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/c3/419cc531235d79f41cb69b766daf94/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/419cc531235d79f41cb69b766daf94/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/3ed35126b02b3f0485d5e6458a9c46/dna_s760.Aligned.sortedByCoord.out.bam
==> 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_s760.Aligned.sortedByCoord.out.bam --OUTPUT dna_s760.md.bam --METRICS_FILE dna_s760.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:44:44.581 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 07:44:44 GMT 2026] MarkDuplicates --INPUT dna_s760.Aligned.sortedByCoord.out.bam --OUTPUT dna_s760.md.bam --METRICS_FILE dna_s760.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 07:44:44 GMT 2026] Executing as ?@nf-c3419cc531235d79f41cb69b766daf94-04db4-64klx 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 07:44:44 MarkDuplicates Start of doWork freeMemory: 105829376; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:44:44 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:44:44 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:44:51 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 4s. Last read position: chr1:3,638,687
INFO 2026-06-08 07:44:51 MarkDuplicates Tracking 2352 as yet unmatched pairs. 210 records in RAM.
INFO 2026-06-08 07:44:55 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 4s. Last read position: chr1:11,216,094
INFO 2026-06-08 07:44:55 MarkDuplicates Tracking 5820 as yet unmatched pairs. 558 records in RAM.
INFO 2026-06-08 07:44:59 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 3s. Last read position: chr1:15,836,182
INFO 2026-06-08 07:44:59 MarkDuplicates Tracking 9493 as yet unmatched pairs. 1784 records in RAM.
INFO 2026-06-08 07:45:03 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 4s. Last read position: chr1:16,945,441
INFO 2026-06-08 07:45:03 MarkDuplicates Tracking 10837 as yet unmatched pairs. 933 records in RAM.
INFO 2026-06-08 07:45:05 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 2s. Last read position: chr1:23,019,630
INFO 2026-06-08 07:45:05 MarkDuplicates Tracking 13741 as yet unmatched pairs. 923 records in RAM.
INFO 2026-06-08 07:45:08 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 2s. Last read position: chr1:28,535,939
INFO 2026-06-08 07:45:08 MarkDuplicates Tracking 16777 as yet unmatched pairs. 1057 records in RAM.
INFO 2026-06-08 07:45:12 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 3s. Last read position: chr1:36,341,961
INFO 2026-06-08 07:45:12 MarkDuplicates Tracking 21372 as yet unmatched pairs. 2360 records in RAM.
INFO 2026-06-08 07:45:16 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 3s. Last read position: chr1:43,272,989
INFO 2026-06-08 07:45:16 MarkDuplicates Tracking 23325 as yet unmatched pairs. 1380 records in RAM.
INFO 2026-06-08 07:45:19 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 3s. Last read position: chr1:46,938,115
INFO 2026-06-08 07:45:19 MarkDuplicates Tracking 25893 as yet unmatched pairs. 1333 records in RAM.
INFO 2026-06-08 07:45:22 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 3s. Last read position: chr1:58,782,756
INFO 2026-06-08 07:45:22 MarkDuplicates Tracking 31085 as yet unmatched pairs. 2605 records in RAM.
INFO 2026-06-08 07:45:26 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 3s. Last read position: chr1:74,489,190
INFO 2026-06-08 07:45:26 MarkDuplicates Tracking 34925 as yet unmatched pairs. 1596 records in RAM.
INFO 2026-06-08 07:45:29 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 3s. Last read position: chr1:92,182,275
INFO 2026-06-08 07:45:29 MarkDuplicates Tracking 40359 as yet unmatched pairs. 1959 records in RAM.
INFO 2026-06-08 07:45:32 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: chr1:103,750,501
INFO 2026-06-08 07:45:32 MarkDuplicates Tracking 43960 as yet unmatched pairs. 1807 records in RAM.
INFO 2026-06-08 07:45:35 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 2s. Last read position: chr1:113,654,009
INFO 2026-06-08 07:45:35 MarkDuplicates Tracking 47250 as yet unmatched pairs. 1776 records in RAM.
INFO 2026-06-08 07:45:38 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 3s. Last read position: chr1:119,997,139
INFO 2026-06-08 07:45:38 MarkDuplicates Tracking 51019 as yet unmatched pairs. 2284 records in RAM.
INFO 2026-06-08 07:45:41 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 2s. Last read position: chr1:146,144,571
INFO 2026-06-08 07:45:41 MarkDuplicates Tracking 53237 as yet unmatched pairs. 1747 records in RAM.
INFO 2026-06-08 07:45:44 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 3s. Last read position: chr1:150,576,784
INFO 2026-06-08 07:45:44 MarkDuplicates Tracking 56608 as yet unmatched pairs. 2994 records in RAM.
INFO 2026-06-08 07:45:47 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 3s. Last read position: chr1:153,741,306
INFO 2026-06-08 07:45:47 MarkDuplicates Tracking 57578 as yet unmatched pairs. 1738 records in RAM.
INFO 2026-06-08 07:45:51 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 3s. Last read position: chr1:156,854,256
INFO 2026-06-08 07:45:51 MarkDuplicates Tracking 60245 as yet unmatched pairs. 1996 records in RAM.
INFO 2026-06-08 07:45:55 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 3s. Last read position: chr1:161,038,496
INFO 2026-06-08 07:45:55 MarkDuplicates Tracking 62572 as yet unmatched pairs. 1661 records in RAM.
INFO 2026-06-08 07:45:58 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 3s. Last read position: chr1:171,196,633
INFO 2026-06-08 07:45:58 MarkDuplicates Tracking 66221 as yet unmatched pairs. 1583 records in RAM.
INFO 2026-06-08 07:46:02 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 3s. Last read position: chr1:182,385,751
INFO 2026-06-08 07:46:02 MarkDuplicates Tracking 69873 as yet unmatched pairs. 1490 records in RAM.
INFO 2026-06-08 07:46:06 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 3s. Last read position: chr1:201,004,881
INFO 2026-06-08 07:46:06 MarkDuplicates Tracking 74811 as yet unmatched pairs. 1284 records in RAM.
INFO 2026-06-08 07:46:08 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 2s. Last read position: chr1:205,228,695
INFO 2026-06-08 07:46:08 MarkDuplicates Tracking 77381 as yet unmatched pairs. 1114 records in RAM.
INFO 2026-06-08 07:46:11 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 3s. Last read position: chr1:208,210,313
INFO 2026-06-08 07:46:11 MarkDuplicates Tracking 79824 as yet unmatched pairs. 1024 records in RAM.
INFO 2026-06-08 07:46:15 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 4s. Last read position: chr1:225,867,874
INFO 2026-06-08 07:46:15 MarkDuplicates Tracking 84303 as yet unmatched pairs. 685 records in RAM.
INFO 2026-06-08 07:46:19 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 3s. Last read position: chr1:232,986,152
INFO 2026-06-08 07:46:19 MarkDuplicates Tracking 87376 as yet unmatched pairs. 536 records in RAM.
INFO 2026-06-08 07:46:21 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 2s. Last read position: chr1:246,850,170
INFO 2026-06-08 07:46:21 MarkDuplicates Tracking 91373 as yet unmatched pairs. 232 records in RAM.
INFO 2026-06-08 07:46:24 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 2s. Last read position: chr2:11,450,024
INFO 2026-06-08 07:46:24 MarkDuplicates Tracking 95192 as yet unmatched pairs. 24423 records in RAM.
INFO 2026-06-08 07:46:27 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 2s. Last read position: chr2:25,281,472
INFO 2026-06-08 07:46:27 MarkDuplicates Tracking 100284 as yet unmatched pairs. 26034 records in RAM.
INFO 2026-06-08 07:46:30 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 3s. Last read position: chr2:29,225,656
INFO 2026-06-08 07:46:30 MarkDuplicates Tracking 102855 as yet unmatched pairs. 26691 records in RAM.
INFO 2026-06-08 07:46:35 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 4s. Last read position: chr2:32,916,425
INFO 2026-06-08 07:46:35 MarkDuplicates Tracking 256410 as yet unmatched pairs. 18243 records in RAM.
INFO 2026-06-08 07:46:38 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 3s. Last read position: chr2:46,384,705
INFO 2026-06-08 07:46:38 MarkDuplicates Tracking 261444 as yet unmatched pairs. 18108 records in RAM.
INFO 2026-06-08 07:46:43 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 4s. Last read position: chr2:58,200,361
INFO 2026-06-08 07:46:43 MarkDuplicates Tracking 263262 as yet unmatched pairs. 16787 records in RAM.
INFO 2026-06-08 07:46:46 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 3s. Last read position: chr2:71,535,254
INFO 2026-06-08 07:46:46 MarkDuplicates Tracking 265838 as yet unmatched pairs. 15835 records in RAM.
INFO 2026-06-08 07:46:49 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 3s. Last read position: chr2:85,596,352
INFO 2026-06-08 07:46:49 MarkDuplicates Tracking 268426 as yet unmatched pairs. 14942 records in RAM.
INFO 2026-06-08 07:46:51 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 2s. Last read position: chr2:95,855,669
INFO 2026-06-08 07:46:51 MarkDuplicates Tracking 270377 as yet unmatched pairs. 14650 records in RAM.
INFO 2026-06-08 07:46:53 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 2s. Last read position: chr2:98,589,067
INFO 2026-06-08 07:46:53 MarkDuplicates Tracking 272433 as yet unmatched pairs. 15173 records in RAM.
INFO 2026-06-08 07:46:57 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 3s. Last read position: chr2:108,765,517
INFO 2026-06-08 07:46:57 MarkDuplicates Tracking 273610 as yet unmatched pairs. 13604 records in RAM.
INFO 2026-06-08 07:46:59 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 1s. Last read position: chr2:112,399,931
INFO 2026-06-08 07:46:59 MarkDuplicates Tracking 275546 as yet unmatched pairs. 14191 records in RAM.
INFO 2026-06-08 07:47:01 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 2s. Last read position: chr2:119,453,041
INFO 2026-06-08 07:47:01 MarkDuplicates Tracking 275212 as yet unmatched pairs. 11556 records in RAM.
INFO 2026-06-08 07:47:05 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 3s. Last read position: chr2:131,482,763
INFO 2026-06-08 07:47:05 MarkDuplicates Tracking 277361 as yet unmatched pairs. 10774 records in RAM.
INFO 2026-06-08 07:47:08 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 3s. Last read position: chr2:151,579,568
INFO 2026-06-08 07:47:08 MarkDuplicates Tracking 280337 as yet unmatched pairs. 9483 records in RAM.
INFO 2026-06-08 07:47:11 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 2s. Last read position: chr2:167,243,406
INFO 2026-06-08 07:47:11 MarkDuplicates Tracking 282916 as yet unmatched pairs. 8533 records in RAM.
INFO 2026-06-08 07:47:14 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 2s. Last read position: chr2:177,263,578
INFO 2026-06-08 07:47:14 MarkDuplicates Tracking 286342 as yet unmatched pairs. 9046 records in RAM.
INFO 2026-06-08 07:47:17 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 2s. Last read position: chr2:182,838,372
INFO 2026-06-08 07:47:17 MarkDuplicates Tracking 286183 as yet unmatched pairs. 6615 records in RAM.
INFO 2026-06-08 07:47:21 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 4s. Last read position: chr2:198,085,943
INFO 2026-06-08 07:47:21 MarkDuplicates Tracking 289060 as yet unmatched pairs. 5696 records in RAM.
INFO 2026-06-08 07:47:24 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 3s. Last read position: chr2:210,437,626
INFO 2026-06-08 07:47:24 MarkDuplicates Tracking 291055 as yet unmatched pairs. 4535 records in RAM.
INFO 2026-06-08 07:47:28 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 3s. Last read position: chr2:219,425,639
INFO 2026-06-08 07:47:28 MarkDuplicates Tracking 292752 as yet unmatched pairs. 3500 records in RAM.
INFO 2026-06-08 07:47:31 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 2s. Last read position: chr2:226,731,992
INFO 2026-06-08 07:47:31 MarkDuplicates Tracking 295180 as yet unmatched pairs. 3313 records in RAM.
INFO 2026-06-08 07:47:34 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 2s. Last read position: chr2:233,960,987
INFO 2026-06-08 07:47:34 MarkDuplicates Tracking 295461 as yet unmatched pairs. 1280 records in RAM.
INFO 2026-06-08 07:47:37 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 3s. Last read position: chr2:241,570,132
INFO 2026-06-08 07:47:37 MarkDuplicates Tracking 296640 as yet unmatched pairs. 284 records in RAM.
INFO 2026-06-08 07:47:41 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 4s. Last read position: chr3:12,292,443
INFO 2026-06-08 07:47:41 MarkDuplicates Tracking 299369 as yet unmatched pairs. 22278 records in RAM.
INFO 2026-06-08 07:47:45 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 3s. Last read position: chr3:12,353,214
INFO 2026-06-08 07:47:45 MarkDuplicates Tracking 300478 as yet unmatched pairs. 21515 records in RAM.
INFO 2026-06-08 07:47:48 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 3s. Last read position: chr3:14,819,496
INFO 2026-06-08 07:47:48 MarkDuplicates Tracking 300402 as yet unmatched pairs. 19585 records in RAM.
INFO 2026-06-08 07:47:51 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 3s. Last read position: chr3:37,040,010
INFO 2026-06-08 07:47:51 MarkDuplicates Tracking 303399 as yet unmatched pairs. 18324 records in RAM.
INFO 2026-06-08 07:47:55 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 3s. Last read position: chr3:44,801,827
INFO 2026-06-08 07:47:55 MarkDuplicates Tracking 304677 as yet unmatched pairs. 17275 records in RAM.
INFO 2026-06-08 07:47:58 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 3s. Last read position: chr3:49,119,275
INFO 2026-06-08 07:47:58 MarkDuplicates Tracking 305338 as yet unmatched pairs. 16213 records in RAM.
INFO 2026-06-08 07:48:02 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 3s. Last read position: chr3:52,385,306
INFO 2026-06-08 07:48:02 MarkDuplicates Tracking 305899 as yet unmatched pairs. 15282 records in RAM.
INFO 2026-06-08 07:48:05 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 3s. Last read position: chr3:62,277,293
INFO 2026-06-08 07:48:05 MarkDuplicates Tracking 307244 as yet unmatched pairs. 14159 records in RAM.
INFO 2026-06-08 07:48:08 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 3s. Last read position: chr3:72,929,543
INFO 2026-06-08 07:48:08 MarkDuplicates Tracking 308811 as yet unmatched pairs. 12841 records in RAM.
INFO 2026-06-08 07:48:11 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 3s. Last read position: chr3:102,452,892
INFO 2026-06-08 07:48:11 MarkDuplicates Tracking 312426 as yet unmatched pairs. 11177 records in RAM.
INFO 2026-06-08 07:48:15 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 3s. Last read position: chr3:121,483,388
INFO 2026-06-08 07:48:15 MarkDuplicates Tracking 315209 as yet unmatched pairs. 10146 records in RAM.
INFO 2026-06-08 07:48:17 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 2s. Last read position: chr3:129,434,036
INFO 2026-06-08 07:48:17 MarkDuplicates Tracking 315568 as yet unmatched pairs. 8347 records in RAM.
INFO 2026-06-08 07:48:20 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 2s. Last read position: chr3:138,653,415
INFO 2026-06-08 07:48:20 MarkDuplicates Tracking 318509 as yet unmatched pairs. 8957 records in RAM.
INFO 2026-06-08 07:48:23 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 3s. Last read position: chr3:154,427,605
INFO 2026-06-08 07:48:23 MarkDuplicates Tracking 318444 as yet unmatched pairs. 5641 records in RAM.
INFO 2026-06-08 07:48:26 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 3s. Last read position: chr3:178,701,261
INFO 2026-06-08 07:48:26 MarkDuplicates Tracking 321067 as yet unmatched pairs. 3659 records in RAM.
INFO 2026-06-08 07:48:29 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 3s. Last read position: chr3:184,385,001
INFO 2026-06-08 07:48:29 MarkDuplicates Tracking 322013 as yet unmatched pairs. 2485 records in RAM.
INFO 2026-06-08 07:48:32 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 2s. Last read position: chr3:189,896,348
INFO 2026-06-08 07:48:32 MarkDuplicates Tracking 323893 as yet unmatched pairs. 2171 records in RAM.
INFO 2026-06-08 07:48:34 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 2s. Last read position: chr4:931,930
INFO 2026-06-08 07:48:34 MarkDuplicates Tracking 323924 as yet unmatched pairs. 18941 records in RAM.
INFO 2026-06-08 07:48:37 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 3s. Last read position: chr4:5,468,031
INFO 2026-06-08 07:48:37 MarkDuplicates Tracking 324373 as yet unmatched pairs. 17732 records in RAM.
INFO 2026-06-08 07:48:40 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 2s. Last read position: chr4:9,985,692
INFO 2026-06-08 07:48:40 MarkDuplicates Tracking 324932 as yet unmatched pairs. 16925 records in RAM.
INFO 2026-06-08 07:48:42 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 2s. Last read position: chr4:38,664,455
INFO 2026-06-08 07:48:42 MarkDuplicates Tracking 328231 as yet unmatched pairs. 15411 records in RAM.
INFO 2026-06-08 07:48:44 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 2s. Last read position: chr4:54,267,622
INFO 2026-06-08 07:48:44 MarkDuplicates Tracking 330178 as yet unmatched pairs. 14353 records in RAM.
INFO 2026-06-08 07:48:47 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 2s. Last read position: chr4:67,646,083
INFO 2026-06-08 07:48:47 MarkDuplicates Tracking 330942 as yet unmatched pairs. 11921 records in RAM.
INFO 2026-06-08 07:48:50 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 2s. Last read position: chr4:80,289,461
INFO 2026-06-08 07:48:50 MarkDuplicates Tracking 333260 as yet unmatched pairs. 11356 records in RAM.
INFO 2026-06-08 07:48:52 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 2s. Last read position: chr4:99,559,436
INFO 2026-06-08 07:48:52 MarkDuplicates Tracking 334376 as yet unmatched pairs. 8754 records in RAM.
INFO 2026-06-08 07:48:55 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 2s. Last read position: chr4:117,084,719
INFO 2026-06-08 07:48:55 MarkDuplicates Tracking 336198 as yet unmatched pairs. 7089 records in RAM.
INFO 2026-06-08 07:48:57 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 2s. Last read position: chr4:142,024,855
INFO 2026-06-08 07:48:57 MarkDuplicates Tracking 339362 as yet unmatched pairs. 5865 records in RAM.
INFO 2026-06-08 07:48:59 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 2s. Last read position: chr4:156,970,666
INFO 2026-06-08 07:48:59 MarkDuplicates Tracking 339740 as yet unmatched pairs. 3175 records in RAM.
INFO 2026-06-08 07:49:02 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 2s. Last read position: chr4:185,589,623
INFO 2026-06-08 07:49:02 MarkDuplicates Tracking 342035 as yet unmatched pairs. 674 records in RAM.
INFO 2026-06-08 07:49:05 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 3s. Last read position: chr5:5,189,968
INFO 2026-06-08 07:49:05 MarkDuplicates Tracking 342888 as yet unmatched pairs. 21770 records in RAM.
INFO 2026-06-08 07:49:08 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 2s. Last read position: chr5:35,654,590
INFO 2026-06-08 07:49:08 MarkDuplicates Tracking 345200 as yet unmatched pairs. 19444 records in RAM.
INFO 2026-06-08 07:49:10 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 2s. Last read position: chr5:49,659,067
INFO 2026-06-08 07:49:10 MarkDuplicates Tracking 346451 as yet unmatched pairs. 17676 records in RAM.
INFO 2026-06-08 07:49:13 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 2s. Last read position: chr5:68,288,338
INFO 2026-06-08 07:49:13 MarkDuplicates Tracking 349440 as yet unmatched pairs. 17504 records in RAM.
INFO 2026-06-08 07:49:16 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 2s. Last read position: chr5:78,415,552
INFO 2026-06-08 07:49:16 MarkDuplicates Tracking 348440 as yet unmatched pairs. 14446 records in RAM.
INFO 2026-06-08 07:49:18 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 2s. Last read position: chr5:97,003,475
INFO 2026-06-08 07:49:18 MarkDuplicates Tracking 349851 as yet unmatched pairs. 12487 records in RAM.
INFO 2026-06-08 07:49:21 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 2s. Last read position: chr5:122,389,202
INFO 2026-06-08 07:49:21 MarkDuplicates Tracking 353227 as yet unmatched pairs. 11756 records in RAM.
INFO 2026-06-08 07:49:24 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 3s. Last read position: chr5:134,750,710
INFO 2026-06-08 07:49:24 MarkDuplicates Tracking 352469 as yet unmatched pairs. 8415 records in RAM.
INFO 2026-06-08 07:49:27 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 3s. Last read position: chr5:141,346,138
INFO 2026-06-08 07:49:27 MarkDuplicates Tracking 353359 as yet unmatched pairs. 7506 records in RAM.
INFO 2026-06-08 07:49:31 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 3s. Last read position: chr5:150,060,626
INFO 2026-06-08 07:49:31 MarkDuplicates Tracking 353241 as yet unmatched pairs. 5441 records in RAM.
INFO 2026-06-08 07:49:34 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 3s. Last read position: chr5:160,413,502
INFO 2026-06-08 07:49:34 MarkDuplicates Tracking 353630 as yet unmatched pairs. 3593 records in RAM.
INFO 2026-06-08 07:49:36 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 2s. Last read position: chr5:177,209,690
INFO 2026-06-08 07:49:36 MarkDuplicates Tracking 354988 as yet unmatched pairs. 1933 records in RAM.
INFO 2026-06-08 07:49:40 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 3s. Last read position: chr5:181,367,587
INFO 2026-06-08 07:49:40 MarkDuplicates Tracking 354559 as yet unmatched pairs. 4 records in RAM.
INFO 2026-06-08 07:49:43 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 2s. Last read position: chr6:19,486,585
INFO 2026-06-08 07:49:43 MarkDuplicates Tracking 355635 as yet unmatched pairs. 26416 records in RAM.
INFO 2026-06-08 07:49:46 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 2s. Last read position: chr6:29,727,070
INFO 2026-06-08 07:49:46 MarkDuplicates Tracking 357186 as yet unmatched pairs. 25794 records in RAM.
INFO 2026-06-08 07:49:49 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 3s. Last read position: chr6:31,828,572
INFO 2026-06-08 07:49:49 MarkDuplicates Tracking 356550 as yet unmatched pairs. 24075 records in RAM.
INFO 2026-06-08 07:49:51 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 2s. Last read position: chr6:33,004,156
INFO 2026-06-08 07:49:51 MarkDuplicates Tracking 356899 as yet unmatched pairs. 23564 records in RAM.
INFO 2026-06-08 07:49:54 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 2s. Last read position: chr6:37,174,863
INFO 2026-06-08 07:49:54 MarkDuplicates Tracking 357111 as yet unmatched pairs. 22411 records in RAM.
INFO 2026-06-08 07:49:56 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 2s. Last read position: chr6:43,785,648
INFO 2026-06-08 07:49:56 MarkDuplicates Tracking 357493 as yet unmatched pairs. 21212 records in RAM.
INFO 2026-06-08 07:50:00 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 3s. Last read position: chr6:61,263,244
INFO 2026-06-08 07:50:00 MarkDuplicates Tracking 356782 as yet unmatched pairs. 17835 records in RAM.
INFO 2026-06-08 07:50:03 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 3s. Last read position: chr6:85,449,886
INFO 2026-06-08 07:50:03 MarkDuplicates Tracking 357863 as yet unmatched pairs. 15362 records in RAM.
INFO 2026-06-08 07:50:06 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 3s. Last read position: chr6:104,742,075
INFO 2026-06-08 07:50:06 MarkDuplicates Tracking 358621 as yet unmatched pairs. 12939 records in RAM.
INFO 2026-06-08 07:50:09 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 3s. Last read position: chr6:116,882,409
INFO 2026-06-08 07:50:09 MarkDuplicates Tracking 359166 as yet unmatched pairs. 11159 records in RAM.
INFO 2026-06-08 07:50:12 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 3s. Last read position: chr6:127,130,085
INFO 2026-06-08 07:50:12 MarkDuplicates Tracking 360459 as yet unmatched pairs. 10070 records in RAM.
INFO 2026-06-08 07:50:16 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 3s. Last read position: chr6:135,210,619
INFO 2026-06-08 07:50:16 MarkDuplicates Tracking 361355 as yet unmatched pairs. 9033 records in RAM.
INFO 2026-06-08 07:50:18 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 2s. Last read position: chr6:147,382,940
INFO 2026-06-08 07:50:18 MarkDuplicates Tracking 359938 as yet unmatched pairs. 5297 records in RAM.
INFO 2026-06-08 07:50:21 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 2s. Last read position: chr6:155,428,819
INFO 2026-06-08 07:50:21 MarkDuplicates Tracking 360057 as yet unmatched pairs. 3480 records in RAM.
INFO 2026-06-08 07:50:24 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 3s. Last read position: chr6:162,201,124
INFO 2026-06-08 07:50:24 MarkDuplicates Tracking 360340 as yet unmatched pairs. 1969 records in RAM.
INFO 2026-06-08 07:50:28 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 4s. Last read position: chr7:2,913,547
INFO 2026-06-08 07:50:28 MarkDuplicates Tracking 360029 as yet unmatched pairs. 30684 records in RAM.
INFO 2026-06-08 07:50:32 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 3s. Last read position: chr7:13,891,029
INFO 2026-06-08 07:50:32 MarkDuplicates Tracking 360035 as yet unmatched pairs. 28756 records in RAM.
INFO 2026-06-08 07:50:35 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 3s. Last read position: chr7:13,978,094
INFO 2026-06-08 07:50:35 MarkDuplicates Tracking 360733 as yet unmatched pairs. 28148 records in RAM.
INFO 2026-06-08 07:50:38 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 3s. Last read position: chr7:31,658,361
INFO 2026-06-08 07:50:38 MarkDuplicates Tracking 360074 as yet unmatched pairs. 24832 records in RAM.
INFO 2026-06-08 07:50:41 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 3s. Last read position: chr7:47,415,098
INFO 2026-06-08 07:50:41 MarkDuplicates Tracking 360740 as yet unmatched pairs. 23028 records in RAM.
INFO 2026-06-08 07:50:44 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 2s. Last read position: chr7:55,180,583
INFO 2026-06-08 07:50:44 MarkDuplicates Tracking 361300 as yet unmatched pairs. 21846 records in RAM.
INFO 2026-06-08 07:50:46 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 2s. Last read position: chr7:72,829,947
INFO 2026-06-08 07:50:46 MarkDuplicates Tracking 360704 as yet unmatched pairs. 18546 records in RAM.
INFO 2026-06-08 07:50:48 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 1s. Last read position: chr7:75,299,673
INFO 2026-06-08 07:50:48 MarkDuplicates Tracking 361039 as yet unmatched pairs. 18202 records in RAM.
INFO 2026-06-08 07:50:50 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 1s. Last read position: chr7:85,022,517
INFO 2026-06-08 07:50:50 MarkDuplicates Tracking 360569 as yet unmatched pairs. 16167 records in RAM.
INFO 2026-06-08 07:50:52 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 2s. Last read position: chr7:97,024,494
INFO 2026-06-08 07:50:52 MarkDuplicates Tracking 360741 as yet unmatched pairs. 14122 records in RAM.
INFO 2026-06-08 07:50:55 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 2s. Last read position: chr7:101,000,946
INFO 2026-06-08 07:50:55 MarkDuplicates Tracking 363099 as yet unmatched pairs. 15362 records in RAM.
INFO 2026-06-08 07:50:58 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 2s. Last read position: chr7:103,388,998
INFO 2026-06-08 07:50:58 MarkDuplicates Tracking 360003 as yet unmatched pairs. 11430 records in RAM.
INFO 2026-06-08 07:51:00 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 2s. Last read position: chr7:116,773,830
INFO 2026-06-08 07:51:00 MarkDuplicates Tracking 361590 as yet unmatched pairs. 10548 records in RAM.
INFO 2026-06-08 07:51:02 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 2s. Last read position: chr7:130,215,846
INFO 2026-06-08 07:51:02 MarkDuplicates Tracking 360258 as yet unmatched pairs. 6884 records in RAM.
INFO 2026-06-08 07:51:04 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 2s. Last read position: chr7:140,760,641
INFO 2026-06-08 07:51:04 MarkDuplicates Tracking 360121 as yet unmatched pairs. 4800 records in RAM.
INFO 2026-06-08 07:51:07 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 2s. Last read position: chr7:144,267,193
INFO 2026-06-08 07:51:07 MarkDuplicates Tracking 359928 as yet unmatched pairs. 3463 records in RAM.
INFO 2026-06-08 07:51:10 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 2s. Last read position: chr7:152,134,921
INFO 2026-06-08 07:51:10 MarkDuplicates Tracking 360138 as yet unmatched pairs. 2267 records in RAM.
INFO 2026-06-08 07:51:14 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 3s. Last read position: chr8:6,811,953
INFO 2026-06-08 07:51:14 MarkDuplicates Tracking 359393 as yet unmatched pairs. 28421 records in RAM.
INFO 2026-06-08 07:51:16 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 2s. Last read position: chr8:19,405,731
INFO 2026-06-08 07:51:16 MarkDuplicates Tracking 359167 as yet unmatched pairs. 26585 records in RAM.
INFO 2026-06-08 07:51:19 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 3s. Last read position: chr8:30,766,292
INFO 2026-06-08 07:51:19 MarkDuplicates Tracking 358956 as yet unmatched pairs. 24539 records in RAM.
INFO 2026-06-08 07:51:23 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 3s. Last read position: chr8:32,656,939
INFO 2026-06-08 07:51:23 MarkDuplicates Tracking 359468 as yet unmatched pairs. 23902 records in RAM.
INFO 2026-06-08 07:51:25 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 2s. Last read position: chr8:32,728,206
INFO 2026-06-08 07:51:25 MarkDuplicates Tracking 359075 as yet unmatched pairs. 22448 records in RAM.
INFO 2026-06-08 07:51:27 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 2s. Last read position: chr8:37,840,774
INFO 2026-06-08 07:51:27 MarkDuplicates Tracking 357914 as yet unmatched pairs. 19815 records in RAM.
INFO 2026-06-08 07:51:30 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 2s. Last read position: chr8:38,459,702
INFO 2026-06-08 07:51:30 MarkDuplicates Tracking 357863 as yet unmatched pairs. 18800 records in RAM.
INFO 2026-06-08 07:51:32 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 2s. Last read position: chr8:47,935,718
INFO 2026-06-08 07:51:32 MarkDuplicates Tracking 356886 as yet unmatched pairs. 16294 records in RAM.
INFO 2026-06-08 07:51:35 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:06:47s. Time for last 1,000,000: 2s. Last read position: chr8:68,231,942
INFO 2026-06-08 07:51:35 MarkDuplicates Tracking 357309 as yet unmatched pairs. 14067 records in RAM.
INFO 2026-06-08 07:51:37 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 2s. Last read position: chr8:90,978,429
INFO 2026-06-08 07:51:37 MarkDuplicates Tracking 355760 as yet unmatched pairs. 9653 records in RAM.
INFO 2026-06-08 07:51:40 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 2s. Last read position: chr8:108,470,860
INFO 2026-06-08 07:51:40 MarkDuplicates Tracking 355376 as yet unmatched pairs. 6770 records in RAM.
INFO 2026-06-08 07:51:43 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 2s. Last read position: chr8:130,724,103
INFO 2026-06-08 07:51:43 MarkDuplicates Tracking 354895 as yet unmatched pairs. 3420 records in RAM.
INFO 2026-06-08 07:51:46 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 2s. Last read position: chr8:143,863,663
INFO 2026-06-08 07:51:46 MarkDuplicates Tracking 355063 as yet unmatched pairs. 1879 records in RAM.
INFO 2026-06-08 07:51:49 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 3s. Last read position: chr9:2,042,042
INFO 2026-06-08 07:51:49 MarkDuplicates Tracking 354416 as yet unmatched pairs. 31838 records in RAM.
INFO 2026-06-08 07:51:52 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 3s. Last read position: chr9:12,218,627
INFO 2026-06-08 07:51:52 MarkDuplicates Tracking 353003 as yet unmatched pairs. 28797 records in RAM.
INFO 2026-06-08 07:51:56 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:07:09s. Time for last 1,000,000: 3s. Last read position: chr9:27,183,574
INFO 2026-06-08 07:51:56 MarkDuplicates Tracking 352526 as yet unmatched pairs. 26279 records in RAM.
INFO 2026-06-08 07:51:59 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:07:12s. Time for last 1,000,000: 3s. Last read position: chr9:36,833,802
INFO 2026-06-08 07:51:59 MarkDuplicates Tracking 352968 as yet unmatched pairs. 25277 records in RAM.
INFO 2026-06-08 07:52:02 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:07:15s. Time for last 1,000,000: 3s. Last read position: chr9:42,386,099
INFO 2026-06-08 07:52:02 MarkDuplicates Tracking 350992 as yet unmatched pairs. 22245 records in RAM.
INFO 2026-06-08 07:52:05 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:07:18s. Time for last 1,000,000: 2s. Last read position: chr9:65,738,427
INFO 2026-06-08 07:52:05 MarkDuplicates Tracking 350994 as yet unmatched pairs. 21479 records in RAM.
INFO 2026-06-08 07:52:08 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:07:20s. Time for last 1,000,000: 2s. Last read position: chr9:77,721,490
INFO 2026-06-08 07:52:08 MarkDuplicates Tracking 350312 as yet unmatched pairs. 19285 records in RAM.
INFO 2026-06-08 07:52:11 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:07:24s. Time for last 1,000,000: 3s. Last read position: chr9:84,863,891
INFO 2026-06-08 07:52:11 MarkDuplicates Tracking 350601 as yet unmatched pairs. 18099 records in RAM.
INFO 2026-06-08 07:52:15 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:07:28s. Time for last 1,000,000: 4s. Last read position: chr9:84,920,286
INFO 2026-06-08 07:52:15 MarkDuplicates Tracking 349788 as yet unmatched pairs. 16245 records in RAM.
INFO 2026-06-08 07:52:18 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:07:31s. Time for last 1,000,000: 2s. Last read position: chr9:93,112,183
INFO 2026-06-08 07:52:18 MarkDuplicates Tracking 347974 as yet unmatched pairs. 12924 records in RAM.
INFO 2026-06-08 07:52:22 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:07:35s. Time for last 1,000,000: 3s. Last read position: chr9:99,828,869
INFO 2026-06-08 07:52:22 MarkDuplicates Tracking 347657 as yet unmatched pairs. 11387 records in RAM.
INFO 2026-06-08 07:52:25 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:07:38s. Time for last 1,000,000: 3s. Last read position: chr9:114,361,614
INFO 2026-06-08 07:52:25 MarkDuplicates Tracking 346667 as yet unmatched pairs. 8323 records in RAM.
INFO 2026-06-08 07:52:28 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:07:41s. Time for last 1,000,000: 3s. Last read position: chr9:127,807,257
INFO 2026-06-08 07:52:28 MarkDuplicates Tracking 345849 as yet unmatched pairs. 5748 records in RAM.
INFO 2026-06-08 07:52:31 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:07:44s. Time for last 1,000,000: 2s. Last read position: chr9:132,587,364
INFO 2026-06-08 07:52:31 MarkDuplicates Tracking 344887 as yet unmatched pairs. 3811 records in RAM.
INFO 2026-06-08 07:52:34 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:07:46s. Time for last 1,000,000: 2s. Last read position: chr9:136,285,353
INFO 2026-06-08 07:52:34 MarkDuplicates Tracking 343973 as yet unmatched pairs. 1943 records in RAM.
INFO 2026-06-08 07:52:37 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:07:50s. Time for last 1,000,000: 3s. Last read position: chr9:137,728,509
INFO 2026-06-08 07:52:37 MarkDuplicates Tracking 342936 as yet unmatched pairs. 216 records in RAM.
INFO 2026-06-08 07:52:40 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:07:53s. Time for last 1,000,000: 3s. Last read position: chr10:17,321,271
INFO 2026-06-08 07:52:40 MarkDuplicates Tracking 342188 as yet unmatched pairs. 27269 records in RAM.
INFO 2026-06-08 07:52:44 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:07:57s. Time for last 1,000,000: 3s. Last read position: chr10:32,286,620
INFO 2026-06-08 07:52:44 MarkDuplicates Tracking 341147 as yet unmatched pairs. 24450 records in RAM.
INFO 2026-06-08 07:52:47 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:08:00s. Time for last 1,000,000: 3s. Last read position: chr10:45,699,108
INFO 2026-06-08 07:52:47 MarkDuplicates Tracking 340104 as yet unmatched pairs. 21722 records in RAM.
INFO 2026-06-08 07:52:50 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:08:03s. Time for last 1,000,000: 3s. Last read position: chr10:53,809,124
INFO 2026-06-08 07:52:50 MarkDuplicates Tracking 339173 as yet unmatched pairs. 19714 records in RAM.
INFO 2026-06-08 07:52:54 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:08:07s. Time for last 1,000,000: 3s. Last read position: chr10:70,255,131
INFO 2026-06-08 07:52:54 MarkDuplicates Tracking 338121 as yet unmatched pairs. 16647 records in RAM.
INFO 2026-06-08 07:52:57 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:08:10s. Time for last 1,000,000: 3s. Last read position: chr10:84,211,158
INFO 2026-06-08 07:52:57 MarkDuplicates Tracking 337019 as yet unmatched pairs. 13947 records in RAM.
INFO 2026-06-08 07:53:00 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:08:13s. Time for last 1,000,000: 3s. Last read position: chr10:89,028,599
INFO 2026-06-08 07:53:00 MarkDuplicates Tracking 337002 as yet unmatched pairs. 12898 records in RAM.
INFO 2026-06-08 07:53:03 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 3s. Last read position: chr10:99,533,159
INFO 2026-06-08 07:53:03 MarkDuplicates Tracking 334937 as yet unmatched pairs. 9412 records in RAM.
INFO 2026-06-08 07:53:06 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 3s. Last read position: chr10:106,667,669
INFO 2026-06-08 07:53:06 MarkDuplicates Tracking 333650 as yet unmatched pairs. 7023 records in RAM.
INFO 2026-06-08 07:53:10 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 3s. Last read position: chr10:121,484,651
INFO 2026-06-08 07:53:10 MarkDuplicates Tracking 333822 as yet unmatched pairs. 5347 records in RAM.
INFO 2026-06-08 07:53:13 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:08:26s. Time for last 1,000,000: 3s. Last read position: chr10:122,994,156
INFO 2026-06-08 07:53:13 MarkDuplicates Tracking 331514 as yet unmatched pairs. 2316 records in RAM.
INFO 2026-06-08 07:53:17 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:08:30s. Time for last 1,000,000: 4s. Last read position: chr11:721,821
INFO 2026-06-08 07:53:17 MarkDuplicates Tracking 330165 as yet unmatched pairs. 35208 records in RAM.
INFO 2026-06-08 07:53:21 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 3s. Last read position: chr11:3,723,309
INFO 2026-06-08 07:53:21 MarkDuplicates Tracking 329198 as yet unmatched pairs. 33636 records in RAM.
INFO 2026-06-08 07:53:24 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 3s. Last read position: chr11:10,802,410
INFO 2026-06-08 07:53:24 MarkDuplicates Tracking 327954 as yet unmatched pairs. 31436 records in RAM.
INFO 2026-06-08 07:53:27 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 2s. Last read position: chr11:26,678,758
INFO 2026-06-08 07:53:27 MarkDuplicates Tracking 326592 as yet unmatched pairs. 28415 records in RAM.
INFO 2026-06-08 07:53:30 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:08:43s. Time for last 1,000,000: 3s. Last read position: chr11:46,725,733
INFO 2026-06-08 07:53:30 MarkDuplicates Tracking 325167 as yet unmatched pairs. 25100 records in RAM.
INFO 2026-06-08 07:53:33 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:08:46s. Time for last 1,000,000: 2s. Last read position: chr11:59,212,133
INFO 2026-06-08 07:53:33 MarkDuplicates Tracking 324056 as yet unmatched pairs. 22707 records in RAM.
INFO 2026-06-08 07:53:36 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 3s. Last read position: chr11:63,945,807
INFO 2026-06-08 07:53:36 MarkDuplicates Tracking 323064 as yet unmatched pairs. 20877 records in RAM.
INFO 2026-06-08 07:53:39 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:08:52s. Time for last 1,000,000: 3s. Last read position: chr11:66,315,529
INFO 2026-06-08 07:53:39 MarkDuplicates Tracking 321947 as yet unmatched pairs. 19154 records in RAM.
INFO 2026-06-08 07:53:43 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:08:56s. Time for last 1,000,000: 3s. Last read position: chr11:71,687,213
INFO 2026-06-08 07:53:43 MarkDuplicates Tracking 320564 as yet unmatched pairs. 16928 records in RAM.
INFO 2026-06-08 07:53:46 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:08:59s. Time for last 1,000,000: 3s. Last read position: chr11:80,921,510
INFO 2026-06-08 07:53:46 MarkDuplicates Tracking 319437 as yet unmatched pairs. 14614 records in RAM.
INFO 2026-06-08 07:53:50 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:09:02s. Time for last 1,000,000: 3s. Last read position: chr11:95,979,606
INFO 2026-06-08 07:53:50 MarkDuplicates Tracking 318149 as yet unmatched pairs. 11634 records in RAM.
INFO 2026-06-08 07:53:53 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:09:06s. Time for last 1,000,000: 3s. Last read position: chr11:108,244,704
INFO 2026-06-08 07:53:53 MarkDuplicates Tracking 317049 as yet unmatched pairs. 8944 records in RAM.
INFO 2026-06-08 07:53:56 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:09:09s. Time for last 1,000,000: 3s. Last read position: chr11:118,449,724
INFO 2026-06-08 07:53:56 MarkDuplicates Tracking 315831 as yet unmatched pairs. 6458 records in RAM.
INFO 2026-06-08 07:54:00 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:09:13s. Time for last 1,000,000: 3s. Last read position: chr11:121,102,560
INFO 2026-06-08 07:54:00 MarkDuplicates Tracking 313708 as yet unmatched pairs. 3512 records in RAM.
INFO 2026-06-08 07:54:03 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 3s. Last read position: chr11:130,880,668
INFO 2026-06-08 07:54:03 MarkDuplicates Tracking 312246 as yet unmatched pairs. 813 records in RAM.
INFO 2026-06-08 07:54:07 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 3s. Last read position: chr12:4,816,213
INFO 2026-06-08 07:54:07 MarkDuplicates Tracking 310742 as yet unmatched pairs. 39539 records in RAM.
INFO 2026-06-08 07:54:11 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:09:24s. Time for last 1,000,000: 3s. Last read position: chr12:10,931,019
INFO 2026-06-08 07:54:11 MarkDuplicates Tracking 309757 as yet unmatched pairs. 37667 records in RAM.
INFO 2026-06-08 07:54:14 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:09:27s. Time for last 1,000,000: 3s. Last read position: chr12:11,801,244
INFO 2026-06-08 07:54:14 MarkDuplicates Tracking 309157 as yet unmatched pairs. 36424 records in RAM.
INFO 2026-06-08 07:54:18 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:09:31s. Time for last 1,000,000: 4s. Last read position: chr12:11,869,618
INFO 2026-06-08 07:54:18 MarkDuplicates Tracking 308283 as yet unmatched pairs. 34889 records in RAM.
INFO 2026-06-08 07:54:22 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 3s. Last read position: chr12:21,437,742
INFO 2026-06-08 07:54:22 MarkDuplicates Tracking 305230 as yet unmatched pairs. 30718 records in RAM.
INFO 2026-06-08 07:54:25 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:09:38s. Time for last 1,000,000: 2s. Last read position: chr12:40,322,236
INFO 2026-06-08 07:54:25 MarkDuplicates Tracking 303288 as yet unmatched pairs. 27370 records in RAM.
INFO 2026-06-08 07:54:28 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:09:41s. Time for last 1,000,000: 3s. Last read position: chr12:49,029,324
INFO 2026-06-08 07:54:28 MarkDuplicates Tracking 301842 as yet unmatched pairs. 24887 records in RAM.
INFO 2026-06-08 07:54:32 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:09:45s. Time for last 1,000,000: 3s. Last read position: chr12:52,056,744
INFO 2026-06-08 07:54:32 MarkDuplicates Tracking 300210 as yet unmatched pairs. 22601 records in RAM.
INFO 2026-06-08 07:54:35 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:09:48s. Time for last 1,000,000: 3s. Last read position: chr12:56,098,468
INFO 2026-06-08 07:54:35 MarkDuplicates Tracking 299832 as yet unmatched pairs. 21516 records in RAM.
INFO 2026-06-08 07:54:38 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:09:51s. Time for last 1,000,000: 3s. Last read position: chr12:57,751,067
INFO 2026-06-08 07:54:38 MarkDuplicates Tracking 298496 as yet unmatched pairs. 19582 records in RAM.
INFO 2026-06-08 07:54:42 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:09:55s. Time for last 1,000,000: 3s. Last read position: chr12:72,653,210
INFO 2026-06-08 07:54:42 MarkDuplicates Tracking 295796 as yet unmatched pairs. 15421 records in RAM.
INFO 2026-06-08 07:54:45 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:09:58s. Time for last 1,000,000: 3s. Last read position: chr12:97,678,881
INFO 2026-06-08 07:54:45 MarkDuplicates Tracking 293275 as yet unmatched pairs. 10875 records in RAM.
INFO 2026-06-08 07:54:49 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:10:02s. Time for last 1,000,000: 3s. Last read position: chr12:109,307,889
INFO 2026-06-08 07:54:49 MarkDuplicates Tracking 291243 as yet unmatched pairs. 7773 records in RAM.
INFO 2026-06-08 07:54:53 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 3s. Last read position: chr12:116,723,025
INFO 2026-06-08 07:54:53 MarkDuplicates Tracking 289684 as yet unmatched pairs. 5270 records in RAM.
INFO 2026-06-08 07:54:56 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 3s. Last read position: chr12:123,223,043
INFO 2026-06-08 07:54:56 MarkDuplicates Tracking 288066 as yet unmatched pairs. 2827 records in RAM.
INFO 2026-06-08 07:54:59 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 3s. Last read position: chr13:18,445,088
INFO 2026-06-08 07:54:59 MarkDuplicates Tracking 286104 as yet unmatched pairs. 20158 records in RAM.
INFO 2026-06-08 07:55:03 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:10:16s. Time for last 1,000,000: 3s. Last read position: chr13:28,303,100
INFO 2026-06-08 07:55:03 MarkDuplicates Tracking 285376 as yet unmatched pairs. 18466 records in RAM.
INFO 2026-06-08 07:55:06 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:10:19s. Time for last 1,000,000: 3s. Last read position: chr13:40,558,730
INFO 2026-06-08 07:55:06 MarkDuplicates Tracking 283343 as yet unmatched pairs. 15240 records in RAM.
INFO 2026-06-08 07:55:10 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:10:23s. Time for last 1,000,000: 3s. Last read position: chr13:57,149,271
INFO 2026-06-08 07:55:10 MarkDuplicates Tracking 280113 as yet unmatched pairs. 10699 records in RAM.
INFO 2026-06-08 07:55:12 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:10:25s. Time for last 1,000,000: 2s. Last read position: chr13:94,612,312
INFO 2026-06-08 07:55:12 MarkDuplicates Tracking 276741 as yet unmatched pairs. 4853 records in RAM.
INFO 2026-06-08 07:55:15 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:10:28s. Time for last 1,000,000: 2s. Last read position: chr13:109,786,006
INFO 2026-06-08 07:55:15 MarkDuplicates Tracking 275471 as yet unmatched pairs. 2234 records in RAM.
INFO 2026-06-08 07:55:18 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:10:31s. Time for last 1,000,000: 2s. Last read position: chr14:21,385,706
INFO 2026-06-08 07:55:18 MarkDuplicates Tracking 272986 as yet unmatched pairs. 21574 records in RAM.
INFO 2026-06-08 07:55:21 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:10:34s. Time for last 1,000,000: 3s. Last read position: chr14:34,152,056
INFO 2026-06-08 07:55:21 MarkDuplicates Tracking 270584 as yet unmatched pairs. 18172 records in RAM.
INFO 2026-06-08 07:55:24 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:10:37s. Time for last 1,000,000: 3s. Last read position: chr14:51,725,957
INFO 2026-06-08 07:55:24 MarkDuplicates Tracking 267960 as yet unmatched pairs. 14254 records in RAM.
INFO 2026-06-08 07:55:27 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:10:40s. Time for last 1,000,000: 3s. Last read position: chr14:67,813,959
INFO 2026-06-08 07:55:27 MarkDuplicates Tracking 265352 as yet unmatched pairs. 10457 records in RAM.
INFO 2026-06-08 07:55:30 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:10:43s. Time for last 1,000,000: 3s. Last read position: chr14:80,916,391
INFO 2026-06-08 07:55:30 MarkDuplicates Tracking 263048 as yet unmatched pairs. 7150 records in RAM.
INFO 2026-06-08 07:55:33 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:10:45s. Time for last 1,000,000: 2s. Last read position: chr14:95,710,450
INFO 2026-06-08 07:55:33 MarkDuplicates Tracking 261762 as yet unmatched pairs. 4672 records in RAM.
INFO 2026-06-08 07:55:35 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:10:48s. Time for last 1,000,000: 2s. Last read position: chr14:104,938,325
INFO 2026-06-08 07:55:35 MarkDuplicates Tracking 258636 as yet unmatched pairs. 668 records in RAM.
INFO 2026-06-08 07:55:38 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:10:51s. Time for last 1,000,000: 2s. Last read position: chr15:23,130,532
INFO 2026-06-08 07:55:38 MarkDuplicates Tracking 257304 as yet unmatched pairs. 35791 records in RAM.
INFO 2026-06-08 07:55:41 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:10:54s. Time for last 1,000,000: 2s. Last read position: chr15:30,555,049
INFO 2026-06-08 07:55:41 MarkDuplicates Tracking 255970 as yet unmatched pairs. 33958 records in RAM.
INFO 2026-06-08 07:55:44 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:10:57s. Time for last 1,000,000: 2s. Last read position: chr15:38,351,322
INFO 2026-06-08 07:55:44 MarkDuplicates Tracking 254547 as yet unmatched pairs. 31874 records in RAM.
INFO 2026-06-08 07:55:47 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:11:00s. Time for last 1,000,000: 3s. Last read position: chr15:42,687,703
INFO 2026-06-08 07:55:47 MarkDuplicates Tracking 252202 as yet unmatched pairs. 29010 records in RAM.
INFO 2026-06-08 07:55:51 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:11:03s. Time for last 1,000,000: 3s. Last read position: chr15:49,425,239
INFO 2026-06-08 07:55:51 MarkDuplicates Tracking 250813 as yet unmatched pairs. 26981 records in RAM.
INFO 2026-06-08 07:55:53 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:11:06s. Time for last 1,000,000: 2s. Last read position: chr15:63,734,670
INFO 2026-06-08 07:55:53 MarkDuplicates Tracking 247675 as yet unmatched pairs. 22839 records in RAM.
INFO 2026-06-08 07:55:56 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:11:09s. Time for last 1,000,000: 2s. Last read position: chr15:73,714,142
INFO 2026-06-08 07:55:56 MarkDuplicates Tracking 246730 as yet unmatched pairs. 21118 records in RAM.
INFO 2026-06-08 07:56:00 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:11:13s. Time for last 1,000,000: 3s. Last read position: chr15:82,349,312
INFO 2026-06-08 07:56:00 MarkDuplicates Tracking 243220 as yet unmatched pairs. 16965 records in RAM.
INFO 2026-06-08 07:56:03 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:11:16s. Time for last 1,000,000: 3s. Last read position: chr15:87,947,627
INFO 2026-06-08 07:56:03 MarkDuplicates Tracking 242352 as yet unmatched pairs. 15580 records in RAM.
INFO 2026-06-08 07:56:06 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:11:19s. Time for last 1,000,000: 3s. Last read position: chr15:88,003,865
INFO 2026-06-08 07:56:06 MarkDuplicates Tracking 240679 as yet unmatched pairs. 13461 records in RAM.
INFO 2026-06-08 07:56:09 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:11:22s. Time for last 1,000,000: 2s. Last read position: chr15:88,047,049
INFO 2026-06-08 07:56:09 MarkDuplicates Tracking 239551 as yet unmatched pairs. 11868 records in RAM.
INFO 2026-06-08 07:56:12 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:11:25s. Time for last 1,000,000: 3s. Last read position: chr15:88,089,416
INFO 2026-06-08 07:56:12 MarkDuplicates Tracking 237170 as yet unmatched pairs. 9007 records in RAM.
INFO 2026-06-08 07:56:16 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:11:29s. Time for last 1,000,000: 3s. Last read position: chr15:88,134,865
INFO 2026-06-08 07:56:16 MarkDuplicates Tracking 235802 as yet unmatched pairs. 7216 records in RAM.
INFO 2026-06-08 07:56:19 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:11:32s. Time for last 1,000,000: 3s. Last read position: chr15:92,899,981
INFO 2026-06-08 07:56:19 MarkDuplicates Tracking 232038 as yet unmatched pairs. 2967 records in RAM.
INFO 2026-06-08 07:56:23 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:11:36s. Time for last 1,000,000: 3s. Last read position: chr16:352,614
INFO 2026-06-08 07:56:23 MarkDuplicates Tracking 230665 as yet unmatched pairs. 33003 records in RAM.
INFO 2026-06-08 07:56:26 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:11:39s. Time for last 1,000,000: 3s. Last read position: chr16:2,171,511
INFO 2026-06-08 07:56:26 MarkDuplicates Tracking 228044 as yet unmatched pairs. 30100 records in RAM.
INFO 2026-06-08 07:56:30 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:11:42s. Time for last 1,000,000: 3s. Last read position: chr16:3,728,521
INFO 2026-06-08 07:56:30 MarkDuplicates Tracking 226992 as yet unmatched pairs. 28787 records in RAM.
INFO 2026-06-08 07:56:33 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:11:46s. Time for last 1,000,000: 3s. Last read position: chr16:13,948,350
INFO 2026-06-08 07:56:33 MarkDuplicates Tracking 224798 as yet unmatched pairs. 25906 records in RAM.
INFO 2026-06-08 07:56:37 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:11:49s. Time for last 1,000,000: 3s. Last read position: chr16:18,394,917
INFO 2026-06-08 07:56:37 MarkDuplicates Tracking 222361 as yet unmatched pairs. 23184 records in RAM.
INFO 2026-06-08 07:56:40 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:11:53s. Time for last 1,000,000: 3s. Last read position: chr16:23,694,749
INFO 2026-06-08 07:56:40 MarkDuplicates Tracking 221050 as yet unmatched pairs. 21429 records in RAM.
INFO 2026-06-08 07:56:43 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:11:56s. Time for last 1,000,000: 3s. Last read position: chr16:29,977,739
INFO 2026-06-08 07:56:43 MarkDuplicates Tracking 219249 as yet unmatched pairs. 19174 records in RAM.
INFO 2026-06-08 07:56:47 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:11:59s. Time for last 1,000,000: 3s. Last read position: chr16:32,770,589
INFO 2026-06-08 07:56:47 MarkDuplicates Tracking 217546 as yet unmatched pairs. 17197 records in RAM.
INFO 2026-06-08 07:56:49 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:12:02s. Time for last 1,000,000: 2s. Last read position: chr16:55,685,272
INFO 2026-06-08 07:56:49 MarkDuplicates Tracking 214666 as yet unmatched pairs. 13253 records in RAM.
INFO 2026-06-08 07:56:51 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:12:04s. Time for last 1,000,000: 2s. Last read position: chr16:67,195,508
INFO 2026-06-08 07:56:51 MarkDuplicates Tracking 211902 as yet unmatched pairs. 9747 records in RAM.
INFO 2026-06-08 07:56:55 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:12:08s. Time for last 1,000,000: 3s. Last read position: chr16:70,860,590
INFO 2026-06-08 07:56:55 MarkDuplicates Tracking 210160 as yet unmatched pairs. 7586 records in RAM.
INFO 2026-06-08 07:56:59 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:12:12s. Time for last 1,000,000: 3s. Last read position: chr16:81,130,406
INFO 2026-06-08 07:56:59 MarkDuplicates Tracking 207780 as yet unmatched pairs. 4492 records in RAM.
INFO 2026-06-08 07:57:02 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:12:15s. Time for last 1,000,000: 3s. Last read position: chr16:89,279,687
INFO 2026-06-08 07:57:02 MarkDuplicates Tracking 206869 as yet unmatched pairs. 2962 records in RAM.
INFO 2026-06-08 07:57:06 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:12:19s. Time for last 1,000,000: 4s. Last read position: chr17:1,653,712
INFO 2026-06-08 07:57:06 MarkDuplicates Tracking 203730 as yet unmatched pairs. 42531 records in RAM.
INFO 2026-06-08 07:57:09 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:12:22s. Time for last 1,000,000: 3s. Last read position: chr17:6,651,934
INFO 2026-06-08 07:57:09 MarkDuplicates Tracking 201733 as yet unmatched pairs. 40191 records in RAM.
INFO 2026-06-08 07:57:13 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:12:26s. Time for last 1,000,000: 3s. Last read position: chr17:8,241,733
INFO 2026-06-08 07:57:13 MarkDuplicates Tracking 199764 as yet unmatched pairs. 37958 records in RAM.
INFO 2026-06-08 07:57:16 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:12:29s. Time for last 1,000,000: 3s. Last read position: chr17:16,101,288
INFO 2026-06-08 07:57:16 MarkDuplicates Tracking 198032 as yet unmatched pairs. 35729 records in RAM.
INFO 2026-06-08 07:57:19 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:12:32s. Time for last 1,000,000: 3s. Last read position: chr17:19,708,577
INFO 2026-06-08 07:57:19 MarkDuplicates Tracking 195640 as yet unmatched pairs. 32995 records in RAM.
INFO 2026-06-08 07:57:22 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:12:35s. Time for last 1,000,000: 2s. Last read position: chr17:30,869,504
INFO 2026-06-08 07:57:22 MarkDuplicates Tracking 193258 as yet unmatched pairs. 30109 records in RAM.
INFO 2026-06-08 07:57:25 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:12:38s. Time for last 1,000,000: 2s. Last read position: chr17:35,773,288
INFO 2026-06-08 07:57:25 MarkDuplicates Tracking 191087 as yet unmatched pairs. 27522 records in RAM.
INFO 2026-06-08 07:57:28 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:12:41s. Time for last 1,000,000: 3s. Last read position: chr17:39,715,866
INFO 2026-06-08 07:57:28 MarkDuplicates Tracking 189887 as yet unmatched pairs. 26051 records in RAM.
INFO 2026-06-08 07:57:31 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:12:44s. Time for last 1,000,000: 3s. Last read position: chr17:40,627,730
INFO 2026-06-08 07:57:31 MarkDuplicates Tracking 188492 as yet unmatched pairs. 24376 records in RAM.
INFO 2026-06-08 07:57:34 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:12:47s. Time for last 1,000,000: 3s. Last read position: chr17:42,315,434
INFO 2026-06-08 07:57:34 MarkDuplicates Tracking 186555 as yet unmatched pairs. 22123 records in RAM.
INFO 2026-06-08 07:57:38 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:12:51s. Time for last 1,000,000: 3s. Last read position: chr17:43,542,213
INFO 2026-06-08 07:57:38 MarkDuplicates Tracking 184722 as yet unmatched pairs. 19956 records in RAM.
INFO 2026-06-08 07:57:41 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:12:54s. Time for last 1,000,000: 2s. Last read position: chr17:46,514,579
INFO 2026-06-08 07:57:41 MarkDuplicates Tracking 181803 as yet unmatched pairs. 16745 records in RAM.
INFO 2026-06-08 07:57:44 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:12:57s. Time for last 1,000,000: 2s. Last read position: chr17:50,655,872
INFO 2026-06-08 07:57:44 MarkDuplicates Tracking 180181 as yet unmatched pairs. 14801 records in RAM.
INFO 2026-06-08 07:59:13 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:14:25s. Time for last 1,000,000: 88s. Last read position: chr17:60,462,092
INFO 2026-06-08 07:59:13 MarkDuplicates Tracking 176917 as yet unmatched pairs. 11013 records in RAM.
INFO 2026-06-08 07:59:17 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:14:30s. Time for last 1,000,000: 4s. Last read position: chr17:65,013,480
INFO 2026-06-08 07:59:17 MarkDuplicates Tracking 175833 as yet unmatched pairs. 9565 records in RAM.
INFO 2026-06-08 07:59:21 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:14:34s. Time for last 1,000,000: 3s. Last read position: chr17:74,863,109
INFO 2026-06-08 07:59:21 MarkDuplicates Tracking 171877 as yet unmatched pairs. 5128 records in RAM.
INFO 2026-06-08 07:59:24 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:14:37s. Time for last 1,000,000: 2s. Last read position: chr17:78,571,590
INFO 2026-06-08 07:59:24 MarkDuplicates Tracking 169822 as yet unmatched pairs. 2727 records in RAM.
INFO 2026-06-08 07:59:26 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:14:39s. Time for last 1,000,000: 2s. Last read position: chr17:82,658,697
INFO 2026-06-08 07:59:26 MarkDuplicates Tracking 167609 as yet unmatched pairs. 206 records in RAM.
INFO 2026-06-08 07:59:29 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:14:42s. Time for last 1,000,000: 2s. Last read position: chr18:21,006,699
INFO 2026-06-08 07:59:29 MarkDuplicates Tracking 163892 as yet unmatched pairs. 16413 records in RAM.
INFO 2026-06-08 07:59:33 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:14:46s. Time for last 1,000,000: 3s. Last read position: chr18:42,087,215
INFO 2026-06-08 07:59:33 MarkDuplicates Tracking 159880 as yet unmatched pairs. 11600 records in RAM.
INFO 2026-06-08 07:59:36 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:14:49s. Time for last 1,000,000: 3s. Last read position: chr18:47,837,678
INFO 2026-06-08 07:59:36 MarkDuplicates Tracking 157837 as yet unmatched pairs. 9171 records in RAM.
INFO 2026-06-08 07:59:39 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:14:52s. Time for last 1,000,000: 3s. Last read position: chr18:63,126,966
INFO 2026-06-08 07:59:39 MarkDuplicates Tracking 154594 as yet unmatched pairs. 5298 records in RAM.
INFO 2026-06-08 07:59:43 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:14:55s. Time for last 1,000,000: 3s. Last read position: chr19:1,206,416
INFO 2026-06-08 07:59:43 MarkDuplicates Tracking 150509 as yet unmatched pairs. 36283 records in RAM.
INFO 2026-06-08 07:59:46 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:14:59s. Time for last 1,000,000: 3s. Last read position: chr19:3,730,464
INFO 2026-06-08 07:59:46 MarkDuplicates Tracking 147205 as yet unmatched pairs. 32756 records in RAM.
INFO 2026-06-08 07:59:49 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:15:02s. Time for last 1,000,000: 3s. Last read position: chr19:7,019,362
INFO 2026-06-08 07:59:49 MarkDuplicates Tracking 144842 as yet unmatched pairs. 30190 records in RAM.
INFO 2026-06-08 07:59:53 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:15:06s. Time for last 1,000,000: 3s. Last read position: chr19:8,960,969
INFO 2026-06-08 07:59:53 MarkDuplicates Tracking 143521 as yet unmatched pairs. 28636 records in RAM.
INFO 2026-06-08 07:59:56 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:15:09s. Time for last 1,000,000: 3s. Last read position: chr19:11,227,240
INFO 2026-06-08 07:59:56 MarkDuplicates Tracking 140823 as yet unmatched pairs. 25737 records in RAM.
INFO 2026-06-08 08:00:00 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:15:13s. Time for last 1,000,000: 3s. Last read position: chr19:15,052,135
INFO 2026-06-08 08:00:00 MarkDuplicates Tracking 138433 as yet unmatched pairs. 23077 records in RAM.
INFO 2026-06-08 08:00:04 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:15:17s. Time for last 1,000,000: 4s. Last read position: chr19:17,832,414
INFO 2026-06-08 08:00:04 MarkDuplicates Tracking 136367 as yet unmatched pairs. 20833 records in RAM.
INFO 2026-06-08 08:00:08 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:15:21s. Time for last 1,000,000: 3s. Last read position: chr19:33,113,970
INFO 2026-06-08 08:00:08 MarkDuplicates Tracking 132876 as yet unmatched pairs. 16941 records in RAM.
INFO 2026-06-08 08:00:11 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:15:24s. Time for last 1,000,000: 3s. Last read position: chr19:38,469,781
INFO 2026-06-08 08:00:11 MarkDuplicates Tracking 130362 as yet unmatched pairs. 14189 records in RAM.
INFO 2026-06-08 08:00:14 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:15:27s. Time for last 1,000,000: 3s. Last read position: chr19:41,248,773
INFO 2026-06-08 08:00:14 MarkDuplicates Tracking 128466 as yet unmatched pairs. 12056 records in RAM.
INFO 2026-06-08 08:00:17 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:15:30s. Time for last 1,000,000: 2s. Last read position: chr19:44,872,002
INFO 2026-06-08 08:00:17 MarkDuplicates Tracking 126040 as yet unmatched pairs. 9384 records in RAM.
INFO 2026-06-08 08:00:20 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:15:33s. Time for last 1,000,000: 2s. Last read position: chr19:48,306,177
INFO 2026-06-08 08:00:20 MarkDuplicates Tracking 123714 as yet unmatched pairs. 6839 records in RAM.
INFO 2026-06-08 08:00:23 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:15:36s. Time for last 1,000,000: 3s. Last read position: chr19:51,341,264
INFO 2026-06-08 08:00:23 MarkDuplicates Tracking 121749 as yet unmatched pairs. 4657 records in RAM.
INFO 2026-06-08 08:00:27 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:15:40s. Time for last 1,000,000: 3s. Last read position: chr19:55,241,310
INFO 2026-06-08 08:00:27 MarkDuplicates Tracking 119404 as yet unmatched pairs. 2088 records in RAM.
INFO 2026-06-08 08:00:30 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:15:43s. Time for last 1,000,000: 3s. Last read position: chr20:2,796,406
INFO 2026-06-08 08:00:30 MarkDuplicates Tracking 116876 as yet unmatched pairs. 21751 records in RAM.
INFO 2026-06-08 08:00:34 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:15:47s. Time for last 1,000,000: 3s. Last read position: chr20:20,511,000
INFO 2026-06-08 08:00:34 MarkDuplicates Tracking 112356 as yet unmatched pairs. 16815 records in RAM.
INFO 2026-06-08 08:00:37 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:15:50s. Time for last 1,000,000: 2s. Last read position: chr20:32,807,986
INFO 2026-06-08 08:00:37 MarkDuplicates Tracking 110329 as yet unmatched pairs. 14434 records in RAM.
INFO 2026-06-08 08:00:39 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:15:52s. Time for last 1,000,000: 2s. Last read position: chr20:38,952,024
INFO 2026-06-08 08:00:39 MarkDuplicates Tracking 106510 as yet unmatched pairs. 10404 records in RAM.
INFO 2026-06-08 08:00:41 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:15:54s. Time for last 1,000,000: 2s. Last read position: chr20:46,241,057
INFO 2026-06-08 08:00:41 MarkDuplicates Tracking 103582 as yet unmatched pairs. 7197 records in RAM.
INFO 2026-06-08 08:00:44 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:15:57s. Time for last 1,000,000: 2s. Last read position: chr20:58,692,925
INFO 2026-06-08 08:00:44 MarkDuplicates Tracking 99909 as yet unmatched pairs. 3197 records in RAM.
INFO 2026-06-08 08:00:46 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:15:59s. Time for last 1,000,000: 2s. Last read position: chr20:63,956,175
INFO 2026-06-08 08:00:46 MarkDuplicates Tracking 97302 as yet unmatched pairs. 354 records in RAM.
INFO 2026-06-08 08:00:49 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:16:02s. Time for last 1,000,000: 2s. Last read position: chr21:8,444,000
INFO 2026-06-08 08:00:49 MarkDuplicates Tracking 95993 as yet unmatched pairs. 13613 records in RAM.
INFO 2026-06-08 08:00:52 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:16:05s. Time for last 1,000,000: 3s. Last read position: chr21:31,968,304
INFO 2026-06-08 08:00:52 MarkDuplicates Tracking 90827 as yet unmatched pairs. 8011 records in RAM.
INFO 2026-06-08 08:00:55 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:16:08s. Time for last 1,000,000: 3s. Last read position: chr21:41,467,723
INFO 2026-06-08 08:00:55 MarkDuplicates Tracking 87733 as yet unmatched pairs. 4668 records in RAM.
INFO 2026-06-08 08:00:58 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:16:11s. Time for last 1,000,000: 3s. Last read position: chr21:44,120,646
INFO 2026-06-08 08:00:58 MarkDuplicates Tracking 85121 as yet unmatched pairs. 1882 records in RAM.
INFO 2026-06-08 08:01:02 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:16:15s. Time for last 1,000,000: 3s. Last read position: chr22:16,189,235
INFO 2026-06-08 08:01:02 MarkDuplicates Tracking 82393 as yet unmatched pairs. 20926 records in RAM.
INFO 2026-06-08 08:01:05 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:16:18s. Time for last 1,000,000: 3s. Last read position: chr22:20,697,313
INFO 2026-06-08 08:01:05 MarkDuplicates Tracking 81631 as yet unmatched pairs. 20038 records in RAM.
INFO 2026-06-08 08:01:07 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:16:20s. Time for last 1,000,000: 2s. Last read position: chr22:21,788,676
INFO 2026-06-08 08:01:07 MarkDuplicates Tracking 78906 as yet unmatched pairs. 17235 records in RAM.
INFO 2026-06-08 08:01:10 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:16:23s. Time for last 1,000,000: 2s. Last read position: chr22:23,292,335
INFO 2026-06-08 08:01:10 MarkDuplicates Tracking 77394 as yet unmatched pairs. 15597 records in RAM.
INFO 2026-06-08 08:01:13 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:16:26s. Time for last 1,000,000: 3s. Last read position: chr22:24,652,025
INFO 2026-06-08 08:01:13 MarkDuplicates Tracking 75878 as yet unmatched pairs. 13961 records in RAM.
INFO 2026-06-08 08:01:16 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:16:29s. Time for last 1,000,000: 3s. Last read position: chr22:29,697,491
INFO 2026-06-08 08:01:16 MarkDuplicates Tracking 71931 as yet unmatched pairs. 9868 records in RAM.
INFO 2026-06-08 08:01:20 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:16:33s. Time for last 1,000,000: 3s. Last read position: chr22:37,851,223
INFO 2026-06-08 08:01:20 MarkDuplicates Tracking 68376 as yet unmatched pairs. 6172 records in RAM.
INFO 2026-06-08 08:01:23 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:16:36s. Time for last 1,000,000: 2s. Last read position: chr22:42,140,278
INFO 2026-06-08 08:01:23 MarkDuplicates Tracking 66538 as yet unmatched pairs. 4214 records in RAM.
INFO 2026-06-08 08:01:25 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:16:38s. Time for last 1,000,000: 2s. Last read position: chr22:50,721,385
INFO 2026-06-08 08:01:25 MarkDuplicates Tracking 62676 as yet unmatched pairs. 191 records in RAM.
INFO 2026-06-08 08:01:28 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:16:41s. Time for last 1,000,000: 3s. Last read position: chrX:15,824,471
INFO 2026-06-08 08:01:28 MarkDuplicates Tracking 59152 as yet unmatched pairs. 52387 records in RAM.
INFO 2026-06-08 08:01:31 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:16:44s. Time for last 1,000,000: 2s. Last read position: chrX:34,943,014
INFO 2026-06-08 08:01:31 MarkDuplicates Tracking 53781 as yet unmatched pairs. 46993 records in RAM.
INFO 2026-06-08 08:01:33 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:16:46s. Time for last 1,000,000: 2s. Last read position: chrX:47,058,691
INFO 2026-06-08 08:01:33 MarkDuplicates Tracking 49219 as yet unmatched pairs. 42422 records in RAM.
INFO 2026-06-08 08:01:35 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:16:48s. Time for last 1,000,000: 2s. Last read position: chrX:49,326,694
INFO 2026-06-08 08:01:35 MarkDuplicates Tracking 46809 as yet unmatched pairs. 40000 records in RAM.
INFO 2026-06-08 08:01:37 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:16:50s. Time for last 1,000,000: 1s. Last read position: chrX:53,374,284
INFO 2026-06-08 08:01:37 MarkDuplicates Tracking 46128 as yet unmatched pairs. 39305 records in RAM.
INFO 2026-06-08 08:01:39 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:16:52s. Time for last 1,000,000: 2s. Last read position: chrX:67,062,599
INFO 2026-06-08 08:01:39 MarkDuplicates Tracking 41046 as yet unmatched pairs. 34195 records in RAM.
INFO 2026-06-08 08:01:42 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:16:55s. Time for last 1,000,000: 2s. Last read position: chrX:67,735,646
INFO 2026-06-08 08:01:42 MarkDuplicates Tracking 38610 as yet unmatched pairs. 31739 records in RAM.
INFO 2026-06-08 08:01:44 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:16:57s. Time for last 1,000,000: 2s. Last read position: chrX:72,938,655
INFO 2026-06-08 08:01:44 MarkDuplicates Tracking 36492 as yet unmatched pairs. 29596 records in RAM.
INFO 2026-06-08 08:01:47 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:17:00s. Time for last 1,000,000: 2s. Last read position: chrX:92,114,125
INFO 2026-06-08 08:01:47 MarkDuplicates Tracking 30422 as yet unmatched pairs. 23499 records in RAM.
INFO 2026-06-08 08:01:51 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:17:03s. Time for last 1,000,000: 3s. Last read position: chrX:107,597,641
INFO 2026-06-08 08:01:51 MarkDuplicates Tracking 25821 as yet unmatched pairs. 18876 records in RAM.
INFO 2026-06-08 08:01:54 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:17:07s. Time for last 1,000,000: 3s. Last read position: chrX:120,873,688
INFO 2026-06-08 08:01:54 MarkDuplicates Tracking 21430 as yet unmatched pairs. 14462 records in RAM.
INFO 2026-06-08 08:01:57 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:17:10s. Time for last 1,000,000: 2s. Last read position: chrX:130,025,102
INFO 2026-06-08 08:01:57 MarkDuplicates Tracking 18477 as yet unmatched pairs. 11493 records in RAM.
INFO 2026-06-08 08:02:00 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:17:13s. Time for last 1,000,000: 2s. Last read position: chrX:135,867,887
INFO 2026-06-08 08:02:00 MarkDuplicates Tracking 17212 as yet unmatched pairs. 10213 records in RAM.
INFO 2026-06-08 08:02:03 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:17:16s. Time for last 1,000,000: 2s. Last read position: chrX:152,652,891
INFO 2026-06-08 08:02:03 MarkDuplicates Tracking 10105 as yet unmatched pairs. 3084 records in RAM.
INFO 2026-06-08 08:02:05 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:17:18s. Time for last 1,000,000: 2s. Last read position: chrX:154,468,730
INFO 2026-06-08 08:02:05 MarkDuplicates Tracking 8530 as yet unmatched pairs. 1504 records in RAM.
INFO 2026-06-08 08:02:07 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:17:20s. Time for last 1,000,000: 2s. Last read position: GL000224.1:6,399
INFO 2026-06-08 08:02:07 MarkDuplicates Tracking 4722 as yet unmatched pairs. 131 records in RAM.
INFO 2026-06-08 08:02:09 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:17:22s. Time for last 1,000,000: 2s. Last read position: KI270733.1:176,055
INFO 2026-06-08 08:02:09 MarkDuplicates Tracking 1527 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 08:02:11 MarkDuplicates Read 309447778 records. 0 pairs never matched.
INFO 2026-06-08 08:02:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 28440419224; totalMemory: 40600862720; maxMemory: 63585648640
INFO 2026-06-08 08:02:44 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:02:59 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:03:28 MarkDuplicates Traversing fragment information and detecting duplicates.
WARNING 2026-06-08 08:03:29 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
INFO 2026-06-08 08:04:25 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:04:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300796448; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-08 08:04:30 MarkDuplicates Marking 61612066 records as duplicates.
INFO 2026-06-08 08:04:30 MarkDuplicates Found 11053760 optical duplicate clusters.
INFO 2026-06-08 08:04:30 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 08:05:03 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:33s. Time for last 10,000,000: 33s. Last read position: chr1:58,782,756
INFO 2026-06-08 08:05:37 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:01:07s. Time for last 10,000,000: 33s. Last read position: chr1:161,038,496
INFO 2026-06-08 08:06:08 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:38s. Time for last 10,000,000: 31s. Last read position: chr2:25,281,472