Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/a8003a48e9154766d573a25cae4276/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/a8003a48e9154766d573a25cae4276/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/eb1b4bc33e6f99dbd09d96c103560c/aih-tih-sc-19e09e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.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 aih-tih-sc-19e09e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bam --METRICS_FILE aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
08:30:08.226 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Jun 08 08:30:08 GMT 2026] MarkDuplicates --INPUT aih-tih-sc-19e09e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bam --METRICS_FILE aih-tih-sc-19e09e-R1_A23WJ53LT4_1.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 08:30:08 GMT 2026] Executing as ?@nf-b1a8003a48e9154766d573a25cae4276-d494e-8htsl on Linux 6.12.88 amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0
INFO 2026-06-08 08:30:08 MarkDuplicates Start of doWork freeMemory: 105828544; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 08:30:08 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 08:30:08 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 08:30:12 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:1,315,562
INFO 2026-06-08 08:30:12 MarkDuplicates Tracking 1612 as yet unmatched pairs. 82 records in RAM.
INFO 2026-06-08 08:30:14 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: chr1:3,825,797
INFO 2026-06-08 08:30:14 MarkDuplicates Tracking 3207 as yet unmatched pairs. 22 records in RAM.
INFO 2026-06-08 08:30:16 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: chr1:8,864,081
INFO 2026-06-08 08:30:16 MarkDuplicates Tracking 6003 as yet unmatched pairs. 1360 records in RAM.
INFO 2026-06-08 08:30:18 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: chr1:11,285,893
INFO 2026-06-08 08:30:18 MarkDuplicates Tracking 6188 as yet unmatched pairs. 64 records in RAM.
INFO 2026-06-08 08:30:20 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 2s. Last read position: chr1:15,937,389
INFO 2026-06-08 08:30:20 MarkDuplicates Tracking 7727 as yet unmatched pairs. 83 records in RAM.
INFO 2026-06-08 08:30:21 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: chr1:19,235,181
INFO 2026-06-08 08:30:21 MarkDuplicates Tracking 9246 as yet unmatched pairs. 209 records in RAM.
INFO 2026-06-08 08:30:24 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: chr1:21,827,891
INFO 2026-06-08 08:30:24 MarkDuplicates Tracking 10766 as yet unmatched pairs. 345 records in RAM.
INFO 2026-06-08 08:30:26 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: chr1:21,875,974
INFO 2026-06-08 08:30:26 MarkDuplicates Tracking 12191 as yet unmatched pairs. 172 records in RAM.
INFO 2026-06-08 08:30:27 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: chr1:22,660,955
INFO 2026-06-08 08:30:27 MarkDuplicates Tracking 14363 as yet unmatched pairs. 791 records in RAM.
INFO 2026-06-08 08:30:29 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 2s. Last read position: chr1:25,352,916
INFO 2026-06-08 08:30:29 MarkDuplicates Tracking 15837 as yet unmatched pairs. 921 records in RAM.
INFO 2026-06-08 08:30:31 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 1s. Last read position: chr1:28,236,268
INFO 2026-06-08 08:30:31 MarkDuplicates Tracking 16687 as yet unmatched pairs. 334 records in RAM.
INFO 2026-06-08 08:30:33 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 2s. Last read position: chr1:32,195,089
INFO 2026-06-08 08:30:33 MarkDuplicates Tracking 17853 as yet unmatched pairs. 30 records in RAM.
INFO 2026-06-08 08:30:35 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 1s. Last read position: chr1:35,883,429
INFO 2026-06-08 08:30:35 MarkDuplicates Tracking 19503 as yet unmatched pairs. 127 records in RAM.
INFO 2026-06-08 08:30:36 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 1s. Last read position: chr1:39,525,808
INFO 2026-06-08 08:30:36 MarkDuplicates Tracking 20871 as yet unmatched pairs. 41 records in RAM.
INFO 2026-06-08 08:30:38 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 1s. Last read position: chr1:43,365,213
INFO 2026-06-08 08:30:38 MarkDuplicates Tracking 22698 as yet unmatched pairs. 428 records in RAM.
INFO 2026-06-08 08:30:39 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 1s. Last read position: chr1:45,568,607
INFO 2026-06-08 08:30:39 MarkDuplicates Tracking 24021 as yet unmatched pairs. 337 records in RAM.
INFO 2026-06-08 08:30:41 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 2s. Last read position: chr1:48,305,787
INFO 2026-06-08 08:30:41 MarkDuplicates Tracking 25368 as yet unmatched pairs. 46 records in RAM.
INFO 2026-06-08 08:30:43 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 1s. Last read position: chr1:55,162,199
INFO 2026-06-08 08:30:43 MarkDuplicates Tracking 26979 as yet unmatched pairs. 236 records in RAM.
INFO 2026-06-08 08:30:45 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 1s. Last read position: chr1:65,431,817
INFO 2026-06-08 08:30:45 MarkDuplicates Tracking 28803 as yet unmatched pairs. 697 records in RAM.
INFO 2026-06-08 08:30:46 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 1s. Last read position: chr1:86,704,835
INFO 2026-06-08 08:30:46 MarkDuplicates Tracking 29375 as yet unmatched pairs. 58 records in RAM.
INFO 2026-06-08 08:30:48 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 1s. Last read position: chr1:98,661,834
INFO 2026-06-08 08:30:48 MarkDuplicates Tracking 30643 as yet unmatched pairs. 44 records in RAM.
INFO 2026-06-08 08:30:49 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 1s. Last read position: chr1:109,656,775
INFO 2026-06-08 08:30:49 MarkDuplicates Tracking 32421 as yet unmatched pairs. 195 records in RAM.
INFO 2026-06-08 08:30:52 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chr1:113,981,666
INFO 2026-06-08 08:30:52 MarkDuplicates Tracking 33743 as yet unmatched pairs. 25 records in RAM.
INFO 2026-06-08 08:30:54 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 2s. Last read position: chr1:119,917,707
INFO 2026-06-08 08:30:54 MarkDuplicates Tracking 36290 as yet unmatched pairs. 1339 records in RAM.
INFO 2026-06-08 08:30:55 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 1s. Last read position: chr1:120,840,461
INFO 2026-06-08 08:30:55 MarkDuplicates Tracking 36192 as yet unmatched pairs. 42 records in RAM.
INFO 2026-06-08 08:30:56 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 1s. Last read position: chr1:146,164,863
INFO 2026-06-08 08:30:56 MarkDuplicates Tracking 37096 as yet unmatched pairs. 100 records in RAM.
INFO 2026-06-08 08:30:58 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 1s. Last read position: chr1:149,082,170
INFO 2026-06-08 08:30:58 MarkDuplicates Tracking 37642 as yet unmatched pairs. 46 records in RAM.
INFO 2026-06-08 08:30:59 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 1s. Last read position: chr1:150,627,517
INFO 2026-06-08 08:30:59 MarkDuplicates Tracking 39391 as yet unmatched pairs. 576 records in RAM.
INFO 2026-06-08 08:31:00 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 1s. Last read position: chr1:152,214,183
INFO 2026-06-08 08:31:00 MarkDuplicates Tracking 40457 as yet unmatched pairs. 209 records in RAM.
INFO 2026-06-08 08:31:02 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 1s. Last read position: chr1:154,157,639
INFO 2026-06-08 08:31:02 MarkDuplicates Tracking 42809 as yet unmatched pairs. 1318 records in RAM.
INFO 2026-06-08 08:31:03 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 1s. Last read position: chr1:155,015,004
INFO 2026-06-08 08:31:03 MarkDuplicates Tracking 42999 as yet unmatched pairs. 42 records in RAM.
INFO 2026-06-08 08:31:05 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 1s. Last read position: chr1:155,753,401
INFO 2026-06-08 08:31:05 MarkDuplicates Tracking 44369 as yet unmatched pairs. 79 records in RAM.
INFO 2026-06-08 08:31:06 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 1s. Last read position: chr1:156,672,646
INFO 2026-06-08 08:31:06 MarkDuplicates Tracking 45907 as yet unmatched pairs. 100 records in RAM.
INFO 2026-06-08 08:31:08 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 1s. Last read position: chr1:160,999,732
INFO 2026-06-08 08:31:08 MarkDuplicates Tracking 47272 as yet unmatched pairs. 116 records in RAM.
INFO 2026-06-08 08:31:09 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 1s. Last read position: chr1:163,152,615
INFO 2026-06-08 08:31:09 MarkDuplicates Tracking 50302 as yet unmatched pairs. 1769 records in RAM.
INFO 2026-06-08 08:31:11 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 1s. Last read position: chr1:169,124,954
INFO 2026-06-08 08:31:11 MarkDuplicates Tracking 55416 as yet unmatched pairs. 5231 records in RAM.
INFO 2026-06-08 08:31:13 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 1s. Last read position: chr1:171,783,887
INFO 2026-06-08 08:31:13 MarkDuplicates Tracking 51658 as yet unmatched pairs. 136 records in RAM.
INFO 2026-06-08 08:31:14 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 1s. Last read position: chr1:182,884,706
INFO 2026-06-08 08:31:14 MarkDuplicates Tracking 53111 as yet unmatched pairs. 171 records in RAM.
INFO 2026-06-08 08:31:16 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 1s. Last read position: chr1:186,426,714
INFO 2026-06-08 08:31:16 MarkDuplicates Tracking 54293 as yet unmatched pairs. 0 records in RAM.
INFO 2026-06-08 08:31:18 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 1s. Last read position: chr1:203,347,413
INFO 2026-06-08 08:31:18 MarkDuplicates Tracking 55854 as yet unmatched pairs. 103 records in RAM.
INFO 2026-06-08 08:31:19 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 1s. Last read position: chr1:206,450,385
INFO 2026-06-08 08:31:19 MarkDuplicates Tracking 57119 as yet unmatched pairs. 40 records in RAM.
INFO 2026-06-08 08:31:21 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 1s. Last read position: chr1:212,442,576
INFO 2026-06-08 08:31:21 MarkDuplicates Tracking 58862 as yet unmatched pairs. 282 records in RAM.
INFO 2026-06-08 08:31:23 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 2s. Last read position: chr1:224,300,562
INFO 2026-06-08 08:31:23 MarkDuplicates Tracking 60005 as yet unmatched pairs. 78 records in RAM.
INFO 2026-06-08 08:31:25 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 1s. Last read position: chr1:228,250,020
INFO 2026-06-08 08:31:25 MarkDuplicates Tracking 61589 as yet unmatched pairs. 100 records in RAM.
INFO 2026-06-08 08:31:26 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 1s. Last read position: chr1:233,054,460
INFO 2026-06-08 08:31:26 MarkDuplicates Tracking 63268 as yet unmatched pairs. 7 records in RAM.
INFO 2026-06-08 08:31:28 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 1s. Last read position: chr1:243,552,907
INFO 2026-06-08 08:31:28 MarkDuplicates Tracking 65013 as yet unmatched pairs. 373 records in RAM.
INFO 2026-06-08 08:31:29 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 1s. Last read position: chr2:6,865,541
INFO 2026-06-08 08:31:29 MarkDuplicates Tracking 66105 as yet unmatched pairs. 66037 records in RAM.
INFO 2026-06-08 08:31:31 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 1s. Last read position: chr2:20,037,538
INFO 2026-06-08 08:31:31 MarkDuplicates Tracking 69736 as yet unmatched pairs. 69666 records in RAM.
INFO 2026-06-08 08:31:32 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 1s. Last read position: chr2:26,215,151
INFO 2026-06-08 08:31:32 MarkDuplicates Tracking 69451 as yet unmatched pairs. 69380 records in RAM.
INFO 2026-06-08 08:31:34 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 1s. Last read position: chr2:27,894,659
INFO 2026-06-08 08:31:34 MarkDuplicates Tracking 70835 as yet unmatched pairs. 70757 records in RAM.
INFO 2026-06-08 08:31:36 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,254
INFO 2026-06-08 08:31:36 MarkDuplicates Tracking 88436 as yet unmatched pairs. 70807 records in RAM.
INFO 2026-06-08 08:31:38 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,395
INFO 2026-06-08 08:31:38 MarkDuplicates Tracking 581028 as yet unmatched pairs. 43888 records in RAM.
INFO 2026-06-08 08:31:39 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 1s. Last read position: chr2:36,441,387
INFO 2026-06-08 08:31:39 MarkDuplicates Tracking 631279 as yet unmatched pairs. 41064 records in RAM.
INFO 2026-06-08 08:31:41 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 1s. Last read position: chr2:42,767,601
INFO 2026-06-08 08:31:41 MarkDuplicates Tracking 629645 as yet unmatched pairs. 39430 records in RAM.
INFO 2026-06-08 08:31:42 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 1s. Last read position: chr2:46,376,710
INFO 2026-06-08 08:31:42 MarkDuplicates Tracking 628624 as yet unmatched pairs. 38409 records in RAM.
INFO 2026-06-08 08:31:44 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 1s. Last read position: chr2:54,973,826
INFO 2026-06-08 08:31:44 MarkDuplicates Tracking 627747 as yet unmatched pairs. 37532 records in RAM.
INFO 2026-06-08 08:31:45 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 1s. Last read position: chr2:64,095,130
INFO 2026-06-08 08:31:45 MarkDuplicates Tracking 625305 as yet unmatched pairs. 35089 records in RAM.
INFO 2026-06-08 08:31:47 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 1s. Last read position: chr2:70,261,328
INFO 2026-06-08 08:31:47 MarkDuplicates Tracking 624112 as yet unmatched pairs. 33891 records in RAM.
INFO 2026-06-08 08:31:48 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 1s. Last read position: chr2:74,208,616
INFO 2026-06-08 08:31:48 MarkDuplicates Tracking 622289 as yet unmatched pairs. 32067 records in RAM.
INFO 2026-06-08 08:31:50 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 1s. Last read position: chr2:85,401,263
INFO 2026-06-08 08:31:50 MarkDuplicates Tracking 620922 as yet unmatched pairs. 30694 records in RAM.
INFO 2026-06-08 08:31:51 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 1s. Last read position: chr2:96,195,443
INFO 2026-06-08 08:31:51 MarkDuplicates Tracking 619759 as yet unmatched pairs. 29528 records in RAM.
INFO 2026-06-08 08:31:52 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 1s. Last read position: chr2:101,022,456
INFO 2026-06-08 08:31:52 MarkDuplicates Tracking 618288 as yet unmatched pairs. 28054 records in RAM.
INFO 2026-06-08 08:31:54 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 1s. Last read position: chr2:108,767,765
INFO 2026-06-08 08:31:54 MarkDuplicates Tracking 617420 as yet unmatched pairs. 27185 records in RAM.
INFO 2026-06-08 08:31:55 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 1s. Last read position: chr2:113,216,426
INFO 2026-06-08 08:31:55 MarkDuplicates Tracking 616430 as yet unmatched pairs. 26193 records in RAM.
INFO 2026-06-08 08:31:57 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 1s. Last read position: chr2:126,656,293
INFO 2026-06-08 08:31:57 MarkDuplicates Tracking 615107 as yet unmatched pairs. 24869 records in RAM.
INFO 2026-06-08 08:31:58 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 1s. Last read position: chr2:136,114,992
INFO 2026-06-08 08:31:58 MarkDuplicates Tracking 614453 as yet unmatched pairs. 24215 records in RAM.
INFO 2026-06-08 08:32:00 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 1s. Last read position: chr2:160,286,975
INFO 2026-06-08 08:32:00 MarkDuplicates Tracking 612061 as yet unmatched pairs. 21820 records in RAM.
INFO 2026-06-08 08:32:02 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 2s. Last read position: chr2:169,185,762
INFO 2026-06-08 08:32:02 MarkDuplicates Tracking 611460 as yet unmatched pairs. 21219 records in RAM.
INFO 2026-06-08 08:32:03 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 1s. Last read position: chr2:169,275,213
INFO 2026-06-08 08:32:03 MarkDuplicates Tracking 610116 as yet unmatched pairs. 19875 records in RAM.
INFO 2026-06-08 08:32:05 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 1s. Last read position: chr2:175,937,398
INFO 2026-06-08 08:32:05 MarkDuplicates Tracking 607675 as yet unmatched pairs. 17434 records in RAM.
INFO 2026-06-08 08:32:06 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 1s. Last read position: chr2:186,652,038
INFO 2026-06-08 08:32:06 MarkDuplicates Tracking 607064 as yet unmatched pairs. 16823 records in RAM.
INFO 2026-06-08 08:32:08 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 1s. Last read position: chr2:196,318,552
INFO 2026-06-08 08:32:08 MarkDuplicates Tracking 604743 as yet unmatched pairs. 14499 records in RAM.
INFO 2026-06-08 08:32:09 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 1s. Last read position: chr2:201,638,999
INFO 2026-06-08 08:32:09 MarkDuplicates Tracking 603214 as yet unmatched pairs. 12970 records in RAM.
INFO 2026-06-08 08:32:11 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 1s. Last read position: chr2:215,361,562
INFO 2026-06-08 08:32:11 MarkDuplicates Tracking 603467 as yet unmatched pairs. 13222 records in RAM.
INFO 2026-06-08 08:32:13 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 1s. Last read position: chr2:215,386,906
INFO 2026-06-08 08:32:13 MarkDuplicates Tracking 602840 as yet unmatched pairs. 12593 records in RAM.
INFO 2026-06-08 08:32:14 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 1s. Last read position: chr2:215,428,312
INFO 2026-06-08 08:32:14 MarkDuplicates Tracking 600162 as yet unmatched pairs. 9915 records in RAM.
INFO 2026-06-08 08:32:16 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 1s. Last read position: chr2:217,818,354
INFO 2026-06-08 08:32:16 MarkDuplicates Tracking 599520 as yet unmatched pairs. 9272 records in RAM.
INFO 2026-06-08 08:32:17 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 1s. Last read position: chr2:218,245,451
INFO 2026-06-08 08:32:17 MarkDuplicates Tracking 596669 as yet unmatched pairs. 6421 records in RAM.
INFO 2026-06-08 08:32:19 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 1s. Last read position: chr2:219,541,738
INFO 2026-06-08 08:32:19 MarkDuplicates Tracking 594973 as yet unmatched pairs. 4724 records in RAM.
INFO 2026-06-08 08:32:20 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 1s. Last read position: chr2:231,165,994
INFO 2026-06-08 08:32:20 MarkDuplicates Tracking 593360 as yet unmatched pairs. 3101 records in RAM.
INFO 2026-06-08 08:32:22 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 2s. Last read position: chr2:236,581,503
INFO 2026-06-08 08:32:22 MarkDuplicates Tracking 591929 as yet unmatched pairs. 1663 records in RAM.
INFO 2026-06-08 08:32:24 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 1s. Last read position: chr2:241,735,285
INFO 2026-06-08 08:32:24 MarkDuplicates Tracking 590806 as yet unmatched pairs. 538 records in RAM.
INFO 2026-06-08 08:32:25 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 1s. Last read position: chr3:12,920,477
INFO 2026-06-08 08:32:25 MarkDuplicates Tracking 588970 as yet unmatched pairs. 30164 records in RAM.
INFO 2026-06-08 08:32:27 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 1s. Last read position: chr3:31,747,998
INFO 2026-06-08 08:32:27 MarkDuplicates Tracking 587605 as yet unmatched pairs. 28798 records in RAM.
INFO 2026-06-08 08:32:29 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 1s. Last read position: chr3:41,233,844
INFO 2026-06-08 08:32:29 MarkDuplicates Tracking 586385 as yet unmatched pairs. 27577 records in RAM.
INFO 2026-06-08 08:32:30 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 1s. Last read position: chr3:47,916,133
INFO 2026-06-08 08:32:30 MarkDuplicates Tracking 584985 as yet unmatched pairs. 26174 records in RAM.
INFO 2026-06-08 08:32:31 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr3:49,286,199
INFO 2026-06-08 08:32:31 MarkDuplicates Tracking 583159 as yet unmatched pairs. 24342 records in RAM.
INFO 2026-06-08 08:32:33 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 1s. Last read position: chr3:51,684,429
INFO 2026-06-08 08:32:33 MarkDuplicates Tracking 581598 as yet unmatched pairs. 22780 records in RAM.
INFO 2026-06-08 08:32:34 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 1s. Last read position: chr3:53,865,019
INFO 2026-06-08 08:32:34 MarkDuplicates Tracking 580091 as yet unmatched pairs. 21272 records in RAM.
INFO 2026-06-08 08:32:36 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 1s. Last read position: chr3:64,681,244
INFO 2026-06-08 08:32:36 MarkDuplicates Tracking 578746 as yet unmatched pairs. 19913 records in RAM.
INFO 2026-06-08 08:32:38 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 1s. Last read position: chr3:100,568,833
INFO 2026-06-08 08:32:38 MarkDuplicates Tracking 578069 as yet unmatched pairs. 19235 records in RAM.
INFO 2026-06-08 08:32:39 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 1s. Last read position: chr3:113,457,163
INFO 2026-06-08 08:32:39 MarkDuplicates Tracking 575686 as yet unmatched pairs. 16851 records in RAM.
INFO 2026-06-08 08:32:40 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 1s. Last read position: chr3:122,699,714
INFO 2026-06-08 08:32:40 MarkDuplicates Tracking 574330 as yet unmatched pairs. 15494 records in RAM.
INFO 2026-06-08 08:32:42 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 1s. Last read position: chr3:123,738,987
INFO 2026-06-08 08:32:42 MarkDuplicates Tracking 572806 as yet unmatched pairs. 13969 records in RAM.
INFO 2026-06-08 08:32:43 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 1s. Last read position: chr3:128,625,578
INFO 2026-06-08 08:32:43 MarkDuplicates Tracking 571159 as yet unmatched pairs. 12320 records in RAM.
INFO 2026-06-08 08:32:45 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 1s. Last read position: chr3:131,501,654
INFO 2026-06-08 08:32:45 MarkDuplicates Tracking 569423 as yet unmatched pairs. 10580 records in RAM.
INFO 2026-06-08 08:32:46 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 1s. Last read position: chr3:138,068,217
INFO 2026-06-08 08:32:46 MarkDuplicates Tracking 567890 as yet unmatched pairs. 9047 records in RAM.
INFO 2026-06-08 08:32:48 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 1s. Last read position: chr3:149,178,611
INFO 2026-06-08 08:32:48 MarkDuplicates Tracking 568939 as yet unmatched pairs. 10096 records in RAM.
INFO 2026-06-08 08:32:49 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 1s. Last read position: chr3:150,567,934
INFO 2026-06-08 08:32:49 MarkDuplicates Tracking 565256 as yet unmatched pairs. 6413 records in RAM.
INFO 2026-06-08 08:32:51 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 1s. Last read position: chr3:171,676,719
INFO 2026-06-08 08:32:51 MarkDuplicates Tracking 563773 as yet unmatched pairs. 4929 records in RAM.
INFO 2026-06-08 08:32:52 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 1s. Last read position: chr3:184,177,036
INFO 2026-06-08 08:32:52 MarkDuplicates Tracking 562701 as yet unmatched pairs. 3848 records in RAM.
INFO 2026-06-08 08:32:53 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 1s. Last read position: chr3:187,729,472
INFO 2026-06-08 08:32:53 MarkDuplicates Tracking 561218 as yet unmatched pairs. 2364 records in RAM.
INFO 2026-06-08 08:32:55 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 1s. Last read position: chr3:195,725,015
INFO 2026-06-08 08:32:55 MarkDuplicates Tracking 559842 as yet unmatched pairs. 987 records in RAM.
INFO 2026-06-08 08:32:56 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 1s. Last read position: chr4:1,025,200
INFO 2026-06-08 08:32:56 MarkDuplicates Tracking 558417 as yet unmatched pairs. 21221 records in RAM.
INFO 2026-06-08 08:32:58 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 1s. Last read position: chr4:3,146,845
INFO 2026-06-08 08:32:58 MarkDuplicates Tracking 556903 as yet unmatched pairs. 19706 records in RAM.
INFO 2026-06-08 08:33:00 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 1s. Last read position: chr4:13,602,065
INFO 2026-06-08 08:33:00 MarkDuplicates Tracking 555195 as yet unmatched pairs. 17998 records in RAM.
INFO 2026-06-08 08:33:01 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 1s. Last read position: chr4:25,670,813
INFO 2026-06-08 08:33:01 MarkDuplicates Tracking 554002 as yet unmatched pairs. 16805 records in RAM.
INFO 2026-06-08 08:33:03 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 1s. Last read position: chr4:41,143,018
INFO 2026-06-08 08:33:03 MarkDuplicates Tracking 552522 as yet unmatched pairs. 15324 records in RAM.
INFO 2026-06-08 08:33:04 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 1s. Last read position: chr4:56,931,062
INFO 2026-06-08 08:33:04 MarkDuplicates Tracking 551012 as yet unmatched pairs. 13811 records in RAM.
INFO 2026-06-08 08:33:06 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 1s. Last read position: chr4:71,450,389
INFO 2026-06-08 08:33:06 MarkDuplicates Tracking 549816 as yet unmatched pairs. 12615 records in RAM.
INFO 2026-06-08 08:33:08 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 1s. Last read position: chr4:78,470,081
INFO 2026-06-08 08:33:08 MarkDuplicates Tracking 548021 as yet unmatched pairs. 10818 records in RAM.
INFO 2026-06-08 08:33:09 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 1s. Last read position: chr4:87,125,095
INFO 2026-06-08 08:33:09 MarkDuplicates Tracking 546668 as yet unmatched pairs. 9465 records in RAM.
INFO 2026-06-08 08:33:11 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 2s. Last read position: chr4:87,982,638
INFO 2026-06-08 08:33:11 MarkDuplicates Tracking 551103 as yet unmatched pairs. 13900 records in RAM.
INFO 2026-06-08 08:33:13 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 1s. Last read position: chr4:105,234,060
INFO 2026-06-08 08:33:13 MarkDuplicates Tracking 544067 as yet unmatched pairs. 6859 records in RAM.
INFO 2026-06-08 08:33:14 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 1s. Last read position: chr4:118,768,237
INFO 2026-06-08 08:33:14 MarkDuplicates Tracking 542729 as yet unmatched pairs. 5519 records in RAM.
INFO 2026-06-08 08:33:16 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 1s. Last read position: chr4:139,472,702
INFO 2026-06-08 08:33:16 MarkDuplicates Tracking 541350 as yet unmatched pairs. 4140 records in RAM.
INFO 2026-06-08 08:33:18 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 1s. Last read position: chr4:153,602,314
INFO 2026-06-08 08:33:18 MarkDuplicates Tracking 540058 as yet unmatched pairs. 2835 records in RAM.
INFO 2026-06-08 08:33:19 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 1s. Last read position: chr4:163,166,615
INFO 2026-06-08 08:33:19 MarkDuplicates Tracking 538680 as yet unmatched pairs. 1456 records in RAM.
INFO 2026-06-08 08:33:21 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 1s. Last read position: chr4:186,708,943
INFO 2026-06-08 08:33:21 MarkDuplicates Tracking 537512 as yet unmatched pairs. 284 records in RAM.
INFO 2026-06-08 08:33:23 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 1s. Last read position: chr5:5,460,942
INFO 2026-06-08 08:33:23 MarkDuplicates Tracking 535791 as yet unmatched pairs. 53527 records in RAM.
INFO 2026-06-08 08:33:24 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 1s. Last read position: chr5:14,316,612
INFO 2026-06-08 08:33:24 MarkDuplicates Tracking 534896 as yet unmatched pairs. 52631 records in RAM.
INFO 2026-06-08 08:33:26 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 1s. Last read position: chr5:31,197,814
INFO 2026-06-08 08:33:26 MarkDuplicates Tracking 532793 as yet unmatched pairs. 50527 records in RAM.
INFO 2026-06-08 08:33:27 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 1s. Last read position: chr5:34,823,461
INFO 2026-06-08 08:33:27 MarkDuplicates Tracking 531409 as yet unmatched pairs. 49143 records in RAM.
INFO 2026-06-08 08:33:29 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 1s. Last read position: chr5:39,394,234
INFO 2026-06-08 08:33:29 MarkDuplicates Tracking 531509 as yet unmatched pairs. 49242 records in RAM.
INFO 2026-06-08 08:33:30 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 1s. Last read position: chr5:54,979,054
INFO 2026-06-08 08:33:30 MarkDuplicates Tracking 528736 as yet unmatched pairs. 46469 records in RAM.
INFO 2026-06-08 08:33:32 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: chr5:66,788,746
INFO 2026-06-08 08:33:32 MarkDuplicates Tracking 527781 as yet unmatched pairs. 45514 records in RAM.
INFO 2026-06-08 08:33:33 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 1s. Last read position: chr5:73,087,642
INFO 2026-06-08 08:33:33 MarkDuplicates Tracking 526376 as yet unmatched pairs. 44104 records in RAM.
INFO 2026-06-08 08:33:35 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 1s. Last read position: chr5:79,077,504
INFO 2026-06-08 08:33:35 MarkDuplicates Tracking 526440 as yet unmatched pairs. 44166 records in RAM.
INFO 2026-06-08 08:33:37 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 1s. Last read position: chr5:83,541,316
INFO 2026-06-08 08:33:37 MarkDuplicates Tracking 523523 as yet unmatched pairs. 41248 records in RAM.
INFO 2026-06-08 08:33:38 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 1s. Last read position: chr5:96,748,516
INFO 2026-06-08 08:33:38 MarkDuplicates Tracking 522005 as yet unmatched pairs. 39712 records in RAM.
INFO 2026-06-08 08:33:40 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 1s. Last read position: chr5:113,008,017
INFO 2026-06-08 08:33:40 MarkDuplicates Tracking 520620 as yet unmatched pairs. 38326 records in RAM.
INFO 2026-06-08 08:33:41 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 1s. Last read position: chr5:131,162,651
INFO 2026-06-08 08:33:41 MarkDuplicates Tracking 521552 as yet unmatched pairs. 39253 records in RAM.
INFO 2026-06-08 08:33:42 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 1s. Last read position: chr5:134,560,926
INFO 2026-06-08 08:33:42 MarkDuplicates Tracking 517694 as yet unmatched pairs. 35392 records in RAM.
INFO 2026-06-08 08:33:44 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 1s. Last read position: chr5:137,753,723
INFO 2026-06-08 08:33:44 MarkDuplicates Tracking 516360 as yet unmatched pairs. 34058 records in RAM.
INFO 2026-06-08 08:33:46 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 1s. Last read position: chr5:139,457,764
INFO 2026-06-08 08:33:46 MarkDuplicates Tracking 514981 as yet unmatched pairs. 32677 records in RAM.
INFO 2026-06-08 08:33:47 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 1s. Last read position: chr5:141,122,610
INFO 2026-06-08 08:33:47 MarkDuplicates Tracking 513284 as yet unmatched pairs. 30937 records in RAM.
INFO 2026-06-08 08:33:48 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 1s. Last read position: chr5:141,376,057
INFO 2026-06-08 08:33:48 MarkDuplicates Tracking 511743 as yet unmatched pairs. 29396 records in RAM.
INFO 2026-06-08 08:33:50 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 1s. Last read position: chr5:142,006,210
INFO 2026-06-08 08:33:50 MarkDuplicates Tracking 510335 as yet unmatched pairs. 27988 records in RAM.
INFO 2026-06-08 08:33:52 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 1s. Last read position: chr5:149,597,836
INFO 2026-06-08 08:33:52 MarkDuplicates Tracking 509350 as yet unmatched pairs. 26998 records in RAM.
INFO 2026-06-08 08:33:53 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 1s. Last read position: chr5:150,401,999
INFO 2026-06-08 08:33:53 MarkDuplicates Tracking 511725 as yet unmatched pairs. 29372 records in RAM.
INFO 2026-06-08 08:33:55 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 1s. Last read position: chr5:150,402,580
INFO 2026-06-08 08:33:55 MarkDuplicates Tracking 532015 as yet unmatched pairs. 49662 records in RAM.
INFO 2026-06-08 08:33:57 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 1s. Last read position: chr5:150,405,093
INFO 2026-06-08 08:33:57 MarkDuplicates Tracking 518797 as yet unmatched pairs. 36442 records in RAM.
INFO 2026-06-08 08:33:59 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 1s. Last read position: chr5:150,406,277
INFO 2026-06-08 08:33:59 MarkDuplicates Tracking 532846 as yet unmatched pairs. 50491 records in RAM.
INFO 2026-06-08 08:34:01 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 2s. Last read position: chr5:150,407,198
INFO 2026-06-08 08:34:01 MarkDuplicates Tracking 511299 as yet unmatched pairs. 28944 records in RAM.
INFO 2026-06-08 08:34:03 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 2s. Last read position: chr5:150,648,052
INFO 2026-06-08 08:34:03 MarkDuplicates Tracking 500310 as yet unmatched pairs. 17955 records in RAM.
INFO 2026-06-08 08:34:05 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 1s. Last read position: chr5:150,656,890
INFO 2026-06-08 08:34:05 MarkDuplicates Tracking 498993 as yet unmatched pairs. 16634 records in RAM.
INFO 2026-06-08 08:34:06 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 1s. Last read position: chr5:151,036,823
INFO 2026-06-08 08:34:06 MarkDuplicates Tracking 497025 as yet unmatched pairs. 14666 records in RAM.
INFO 2026-06-08 08:34:08 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 1s. Last read position: chr5:154,917,995
INFO 2026-06-08 08:34:08 MarkDuplicates Tracking 495125 as yet unmatched pairs. 12766 records in RAM.
INFO 2026-06-08 08:34:09 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 1s. Last read position: chr5:168,414,495
INFO 2026-06-08 08:34:09 MarkDuplicates Tracking 493668 as yet unmatched pairs. 11309 records in RAM.
INFO 2026-06-08 08:34:11 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 1s. Last read position: chr5:171,391,410
INFO 2026-06-08 08:34:11 MarkDuplicates Tracking 494983 as yet unmatched pairs. 12623 records in RAM.
INFO 2026-06-08 08:34:12 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 1s. Last read position: chr5:172,909,695
INFO 2026-06-08 08:34:12 MarkDuplicates Tracking 491483 as yet unmatched pairs. 9123 records in RAM.
INFO 2026-06-08 08:34:14 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 1s. Last read position: chr5:177,135,351
INFO 2026-06-08 08:34:14 MarkDuplicates Tracking 490117 as yet unmatched pairs. 7757 records in RAM.
INFO 2026-06-08 08:34:15 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 1s. Last read position: chr5:178,210,124
INFO 2026-06-08 08:34:15 MarkDuplicates Tracking 488777 as yet unmatched pairs. 6415 records in RAM.
INFO 2026-06-08 08:34:17 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 1s. Last read position: chr5:179,720,424
INFO 2026-06-08 08:34:17 MarkDuplicates Tracking 487748 as yet unmatched pairs. 5380 records in RAM.
INFO 2026-06-08 08:34:19 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 1s. Last read position: chr5:179,824,229
INFO 2026-06-08 08:34:19 MarkDuplicates Tracking 491665 as yet unmatched pairs. 9297 records in RAM.
INFO 2026-06-08 08:34:20 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 1s. Last read position: chr5:180,621,711
INFO 2026-06-08 08:34:20 MarkDuplicates Tracking 483965 as yet unmatched pairs. 1597 records in RAM.
INFO 2026-06-08 08:34:22 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 1s. Last read position: chr6:348,200
INFO 2026-06-08 08:34:22 MarkDuplicates Tracking 482548 as yet unmatched pairs. 39829 records in RAM.
INFO 2026-06-08 08:34:23 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 1s. Last read position: chr6:11,185,131
INFO 2026-06-08 08:34:23 MarkDuplicates Tracking 480840 as yet unmatched pairs. 38119 records in RAM.
INFO 2026-06-08 08:34:25 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 1s. Last read position: chr6:25,983,454
INFO 2026-06-08 08:34:25 MarkDuplicates Tracking 479476 as yet unmatched pairs. 36751 records in RAM.
INFO 2026-06-08 08:34:27 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 1s. Last read position: chr6:29,553,876
INFO 2026-06-08 08:34:27 MarkDuplicates Tracking 478195 as yet unmatched pairs. 35470 records in RAM.
INFO 2026-06-08 08:34:28 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 1s. Last read position: chr6:30,068,683
INFO 2026-06-08 08:34:28 MarkDuplicates Tracking 476880 as yet unmatched pairs. 34155 records in RAM.
INFO 2026-06-08 08:34:30 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 1s. Last read position: chr6:31,269,134
INFO 2026-06-08 08:34:30 MarkDuplicates Tracking 477051 as yet unmatched pairs. 34321 records in RAM.
INFO 2026-06-08 08:34:32 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 1s. Last read position: chr6:31,626,783
INFO 2026-06-08 08:34:32 MarkDuplicates Tracking 473883 as yet unmatched pairs. 31153 records in RAM.
INFO 2026-06-08 08:34:33 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 1s. Last read position: chr6:31,860,502
INFO 2026-06-08 08:34:33 MarkDuplicates Tracking 472625 as yet unmatched pairs. 29895 records in RAM.
INFO 2026-06-08 08:34:34 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 1s. Last read position: chr6:31,994,678
INFO 2026-06-08 08:34:34 MarkDuplicates Tracking 474568 as yet unmatched pairs. 31838 records in RAM.
INFO 2026-06-08 08:34:36 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr6:32,024,910
INFO 2026-06-08 08:34:36 MarkDuplicates Tracking 474271 as yet unmatched pairs. 31541 records in RAM.
INFO 2026-06-08 08:34:37 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 1s. Last read position: chr6:32,121,009
INFO 2026-06-08 08:34:37 MarkDuplicates Tracking 469661 as yet unmatched pairs. 26931 records in RAM.
INFO 2026-06-08 08:34:38 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 1s. Last read position: chr6:32,757,773
INFO 2026-06-08 08:34:38 MarkDuplicates Tracking 468569 as yet unmatched pairs. 25838 records in RAM.
INFO 2026-06-08 08:34:40 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 1s. Last read position: chr6:33,275,849
INFO 2026-06-08 08:34:40 MarkDuplicates Tracking 467057 as yet unmatched pairs. 24326 records in RAM.
INFO 2026-06-08 08:34:41 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 1s. Last read position: chr6:34,418,414
INFO 2026-06-08 08:34:41 MarkDuplicates Tracking 465534 as yet unmatched pairs. 22803 records in RAM.
INFO 2026-06-08 08:34:43 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 1s. Last read position: chr6:41,084,117
INFO 2026-06-08 08:34:43 MarkDuplicates Tracking 463767 as yet unmatched pairs. 21036 records in RAM.
INFO 2026-06-08 08:34:44 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 1s. Last read position: chr6:43,770,673
INFO 2026-06-08 08:34:44 MarkDuplicates Tracking 463449 as yet unmatched pairs. 20718 records in RAM.
INFO 2026-06-08 08:34:46 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 1s. Last read position: chr6:44,135,058
INFO 2026-06-08 08:34:46 MarkDuplicates Tracking 460587 as yet unmatched pairs. 17856 records in RAM.
INFO 2026-06-08 08:34:47 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 1s. Last read position: chr6:52,507,587
INFO 2026-06-08 08:34:47 MarkDuplicates Tracking 459006 as yet unmatched pairs. 16274 records in RAM.
INFO 2026-06-08 08:34:49 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 1s. Last read position: chr6:69,700,789
INFO 2026-06-08 08:34:49 MarkDuplicates Tracking 457952 as yet unmatched pairs. 15211 records in RAM.
INFO 2026-06-08 08:34:51 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 1s. Last read position: chr6:87,215,974
INFO 2026-06-08 08:34:51 MarkDuplicates Tracking 456752 as yet unmatched pairs. 14009 records in RAM.
INFO 2026-06-08 08:34:52 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 1s. Last read position: chr6:106,561,466
INFO 2026-06-08 08:34:52 MarkDuplicates Tracking 455081 as yet unmatched pairs. 12338 records in RAM.
INFO 2026-06-08 08:34:54 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 1s. Last read position: chr6:112,140,844
INFO 2026-06-08 08:34:54 MarkDuplicates Tracking 453630 as yet unmatched pairs. 10885 records in RAM.
INFO 2026-06-08 08:34:56 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 2s. Last read position: chr6:127,981,155
INFO 2026-06-08 08:34:56 MarkDuplicates Tracking 452269 as yet unmatched pairs. 9523 records in RAM.
INFO 2026-06-08 08:34:57 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 1s. Last read position: chr6:138,405,153
INFO 2026-06-08 08:34:57 MarkDuplicates Tracking 450749 as yet unmatched pairs. 8002 records in RAM.
INFO 2026-06-08 08:34:59 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 1s. Last read position: chr6:149,399,104
INFO 2026-06-08 08:34:59 MarkDuplicates Tracking 449272 as yet unmatched pairs. 6525 records in RAM.
INFO 2026-06-08 08:35:01 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 2s. Last read position: chr6:152,353,373
INFO 2026-06-08 08:35:01 MarkDuplicates Tracking 447809 as yet unmatched pairs. 5062 records in RAM.
INFO 2026-06-08 08:35:03 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 1s. Last read position: chr6:158,776,487
INFO 2026-06-08 08:35:03 MarkDuplicates Tracking 449385 as yet unmatched pairs. 6637 records in RAM.
INFO 2026-06-08 08:35:04 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 1s. Last read position: chr6:160,063,537
INFO 2026-06-08 08:35:04 MarkDuplicates Tracking 444962 as yet unmatched pairs. 2214 records in RAM.
INFO 2026-06-08 08:35:06 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 1s. Last read position: chr6:166,956,205
INFO 2026-06-08 08:35:06 MarkDuplicates Tracking 443686 as yet unmatched pairs. 938 records in RAM.
INFO 2026-06-08 08:35:07 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 1s. Last read position: chr7:2,364,402
INFO 2026-06-08 08:35:07 MarkDuplicates Tracking 441878 as yet unmatched pairs. 34259 records in RAM.
INFO 2026-06-08 08:35:09 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 1s. Last read position: chr7:5,528,101
INFO 2026-06-08 08:35:09 MarkDuplicates Tracking 443493 as yet unmatched pairs. 35874 records in RAM.
INFO 2026-06-08 08:35:10 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 1s. Last read position: chr7:8,221,332
INFO 2026-06-08 08:35:10 MarkDuplicates Tracking 438916 as yet unmatched pairs. 31295 records in RAM.
INFO 2026-06-08 08:35:12 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 1s. Last read position: chr7:25,136,503
INFO 2026-06-08 08:35:12 MarkDuplicates Tracking 437485 as yet unmatched pairs. 29861 records in RAM.
INFO 2026-06-08 08:35:13 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 1s. Last read position: chr7:35,801,222
INFO 2026-06-08 08:35:13 MarkDuplicates Tracking 436018 as yet unmatched pairs. 28393 records in RAM.
INFO 2026-06-08 08:35:14 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 1s. Last read position: chr7:44,572,696
INFO 2026-06-08 08:35:14 MarkDuplicates Tracking 434414 as yet unmatched pairs. 26787 records in RAM.
INFO 2026-06-08 08:35:16 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 1s. Last read position: chr7:47,346,227
INFO 2026-06-08 08:35:16 MarkDuplicates Tracking 432624 as yet unmatched pairs. 24994 records in RAM.
INFO 2026-06-08 08:35:17 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 1s. Last read position: chr7:55,163,767
INFO 2026-06-08 08:35:17 MarkDuplicates Tracking 432147 as yet unmatched pairs. 24514 records in RAM.
INFO 2026-06-08 08:35:19 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr7:56,068,493
INFO 2026-06-08 08:35:19 MarkDuplicates Tracking 429986 as yet unmatched pairs. 22353 records in RAM.
INFO 2026-06-08 08:35:20 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 1s. Last read position: chr7:73,298,410
INFO 2026-06-08 08:35:20 MarkDuplicates Tracking 428540 as yet unmatched pairs. 20907 records in RAM.
INFO 2026-06-08 08:35:22 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 1s. Last read position: chr7:75,422,566
INFO 2026-06-08 08:35:22 MarkDuplicates Tracking 427531 as yet unmatched pairs. 19897 records in RAM.
INFO 2026-06-08 08:35:23 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 1s. Last read position: chr7:77,592,196
INFO 2026-06-08 08:35:23 MarkDuplicates Tracking 426139 as yet unmatched pairs. 18505 records in RAM.
INFO 2026-06-08 08:35:24 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 1s. Last read position: chr7:93,999,278
INFO 2026-06-08 08:35:24 MarkDuplicates Tracking 424506 as yet unmatched pairs. 16863 records in RAM.
INFO 2026-06-08 08:35:26 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 1s. Last read position: chr7:98,962,408
INFO 2026-06-08 08:35:26 MarkDuplicates Tracking 422908 as yet unmatched pairs. 15264 records in RAM.
INFO 2026-06-08 08:35:28 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 1s. Last read position: chr7:100,676,559
INFO 2026-06-08 08:35:28 MarkDuplicates Tracking 421575 as yet unmatched pairs. 13930 records in RAM.
INFO 2026-06-08 08:35:29 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 1s. Last read position: chr7:102,595,651
INFO 2026-06-08 08:35:29 MarkDuplicates Tracking 419950 as yet unmatched pairs. 12303 records in RAM.
INFO 2026-06-08 08:35:31 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 1s. Last read position: chr7:113,117,386
INFO 2026-06-08 08:35:31 MarkDuplicates Tracking 418792 as yet unmatched pairs. 11144 records in RAM.
INFO 2026-06-08 08:35:33 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 1s. Last read position: chr7:123,512,206
INFO 2026-06-08 08:35:33 MarkDuplicates Tracking 417159 as yet unmatched pairs. 9510 records in RAM.
INFO 2026-06-08 08:35:34 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 1s. Last read position: chr7:128,865,451
INFO 2026-06-08 08:35:34 MarkDuplicates Tracking 416063 as yet unmatched pairs. 8414 records in RAM.
INFO 2026-06-08 08:35:36 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 1s. Last read position: chr7:135,622,866
INFO 2026-06-08 08:35:36 MarkDuplicates Tracking 414422 as yet unmatched pairs. 6773 records in RAM.
INFO 2026-06-08 08:35:38 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 1s. Last read position: chr7:139,716,668
INFO 2026-06-08 08:35:38 MarkDuplicates Tracking 413546 as yet unmatched pairs. 5897 records in RAM.
INFO 2026-06-08 08:35:39 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 1s. Last read position: chr7:143,646,934
INFO 2026-06-08 08:35:39 MarkDuplicates Tracking 411780 as yet unmatched pairs. 4131 records in RAM.
INFO 2026-06-08 08:35:41 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 1s. Last read position: chr7:150,626,322
INFO 2026-06-08 08:35:41 MarkDuplicates Tracking 410584 as yet unmatched pairs. 2935 records in RAM.
INFO 2026-06-08 08:35:42 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 1s. Last read position: chr7:151,241,590
INFO 2026-06-08 08:35:42 MarkDuplicates Tracking 408803 as yet unmatched pairs. 1154 records in RAM.
INFO 2026-06-08 08:35:44 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 1s. Last read position: chr8:6,527,568
INFO 2026-06-08 08:35:44 MarkDuplicates Tracking 407455 as yet unmatched pairs. 26087 records in RAM.
INFO 2026-06-08 08:35:45 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 1s. Last read position: chr8:18,057,534
INFO 2026-06-08 08:35:45 MarkDuplicates Tracking 406244 as yet unmatched pairs. 24871 records in RAM.
INFO 2026-06-08 08:35:47 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 1s. Last read position: chr8:23,191,714
INFO 2026-06-08 08:35:47 MarkDuplicates Tracking 404328 as yet unmatched pairs. 22955 records in RAM.
INFO 2026-06-08 08:35:48 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 1s. Last read position: chr8:27,605,052
INFO 2026-06-08 08:35:48 MarkDuplicates Tracking 405153 as yet unmatched pairs. 23779 records in RAM.
INFO 2026-06-08 08:35:50 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 1s. Last read position: chr8:30,681,960
INFO 2026-06-08 08:35:50 MarkDuplicates Tracking 401557 as yet unmatched pairs. 20183 records in RAM.
INFO 2026-06-08 08:35:51 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 1s. Last read position: chr8:38,457,379
INFO 2026-06-08 08:35:51 MarkDuplicates Tracking 400665 as yet unmatched pairs. 19289 records in RAM.
INFO 2026-06-08 08:35:53 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:05:43s. Time for last 1,000,000: 1s. Last read position: chr8:43,199,417
INFO 2026-06-08 08:35:53 MarkDuplicates Tracking 398684 as yet unmatched pairs. 17306 records in RAM.
INFO 2026-06-08 08:35:54 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 1s. Last read position: chr8:60,741,681
INFO 2026-06-08 08:35:54 MarkDuplicates Tracking 396921 as yet unmatched pairs. 15543 records in RAM.
INFO 2026-06-08 08:35:56 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 1s. Last read position: chr8:71,843,838
INFO 2026-06-08 08:35:56 MarkDuplicates Tracking 395600 as yet unmatched pairs. 14222 records in RAM.
INFO 2026-06-08 08:35:57 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 1s. Last read position: chr8:94,788,003
INFO 2026-06-08 08:35:57 MarkDuplicates Tracking 394331 as yet unmatched pairs. 12951 records in RAM.
INFO 2026-06-08 08:35:59 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 1s. Last read position: chr8:100,721,640
INFO 2026-06-08 08:35:59 MarkDuplicates Tracking 392910 as yet unmatched pairs. 11528 records in RAM.
INFO 2026-06-08 08:36:00 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 1s. Last read position: chr8:119,564,941
INFO 2026-06-08 08:36:00 MarkDuplicates Tracking 392846 as yet unmatched pairs. 11463 records in RAM.
INFO 2026-06-08 08:36:02 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 1s. Last read position: chr8:127,740,430
INFO 2026-06-08 08:36:02 MarkDuplicates Tracking 390310 as yet unmatched pairs. 8926 records in RAM.
INFO 2026-06-08 08:36:04 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 2s. Last read position: chr8:133,250,489
INFO 2026-06-08 08:36:04 MarkDuplicates Tracking 393416 as yet unmatched pairs. 12032 records in RAM.
INFO 2026-06-08 08:36:05 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 1s. Last read position: chr8:141,424,940
INFO 2026-06-08 08:36:05 MarkDuplicates Tracking 387032 as yet unmatched pairs. 5647 records in RAM.
INFO 2026-06-08 08:36:07 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 1s. Last read position: chr8:143,858,430
INFO 2026-06-08 08:36:07 MarkDuplicates Tracking 385557 as yet unmatched pairs. 4170 records in RAM.
INFO 2026-06-08 08:36:09 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 1s. Last read position: chr8:143,863,207
INFO 2026-06-08 08:36:09 MarkDuplicates Tracking 385349 as yet unmatched pairs. 3962 records in RAM.
INFO 2026-06-08 08:36:10 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 1s. Last read position: chr8:143,919,356
INFO 2026-06-08 08:36:10 MarkDuplicates Tracking 384601 as yet unmatched pairs. 3214 records in RAM.
INFO 2026-06-08 08:36:11 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 1s. Last read position: chr8:144,311,544
INFO 2026-06-08 08:36:11 MarkDuplicates Tracking 382508 as yet unmatched pairs. 1121 records in RAM.
INFO 2026-06-08 08:36:13 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 1s. Last read position: chr9:2,651,887
INFO 2026-06-08 08:36:13 MarkDuplicates Tracking 380950 as yet unmatched pairs. 18186 records in RAM.
INFO 2026-06-08 08:36:14 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 1s. Last read position: chr9:19,290,703
INFO 2026-06-08 08:36:14 MarkDuplicates Tracking 379696 as yet unmatched pairs. 16932 records in RAM.
INFO 2026-06-08 08:36:16 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 1s. Last read position: chr9:35,547,502
INFO 2026-06-08 08:36:16 MarkDuplicates Tracking 378121 as yet unmatched pairs. 15357 records in RAM.
INFO 2026-06-08 08:36:17 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 1s. Last read position: chr9:62,376,513
INFO 2026-06-08 08:36:17 MarkDuplicates Tracking 376697 as yet unmatched pairs. 13928 records in RAM.
INFO 2026-06-08 08:36:19 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:06:09s. Time for last 1,000,000: 1s. Last read position: chr9:81,709,717
INFO 2026-06-08 08:36:19 MarkDuplicates Tracking 375559 as yet unmatched pairs. 12790 records in RAM.
INFO 2026-06-08 08:36:20 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 1s. Last read position: chr9:93,557,959
INFO 2026-06-08 08:36:20 MarkDuplicates Tracking 374208 as yet unmatched pairs. 11437 records in RAM.
INFO 2026-06-08 08:36:21 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 1s. Last read position: chr9:108,903,616
INFO 2026-06-08 08:36:21 MarkDuplicates Tracking 372802 as yet unmatched pairs. 10030 records in RAM.
INFO 2026-06-08 08:36:23 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 1s. Last read position: chr9:117,714,247
INFO 2026-06-08 08:36:23 MarkDuplicates Tracking 371340 as yet unmatched pairs. 8568 records in RAM.
INFO 2026-06-08 08:36:24 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 1s. Last read position: chr9:125,236,910
INFO 2026-06-08 08:36:24 MarkDuplicates Tracking 370402 as yet unmatched pairs. 7627 records in RAM.
INFO 2026-06-08 08:36:26 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:06:16s. Time for last 1,000,000: 1s. Last read position: chr9:128,566,762
INFO 2026-06-08 08:36:26 MarkDuplicates Tracking 368472 as yet unmatched pairs. 5697 records in RAM.
INFO 2026-06-08 08:36:27 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 1s. Last read position: chr9:131,474,870
INFO 2026-06-08 08:36:27 MarkDuplicates Tracking 366921 as yet unmatched pairs. 4146 records in RAM.
INFO 2026-06-08 08:36:28 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 1s. Last read position: chr9:136,016,331
INFO 2026-06-08 08:36:28 MarkDuplicates Tracking 365261 as yet unmatched pairs. 2486 records in RAM.
INFO 2026-06-08 08:36:30 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 1s. Last read position: chr9:137,114,330
INFO 2026-06-08 08:36:30 MarkDuplicates Tracking 363491 as yet unmatched pairs. 716 records in RAM.
INFO 2026-06-08 08:36:32 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 1s. Last read position: chr10:3,781,645
INFO 2026-06-08 08:36:32 MarkDuplicates Tracking 361885 as yet unmatched pairs. 24814 records in RAM.
INFO 2026-06-08 08:36:33 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 1s. Last read position: chr10:13,118,988
INFO 2026-06-08 08:36:33 MarkDuplicates Tracking 360407 as yet unmatched pairs. 23336 records in RAM.
INFO 2026-06-08 08:36:35 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 1s. Last read position: chr10:16,954,468
INFO 2026-06-08 08:36:35 MarkDuplicates Tracking 359441 as yet unmatched pairs. 22370 records in RAM.
INFO 2026-06-08 08:36:36 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 1s. Last read position: chr10:18,260,884
INFO 2026-06-08 08:36:36 MarkDuplicates Tracking 357220 as yet unmatched pairs. 20149 records in RAM.
INFO 2026-06-08 08:36:38 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 1s. Last read position: chr10:31,854,066
INFO 2026-06-08 08:36:38 MarkDuplicates Tracking 355937 as yet unmatched pairs. 18865 records in RAM.
INFO 2026-06-08 08:36:39 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:06:30s. Time for last 1,000,000: 1s. Last read position: chr10:35,566,115
INFO 2026-06-08 08:36:39 MarkDuplicates Tracking 354766 as yet unmatched pairs. 17693 records in RAM.
INFO 2026-06-08 08:36:41 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:06:31s. Time for last 1,000,000: 1s. Last read position: chr10:46,016,544
INFO 2026-06-08 08:36:41 MarkDuplicates Tracking 356568 as yet unmatched pairs. 19495 records in RAM.
INFO 2026-06-08 08:36:43 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:06:33s. Time for last 1,000,000: 1s. Last read position: chr10:58,789,760
INFO 2026-06-08 08:36:43 MarkDuplicates Tracking 352279 as yet unmatched pairs. 15204 records in RAM.
INFO 2026-06-08 08:37:47 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:07:38s. Time for last 1,000,000: 64s. Last read position: chr10:69,180,433
INFO 2026-06-08 08:37:47 MarkDuplicates Tracking 350760 as yet unmatched pairs. 13684 records in RAM.
INFO 2026-06-08 08:37:49 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:07:39s. Time for last 1,000,000: 1s. Last read position: chr10:73,134,695
INFO 2026-06-08 08:37:49 MarkDuplicates Tracking 349333 as yet unmatched pairs. 12251 records in RAM.
INFO 2026-06-08 08:37:51 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:07:41s. Time for last 1,000,000: 1s. Last read position: chr10:78,037,259
INFO 2026-06-08 08:37:51 MarkDuplicates Tracking 347989 as yet unmatched pairs. 10907 records in RAM.
INFO 2026-06-08 08:37:52 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:07:42s. Time for last 1,000,000: 1s. Last read position: chr10:87,862,373
INFO 2026-06-08 08:37:52 MarkDuplicates Tracking 346666 as yet unmatched pairs. 9584 records in RAM.
INFO 2026-06-08 08:37:54 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:07:44s. Time for last 1,000,000: 1s. Last read position: chr10:93,600,451
INFO 2026-06-08 08:37:54 MarkDuplicates Tracking 346107 as yet unmatched pairs. 9025 records in RAM.
INFO 2026-06-08 08:37:55 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:07:45s. Time for last 1,000,000: 1s. Last read position: chr10:97,468,966
INFO 2026-06-08 08:37:55 MarkDuplicates Tracking 344068 as yet unmatched pairs. 6986 records in RAM.
INFO 2026-06-08 08:37:57 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:07:47s. Time for last 1,000,000: 1s. Last read position: chr10:101,803,908
INFO 2026-06-08 08:37:57 MarkDuplicates Tracking 342656 as yet unmatched pairs. 5572 records in RAM.
INFO 2026-06-08 08:37:58 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:07:48s. Time for last 1,000,000: 1s. Last read position: chr10:110,100,694
INFO 2026-06-08 08:37:58 MarkDuplicates Tracking 340900 as yet unmatched pairs. 3814 records in RAM.
INFO 2026-06-08 08:38:00 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:07:50s. Time for last 1,000,000: 1s. Last read position: chr10:119,806,373
INFO 2026-06-08 08:38:00 MarkDuplicates Tracking 339377 as yet unmatched pairs. 2290 records in RAM.
INFO 2026-06-08 08:38:01 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:07:52s. Time for last 1,000,000: 1s. Last read position: chr10:127,410,823
INFO 2026-06-08 08:38:01 MarkDuplicates Tracking 338015 as yet unmatched pairs. 928 records in RAM.
INFO 2026-06-08 08:38:03 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:07:53s. Time for last 1,000,000: 1s. Last read position: chr11:319,864
INFO 2026-06-08 08:38:03 MarkDuplicates Tracking 338436 as yet unmatched pairs. 45953 records in RAM.
INFO 2026-06-08 08:38:05 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:07:55s. Time for last 1,000,000: 1s. Last read position: chr11:747,519
INFO 2026-06-08 08:38:05 MarkDuplicates Tracking 335007 as yet unmatched pairs. 42523 records in RAM.
INFO 2026-06-08 08:38:06 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:07:56s. Time for last 1,000,000: 1s. Last read position: chr11:1,759,577
INFO 2026-06-08 08:38:06 MarkDuplicates Tracking 336704 as yet unmatched pairs. 44220 records in RAM.
INFO 2026-06-08 08:38:08 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:07:58s. Time for last 1,000,000: 1s. Last read position: chr11:5,679,769
INFO 2026-06-08 08:38:08 MarkDuplicates Tracking 331818 as yet unmatched pairs. 39334 records in RAM.
INFO 2026-06-08 08:38:10 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:08:00s. Time for last 1,000,000: 1s. Last read position: chr11:9,142,016
INFO 2026-06-08 08:38:10 MarkDuplicates Tracking 330203 as yet unmatched pairs. 37719 records in RAM.
INFO 2026-06-08 08:38:11 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:08:01s. Time for last 1,000,000: 1s. Last read position: chr11:14,517,889
INFO 2026-06-08 08:38:11 MarkDuplicates Tracking 329237 as yet unmatched pairs. 36751 records in RAM.
INFO 2026-06-08 08:38:13 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:08:03s. Time for last 1,000,000: 1s. Last read position: chr11:20,054,094
INFO 2026-06-08 08:38:13 MarkDuplicates Tracking 327260 as yet unmatched pairs. 34773 records in RAM.
INFO 2026-06-08 08:38:14 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:08:04s. Time for last 1,000,000: 1s. Last read position: chr11:34,909,107
INFO 2026-06-08 08:38:14 MarkDuplicates Tracking 325731 as yet unmatched pairs. 33243 records in RAM.
INFO 2026-06-08 08:38:16 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:08:06s. Time for last 1,000,000: 1s. Last read position: chr11:47,172,311
INFO 2026-06-08 08:38:16 MarkDuplicates Tracking 324459 as yet unmatched pairs. 31970 records in RAM.
INFO 2026-06-08 08:38:18 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:08:08s. Time for last 1,000,000: 1s. Last read position: chr11:57,600,255
INFO 2026-06-08 08:38:18 MarkDuplicates Tracking 323818 as yet unmatched pairs. 31329 records in RAM.
INFO 2026-06-08 08:38:19 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:08:09s. Time for last 1,000,000: 1s. Last read position: chr11:60,919,830
INFO 2026-06-08 08:38:19 MarkDuplicates Tracking 321604 as yet unmatched pairs. 29114 records in RAM.
INFO 2026-06-08 08:38:20 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:08:10s. Time for last 1,000,000: 1s. Last read position: chr11:62,518,257
INFO 2026-06-08 08:38:20 MarkDuplicates Tracking 320278 as yet unmatched pairs. 27783 records in RAM.
INFO 2026-06-08 08:38:22 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:08:12s. Time for last 1,000,000: 1s. Last read position: chr11:62,527,830
INFO 2026-06-08 08:38:22 MarkDuplicates Tracking 319594 as yet unmatched pairs. 27099 records in RAM.
INFO 2026-06-08 08:38:23 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:08:13s. Time for last 1,000,000: 1s. Last read position: chr11:62,581,447
INFO 2026-06-08 08:38:23 MarkDuplicates Tracking 317574 as yet unmatched pairs. 25079 records in RAM.
INFO 2026-06-08 08:38:25 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:08:15s. Time for last 1,000,000: 1s. Last read position: chr11:63,904,118
INFO 2026-06-08 08:38:25 MarkDuplicates Tracking 316070 as yet unmatched pairs. 23575 records in RAM.
INFO 2026-06-08 08:38:26 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 1s. Last read position: chr11:64,912,152
INFO 2026-06-08 08:38:26 MarkDuplicates Tracking 314442 as yet unmatched pairs. 21947 records in RAM.
INFO 2026-06-08 08:38:28 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:08:18s. Time for last 1,000,000: 1s. Last read position: chr11:65,616,974
INFO 2026-06-08 08:38:28 MarkDuplicates Tracking 312690 as yet unmatched pairs. 20195 records in RAM.
INFO 2026-06-08 08:38:29 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 1s. Last read position: chr11:66,435,950
INFO 2026-06-08 08:38:29 MarkDuplicates Tracking 310993 as yet unmatched pairs. 18498 records in RAM.
INFO 2026-06-08 08:38:31 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 1s. Last read position: chr11:67,611,133
INFO 2026-06-08 08:38:31 MarkDuplicates Tracking 309356 as yet unmatched pairs. 16861 records in RAM.
INFO 2026-06-08 08:38:32 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:08:22s. Time for last 1,000,000: 1s. Last read position: chr11:69,643,154
INFO 2026-06-08 08:38:32 MarkDuplicates Tracking 311837 as yet unmatched pairs. 19342 records in RAM.
INFO 2026-06-08 08:38:34 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 2s. Last read position: chr11:72,004,688
INFO 2026-06-08 08:38:34 MarkDuplicates Tracking 306392 as yet unmatched pairs. 13891 records in RAM.
INFO 2026-06-08 08:38:36 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:08:27s. Time for last 1,000,000: 1s. Last read position: chr11:73,844,830
INFO 2026-06-08 08:38:36 MarkDuplicates Tracking 304723 as yet unmatched pairs. 12222 records in RAM.
INFO 2026-06-08 08:38:38 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:08:28s. Time for last 1,000,000: 1s. Last read position: chr11:78,196,346
INFO 2026-06-08 08:38:38 MarkDuplicates Tracking 303183 as yet unmatched pairs. 10681 records in RAM.
INFO 2026-06-08 08:38:39 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:08:30s. Time for last 1,000,000: 1s. Last read position: chr11:94,859,605
INFO 2026-06-08 08:38:39 MarkDuplicates Tracking 301797 as yet unmatched pairs. 9293 records in RAM.
INFO 2026-06-08 08:38:41 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:08:31s. Time for last 1,000,000: 1s. Last read position: chr11:105,611,013
INFO 2026-06-08 08:38:41 MarkDuplicates Tracking 300614 as yet unmatched pairs. 8110 records in RAM.
INFO 2026-06-08 08:38:42 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 1s. Last read position: chr11:112,074,890
INFO 2026-06-08 08:38:42 MarkDuplicates Tracking 299083 as yet unmatched pairs. 6579 records in RAM.
INFO 2026-06-08 08:38:44 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 1s. Last read position: chr11:117,820,861
INFO 2026-06-08 08:38:44 MarkDuplicates Tracking 303755 as yet unmatched pairs. 11248 records in RAM.
INFO 2026-06-08 08:38:45 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 1s. Last read position: chr11:119,025,972
INFO 2026-06-08 08:38:45 MarkDuplicates Tracking 296506 as yet unmatched pairs. 3999 records in RAM.
INFO 2026-06-08 08:38:47 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 1s. Last read position: chr11:123,058,312
INFO 2026-06-08 08:38:47 MarkDuplicates Tracking 294894 as yet unmatched pairs. 2387 records in RAM.
INFO 2026-06-08 08:38:48 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:08:38s. Time for last 1,000,000: 1s. Last read position: chr11:128,969,419
INFO 2026-06-08 08:38:48 MarkDuplicates Tracking 293417 as yet unmatched pairs. 908 records in RAM.
INFO 2026-06-08 08:38:50 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 1s. Last read position: chr12:900,547
INFO 2026-06-08 08:38:50 MarkDuplicates Tracking 292131 as yet unmatched pairs. 39511 records in RAM.
INFO 2026-06-08 08:38:51 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:08:42s. Time for last 1,000,000: 1s. Last read position: chr12:6,011,751
INFO 2026-06-08 08:38:51 MarkDuplicates Tracking 292234 as yet unmatched pairs. 39613 records in RAM.
INFO 2026-06-08 08:38:53 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:08:43s. Time for last 1,000,000: 1s. Last read position: chr12:6,121,268
INFO 2026-06-08 08:38:53 MarkDuplicates Tracking 290836 as yet unmatched pairs. 38215 records in RAM.
INFO 2026-06-08 08:38:55 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:08:45s. Time for last 1,000,000: 1s. Last read position: chr12:6,862,500
INFO 2026-06-08 08:38:55 MarkDuplicates Tracking 287310 as yet unmatched pairs. 34689 records in RAM.
INFO 2026-06-08 08:38:57 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:08:47s. Time for last 1,000,000: 2s. Last read position: chr12:7,130,638
INFO 2026-06-08 08:38:57 MarkDuplicates Tracking 285968 as yet unmatched pairs. 33347 records in RAM.
INFO 2026-06-08 08:38:59 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 1s. Last read position: chr12:9,240,061
INFO 2026-06-08 08:38:59 MarkDuplicates Tracking 284342 as yet unmatched pairs. 31719 records in RAM.
INFO 2026-06-08 08:39:00 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 1s. Last read position: chr12:15,647,102
INFO 2026-06-08 08:39:00 MarkDuplicates Tracking 283178 as yet unmatched pairs. 30555 records in RAM.
INFO 2026-06-08 08:39:02 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:08:52s. Time for last 1,000,000: 1s. Last read position: chr12:28,362,505
INFO 2026-06-08 08:39:02 MarkDuplicates Tracking 281686 as yet unmatched pairs. 29062 records in RAM.
INFO 2026-06-08 08:39:03 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 1s. Last read position: chr12:46,204,408
INFO 2026-06-08 08:39:03 MarkDuplicates Tracking 281042 as yet unmatched pairs. 28415 records in RAM.
INFO 2026-06-08 08:39:05 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:08:55s. Time for last 1,000,000: 1s. Last read position: chr12:49,128,396
INFO 2026-06-08 08:39:05 MarkDuplicates Tracking 279420 as yet unmatched pairs. 26792 records in RAM.
INFO 2026-06-08 08:39:06 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:08:57s. Time for last 1,000,000: 1s. Last read position: chr12:50,353,934
INFO 2026-06-08 08:39:06 MarkDuplicates Tracking 277699 as yet unmatched pairs. 25071 records in RAM.
INFO 2026-06-08 08:39:08 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:08:58s. Time for last 1,000,000: 1s. Last read position: chr12:53,059,195
INFO 2026-06-08 08:39:08 MarkDuplicates Tracking 276516 as yet unmatched pairs. 23888 records in RAM.
INFO 2026-06-08 08:39:09 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:08:59s. Time for last 1,000,000: 1s. Last read position: chr12:53,537,517
INFO 2026-06-08 08:39:09 MarkDuplicates Tracking 275187 as yet unmatched pairs. 22559 records in RAM.
INFO 2026-06-08 08:39:11 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:09:01s. Time for last 1,000,000: 1s. Last read position: chr12:55,725,550
INFO 2026-06-08 08:39:11 MarkDuplicates Tracking 274132 as yet unmatched pairs. 21504 records in RAM.
INFO 2026-06-08 08:39:12 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:09:03s. Time for last 1,000,000: 1s. Last read position: chr12:56,206,578
INFO 2026-06-08 08:39:12 MarkDuplicates Tracking 272389 as yet unmatched pairs. 19761 records in RAM.
INFO 2026-06-08 08:39:14 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:09:04s. Time for last 1,000,000: 1s. Last read position: chr12:57,089,247
INFO 2026-06-08 08:39:14 MarkDuplicates Tracking 271084 as yet unmatched pairs. 18456 records in RAM.
INFO 2026-06-08 08:39:15 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:09:06s. Time for last 1,000,000: 1s. Last read position: chr12:57,190,914
INFO 2026-06-08 08:39:15 MarkDuplicates Tracking 269880 as yet unmatched pairs. 17252 records in RAM.
INFO 2026-06-08 08:39:17 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:09:07s. Time for last 1,000,000: 1s. Last read position: chr12:57,528,192
INFO 2026-06-08 08:39:17 MarkDuplicates Tracking 268099 as yet unmatched pairs. 15471 records in RAM.
INFO 2026-06-08 08:39:19 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:09:09s. Time for last 1,000,000: 1s. Last read position: chr12:65,463,161
INFO 2026-06-08 08:39:19 MarkDuplicates Tracking 266737 as yet unmatched pairs. 14097 records in RAM.
INFO 2026-06-08 08:39:21 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:09:11s. Time for last 1,000,000: 1s. Last read position: chr12:76,060,259
INFO 2026-06-08 08:39:21 MarkDuplicates Tracking 266310 as yet unmatched pairs. 13670 records in RAM.
INFO 2026-06-08 08:39:22 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:09:12s. Time for last 1,000,000: 1s. Last read position: chr12:96,247,002
INFO 2026-06-08 08:39:22 MarkDuplicates Tracking 264309 as yet unmatched pairs. 11668 records in RAM.
INFO 2026-06-08 08:39:24 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 1s. Last read position: chr12:104,265,795
INFO 2026-06-08 08:39:24 MarkDuplicates Tracking 262675 as yet unmatched pairs. 10034 records in RAM.
INFO 2026-06-08 08:39:25 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:09:15s. Time for last 1,000,000: 1s. Last read position: chr12:110,013,145
INFO 2026-06-08 08:39:25 MarkDuplicates Tracking 261451 as yet unmatched pairs. 8809 records in RAM.
INFO 2026-06-08 08:39:27 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:09:17s. Time for last 1,000,000: 1s. Last read position: chr12:112,408,246
INFO 2026-06-08 08:39:27 MarkDuplicates Tracking 260498 as yet unmatched pairs. 7855 records in RAM.
INFO 2026-06-08 08:39:28 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:09:19s. Time for last 1,000,000: 1s. Last read position: chr12:118,246,171
INFO 2026-06-08 08:39:28 MarkDuplicates Tracking 258282 as yet unmatched pairs. 5639 records in RAM.
INFO 2026-06-08 08:39:30 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 1s. Last read position: chr12:120,994,379
INFO 2026-06-08 08:39:30 MarkDuplicates Tracking 256666 as yet unmatched pairs. 4023 records in RAM.
INFO 2026-06-08 08:39:31 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:09:21s. Time for last 1,000,000: 1s. Last read position: chr12:123,673,768
INFO 2026-06-08 08:39:31 MarkDuplicates Tracking 255206 as yet unmatched pairs. 2563 records in RAM.
INFO 2026-06-08 08:39:33 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:09:23s. Time for last 1,000,000: 1s. Last read position: chr12:131,916,051
INFO 2026-06-08 08:39:33 MarkDuplicates Tracking 253610 as yet unmatched pairs. 967 records in RAM.
INFO 2026-06-08 08:39:34 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:09:24s. Time for last 1,000,000: 1s. Last read position: chr13:20,961,309
INFO 2026-06-08 08:39:34 MarkDuplicates Tracking 252075 as yet unmatched pairs. 10829 records in RAM.
INFO 2026-06-08 08:39:36 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:09:26s. Time for last 1,000,000: 1s. Last read position: chr13:29,078,444
INFO 2026-06-08 08:39:36 MarkDuplicates Tracking 250715 as yet unmatched pairs. 9469 records in RAM.
INFO 2026-06-08 08:39:37 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:09:27s. Time for last 1,000,000: 1s. Last read position: chr13:44,434,678
INFO 2026-06-08 08:39:37 MarkDuplicates Tracking 249987 as yet unmatched pairs. 8724 records in RAM.
INFO 2026-06-08 08:39:39 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:09:29s. Time for last 1,000,000: 1s. Last read position: chr13:48,261,143
INFO 2026-06-08 08:39:39 MarkDuplicates Tracking 248930 as yet unmatched pairs. 7667 records in RAM.
INFO 2026-06-08 08:39:41 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:09:31s. Time for last 1,000,000: 1s. Last read position: chr13:77,903,279
INFO 2026-06-08 08:39:41 MarkDuplicates Tracking 247024 as yet unmatched pairs. 5760 records in RAM.
INFO 2026-06-08 08:39:42 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:09:32s. Time for last 1,000,000: 1s. Last read position: chr13:102,767,360
INFO 2026-06-08 08:39:42 MarkDuplicates Tracking 245236 as yet unmatched pairs. 3968 records in RAM.
INFO 2026-06-08 08:39:44 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:09:34s. Time for last 1,000,000: 1s. Last read position: chr13:110,357,524
INFO 2026-06-08 08:39:44 MarkDuplicates Tracking 244341 as yet unmatched pairs. 3073 records in RAM.
INFO 2026-06-08 08:39:46 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:09:36s. Time for last 1,000,000: 1s. Last read position: chr13:112,881,870
INFO 2026-06-08 08:39:46 MarkDuplicates Tracking 242352 as yet unmatched pairs. 1084 records in RAM.
INFO 2026-06-08 08:39:47 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:09:38s. Time for last 1,000,000: 1s. Last read position: chr14:21,231,041
INFO 2026-06-08 08:39:47 MarkDuplicates Tracking 241292 as yet unmatched pairs. 19812 records in RAM.
INFO 2026-06-08 08:39:49 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:09:39s. Time for last 1,000,000: 1s. Last read position: chr14:23,470,908
INFO 2026-06-08 08:39:49 MarkDuplicates Tracking 239111 as yet unmatched pairs. 17631 records in RAM.
INFO 2026-06-08 08:39:50 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:09:40s. Time for last 1,000,000: 1s. Last read position: chr14:31,106,867
INFO 2026-06-08 08:39:50 MarkDuplicates Tracking 237612 as yet unmatched pairs. 16132 records in RAM.
INFO 2026-06-08 08:39:52 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:09:42s. Time for last 1,000,000: 1s. Last read position: chr14:45,136,198
INFO 2026-06-08 08:39:52 MarkDuplicates Tracking 236026 as yet unmatched pairs. 14546 records in RAM.
INFO 2026-06-08 08:39:53 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:09:43s. Time for last 1,000,000: 1s. Last read position: chr14:55,140,274
INFO 2026-06-08 08:39:53 MarkDuplicates Tracking 235329 as yet unmatched pairs. 13849 records in RAM.
INFO 2026-06-08 08:39:54 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:09:45s. Time for last 1,000,000: 1s. Last read position: chr14:64,087,764
INFO 2026-06-08 08:39:54 MarkDuplicates Tracking 233660 as yet unmatched pairs. 12179 records in RAM.
INFO 2026-06-08 08:39:56 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:09:46s. Time for last 1,000,000: 1s. Last read position: chr14:68,892,266
INFO 2026-06-08 08:39:56 MarkDuplicates Tracking 232171 as yet unmatched pairs. 10690 records in RAM.
INFO 2026-06-08 08:39:58 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:09:48s. Time for last 1,000,000: 1s. Last read position: chr14:73,986,862
INFO 2026-06-08 08:39:58 MarkDuplicates Tracking 230578 as yet unmatched pairs. 9097 records in RAM.
INFO 2026-06-08 08:39:59 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:09:49s. Time for last 1,000,000: 1s. Last read position: chr14:76,763,054
INFO 2026-06-08 08:39:59 MarkDuplicates Tracking 228938 as yet unmatched pairs. 7457 records in RAM.
INFO 2026-06-08 08:40:00 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:09:50s. Time for last 1,000,000: 1s. Last read position: chr14:92,711,852
INFO 2026-06-08 08:40:00 MarkDuplicates Tracking 227414 as yet unmatched pairs. 5930 records in RAM.
INFO 2026-06-08 08:40:02 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:09:52s. Time for last 1,000,000: 1s. Last read position: chr14:96,303,202
INFO 2026-06-08 08:40:02 MarkDuplicates Tracking 225955 as yet unmatched pairs. 4470 records in RAM.
INFO 2026-06-08 08:40:03 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:09:54s. Time for last 1,000,000: 1s. Last read position: chr14:102,930,456
INFO 2026-06-08 08:40:03 MarkDuplicates Tracking 224679 as yet unmatched pairs. 3185 records in RAM.
INFO 2026-06-08 08:40:05 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:09:55s. Time for last 1,000,000: 1s. Last read position: chr14:105,148,844
INFO 2026-06-08 08:40:05 MarkDuplicates Tracking 223010 as yet unmatched pairs. 1515 records in RAM.
INFO 2026-06-08 08:40:06 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:09:56s. Time for last 1,000,000: 1s. Last read position: chr14:105,742,177
INFO 2026-06-08 08:40:06 MarkDuplicates Tracking 223179 as yet unmatched pairs. 1683 records in RAM.
INFO 2026-06-08 08:40:08 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:09:58s. Time for last 1,000,000: 1s. Last read position: chr15:28,702,752
INFO 2026-06-08 08:40:08 MarkDuplicates Tracking 220719 as yet unmatched pairs. 19842 records in RAM.
INFO 2026-06-08 08:40:09 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 1s. Last read position: chr15:39,581,151
INFO 2026-06-08 08:40:09 MarkDuplicates Tracking 219868 as yet unmatched pairs. 18978 records in RAM.
INFO 2026-06-08 08:40:10 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:10:01s. Time for last 1,000,000: 1s. Last read position: chr15:41,696,133
INFO 2026-06-08 08:40:10 MarkDuplicates Tracking 218346 as yet unmatched pairs. 17456 records in RAM.
INFO 2026-06-08 08:40:12 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:10:02s. Time for last 1,000,000: 1s. Last read position: chr15:43,769,536
INFO 2026-06-08 08:40:12 MarkDuplicates Tracking 217812 as yet unmatched pairs. 16922 records in RAM.
INFO 2026-06-08 08:40:14 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:10:04s. Time for last 1,000,000: 1s. Last read position: chr15:48,878,342
INFO 2026-06-08 08:40:14 MarkDuplicates Tracking 215525 as yet unmatched pairs. 14633 records in RAM.
INFO 2026-06-08 08:40:16 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 2s. Last read position: chr15:57,438,622
INFO 2026-06-08 08:40:16 MarkDuplicates Tracking 214197 as yet unmatched pairs. 13305 records in RAM.
INFO 2026-06-08 08:40:18 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:10:08s. Time for last 1,000,000: 1s. Last read position: chr15:63,153,982
INFO 2026-06-08 08:40:18 MarkDuplicates Tracking 213232 as yet unmatched pairs. 12340 records in RAM.
INFO 2026-06-08 08:40:19 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 1s. Last read position: chr15:66,293,617
INFO 2026-06-08 08:40:19 MarkDuplicates Tracking 210870 as yet unmatched pairs. 9978 records in RAM.
INFO 2026-06-08 08:40:21 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:10:11s. Time for last 1,000,000: 1s. Last read position: chr15:72,199,734
INFO 2026-06-08 08:40:21 MarkDuplicates Tracking 210780 as yet unmatched pairs. 9888 records in RAM.
INFO 2026-06-08 08:40:22 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 1s. Last read position: chr15:74,035,771
INFO 2026-06-08 08:40:22 MarkDuplicates Tracking 208960 as yet unmatched pairs. 8068 records in RAM.
INFO 2026-06-08 08:40:23 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:10:14s. Time for last 1,000,000: 1s. Last read position: chr15:76,295,726
INFO 2026-06-08 08:40:23 MarkDuplicates Tracking 206679 as yet unmatched pairs. 5787 records in RAM.
INFO 2026-06-08 08:40:25 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:10:15s. Time for last 1,000,000: 1s. Last read position: chr15:83,773,593
INFO 2026-06-08 08:40:25 MarkDuplicates Tracking 205285 as yet unmatched pairs. 4392 records in RAM.
INFO 2026-06-08 08:40:26 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:10:17s. Time for last 1,000,000: 1s. Last read position: chr15:88,856,229
INFO 2026-06-08 08:40:26 MarkDuplicates Tracking 204119 as yet unmatched pairs. 3226 records in RAM.
INFO 2026-06-08 08:40:28 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:10:18s. Time for last 1,000,000: 1s. Last read position: chr15:90,388,316
INFO 2026-06-08 08:40:28 MarkDuplicates Tracking 203011 as yet unmatched pairs. 2117 records in RAM.
INFO 2026-06-08 08:40:29 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:10:19s. Time for last 1,000,000: 1s. Last read position: chr15:101,305,171
INFO 2026-06-08 08:40:29 MarkDuplicates Tracking 201936 as yet unmatched pairs. 1026 records in RAM.
INFO 2026-06-08 08:40:31 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:10:21s. Time for last 1,000,000: 1s. Last read position: chr16:672,985
INFO 2026-06-08 08:40:31 MarkDuplicates Tracking 200014 as yet unmatched pairs. 33199 records in RAM.
INFO 2026-06-08 08:40:32 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:10:22s. Time for last 1,000,000: 1s. Last read position: chr16:1,939,083
INFO 2026-06-08 08:40:32 MarkDuplicates Tracking 198541 as yet unmatched pairs. 31726 records in RAM.
INFO 2026-06-08 08:40:34 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:10:24s. Time for last 1,000,000: 1s. Last read position: chr16:2,530,386
INFO 2026-06-08 08:40:34 MarkDuplicates Tracking 196365 as yet unmatched pairs. 29550 records in RAM.
INFO 2026-06-08 08:40:35 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:10:25s. Time for last 1,000,000: 1s. Last read position: chr16:3,065,660
INFO 2026-06-08 08:40:35 MarkDuplicates Tracking 196364 as yet unmatched pairs. 29549 records in RAM.
INFO 2026-06-08 08:40:37 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:10:27s. Time for last 1,000,000: 1s. Last read position: chr16:4,657,298
INFO 2026-06-08 08:40:37 MarkDuplicates Tracking 193704 as yet unmatched pairs. 26889 records in RAM.
INFO 2026-06-08 08:40:38 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:10:28s. Time for last 1,000,000: 1s. Last read position: chr16:11,927,750
INFO 2026-06-08 08:40:38 MarkDuplicates Tracking 192231 as yet unmatched pairs. 25416 records in RAM.
INFO 2026-06-08 08:40:40 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:10:30s. Time for last 1,000,000: 1s. Last read position: chr16:15,127,543
INFO 2026-06-08 08:40:40 MarkDuplicates Tracking 191186 as yet unmatched pairs. 24371 records in RAM.
INFO 2026-06-08 08:40:41 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:10:31s. Time for last 1,000,000: 1s. Last read position: chr16:16,361,326
INFO 2026-06-08 08:40:41 MarkDuplicates Tracking 190363 as yet unmatched pairs. 23547 records in RAM.
INFO 2026-06-08 08:40:42 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:10:32s. Time for last 1,000,000: 1s. Last read position: chr16:18,849,333
INFO 2026-06-08 08:40:42 MarkDuplicates Tracking 189618 as yet unmatched pairs. 22802 records in RAM.
INFO 2026-06-08 08:40:44 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:10:34s. Time for last 1,000,000: 1s. Last read position: chr16:21,415,065
INFO 2026-06-08 08:40:44 MarkDuplicates Tracking 188718 as yet unmatched pairs. 21901 records in RAM.
INFO 2026-06-08 08:40:45 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:10:36s. Time for last 1,000,000: 1s. Last read position: chr16:22,533,650
INFO 2026-06-08 08:40:45 MarkDuplicates Tracking 187780 as yet unmatched pairs. 20963 records in RAM.
INFO 2026-06-08 08:40:48 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:10:38s. Time for last 1,000,000: 2s. Last read position: chr16:28,399,897
INFO 2026-06-08 08:40:48 MarkDuplicates Tracking 187049 as yet unmatched pairs. 20232 records in RAM.
INFO 2026-06-08 08:40:49 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:10:40s. Time for last 1,000,000: 1s. Last read position: chr16:29,454,794
INFO 2026-06-08 08:40:49 MarkDuplicates Tracking 185981 as yet unmatched pairs. 19164 records in RAM.
INFO 2026-06-08 08:40:51 MarkDuplicates Read 368,000,000 records. Elapsed time: 00:10:41s. Time for last 1,000,000: 1s. Last read position: chr16:29,991,251
INFO 2026-06-08 08:40:51 MarkDuplicates Tracking 184270 as yet unmatched pairs. 17451 records in RAM.
INFO 2026-06-08 08:40:53 MarkDuplicates Read 369,000,000 records. Elapsed time: 00:10:43s. Time for last 1,000,000: 1s. Last read position: chr16:30,223,039
INFO 2026-06-08 08:40:53 MarkDuplicates Tracking 182580 as yet unmatched pairs. 15761 records in RAM.
INFO 2026-06-08 08:40:54 MarkDuplicates Read 370,000,000 records. Elapsed time: 00:10:44s. Time for last 1,000,000: 1s. Last read position: chr16:30,930,329
INFO 2026-06-08 08:40:54 MarkDuplicates Tracking 181331 as yet unmatched pairs. 14509 records in RAM.
INFO 2026-06-08 08:40:56 MarkDuplicates Read 371,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 1s. Last read position: chr16:31,424,564
INFO 2026-06-08 08:40:56 MarkDuplicates Tracking 179597 as yet unmatched pairs. 12775 records in RAM.
INFO 2026-06-08 08:40:57 MarkDuplicates Read 372,000,000 records. Elapsed time: 00:10:47s. Time for last 1,000,000: 1s. Last read position: chr16:54,111,770
INFO 2026-06-08 08:40:57 MarkDuplicates Tracking 178589 as yet unmatched pairs. 11766 records in RAM.
INFO 2026-06-08 08:40:59 MarkDuplicates Read 373,000,000 records. Elapsed time: 00:10:49s. Time for last 1,000,000: 1s. Last read position: chr16:57,798,121
INFO 2026-06-08 08:40:59 MarkDuplicates Tracking 177646 as yet unmatched pairs. 10823 records in RAM.
INFO 2026-06-08 08:41:00 MarkDuplicates Read 374,000,000 records. Elapsed time: 00:10:51s. Time for last 1,000,000: 1s. Last read position: chr16:67,154,741
INFO 2026-06-08 08:41:00 MarkDuplicates Tracking 175344 as yet unmatched pairs. 8520 records in RAM.
INFO 2026-06-08 08:41:02 MarkDuplicates Read 375,000,000 records. Elapsed time: 00:10:52s. Time for last 1,000,000: 1s. Last read position: chr16:68,357,065
INFO 2026-06-08 08:41:02 MarkDuplicates Tracking 173574 as yet unmatched pairs. 6750 records in RAM.
INFO 2026-06-08 08:41:03 MarkDuplicates Read 376,000,000 records. Elapsed time: 00:10:54s. Time for last 1,000,000: 1s. Last read position: chr16:70,184,596
INFO 2026-06-08 08:41:03 MarkDuplicates Tracking 172871 as yet unmatched pairs. 6046 records in RAM.
INFO 2026-06-08 08:41:06 MarkDuplicates Read 377,000,000 records. Elapsed time: 00:10:56s. Time for last 1,000,000: 2s. Last read position: chr16:74,412,190
INFO 2026-06-08 08:41:06 MarkDuplicates Tracking 172469 as yet unmatched pairs. 5644 records in RAM.
INFO 2026-06-08 08:41:08 MarkDuplicates Read 378,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 2s. Last read position: chr16:83,783,397
INFO 2026-06-08 08:41:08 MarkDuplicates Tracking 169988 as yet unmatched pairs. 3161 records in RAM.
INFO 2026-06-08 08:41:10 MarkDuplicates Read 379,000,000 records. Elapsed time: 00:11:00s. Time for last 1,000,000: 1s. Last read position: chr16:88,719,614
INFO 2026-06-08 08:41:10 MarkDuplicates Tracking 168366 as yet unmatched pairs. 1538 records in RAM.
INFO 2026-06-08 08:41:12 MarkDuplicates Read 380,000,000 records. Elapsed time: 00:11:02s. Time for last 1,000,000: 1s. Last read position: chr17:747,651
INFO 2026-06-08 08:41:12 MarkDuplicates Tracking 166795 as yet unmatched pairs. 43108 records in RAM.
INFO 2026-06-08 08:41:13 MarkDuplicates Read 381,000,000 records. Elapsed time: 00:11:03s. Time for last 1,000,000: 1s. Last read position: chr17:1,678,532
INFO 2026-06-08 08:41:13 MarkDuplicates Tracking 165469 as yet unmatched pairs. 41782 records in RAM.
INFO 2026-06-08 08:41:15 MarkDuplicates Read 382,000,000 records. Elapsed time: 00:11:05s. Time for last 1,000,000: 1s. Last read position: chr17:3,669,112
INFO 2026-06-08 08:41:15 MarkDuplicates Tracking 163777 as yet unmatched pairs. 40090 records in RAM.
INFO 2026-06-08 08:41:16 MarkDuplicates Read 383,000,000 records. Elapsed time: 00:11:07s. Time for last 1,000,000: 1s. Last read position: chr17:5,433,023
INFO 2026-06-08 08:41:16 MarkDuplicates Tracking 162101 as yet unmatched pairs. 38413 records in RAM.
INFO 2026-06-08 08:41:18 MarkDuplicates Read 384,000,000 records. Elapsed time: 00:11:08s. Time for last 1,000,000: 1s. Last read position: chr17:7,444,824
INFO 2026-06-08 08:41:18 MarkDuplicates Tracking 160407 as yet unmatched pairs. 36719 records in RAM.
INFO 2026-06-08 08:41:21 MarkDuplicates Read 385,000,000 records. Elapsed time: 00:11:11s. Time for last 1,000,000: 2s. Last read position: chr17:7,856,826
INFO 2026-06-08 08:41:21 MarkDuplicates Tracking 159759 as yet unmatched pairs. 36071 records in RAM.
INFO 2026-06-08 08:41:22 MarkDuplicates Read 386,000,000 records. Elapsed time: 00:11:12s. Time for last 1,000,000: 1s. Last read position: chr17:16,068,007
INFO 2026-06-08 08:41:22 MarkDuplicates Tracking 157751 as yet unmatched pairs. 34062 records in RAM.
INFO 2026-06-08 08:41:24 MarkDuplicates Read 387,000,000 records. Elapsed time: 00:11:14s. Time for last 1,000,000: 1s. Last read position: chr17:18,250,946
INFO 2026-06-08 08:41:24 MarkDuplicates Tracking 156142 as yet unmatched pairs. 32452 records in RAM.
INFO 2026-06-08 08:41:25 MarkDuplicates Read 388,000,000 records. Elapsed time: 00:11:15s. Time for last 1,000,000: 1s. Last read position: chr17:27,301,856
INFO 2026-06-08 08:41:25 MarkDuplicates Tracking 155561 as yet unmatched pairs. 31871 records in RAM.
INFO 2026-06-08 08:41:27 MarkDuplicates Read 389,000,000 records. Elapsed time: 00:11:17s. Time for last 1,000,000: 1s. Last read position: chr17:29,082,392
INFO 2026-06-08 08:41:27 MarkDuplicates Tracking 153391 as yet unmatched pairs. 29701 records in RAM.
INFO 2026-06-08 08:41:28 MarkDuplicates Read 390,000,000 records. Elapsed time: 00:11:18s. Time for last 1,000,000: 1s. Last read position: chr17:32,767,734
INFO 2026-06-08 08:41:28 MarkDuplicates Tracking 152100 as yet unmatched pairs. 28410 records in RAM.
INFO 2026-06-08 08:41:30 MarkDuplicates Read 391,000,000 records. Elapsed time: 00:11:20s. Time for last 1,000,000: 1s. Last read position: chr17:37,934,548
INFO 2026-06-08 08:41:30 MarkDuplicates Tracking 150488 as yet unmatched pairs. 26798 records in RAM.
INFO 2026-06-08 08:41:31 MarkDuplicates Read 392,000,000 records. Elapsed time: 00:11:21s. Time for last 1,000,000: 1s. Last read position: chr17:39,410,386
INFO 2026-06-08 08:41:31 MarkDuplicates Tracking 149239 as yet unmatched pairs. 25549 records in RAM.
INFO 2026-06-08 08:41:33 MarkDuplicates Read 393,000,000 records. Elapsed time: 00:11:23s. Time for last 1,000,000: 1s. Last read position: chr17:40,169,333
INFO 2026-06-08 08:41:33 MarkDuplicates Tracking 147463 as yet unmatched pairs. 23772 records in RAM.
INFO 2026-06-08 08:41:35 MarkDuplicates Read 394,000,000 records. Elapsed time: 00:11:25s. Time for last 1,000,000: 2s. Last read position: chr17:41,966,860
INFO 2026-06-08 08:41:35 MarkDuplicates Tracking 146002 as yet unmatched pairs. 22311 records in RAM.
INFO 2026-06-08 08:41:37 MarkDuplicates Read 395,000,000 records. Elapsed time: 00:11:27s. Time for last 1,000,000: 1s. Last read position: chr17:42,854,668
INFO 2026-06-08 08:41:37 MarkDuplicates Tracking 144466 as yet unmatched pairs. 20775 records in RAM.
INFO 2026-06-08 08:41:39 MarkDuplicates Read 396,000,000 records. Elapsed time: 00:11:29s. Time for last 1,000,000: 1s. Last read position: chr17:44,967,953
INFO 2026-06-08 08:41:39 MarkDuplicates Tracking 142846 as yet unmatched pairs. 19155 records in RAM.
INFO 2026-06-08 08:41:40 MarkDuplicates Read 397,000,000 records. Elapsed time: 00:11:30s. Time for last 1,000,000: 1s. Last read position: chr17:47,840,337
INFO 2026-06-08 08:41:40 MarkDuplicates Tracking 141677 as yet unmatched pairs. 17986 records in RAM.
INFO 2026-06-08 08:41:42 MarkDuplicates Read 398,000,000 records. Elapsed time: 00:11:32s. Time for last 1,000,000: 1s. Last read position: chr17:50,187,918
INFO 2026-06-08 08:41:42 MarkDuplicates Tracking 140681 as yet unmatched pairs. 16981 records in RAM.
INFO 2026-06-08 08:41:43 MarkDuplicates Read 399,000,000 records. Elapsed time: 00:11:33s. Time for last 1,000,000: 1s. Last read position: chr17:50,660,963
INFO 2026-06-08 08:41:43 MarkDuplicates Tracking 138755 as yet unmatched pairs. 15055 records in RAM.
INFO 2026-06-08 08:41:45 MarkDuplicates Read 400,000,000 records. Elapsed time: 00:11:35s. Time for last 1,000,000: 1s. Last read position: chr17:58,525,700
INFO 2026-06-08 08:41:45 MarkDuplicates Tracking 137037 as yet unmatched pairs. 13337 records in RAM.
INFO 2026-06-08 08:41:46 MarkDuplicates Read 401,000,000 records. Elapsed time: 00:11:36s. Time for last 1,000,000: 1s. Last read position: chr17:60,214,620
INFO 2026-06-08 08:41:46 MarkDuplicates Tracking 135462 as yet unmatched pairs. 11762 records in RAM.
INFO 2026-06-08 08:41:48 MarkDuplicates Read 402,000,000 records. Elapsed time: 00:11:38s. Time for last 1,000,000: 1s. Last read position: chr17:64,375,296
INFO 2026-06-08 08:41:48 MarkDuplicates Tracking 134304 as yet unmatched pairs. 10604 records in RAM.
INFO 2026-06-08 08:41:49 MarkDuplicates Read 403,000,000 records. Elapsed time: 00:11:40s. Time for last 1,000,000: 1s. Last read position: chr17:68,530,341
INFO 2026-06-08 08:41:49 MarkDuplicates Tracking 134093 as yet unmatched pairs. 10392 records in RAM.
INFO 2026-06-08 08:41:52 MarkDuplicates Read 404,000,000 records. Elapsed time: 00:11:42s. Time for last 1,000,000: 2s. Last read position: chr17:75,588,510
INFO 2026-06-08 08:41:52 MarkDuplicates Tracking 131212 as yet unmatched pairs. 7508 records in RAM.
INFO 2026-06-08 08:41:53 MarkDuplicates Read 405,000,000 records. Elapsed time: 00:11:43s. Time for last 1,000,000: 1s. Last read position: chr17:77,194,753
INFO 2026-06-08 08:41:53 MarkDuplicates Tracking 130027 as yet unmatched pairs. 6323 records in RAM.
INFO 2026-06-08 08:41:55 MarkDuplicates Read 406,000,000 records. Elapsed time: 00:11:45s. Time for last 1,000,000: 1s. Last read position: chr17:80,110,785
INFO 2026-06-08 08:41:55 MarkDuplicates Tracking 128425 as yet unmatched pairs. 4721 records in RAM.
INFO 2026-06-08 08:41:56 MarkDuplicates Read 407,000,000 records. Elapsed time: 00:11:46s. Time for last 1,000,000: 1s. Last read position: chr17:81,280,618
INFO 2026-06-08 08:41:56 MarkDuplicates Tracking 126608 as yet unmatched pairs. 2904 records in RAM.
INFO 2026-06-08 08:41:58 MarkDuplicates Read 408,000,000 records. Elapsed time: 00:11:48s. Time for last 1,000,000: 1s. Last read position: chr17:81,983,479
INFO 2026-06-08 08:41:58 MarkDuplicates Tracking 124804 as yet unmatched pairs. 1100 records in RAM.
INFO 2026-06-08 08:41:59 MarkDuplicates Read 409,000,000 records. Elapsed time: 00:11:50s. Time for last 1,000,000: 1s. Last read position: chr18:4,637,729
INFO 2026-06-08 08:41:59 MarkDuplicates Tracking 123267 as yet unmatched pairs. 7889 records in RAM.
INFO 2026-06-08 08:42:01 MarkDuplicates Read 410,000,000 records. Elapsed time: 00:11:51s. Time for last 1,000,000: 1s. Last read position: chr18:12,325,264
INFO 2026-06-08 08:42:01 MarkDuplicates Tracking 122039 as yet unmatched pairs. 6661 records in RAM.
INFO 2026-06-08 08:42:02 MarkDuplicates Read 411,000,000 records. Elapsed time: 00:11:52s. Time for last 1,000,000: 1s. Last read position: chr18:32,018,945
INFO 2026-06-08 08:42:02 MarkDuplicates Tracking 120510 as yet unmatched pairs. 5131 records in RAM.
INFO 2026-06-08 08:42:04 MarkDuplicates Read 412,000,000 records. Elapsed time: 00:11:54s. Time for last 1,000,000: 1s. Last read position: chr18:49,490,861
INFO 2026-06-08 08:42:04 MarkDuplicates Tracking 121055 as yet unmatched pairs. 5676 records in RAM.
INFO 2026-06-08 08:42:06 MarkDuplicates Read 413,000,000 records. Elapsed time: 00:11:56s. Time for last 1,000,000: 2s. Last read position: chr18:58,984,238
INFO 2026-06-08 08:42:06 MarkDuplicates Tracking 117712 as yet unmatched pairs. 2333 records in RAM.
INFO 2026-06-08 08:42:08 MarkDuplicates Read 414,000,000 records. Elapsed time: 00:11:58s. Time for last 1,000,000: 1s. Last read position: chr18:74,510,922
INFO 2026-06-08 08:42:08 MarkDuplicates Tracking 117144 as yet unmatched pairs. 1765 records in RAM.
INFO 2026-06-08 08:42:10 MarkDuplicates Read 415,000,000 records. Elapsed time: 00:12:00s. Time for last 1,000,000: 1s. Last read position: chr19:726,161
INFO 2026-06-08 08:42:10 MarkDuplicates Tracking 114611 as yet unmatched pairs. 48055 records in RAM.
INFO 2026-06-08 08:42:11 MarkDuplicates Read 416,000,000 records. Elapsed time: 00:12:02s. Time for last 1,000,000: 1s. Last read position: chr19:1,271,995
INFO 2026-06-08 08:42:11 MarkDuplicates Tracking 113980 as yet unmatched pairs. 47423 records in RAM.
INFO 2026-06-08 08:42:13 MarkDuplicates Read 417,000,000 records. Elapsed time: 00:12:03s. Time for last 1,000,000: 1s. Last read position: chr19:2,244,734
INFO 2026-06-08 08:42:13 MarkDuplicates Tracking 111340 as yet unmatched pairs. 44783 records in RAM.
INFO 2026-06-08 08:42:14 MarkDuplicates Read 418,000,000 records. Elapsed time: 00:12:05s. Time for last 1,000,000: 1s. Last read position: chr19:4,327,361
INFO 2026-06-08 08:42:14 MarkDuplicates Tracking 109577 as yet unmatched pairs. 43020 records in RAM.
INFO 2026-06-08 08:42:17 MarkDuplicates Read 419,000,000 records. Elapsed time: 00:12:07s. Time for last 1,000,000: 2s. Last read position: chr19:5,691,368
INFO 2026-06-08 08:42:17 MarkDuplicates Tracking 108178 as yet unmatched pairs. 41621 records in RAM.
INFO 2026-06-08 08:42:18 MarkDuplicates Read 420,000,000 records. Elapsed time: 00:12:09s. Time for last 1,000,000: 1s. Last read position: chr19:6,693,019
INFO 2026-06-08 08:42:18 MarkDuplicates Tracking 107909 as yet unmatched pairs. 41352 records in RAM.
INFO 2026-06-08 08:42:20 MarkDuplicates Read 421,000,000 records. Elapsed time: 00:12:10s. Time for last 1,000,000: 1s. Last read position: chr19:6,822,305
INFO 2026-06-08 08:42:20 MarkDuplicates Tracking 104990 as yet unmatched pairs. 38433 records in RAM.
INFO 2026-06-08 08:42:22 MarkDuplicates Read 422,000,000 records. Elapsed time: 00:12:12s. Time for last 1,000,000: 1s. Last read position: chr19:8,333,083
INFO 2026-06-08 08:42:22 MarkDuplicates Tracking 103565 as yet unmatched pairs. 37008 records in RAM.
INFO 2026-06-08 08:42:23 MarkDuplicates Read 423,000,000 records. Elapsed time: 00:12:13s. Time for last 1,000,000: 1s. Last read position: chr19:10,086,952
INFO 2026-06-08 08:42:23 MarkDuplicates Tracking 101816 as yet unmatched pairs. 35259 records in RAM.
INFO 2026-06-08 08:42:25 MarkDuplicates Read 424,000,000 records. Elapsed time: 00:12:15s. Time for last 1,000,000: 1s. Last read position: chr19:11,019,567
INFO 2026-06-08 08:42:25 MarkDuplicates Tracking 100268 as yet unmatched pairs. 33710 records in RAM.
INFO 2026-06-08 08:42:26 MarkDuplicates Read 425,000,000 records. Elapsed time: 00:12:16s. Time for last 1,000,000: 1s. Last read position: chr19:12,665,515
INFO 2026-06-08 08:42:26 MarkDuplicates Tracking 99040 as yet unmatched pairs. 32482 records in RAM.
INFO 2026-06-08 08:42:28 MarkDuplicates Read 426,000,000 records. Elapsed time: 00:12:18s. Time for last 1,000,000: 1s. Last read position: chr19:14,090,391
INFO 2026-06-08 08:42:28 MarkDuplicates Tracking 97076 as yet unmatched pairs. 30518 records in RAM.
INFO 2026-06-08 08:42:29 MarkDuplicates Read 427,000,000 records. Elapsed time: 00:12:19s. Time for last 1,000,000: 1s. Last read position: chr19:15,179,395
INFO 2026-06-08 08:42:29 MarkDuplicates Tracking 95572 as yet unmatched pairs. 29014 records in RAM.
INFO 2026-06-08 08:42:31 MarkDuplicates Read 428,000,000 records. Elapsed time: 00:12:21s. Time for last 1,000,000: 1s. Last read position: chr19:16,525,401
INFO 2026-06-08 08:42:31 MarkDuplicates Tracking 93926 as yet unmatched pairs. 27368 records in RAM.
INFO 2026-06-08 08:42:33 MarkDuplicates Read 429,000,000 records. Elapsed time: 00:12:23s. Time for last 1,000,000: 1s. Last read position: chr19:17,861,297
INFO 2026-06-08 08:42:33 MarkDuplicates Tracking 93034 as yet unmatched pairs. 26476 records in RAM.
INFO 2026-06-08 08:42:35 MarkDuplicates Read 430,000,000 records. Elapsed time: 00:12:25s. Time for last 1,000,000: 1s. Last read position: chr19:18,786,633
INFO 2026-06-08 08:42:35 MarkDuplicates Tracking 90751 as yet unmatched pairs. 24193 records in RAM.
INFO 2026-06-08 08:42:36 MarkDuplicates Read 431,000,000 records. Elapsed time: 00:12:26s. Time for last 1,000,000: 1s. Last read position: chr19:33,511,064
INFO 2026-06-08 08:42:36 MarkDuplicates Tracking 89669 as yet unmatched pairs. 23111 records in RAM.
INFO 2026-06-08 08:42:38 MarkDuplicates Read 432,000,000 records. Elapsed time: 00:12:28s. Time for last 1,000,000: 1s. Last read position: chr19:35,658,599
INFO 2026-06-08 08:42:38 MarkDuplicates Tracking 87621 as yet unmatched pairs. 21063 records in RAM.
INFO 2026-06-08 08:42:39 MarkDuplicates Read 433,000,000 records. Elapsed time: 00:12:29s. Time for last 1,000,000: 1s. Last read position: chr19:38,634,996
INFO 2026-06-08 08:42:39 MarkDuplicates Tracking 85812 as yet unmatched pairs. 19254 records in RAM.
INFO 2026-06-08 08:42:40 MarkDuplicates Read 434,000,000 records. Elapsed time: 00:12:31s. Time for last 1,000,000: 1s. Last read position: chr19:39,433,394
INFO 2026-06-08 08:42:40 MarkDuplicates Tracking 86331 as yet unmatched pairs. 19773 records in RAM.
INFO 2026-06-08 08:42:42 MarkDuplicates Read 435,000,000 records. Elapsed time: 00:12:32s. Time for last 1,000,000: 1s. Last read position: chr19:40,677,318
INFO 2026-06-08 08:42:42 MarkDuplicates Tracking 82481 as yet unmatched pairs. 15923 records in RAM.
INFO 2026-06-08 08:42:44 MarkDuplicates Read 436,000,000 records. Elapsed time: 00:12:34s. Time for last 1,000,000: 1s. Last read position: chr19:42,250,526
INFO 2026-06-08 08:42:44 MarkDuplicates Tracking 80846 as yet unmatched pairs. 14287 records in RAM.
INFO 2026-06-08 08:42:45 MarkDuplicates Read 437,000,000 records. Elapsed time: 00:12:35s. Time for last 1,000,000: 1s. Last read position: chr19:43,546,917
INFO 2026-06-08 08:42:45 MarkDuplicates Tracking 79398 as yet unmatched pairs. 12825 records in RAM.
INFO 2026-06-08 08:42:47 MarkDuplicates Read 438,000,000 records. Elapsed time: 00:12:37s. Time for last 1,000,000: 1s. Last read position: chr19:45,398,120
INFO 2026-06-08 08:42:47 MarkDuplicates Tracking 77742 as yet unmatched pairs. 11169 records in RAM.
INFO 2026-06-08 08:42:48 MarkDuplicates Read 439,000,000 records. Elapsed time: 00:12:39s. Time for last 1,000,000: 1s. Last read position: chr19:47,086,384
INFO 2026-06-08 08:42:48 MarkDuplicates Tracking 75907 as yet unmatched pairs. 9334 records in RAM.
INFO 2026-06-08 08:42:50 MarkDuplicates Read 440,000,000 records. Elapsed time: 00:12:40s. Time for last 1,000,000: 1s. Last read position: chr19:48,859,506
INFO 2026-06-08 08:42:50 MarkDuplicates Tracking 74265 as yet unmatched pairs. 7692 records in RAM.
INFO 2026-06-08 08:42:53 MarkDuplicates Read 441,000,000 records. Elapsed time: 00:12:43s. Time for last 1,000,000: 2s. Last read position: chr19:49,524,517
INFO 2026-06-08 08:42:53 MarkDuplicates Tracking 73152 as yet unmatched pairs. 6579 records in RAM.
INFO 2026-06-08 08:42:55 MarkDuplicates Read 442,000,000 records. Elapsed time: 00:12:45s. Time for last 1,000,000: 2s. Last read position: chr19:50,506,379
INFO 2026-06-08 08:42:55 MarkDuplicates Tracking 71224 as yet unmatched pairs. 4651 records in RAM.
INFO 2026-06-08 08:42:57 MarkDuplicates Read 443,000,000 records. Elapsed time: 00:12:47s. Time for last 1,000,000: 1s. Last read position: chr19:54,207,415
INFO 2026-06-08 08:42:57 MarkDuplicates Tracking 70680 as yet unmatched pairs. 4107 records in RAM.
INFO 2026-06-08 08:42:58 MarkDuplicates Read 444,000,000 records. Elapsed time: 00:12:48s. Time for last 1,000,000: 1s. Last read position: chr19:55,688,919
INFO 2026-06-08 08:42:58 MarkDuplicates Tracking 68339 as yet unmatched pairs. 1766 records in RAM.
INFO 2026-06-08 08:43:00 MarkDuplicates Read 445,000,000 records. Elapsed time: 00:12:50s. Time for last 1,000,000: 1s. Last read position: chr19:58,556,171
INFO 2026-06-08 08:43:00 MarkDuplicates Tracking 66737 as yet unmatched pairs. 163 records in RAM.
INFO 2026-06-08 08:43:01 MarkDuplicates Read 446,000,000 records. Elapsed time: 00:12:51s. Time for last 1,000,000: 1s. Last read position: chr20:3,692,019
INFO 2026-06-08 08:43:01 MarkDuplicates Tracking 65151 as yet unmatched pairs. 13914 records in RAM.
INFO 2026-06-08 08:43:04 MarkDuplicates Read 447,000,000 records. Elapsed time: 00:12:54s. Time for last 1,000,000: 2s. Last read position: chr20:17,659,065
INFO 2026-06-08 08:43:04 MarkDuplicates Tracking 63691 as yet unmatched pairs. 12452 records in RAM.
INFO 2026-06-08 08:43:05 MarkDuplicates Read 448,000,000 records. Elapsed time: 00:12:55s. Time for last 1,000,000: 1s. Last read position: chr20:31,561,642
INFO 2026-06-08 08:43:05 MarkDuplicates Tracking 62362 as yet unmatched pairs. 11123 records in RAM.
INFO 2026-06-08 08:43:07 MarkDuplicates Read 449,000,000 records. Elapsed time: 00:12:57s. Time for last 1,000,000: 1s. Last read position: chr20:35,284,191
INFO 2026-06-08 08:43:07 MarkDuplicates Tracking 61390 as yet unmatched pairs. 10151 records in RAM.
INFO 2026-06-08 08:43:08 MarkDuplicates Read 450,000,000 records. Elapsed time: 00:12:58s. Time for last 1,000,000: 1s. Last read position: chr20:38,130,262
INFO 2026-06-08 08:43:08 MarkDuplicates Tracking 59600 as yet unmatched pairs. 8361 records in RAM.
INFO 2026-06-08 08:43:10 MarkDuplicates Read 451,000,000 records. Elapsed time: 00:13:00s. Time for last 1,000,000: 1s. Last read position: chr20:44,906,000
INFO 2026-06-08 08:43:10 MarkDuplicates Tracking 57934 as yet unmatched pairs. 6695 records in RAM.
INFO 2026-06-08 08:43:12 MarkDuplicates Read 452,000,000 records. Elapsed time: 00:13:02s. Time for last 1,000,000: 2s. Last read position: chr20:47,684,548
INFO 2026-06-08 08:43:12 MarkDuplicates Tracking 56435 as yet unmatched pairs. 5196 records in RAM.
INFO 2026-06-08 08:43:13 MarkDuplicates Read 453,000,000 records. Elapsed time: 00:13:04s. Time for last 1,000,000: 1s. Last read position: chr20:57,565,531
INFO 2026-06-08 08:43:13 MarkDuplicates Tracking 55121 as yet unmatched pairs. 3881 records in RAM.
INFO 2026-06-08 08:43:15 MarkDuplicates Read 454,000,000 records. Elapsed time: 00:13:05s. Time for last 1,000,000: 1s. Last read position: chr20:62,325,443
INFO 2026-06-08 08:43:15 MarkDuplicates Tracking 53456 as yet unmatched pairs. 2216 records in RAM.
INFO 2026-06-08 08:43:16 MarkDuplicates Read 455,000,000 records. Elapsed time: 00:13:07s. Time for last 1,000,000: 1s. Last read position: chr20:63,873,681
INFO 2026-06-08 08:43:16 MarkDuplicates Tracking 51782 as yet unmatched pairs. 542 records in RAM.
INFO 2026-06-08 08:43:18 MarkDuplicates Read 456,000,000 records. Elapsed time: 00:13:08s. Time for last 1,000,000: 1s. Last read position: chr21:8,217,335
INFO 2026-06-08 08:43:18 MarkDuplicates Tracking 50217 as yet unmatched pairs. 8719 records in RAM.
INFO 2026-06-08 08:43:19 MarkDuplicates Read 457,000,000 records. Elapsed time: 00:13:09s. Time for last 1,000,000: 1s. Last read position: chr21:8,400,429
INFO 2026-06-08 08:43:19 MarkDuplicates Tracking 49569 as yet unmatched pairs. 8069 records in RAM.
INFO 2026-06-08 08:43:20 MarkDuplicates Read 458,000,000 records. Elapsed time: 00:13:10s. Time for last 1,000,000: 1s. Last read position: chr21:25,911,804
INFO 2026-06-08 08:43:20 MarkDuplicates Tracking 49632 as yet unmatched pairs. 8132 records in RAM.
INFO 2026-06-08 08:43:22 MarkDuplicates Read 459,000,000 records. Elapsed time: 00:13:12s. Time for last 1,000,000: 1s. Last read position: chr21:33,546,228
INFO 2026-06-08 08:43:22 MarkDuplicates Tracking 47300 as yet unmatched pairs. 5800 records in RAM.
INFO 2026-06-08 08:43:23 MarkDuplicates Read 460,000,000 records. Elapsed time: 00:13:14s. Time for last 1,000,000: 1s. Last read position: chr21:38,383,489
INFO 2026-06-08 08:43:23 MarkDuplicates Tracking 45794 as yet unmatched pairs. 4293 records in RAM.
INFO 2026-06-08 08:43:25 MarkDuplicates Read 461,000,000 records. Elapsed time: 00:13:15s. Time for last 1,000,000: 1s. Last read position: chr21:44,319,352
INFO 2026-06-08 08:43:25 MarkDuplicates Tracking 44671 as yet unmatched pairs. 3170 records in RAM.
INFO 2026-06-08 08:43:27 MarkDuplicates Read 462,000,000 records. Elapsed time: 00:13:17s. Time for last 1,000,000: 2s. Last read position: chr21:45,509,504
INFO 2026-06-08 08:43:27 MarkDuplicates Tracking 43179 as yet unmatched pairs. 1671 records in RAM.
INFO 2026-06-08 08:43:29 MarkDuplicates Read 463,000,000 records. Elapsed time: 00:13:19s. Time for last 1,000,000: 1s. Last read position: chr22:17,818,935
INFO 2026-06-08 08:43:29 MarkDuplicates Tracking 41278 as yet unmatched pairs. 18929 records in RAM.
INFO 2026-06-08 08:43:31 MarkDuplicates Read 464,000,000 records. Elapsed time: 00:13:21s. Time for last 1,000,000: 1s. Last read position: chr22:20,996,957
INFO 2026-06-08 08:43:31 MarkDuplicates Tracking 39606 as yet unmatched pairs. 17257 records in RAM.
INFO 2026-06-08 08:43:32 MarkDuplicates Read 465,000,000 records. Elapsed time: 00:13:22s. Time for last 1,000,000: 1s. Last read position: chr22:23,894,831
INFO 2026-06-08 08:43:32 MarkDuplicates Tracking 39796 as yet unmatched pairs. 17447 records in RAM.
INFO 2026-06-08 08:43:33 MarkDuplicates Read 466,000,000 records. Elapsed time: 00:13:24s. Time for last 1,000,000: 1s. Last read position: chr22:27,998,950
INFO 2026-06-08 08:43:33 MarkDuplicates Tracking 36631 as yet unmatched pairs. 14282 records in RAM.
INFO 2026-06-08 08:43:35 MarkDuplicates Read 467,000,000 records. Elapsed time: 00:13:25s. Time for last 1,000,000: 1s. Last read position: chr22:30,340,702
INFO 2026-06-08 08:43:35 MarkDuplicates Tracking 35033 as yet unmatched pairs. 12684 records in RAM.
INFO 2026-06-08 08:43:36 MarkDuplicates Read 468,000,000 records. Elapsed time: 00:13:27s. Time for last 1,000,000: 1s. Last read position: chr22:32,066,934
INFO 2026-06-08 08:43:36 MarkDuplicates Tracking 33590 as yet unmatched pairs. 11241 records in RAM.
INFO 2026-06-08 08:43:39 MarkDuplicates Read 469,000,000 records. Elapsed time: 00:13:29s. Time for last 1,000,000: 2s. Last read position: chr22:36,341,418
INFO 2026-06-08 08:43:39 MarkDuplicates Tracking 31915 as yet unmatched pairs. 9566 records in RAM.
INFO 2026-06-08 08:43:40 MarkDuplicates Read 470,000,000 records. Elapsed time: 00:13:30s. Time for last 1,000,000: 1s. Last read position: chr22:38,485,993
INFO 2026-06-08 08:43:40 MarkDuplicates Tracking 30574 as yet unmatched pairs. 8225 records in RAM.
INFO 2026-06-08 08:43:42 MarkDuplicates Read 471,000,000 records. Elapsed time: 00:13:32s. Time for last 1,000,000: 1s. Last read position: chr22:40,361,286
INFO 2026-06-08 08:43:42 MarkDuplicates Tracking 28468 as yet unmatched pairs. 6119 records in RAM.
INFO 2026-06-08 08:43:43 MarkDuplicates Read 472,000,000 records. Elapsed time: 00:13:33s. Time for last 1,000,000: 1s. Last read position: chr22:42,214,276
INFO 2026-06-08 08:43:43 MarkDuplicates Tracking 27013 as yet unmatched pairs. 4664 records in RAM.
INFO 2026-06-08 08:43:45 MarkDuplicates Read 473,000,000 records. Elapsed time: 00:13:35s. Time for last 1,000,000: 1s. Last read position: chr22:46,534,188
INFO 2026-06-08 08:43:45 MarkDuplicates Tracking 25599 as yet unmatched pairs. 3250 records in RAM.
INFO 2026-06-08 08:43:46 MarkDuplicates Read 474,000,000 records. Elapsed time: 00:13:36s. Time for last 1,000,000: 1s. Last read position: chr22:50,440,884
INFO 2026-06-08 08:43:46 MarkDuplicates Tracking 23832 as yet unmatched pairs. 1483 records in RAM.
INFO 2026-06-08 08:43:48 MarkDuplicates Read 475,000,000 records. Elapsed time: 00:13:39s. Time for last 1,000,000: 2s. Last read position: chrX:2,740,814
INFO 2026-06-08 08:43:48 MarkDuplicates Tracking 22091 as yet unmatched pairs. 18711 records in RAM.
INFO 2026-06-08 08:43:50 MarkDuplicates Read 476,000,000 records. Elapsed time: 00:13:41s. Time for last 1,000,000: 1s. Last read position: chrX:16,869,096
INFO 2026-06-08 08:43:50 MarkDuplicates Tracking 20608 as yet unmatched pairs. 17228 records in RAM.
INFO 2026-06-08 08:43:52 MarkDuplicates Read 477,000,000 records. Elapsed time: 00:13:42s. Time for last 1,000,000: 1s. Last read position: chrX:40,053,926
INFO 2026-06-08 08:43:52 MarkDuplicates Tracking 19196 as yet unmatched pairs. 15812 records in RAM.
INFO 2026-06-08 08:43:53 MarkDuplicates Read 478,000,000 records. Elapsed time: 00:13:44s. Time for last 1,000,000: 1s. Last read position: chrX:47,200,992
INFO 2026-06-08 08:43:53 MarkDuplicates Tracking 18067 as yet unmatched pairs. 14682 records in RAM.
INFO 2026-06-08 08:43:55 MarkDuplicates Read 479,000,000 records. Elapsed time: 00:13:45s. Time for last 1,000,000: 1s. Last read position: chrX:49,075,395
INFO 2026-06-08 08:43:55 MarkDuplicates Tracking 16182 as yet unmatched pairs. 12797 records in RAM.
INFO 2026-06-08 08:43:56 MarkDuplicates Read 480,000,000 records. Elapsed time: 00:13:47s. Time for last 1,000,000: 1s. Last read position: chrX:54,809,301
INFO 2026-06-08 08:43:56 MarkDuplicates Tracking 14772 as yet unmatched pairs. 11387 records in RAM.
INFO 2026-06-08 08:43:58 MarkDuplicates Read 481,000,000 records. Elapsed time: 00:13:48s. Time for last 1,000,000: 1s. Last read position: chrX:71,294,380
INFO 2026-06-08 08:43:58 MarkDuplicates Tracking 13376 as yet unmatched pairs. 9991 records in RAM.
INFO 2026-06-08 08:43:59 MarkDuplicates Read 482,000,000 records. Elapsed time: 00:13:49s. Time for last 1,000,000: 1s. Last read position: chrX:78,113,821
INFO 2026-06-08 08:43:59 MarkDuplicates Tracking 12448 as yet unmatched pairs. 9063 records in RAM.
INFO 2026-06-08 08:44:01 MarkDuplicates Read 483,000,000 records. Elapsed time: 00:13:51s. Time for last 1,000,000: 1s. Last read position: chrX:107,714,583
INFO 2026-06-08 08:44:01 MarkDuplicates Tracking 10498 as yet unmatched pairs. 7113 records in RAM.
INFO 2026-06-08 08:44:02 MarkDuplicates Read 484,000,000 records. Elapsed time: 00:13:52s. Time for last 1,000,000: 1s. Last read position: chrX:129,576,307
INFO 2026-06-08 08:44:02 MarkDuplicates Tracking 9021 as yet unmatched pairs. 5636 records in RAM.
INFO 2026-06-08 08:44:04 MarkDuplicates Read 485,000,000 records. Elapsed time: 00:13:54s. Time for last 1,000,000: 1s. Last read position: chrX:149,631,731
INFO 2026-06-08 08:44:04 MarkDuplicates Tracking 7730 as yet unmatched pairs. 4345 records in RAM.
INFO 2026-06-08 08:44:05 MarkDuplicates Read 486,000,000 records. Elapsed time: 00:13:56s. Time for last 1,000,000: 1s. Last read position: chrX:153,695,124
INFO 2026-06-08 08:44:05 MarkDuplicates Tracking 7661 as yet unmatched pairs. 4275 records in RAM.
INFO 2026-06-08 08:44:07 MarkDuplicates Read 487,000,000 records. Elapsed time: 00:13:58s. Time for last 1,000,000: 2s. Last read position: chrX:154,366,029
INFO 2026-06-08 08:44:07 MarkDuplicates Tracking 4993 as yet unmatched pairs. 1607 records in RAM.
INFO 2026-06-08 08:44:09 MarkDuplicates Read 488,000,000 records. Elapsed time: 00:14:00s. Time for last 1,000,000: 2s. Last read position: chrY:19,707,727
INFO 2026-06-08 08:44:09 MarkDuplicates Tracking 3278 as yet unmatched pairs. 51 records in RAM.
INFO 2026-06-08 08:44:11 MarkDuplicates Read 489,000,000 records. Elapsed time: 00:14:01s. Time for last 1,000,000: 1s. Last read position: GL000220.1:159,525
INFO 2026-06-08 08:44:11 MarkDuplicates Tracking 1946 as yet unmatched pairs. 14 records in RAM.
INFO 2026-06-08 08:44:12 MarkDuplicates Read 490,000,000 records. Elapsed time: 00:14:02s. Time for last 1,000,000: 1s. Last read position: KI270733.1:149,710
INFO 2026-06-08 08:44:12 MarkDuplicates Tracking 122 as yet unmatched pairs. 104 records in RAM.
INFO 2026-06-08 08:44:13 MarkDuplicates Read 490617788 records. 0 pairs never matched.
INFO 2026-06-08 08:45:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 42394139968; totalMemory: 60532195328; maxMemory: 63585648640
INFO 2026-06-08 08:45:20 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:45:28 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:45:46 OpticalDuplicateFinder Large duplicate set. size = 1312
INFO 2026-06-08 08:45:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,128
INFO 2026-06-08 08:45:54 OpticalDuplicateFinder Large duplicate set. size = 1054
INFO 2026-06-08 08:45:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,507
INFO 2026-06-08 08:45:54 OpticalDuplicateFinder Large duplicate set. size = 1394
INFO 2026-06-08 08:45:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,043
INFO 2026-06-08 08:45:54 OpticalDuplicateFinder Large duplicate set. size = 1265
INFO 2026-06-08 08:45:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,138
INFO 2026-06-08 08:45:54 OpticalDuplicateFinder Large duplicate set. size = 1235
INFO 2026-06-08 08:45:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-19,790
INFO 2026-06-08 08:45:54 OpticalDuplicateFinder Large duplicate set. size = 1007
INFO 2026-06-08 08:45:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:10,943
INFO 2026-06-08 08:45:54 OpticalDuplicateFinder Large duplicate set. size = 1700
INFO 2026-06-08 08:45:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,794
INFO 2026-06-08 08:45:54 OpticalDuplicateFinder Large duplicate set. size = 1973
INFO 2026-06-08 08:45:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,600
INFO 2026-06-08 08:45:54 OpticalDuplicateFinder Large duplicate set. size = 4546
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:15,457
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,767
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder compared 3,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,224
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder compared 4,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:7,302
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder Large duplicate set. size = 1258
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-25,696
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder Large duplicate set. size = 1404
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,269
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder Large duplicate set. size = 2194
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,025
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-14,111
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder Large duplicate set. size = 1147
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-14,038
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder Large duplicate set. size = 2018
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,445
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:25,626
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder Large duplicate set. size = 1122
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,407
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder Large duplicate set. size = 2771
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-14,127
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:24,275
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder Large duplicate set. size = 1323
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:15,797
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder Large duplicate set. size = 1810
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,361
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder Large duplicate set. size = 2274
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-25,963
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:25,618
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder Large duplicate set. size = 1368
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,545
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder Large duplicate set. size = 1211
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,557
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder Large duplicate set. size = 1036
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-21,093
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder Large duplicate set. size = 1089
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:6,129
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder Large duplicate set. size = 1238
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,740
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder Large duplicate set. size = 1171
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:17,261
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder Large duplicate set. size = 1491
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-27,896
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder Large duplicate set. size = 1670
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,327
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder Large duplicate set. size = 1507
INFO 2026-06-08 08:45:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,169
INFO 2026-06-08 08:45:59 OpticalDuplicateFinder Large duplicate set. size = 1186
INFO 2026-06-08 08:45:59 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,925
INFO 2026-06-08 08:46:05 OpticalDuplicateFinder Large duplicate set. size = 1283
INFO 2026-06-08 08:46:05 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,543
INFO 2026-06-08 08:46:05 OpticalDuplicateFinder Large duplicate set. size = 1318
INFO 2026-06-08 08:46:05 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,533
INFO 2026-06-08 08:46:05 OpticalDuplicateFinder Large duplicate set. size = 1035
INFO 2026-06-08 08:46:05 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,422
INFO 2026-06-08 08:46:44 MarkDuplicates Traversing fragment information and detecting duplicates.
WARNING 2026-06-08 08:46:45 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
INFO 2026-06-08 08:47:37 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:47:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 203954840; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:47:40 MarkDuplicates Marking 334570254 records as duplicates.
INFO 2026-06-08 08:47:40 MarkDuplicates Found 9304211 optical duplicate clusters.
INFO 2026-06-08 08:47:40 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 08:47:58 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:17s. Time for last 10,000,000: 17s. Last read position: chr1:25,352,916
INFO 2026-06-08 08:48:14 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:34s. Time for last 10,000,000: 16s. Last read position: chr1:86,704,835
INFO 2026-06-08 08:48:31 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:50s. Time for last 10,000,000: 16s. Last read position: chr1:154,157,639
INFO 2026-06-08 08:48:47 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:06s. Time for last 10,000,000: 15s. Last read position: chr1:203,347,413
INFO 2026-06-08 08:49:03 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:22s. Time for last 10,000,000: 16s. Last read position: chr2:27,894,659
INFO 2026-06-08 08:49:19 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:38s. Time for last 10,000,000: 16s. Last read position: chr2:85,401,263
INFO 2026-06-08 08:49:35 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:01:54s. Time for last 10,000,000: 16s. Last read position: chr2:175,937,398
INFO 2026-06-08 08:49:51 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:11s. Time for last 10,000,000: 16s. Last read position: chr2:231,165,994
INFO 2026-06-08 08:50:07 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:27s. Time for last 10,000,000: 16s. Last read position: chr3:64,681,244
INFO 2026-06-08 08:50:24 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:43s. Time for last 10,000,000: 16s. Last read position: chr3:171,676,719
INFO 2026-06-08 08:50:40 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:03:00s. Time for last 10,000,000: 16s. Last read position: chr4:71,450,389
INFO 2026-06-08 08:50:57 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:16s. Time for last 10,000,000: 16s. Last read position: chr5:5,460,942
INFO 2026-06-08 08:51:14 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:33s. Time for last 10,000,000: 17s. Last read position: chr5:96,748,516
INFO 2026-06-08 08:51:32 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:03:51s. Time for last 10,000,000: 17s. Last read position: chr5:150,401,999
INFO 2026-06-08 08:51:47 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:04:07s. Time for last 10,000,000: 15s. Last read position: chr5:171,391,410
INFO 2026-06-08 08:52:04 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:23s. Time for last 10,000,000: 16s. Last read position: chr6:29,553,876
INFO 2026-06-08 08:52:19 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:04:38s. Time for last 10,000,000: 15s. Last read position: chr6:34,418,414
INFO 2026-06-08 08:52:37 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:04:56s. Time for last 10,000,000: 17s. Last read position: chr6:138,405,153
INFO 2026-06-08 08:52:54 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:05:13s. Time for last 10,000,000: 16s. Last read position: chr7:35,801,222
INFO 2026-06-08 08:53:10 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:05:29s. Time for last 10,000,000: 16s. Last read position: chr7:100,676,559
INFO 2026-06-08 08:53:27 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:05:47s. Time for last 10,000,000: 17s. Last read position: chr8:6,527,568
INFO 2026-06-08 08:53:44 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:06:03s. Time for last 10,000,000: 16s. Last read position: chr8:100,721,640
INFO 2026-06-08 08:54:00 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:06:19s. Time for last 10,000,000: 16s. Last read position: chr9:19,290,703
INFO 2026-06-08 08:54:17 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:06:37s. Time for last 10,000,000: 17s. Last read position: chr9:136,016,331
INFO 2026-06-08 08:54:38 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:06:58s. Time for last 10,000,000: 21s. Last read position: chr10:69,180,433
INFO 2026-06-08 08:54:57 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:07:17s. Time for last 10,000,000: 18s. Last read position: chr11:319,864
INFO 2026-06-08 08:55:13 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:07:32s. Time for last 10,000,000: 15s. Last read position: chr11:60,919,830
INFO 2026-06-08 08:55:28 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:07:47s. Time for last 10,000,000: 15s. Last read position: chr11:72,004,688
INFO 2026-06-08 08:55:43 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:08:03s. Time for last 10,000,000: 15s. Last read position: chr12:900,547
INFO 2026-06-08 08:55:59 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:08:18s. Time for last 10,000,000: 15s. Last read position: chr12:50,353,934
INFO 2026-06-08 08:56:16 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:08:35s. Time for last 10,000,000: 17s. Last read position: chr12:96,247,002
INFO 2026-06-08 08:56:34 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:08:54s. Time for last 10,000,000: 18s. Last read position: chr13:44,434,678
INFO 2026-06-08 08:56:52 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:09:11s. Time for last 10,000,000: 17s. Last read position: chr14:55,140,274
INFO 2026-06-08 08:57:08 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:09:28s. Time for last 10,000,000: 16s. Last read position: chr15:28,702,752
INFO 2026-06-08 08:57:25 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:09:44s. Time for last 10,000,000: 16s. Last read position: chr15:76,295,726
INFO 2026-06-08 08:57:41 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:10:01s. Time for last 10,000,000: 16s. Last read position: chr16:11,927,750
INFO 2026-06-08 08:57:58 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:10:17s. Time for last 10,000,000: 16s. Last read position: chr16:30,930,329
INFO 2026-06-08 08:58:14 MarkDuplicates Written 380,000,000 records. Elapsed time: 00:10:33s. Time for last 10,000,000: 16s. Last read position: chr17:747,651
INFO 2026-06-08 08:58:30 MarkDuplicates Written 390,000,000 records. Elapsed time: 00:10:50s. Time for last 10,000,000: 16s. Last read position: chr17:32,767,734
INFO 2026-06-08 08:58:45 MarkDuplicates Written 400,000,000 records. Elapsed time: 00:11:04s. Time for last 10,000,000: 14s. Last read position: chr17:58,525,700
INFO 2026-06-08 08:58:59 MarkDuplicates Written 410,000,000 records. Elapsed time: 00:11:19s. Time for last 10,000,000: 14s. Last read position: chr18:12,325,264
INFO 2026-06-08 08:59:14 MarkDuplicates Written 420,000,000 records. Elapsed time: 00:11:33s. Time for last 10,000,000: 14s. Last read position: chr19:6,693,019
INFO 2026-06-08 08:59:28 MarkDuplicates Written 430,000,000 records. Elapsed time: 00:11:47s. Time for last 10,000,000: 14s. Last read position: chr19:18,786,633
INFO 2026-06-08 08:59:42 MarkDuplicates Written 440,000,000 records. Elapsed time: 00:12:01s. Time for last 10,000,000: 14s. Last read position: chr19:48,859,506
INFO 2026-06-08 08:59:56 MarkDuplicates Written 450,000,000 records. Elapsed time: 00:12:16s. Time for last 10,000,000: 14s. Last read position: chr20:38,130,262
INFO 2026-06-08 09:00:10 MarkDuplicates Written 460,000,000 records. Elapsed time: 00:12:29s. Time for last 10,000,000: 13s. Last read position: chr21:38,383,489
INFO 2026-06-08 09:00:24 MarkDuplicates Written 470,000,000 records. Elapsed time: 00:12:43s. Time for last 10,000,000: 14s. Last read position: chr22:38,485,993
INFO 2026-06-08 09:00:38 MarkDuplicates Written 480,000,000 records. Elapsed time: 00:12:58s. Time for last 10,000,000: 14s. Last read position: chrX:54,809,301
INFO 2026-06-08 09:00:52 MarkDuplicates Written 490,000,000 records. Elapsed time: 00:13:11s. Time for last 10,000,000: 13s. Last read position: KI270733.1:149,710
INFO 2026-06-08 09:00:58 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 09:00:58 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 09:00:58 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 09:00:58 MarkDuplicates Before output close freeMemory: 203916544; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 09:00:58 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 09:00:58 MarkDuplicates After output close freeMemory: 104163312; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 09:00:58 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 30.84 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory