Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/414d781812c15a8d1e5e8f7566a121/aih-tih-sc-0419d4-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
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/5138825491b00634cbd1f002f858c8/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/5138825491b00634cbd1f002f858c8/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai
==> STAGING COMPLETE (5 inputs)
Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT aih-tih-sc-0419d4-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-0419d4-R1_A23WJ53LT4_1.md.bam --METRICS_FILE aih-tih-sc-0419d4-R1_A23WJ53LT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
08:24:01.931 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 08:24:01 GMT 2026] MarkDuplicates --INPUT aih-tih-sc-0419d4-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-0419d4-R1_A23WJ53LT4_1.md.bam --METRICS_FILE aih-tih-sc-0419d4-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 08:24:01 GMT 2026] Executing as ?@nf-2e5138825491b00634cbd1f002f858c8-8a15b-v89nx 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 08:24:01 MarkDuplicates Start of doWork freeMemory: 105826280; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 08:24:01 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 08:24:01 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 08:24:05 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:1,529,279
INFO 2026-06-08 08:24:05 MarkDuplicates Tracking 2200 as yet unmatched pairs. 90 records in RAM.
INFO 2026-06-08 08:24:08 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 2s. Last read position: chr1:6,620,003
INFO 2026-06-08 08:24:08 MarkDuplicates Tracking 4372 as yet unmatched pairs. 29 records in RAM.
INFO 2026-06-08 08:24:10 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: chr1:11,115,441
INFO 2026-06-08 08:24:10 MarkDuplicates Tracking 6113 as yet unmatched pairs. 68 records in RAM.
INFO 2026-06-08 08:24:11 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: chr1:15,932,264
INFO 2026-06-08 08:24:11 MarkDuplicates Tracking 7896 as yet unmatched pairs. 51 records in RAM.
INFO 2026-06-08 08:24:13 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: chr1:19,243,659
INFO 2026-06-08 08:24:13 MarkDuplicates Tracking 9554 as yet unmatched pairs. 80 records in RAM.
INFO 2026-06-08 08:24:14 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: chr1:21,874,890
INFO 2026-06-08 08:24:14 MarkDuplicates Tracking 11529 as yet unmatched pairs. 421 records in RAM.
INFO 2026-06-08 08:24:17 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 2s. Last read position: chr1:25,815,574
INFO 2026-06-08 08:24:17 MarkDuplicates Tracking 13078 as yet unmatched pairs. 206 records in RAM.
INFO 2026-06-08 08:24:18 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: chr1:29,053,219
INFO 2026-06-08 08:24:18 MarkDuplicates Tracking 14730 as yet unmatched pairs. 141 records in RAM.
INFO 2026-06-08 08:24:20 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: chr1:32,895,569
INFO 2026-06-08 08:24:20 MarkDuplicates Tracking 16599 as yet unmatched pairs. 165 records in RAM.
INFO 2026-06-08 08:24:22 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 2s. Last read position: chr1:37,885,667
INFO 2026-06-08 08:24:22 MarkDuplicates Tracking 18394 as yet unmatched pairs. 89 records in RAM.
INFO 2026-06-08 08:24:24 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: chr1:42,682,592
INFO 2026-06-08 08:24:24 MarkDuplicates Tracking 20067 as yet unmatched pairs. 110 records in RAM.
INFO 2026-06-08 08:24:26 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: chr1:44,776,129
INFO 2026-06-08 08:24:26 MarkDuplicates Tracking 23022 as yet unmatched pairs. 1148 records in RAM.
INFO 2026-06-08 08:24:27 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 1s. Last read position: chr1:47,144,536
INFO 2026-06-08 08:24:27 MarkDuplicates Tracking 23623 as yet unmatched pairs. 33 records in RAM.
INFO 2026-06-08 08:24:29 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 2s. Last read position: chr1:53,078,887
INFO 2026-06-08 08:24:29 MarkDuplicates Tracking 25453 as yet unmatched pairs. 67 records in RAM.
INFO 2026-06-08 08:24:31 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 1s. Last read position: chr1:64,663,701
INFO 2026-06-08 08:24:31 MarkDuplicates Tracking 27071 as yet unmatched pairs. 15 records in RAM.
INFO 2026-06-08 08:24:33 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 1s. Last read position: chr1:86,447,760
INFO 2026-06-08 08:24:33 MarkDuplicates Tracking 28890 as yet unmatched pairs. 143 records in RAM.
INFO 2026-06-08 08:24:34 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 1s. Last read position: chr1:108,922,560
INFO 2026-06-08 08:24:34 MarkDuplicates Tracking 30229 as yet unmatched pairs. 20 records in RAM.
INFO 2026-06-08 08:24:36 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 1s. Last read position: chr1:112,616,879
INFO 2026-06-08 08:24:36 MarkDuplicates Tracking 31991 as yet unmatched pairs. 28 records in RAM.
INFO 2026-06-08 08:24:38 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 1s. Last read position: chr1:114,734,007
INFO 2026-06-08 08:24:38 MarkDuplicates Tracking 33846 as yet unmatched pairs. 335 records in RAM.
INFO 2026-06-08 08:24:39 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 1s. Last read position: chr1:119,929,025
INFO 2026-06-08 08:24:39 MarkDuplicates Tracking 36166 as yet unmatched pairs. 1017 records in RAM.
INFO 2026-06-08 08:24:40 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 1s. Last read position: chr1:145,388,385
INFO 2026-06-08 08:24:40 MarkDuplicates Tracking 36527 as yet unmatched pairs. 7 records in RAM.
INFO 2026-06-08 08:24:43 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 2s. Last read position: chr1:147,758,607
INFO 2026-06-08 08:24:43 MarkDuplicates Tracking 37392 as yet unmatched pairs. 16 records in RAM.
INFO 2026-06-08 08:24:44 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 1s. Last read position: chr1:149,812,218
INFO 2026-06-08 08:24:44 MarkDuplicates Tracking 37995 as yet unmatched pairs. 3 records in RAM.
INFO 2026-06-08 08:24:45 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 1s. Last read position: chr1:150,968,944
INFO 2026-06-08 08:24:45 MarkDuplicates Tracking 39788 as yet unmatched pairs. 192 records in RAM.
INFO 2026-06-08 08:24:47 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 1s. Last read position: chr1:153,984,720
INFO 2026-06-08 08:24:47 MarkDuplicates Tracking 41295 as yet unmatched pairs. 30 records in RAM.
INFO 2026-06-08 08:24:48 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 1s. Last read position: chr1:155,058,729
INFO 2026-06-08 08:24:48 MarkDuplicates Tracking 43266 as yet unmatched pairs. 302 records in RAM.
INFO 2026-06-08 08:24:49 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 1s. Last read position: chr1:155,481,770
INFO 2026-06-08 08:24:49 MarkDuplicates Tracking 44592 as yet unmatched pairs. 128 records in RAM.
INFO 2026-06-08 08:24:51 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 1s. Last read position: chr1:156,251,459
INFO 2026-06-08 08:24:51 MarkDuplicates Tracking 46565 as yet unmatched pairs. 118 records in RAM.
INFO 2026-06-08 08:24:52 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 1s. Last read position: chr1:160,681,368
INFO 2026-06-08 08:24:52 MarkDuplicates Tracking 48081 as yet unmatched pairs. 8 records in RAM.
INFO 2026-06-08 08:24:54 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 1s. Last read position: chr1:169,106,800
INFO 2026-06-08 08:24:54 MarkDuplicates Tracking 49584 as yet unmatched pairs. 63 records in RAM.
INFO 2026-06-08 08:24:56 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 2s. Last read position: chr1:181,089,341
INFO 2026-06-08 08:24:56 MarkDuplicates Tracking 51157 as yet unmatched pairs. 186 records in RAM.
INFO 2026-06-08 08:24:58 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 2s. Last read position: chr1:198,262,579
INFO 2026-06-08 08:24:58 MarkDuplicates Tracking 52617 as yet unmatched pairs. 95 records in RAM.
INFO 2026-06-08 08:25:00 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 1s. Last read position: chr1:203,852,196
INFO 2026-06-08 08:25:00 MarkDuplicates Tracking 54900 as yet unmatched pairs. 672 records in RAM.
INFO 2026-06-08 08:25:01 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 1s. Last read position: chr1:211,578,064
INFO 2026-06-08 08:25:01 MarkDuplicates Tracking 55896 as yet unmatched pairs. 122 records in RAM.
INFO 2026-06-08 08:25:03 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 1s. Last read position: chr1:225,856,881
INFO 2026-06-08 08:25:03 MarkDuplicates Tracking 57519 as yet unmatched pairs. 102 records in RAM.
INFO 2026-06-08 08:25:05 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 1s. Last read position: chr1:232,514,612
INFO 2026-06-08 08:25:05 MarkDuplicates Tracking 59413 as yet unmatched pairs. 23 records in RAM.
INFO 2026-06-08 08:25:06 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 1s. Last read position: chr1:247,310,435
INFO 2026-06-08 08:25:06 MarkDuplicates Tracking 61263 as yet unmatched pairs. 16 records in RAM.
INFO 2026-06-08 08:25:08 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 2s. Last read position: chr2:15,488,860
INFO 2026-06-08 08:25:08 MarkDuplicates Tracking 62911 as yet unmatched pairs. 62773 records in RAM.
INFO 2026-06-08 08:25:10 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 1s. Last read position: chr2:25,744,190
INFO 2026-06-08 08:25:10 MarkDuplicates Tracking 64655 as yet unmatched pairs. 64516 records in RAM.
INFO 2026-06-08 08:25:12 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 1s. Last read position: chr2:28,793,875
INFO 2026-06-08 08:25:12 MarkDuplicates Tracking 67531 as yet unmatched pairs. 67392 records in RAM.
INFO 2026-06-08 08:25:14 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,264
INFO 2026-06-08 08:25:14 MarkDuplicates Tracking 224186 as yet unmatched pairs. 57734 records in RAM.
INFO 2026-06-08 08:25:15 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,406
INFO 2026-06-08 08:25:15 MarkDuplicates Tracking 583268 as yet unmatched pairs. 36917 records in RAM.
INFO 2026-06-08 08:25:17 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 1s. Last read position: chr2:42,169,506
INFO 2026-06-08 08:25:17 MarkDuplicates Tracking 618063 as yet unmatched pairs. 34271 records in RAM.
INFO 2026-06-08 08:25:18 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 1s. Last read position: chr2:47,799,121
INFO 2026-06-08 08:25:18 MarkDuplicates Tracking 616051 as yet unmatched pairs. 32258 records in RAM.
INFO 2026-06-08 08:25:19 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 1s. Last read position: chr2:61,076,919
INFO 2026-06-08 08:25:19 MarkDuplicates Tracking 614290 as yet unmatched pairs. 30497 records in RAM.
INFO 2026-06-08 08:25:21 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 1s. Last read position: chr2:70,297,329
INFO 2026-06-08 08:25:21 MarkDuplicates Tracking 612734 as yet unmatched pairs. 28938 records in RAM.
INFO 2026-06-08 08:25:23 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 1s. Last read position: chr2:74,880,385
INFO 2026-06-08 08:25:23 MarkDuplicates Tracking 611026 as yet unmatched pairs. 27223 records in RAM.
INFO 2026-06-08 08:25:24 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 1s. Last read position: chr2:88,067,851
INFO 2026-06-08 08:25:24 MarkDuplicates Tracking 609438 as yet unmatched pairs. 25635 records in RAM.
INFO 2026-06-08 08:25:26 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 1s. Last read position: chr2:99,399,313
INFO 2026-06-08 08:25:26 MarkDuplicates Tracking 607860 as yet unmatched pairs. 24057 records in RAM.
INFO 2026-06-08 08:25:27 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 1s. Last read position: chr2:108,258,967
INFO 2026-06-08 08:25:27 MarkDuplicates Tracking 609205 as yet unmatched pairs. 25402 records in RAM.
INFO 2026-06-08 08:25:28 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 1s. Last read position: chr2:110,534,647
INFO 2026-06-08 08:25:28 MarkDuplicates Tracking 605399 as yet unmatched pairs. 21595 records in RAM.
INFO 2026-06-08 08:25:30 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 1s. Last read position: chr2:119,367,580
INFO 2026-06-08 08:25:30 MarkDuplicates Tracking 605909 as yet unmatched pairs. 22105 records in RAM.
INFO 2026-06-08 08:25:31 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 1s. Last read position: chr2:135,780,210
INFO 2026-06-08 08:25:31 MarkDuplicates Tracking 602696 as yet unmatched pairs. 18884 records in RAM.
INFO 2026-06-08 08:25:32 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 1s. Last read position: chr2:162,318,174
INFO 2026-06-08 08:25:32 MarkDuplicates Tracking 601126 as yet unmatched pairs. 17303 records in RAM.
INFO 2026-06-08 08:25:34 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 1s. Last read position: chr2:178,560,867
INFO 2026-06-08 08:25:34 MarkDuplicates Tracking 599632 as yet unmatched pairs. 15807 records in RAM.
INFO 2026-06-08 08:25:35 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 1s. Last read position: chr2:188,994,724
INFO 2026-06-08 08:25:35 MarkDuplicates Tracking 598327 as yet unmatched pairs. 14494 records in RAM.
INFO 2026-06-08 08:25:37 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 1s. Last read position: chr2:199,925,171
INFO 2026-06-08 08:25:37 MarkDuplicates Tracking 596480 as yet unmatched pairs. 12647 records in RAM.
INFO 2026-06-08 08:25:38 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 1s. Last read position: chr2:210,216,377
INFO 2026-06-08 08:25:38 MarkDuplicates Tracking 595071 as yet unmatched pairs. 11238 records in RAM.
INFO 2026-06-08 08:25:40 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 1s. Last read position: chr2:215,386,702
INFO 2026-06-08 08:25:40 MarkDuplicates Tracking 594014 as yet unmatched pairs. 10179 records in RAM.
INFO 2026-06-08 08:25:41 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 1s. Last read position: chr2:216,119,052
INFO 2026-06-08 08:25:41 MarkDuplicates Tracking 592062 as yet unmatched pairs. 8227 records in RAM.
INFO 2026-06-08 08:25:43 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 1s. Last read position: chr2:219,175,642
INFO 2026-06-08 08:25:43 MarkDuplicates Tracking 590594 as yet unmatched pairs. 6759 records in RAM.
INFO 2026-06-08 08:25:45 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 2s. Last read position: chr2:226,797,803
INFO 2026-06-08 08:25:45 MarkDuplicates Tracking 588614 as yet unmatched pairs. 4775 records in RAM.
INFO 2026-06-08 08:25:47 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 1s. Last read position: chr2:236,581,054
INFO 2026-06-08 08:25:47 MarkDuplicates Tracking 587032 as yet unmatched pairs. 3190 records in RAM.
INFO 2026-06-08 08:25:48 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 1s. Last read position: chr2:240,572,490
INFO 2026-06-08 08:25:48 MarkDuplicates Tracking 585313 as yet unmatched pairs. 1470 records in RAM.
INFO 2026-06-08 08:25:50 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 1s. Last read position: chr3:8,958,946
INFO 2026-06-08 08:25:50 MarkDuplicates Tracking 583519 as yet unmatched pairs. 33021 records in RAM.
INFO 2026-06-08 08:25:51 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 1s. Last read position: chr3:12,936,556
INFO 2026-06-08 08:25:51 MarkDuplicates Tracking 581761 as yet unmatched pairs. 31261 records in RAM.
INFO 2026-06-08 08:25:53 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 1s. Last read position: chr3:31,533,028
INFO 2026-06-08 08:25:53 MarkDuplicates Tracking 580605 as yet unmatched pairs. 30105 records in RAM.
INFO 2026-06-08 08:25:54 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 1s. Last read position: chr3:39,411,746
INFO 2026-06-08 08:25:54 MarkDuplicates Tracking 580114 as yet unmatched pairs. 29613 records in RAM.
INFO 2026-06-08 08:25:56 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 1s. Last read position: chr3:46,459,792
INFO 2026-06-08 08:25:56 MarkDuplicates Tracking 576864 as yet unmatched pairs. 26363 records in RAM.
INFO 2026-06-08 08:25:58 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 1s. Last read position: chr3:48,440,619
INFO 2026-06-08 08:25:58 MarkDuplicates Tracking 575207 as yet unmatched pairs. 24706 records in RAM.
INFO 2026-06-08 08:25:59 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 1s. Last read position: chr3:49,123,619
INFO 2026-06-08 08:25:59 MarkDuplicates Tracking 573381 as yet unmatched pairs. 22880 records in RAM.
INFO 2026-06-08 08:26:01 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 1s. Last read position: chr3:50,297,133
INFO 2026-06-08 08:26:01 MarkDuplicates Tracking 571275 as yet unmatched pairs. 20774 records in RAM.
INFO 2026-06-08 08:26:02 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 1s. Last read position: chr3:52,513,776
INFO 2026-06-08 08:26:02 MarkDuplicates Tracking 569825 as yet unmatched pairs. 19324 records in RAM.
INFO 2026-06-08 08:26:04 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 1s. Last read position: chr3:58,138,414
INFO 2026-06-08 08:26:04 MarkDuplicates Tracking 568256 as yet unmatched pairs. 17754 records in RAM.
INFO 2026-06-08 08:26:06 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 1s. Last read position: chr3:97,942,431
INFO 2026-06-08 08:26:06 MarkDuplicates Tracking 566274 as yet unmatched pairs. 15767 records in RAM.
INFO 2026-06-08 08:26:08 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 2s. Last read position: chr3:113,611,132
INFO 2026-06-08 08:26:08 MarkDuplicates Tracking 564954 as yet unmatched pairs. 14438 records in RAM.
INFO 2026-06-08 08:26:09 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 1s. Last read position: chr3:124,809,022
INFO 2026-06-08 08:26:09 MarkDuplicates Tracking 563291 as yet unmatched pairs. 12774 records in RAM.
INFO 2026-06-08 08:26:11 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 1s. Last read position: chr3:129,272,806
INFO 2026-06-08 08:26:11 MarkDuplicates Tracking 561660 as yet unmatched pairs. 11143 records in RAM.
INFO 2026-06-08 08:26:12 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 1s. Last read position: chr3:139,367,061
INFO 2026-06-08 08:26:12 MarkDuplicates Tracking 559673 as yet unmatched pairs. 9156 records in RAM.
INFO 2026-06-08 08:26:14 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 1s. Last read position: chr3:155,147,206
INFO 2026-06-08 08:26:14 MarkDuplicates Tracking 557937 as yet unmatched pairs. 7419 records in RAM.
INFO 2026-06-08 08:26:15 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 1s. Last read position: chr3:180,616,262
INFO 2026-06-08 08:26:15 MarkDuplicates Tracking 556331 as yet unmatched pairs. 5811 records in RAM.
INFO 2026-06-08 08:26:17 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 1s. Last read position: chr3:186,596,981
INFO 2026-06-08 08:26:17 MarkDuplicates Tracking 554586 as yet unmatched pairs. 4052 records in RAM.
INFO 2026-06-08 08:26:18 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 1s. Last read position: chr3:195,568,846
INFO 2026-06-08 08:26:18 MarkDuplicates Tracking 561620 as yet unmatched pairs. 11071 records in RAM.
INFO 2026-06-08 08:26:20 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 1s. Last read position: chr3:195,579,398
INFO 2026-06-08 08:26:20 MarkDuplicates Tracking 551678 as yet unmatched pairs. 1128 records in RAM.
INFO 2026-06-08 08:26:21 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 1s. Last read position: chr4:991,230
INFO 2026-06-08 08:26:21 MarkDuplicates Tracking 550059 as yet unmatched pairs. 16792 records in RAM.
INFO 2026-06-08 08:26:23 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 1s. Last read position: chr4:3,767,808
INFO 2026-06-08 08:26:23 MarkDuplicates Tracking 548083 as yet unmatched pairs. 14814 records in RAM.
INFO 2026-06-08 08:26:24 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 1s. Last read position: chr4:20,616,932
INFO 2026-06-08 08:26:24 MarkDuplicates Tracking 546329 as yet unmatched pairs. 13059 records in RAM.
INFO 2026-06-08 08:26:25 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr4:42,735,219
INFO 2026-06-08 08:26:25 MarkDuplicates Tracking 544702 as yet unmatched pairs. 11426 records in RAM.
INFO 2026-06-08 08:26:27 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 1s. Last read position: chr4:69,214,492
INFO 2026-06-08 08:26:27 MarkDuplicates Tracking 544825 as yet unmatched pairs. 11546 records in RAM.
INFO 2026-06-08 08:26:28 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 1s. Last read position: chr4:77,055,332
INFO 2026-06-08 08:26:28 MarkDuplicates Tracking 542430 as yet unmatched pairs. 9151 records in RAM.
INFO 2026-06-08 08:26:30 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 1s. Last read position: chr4:88,676,366
INFO 2026-06-08 08:26:30 MarkDuplicates Tracking 540459 as yet unmatched pairs. 7177 records in RAM.
INFO 2026-06-08 08:26:31 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 1s. Last read position: chr4:113,454,343
INFO 2026-06-08 08:26:31 MarkDuplicates Tracking 538879 as yet unmatched pairs. 5593 records in RAM.
INFO 2026-06-08 08:26:33 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 1s. Last read position: chr4:142,305,468
INFO 2026-06-08 08:26:33 MarkDuplicates Tracking 537376 as yet unmatched pairs. 4088 records in RAM.
INFO 2026-06-08 08:26:34 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 1s. Last read position: chr4:159,268,102
INFO 2026-06-08 08:26:34 MarkDuplicates Tracking 535788 as yet unmatched pairs. 2493 records in RAM.
INFO 2026-06-08 08:26:35 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 1s. Last read position: chr4:184,716,421
INFO 2026-06-08 08:26:35 MarkDuplicates Tracking 534144 as yet unmatched pairs. 844 records in RAM.
INFO 2026-06-08 08:26:38 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 2s. Last read position: chr5:5,454,612
INFO 2026-06-08 08:26:38 MarkDuplicates Tracking 532491 as yet unmatched pairs. 30311 records in RAM.
INFO 2026-06-08 08:26:40 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 1s. Last read position: chr5:14,472,596
INFO 2026-06-08 08:26:40 MarkDuplicates Tracking 531014 as yet unmatched pairs. 28834 records in RAM.
INFO 2026-06-08 08:26:42 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 1s. Last read position: chr5:37,022,268
INFO 2026-06-08 08:26:42 MarkDuplicates Tracking 529123 as yet unmatched pairs. 26940 records in RAM.
INFO 2026-06-08 08:26:44 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 1s. Last read position: chr5:56,864,897
INFO 2026-06-08 08:26:44 MarkDuplicates Tracking 527634 as yet unmatched pairs. 25447 records in RAM.
INFO 2026-06-08 08:26:45 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 1s. Last read position: chr5:72,893,157
INFO 2026-06-08 08:26:45 MarkDuplicates Tracking 526231 as yet unmatched pairs. 24040 records in RAM.
INFO 2026-06-08 08:26:47 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 1s. Last read position: chr5:83,537,176
INFO 2026-06-08 08:26:47 MarkDuplicates Tracking 524613 as yet unmatched pairs. 22413 records in RAM.
INFO 2026-06-08 08:26:48 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 1s. Last read position: chr5:113,049,092
INFO 2026-06-08 08:26:48 MarkDuplicates Tracking 523032 as yet unmatched pairs. 20832 records in RAM.
INFO 2026-06-08 08:26:50 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 1s. Last read position: chr5:132,887,890
INFO 2026-06-08 08:26:50 MarkDuplicates Tracking 521346 as yet unmatched pairs. 19139 records in RAM.
INFO 2026-06-08 08:26:51 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 1s. Last read position: chr5:139,137,333
INFO 2026-06-08 08:26:51 MarkDuplicates Tracking 519580 as yet unmatched pairs. 17367 records in RAM.
INFO 2026-06-08 08:26:53 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 1s. Last read position: chr5:141,332,463
INFO 2026-06-08 08:26:53 MarkDuplicates Tracking 518022 as yet unmatched pairs. 15788 records in RAM.
INFO 2026-06-08 08:26:54 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 1s. Last read position: chr5:141,863,567
INFO 2026-06-08 08:26:54 MarkDuplicates Tracking 516507 as yet unmatched pairs. 14273 records in RAM.
INFO 2026-06-08 08:26:55 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 1s. Last read position: chr5:150,118,771
INFO 2026-06-08 08:26:55 MarkDuplicates Tracking 515596 as yet unmatched pairs. 13356 records in RAM.
INFO 2026-06-08 08:26:57 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 1s. Last read position: chr5:150,406,282
INFO 2026-06-08 08:26:57 MarkDuplicates Tracking 517304 as yet unmatched pairs. 15064 records in RAM.
INFO 2026-06-08 08:26:58 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 1s. Last read position: chr5:151,671,614
INFO 2026-06-08 08:26:58 MarkDuplicates Tracking 511533 as yet unmatched pairs. 9292 records in RAM.
INFO 2026-06-08 08:27:00 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 1s. Last read position: chr5:170,106,127
INFO 2026-06-08 08:27:00 MarkDuplicates Tracking 509767 as yet unmatched pairs. 7526 records in RAM.
INFO 2026-06-08 08:27:02 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 1s. Last read position: chr5:173,328,062
INFO 2026-06-08 08:27:02 MarkDuplicates Tracking 508227 as yet unmatched pairs. 5984 records in RAM.
INFO 2026-06-08 08:27:03 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 1s. Last read position: chr5:177,595,311
INFO 2026-06-08 08:27:03 MarkDuplicates Tracking 506822 as yet unmatched pairs. 4579 records in RAM.
INFO 2026-06-08 08:27:04 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 1s. Last read position: chr5:179,821,091
INFO 2026-06-08 08:27:04 MarkDuplicates Tracking 507664 as yet unmatched pairs. 5420 records in RAM.
INFO 2026-06-08 08:27:06 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 1s. Last read position: chr5:180,791,854
INFO 2026-06-08 08:27:06 MarkDuplicates Tracking 503830 as yet unmatched pairs. 1586 records in RAM.
INFO 2026-06-08 08:27:08 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 1s. Last read position: chr6:7,182,012
INFO 2026-06-08 08:27:08 MarkDuplicates Tracking 502149 as yet unmatched pairs. 29966 records in RAM.
INFO 2026-06-08 08:27:09 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 1s. Last read position: chr6:11,191,078
INFO 2026-06-08 08:27:09 MarkDuplicates Tracking 499610 as yet unmatched pairs. 27420 records in RAM.
INFO 2026-06-08 08:27:11 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 1s. Last read position: chr6:26,216,299
INFO 2026-06-08 08:27:11 MarkDuplicates Tracking 498145 as yet unmatched pairs. 25931 records in RAM.
INFO 2026-06-08 08:27:12 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 1s. Last read position: chr6:30,730,024
INFO 2026-06-08 08:27:12 MarkDuplicates Tracking 496573 as yet unmatched pairs. 24359 records in RAM.
INFO 2026-06-08 08:27:14 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 1s. Last read position: chr6:31,649,617
INFO 2026-06-08 08:27:14 MarkDuplicates Tracking 494746 as yet unmatched pairs. 22527 records in RAM.
INFO 2026-06-08 08:27:15 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 1s. Last read position: chr6:31,983,917
INFO 2026-06-08 08:27:15 MarkDuplicates Tracking 493585 as yet unmatched pairs. 21365 records in RAM.
INFO 2026-06-08 08:27:17 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 1s. Last read position: chr6:32,025,834
INFO 2026-06-08 08:27:17 MarkDuplicates Tracking 494223 as yet unmatched pairs. 22003 records in RAM.
INFO 2026-06-08 08:27:18 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 1s. Last read position: chr6:32,097,026
INFO 2026-06-08 08:27:18 MarkDuplicates Tracking 491293 as yet unmatched pairs. 19064 records in RAM.
INFO 2026-06-08 08:27:19 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 1s. Last read position: chr6:33,280,673
INFO 2026-06-08 08:27:19 MarkDuplicates Tracking 489469 as yet unmatched pairs. 17240 records in RAM.
INFO 2026-06-08 08:27:21 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 1s. Last read position: chr6:34,421,756
INFO 2026-06-08 08:27:21 MarkDuplicates Tracking 488216 as yet unmatched pairs. 15986 records in RAM.
INFO 2026-06-08 08:27:23 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 1s. Last read position: chr6:36,972,735
INFO 2026-06-08 08:27:23 MarkDuplicates Tracking 486603 as yet unmatched pairs. 14360 records in RAM.
INFO 2026-06-08 08:27:25 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 2s. Last read position: chr6:43,073,914
INFO 2026-06-08 08:27:25 MarkDuplicates Tracking 484112 as yet unmatched pairs. 11860 records in RAM.
INFO 2026-06-08 08:27:26 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 1s. Last read position: chr6:47,595,867
INFO 2026-06-08 08:27:26 MarkDuplicates Tracking 482304 as yet unmatched pairs. 10051 records in RAM.
INFO 2026-06-08 08:27:28 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 1s. Last read position: chr6:75,152,349
INFO 2026-06-08 08:27:28 MarkDuplicates Tracking 480746 as yet unmatched pairs. 8485 records in RAM.
INFO 2026-06-08 08:27:30 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 1s. Last read position: chr6:108,664,198
INFO 2026-06-08 08:27:30 MarkDuplicates Tracking 479112 as yet unmatched pairs. 6845 records in RAM.
INFO 2026-06-08 08:27:31 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 1s. Last read position: chr6:130,869,755
INFO 2026-06-08 08:27:31 MarkDuplicates Tracking 477426 as yet unmatched pairs. 5151 records in RAM.
INFO 2026-06-08 08:27:33 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 1s. Last read position: chr6:143,862,158
INFO 2026-06-08 08:27:33 MarkDuplicates Tracking 475792 as yet unmatched pairs. 3517 records in RAM.
INFO 2026-06-08 08:27:34 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 1s. Last read position: chr6:157,299,559
INFO 2026-06-08 08:27:34 MarkDuplicates Tracking 474265 as yet unmatched pairs. 1990 records in RAM.
INFO 2026-06-08 08:27:35 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 1s. Last read position: chr6:168,598,817
INFO 2026-06-08 08:27:35 MarkDuplicates Tracking 472827 as yet unmatched pairs. 551 records in RAM.
INFO 2026-06-08 08:27:37 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 1s. Last read position: chr7:2,538,580
INFO 2026-06-08 08:27:37 MarkDuplicates Tracking 470605 as yet unmatched pairs. 36175 records in RAM.
INFO 2026-06-08 08:27:39 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 1s. Last read position: chr7:5,528,106
INFO 2026-06-08 08:27:39 MarkDuplicates Tracking 470634 as yet unmatched pairs. 36204 records in RAM.
INFO 2026-06-08 08:27:40 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 1s. Last read position: chr7:7,436,351
INFO 2026-06-08 08:27:40 MarkDuplicates Tracking 466785 as yet unmatched pairs. 32352 records in RAM.
INFO 2026-06-08 08:27:42 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 1s. Last read position: chr7:29,095,124
INFO 2026-06-08 08:27:42 MarkDuplicates Tracking 465356 as yet unmatched pairs. 30921 records in RAM.
INFO 2026-06-08 08:27:43 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 1s. Last read position: chr7:44,056,790
INFO 2026-06-08 08:27:43 MarkDuplicates Tracking 463835 as yet unmatched pairs. 29400 records in RAM.
INFO 2026-06-08 08:27:45 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 1s. Last read position: chr7:51,191,020
INFO 2026-06-08 08:27:45 MarkDuplicates Tracking 462024 as yet unmatched pairs. 27588 records in RAM.
INFO 2026-06-08 08:27:46 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 1s. Last read position: chr7:65,967,758
INFO 2026-06-08 08:27:46 MarkDuplicates Tracking 461892 as yet unmatched pairs. 27455 records in RAM.
INFO 2026-06-08 08:27:48 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 1s. Last read position: chr7:66,808,873
INFO 2026-06-08 08:27:48 MarkDuplicates Tracking 458844 as yet unmatched pairs. 24407 records in RAM.
INFO 2026-06-08 08:27:49 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 1s. Last read position: chr7:74,042,998
INFO 2026-06-08 08:27:49 MarkDuplicates Tracking 457737 as yet unmatched pairs. 23293 records in RAM.
INFO 2026-06-08 08:27:51 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 1s. Last read position: chr7:75,985,682
INFO 2026-06-08 08:27:51 MarkDuplicates Tracking 456243 as yet unmatched pairs. 21799 records in RAM.
INFO 2026-06-08 08:27:52 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 1s. Last read position: chr7:80,673,358
INFO 2026-06-08 08:27:52 MarkDuplicates Tracking 454615 as yet unmatched pairs. 20171 records in RAM.
INFO 2026-06-08 08:27:54 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 1s. Last read position: chr7:94,405,216
INFO 2026-06-08 08:27:54 MarkDuplicates Tracking 453231 as yet unmatched pairs. 18768 records in RAM.
INFO 2026-06-08 08:27:55 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 1s. Last read position: chr7:99,396,602
INFO 2026-06-08 08:27:55 MarkDuplicates Tracking 451251 as yet unmatched pairs. 16779 records in RAM.
INFO 2026-06-08 08:27:56 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 1s. Last read position: chr7:100,374,073
INFO 2026-06-08 08:27:56 MarkDuplicates Tracking 449994 as yet unmatched pairs. 15522 records in RAM.
INFO 2026-06-08 08:27:58 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 1s. Last read position: chr7:102,355,851
INFO 2026-06-08 08:27:58 MarkDuplicates Tracking 447631 as yet unmatched pairs. 13157 records in RAM.
INFO 2026-06-08 08:27:59 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 1s. Last read position: chr7:107,917,943
INFO 2026-06-08 08:27:59 MarkDuplicates Tracking 446385 as yet unmatched pairs. 11910 records in RAM.
INFO 2026-06-08 08:28:01 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 1s. Last read position: chr7:127,703,232
INFO 2026-06-08 08:28:01 MarkDuplicates Tracking 446160 as yet unmatched pairs. 11685 records in RAM.
INFO 2026-06-08 08:28:03 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 1s. Last read position: chr7:130,070,770
INFO 2026-06-08 08:28:03 MarkDuplicates Tracking 443040 as yet unmatched pairs. 8565 records in RAM.
INFO 2026-06-08 08:28:05 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 2s. Last read position: chr7:137,912,865
INFO 2026-06-08 08:28:05 MarkDuplicates Tracking 442880 as yet unmatched pairs. 8392 records in RAM.
INFO 2026-06-08 08:28:07 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 1s. Last read position: chr7:141,652,853
INFO 2026-06-08 08:28:07 MarkDuplicates Tracking 440245 as yet unmatched pairs. 5757 records in RAM.
INFO 2026-06-08 08:28:09 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 1s. Last read position: chr7:144,188,162
INFO 2026-06-08 08:28:09 MarkDuplicates Tracking 438372 as yet unmatched pairs. 3884 records in RAM.
INFO 2026-06-08 08:28:10 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 1s. Last read position: chr7:151,010,623
INFO 2026-06-08 08:28:10 MarkDuplicates Tracking 436827 as yet unmatched pairs. 2319 records in RAM.
INFO 2026-06-08 08:28:12 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 1s. Last read position: chr7:156,725,808
INFO 2026-06-08 08:28:12 MarkDuplicates Tracking 435131 as yet unmatched pairs. 622 records in RAM.
INFO 2026-06-08 08:28:14 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 1s. Last read position: chr8:11,831,538
INFO 2026-06-08 08:28:14 MarkDuplicates Tracking 434209 as yet unmatched pairs. 29636 records in RAM.
INFO 2026-06-08 08:28:15 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 1s. Last read position: chr8:22,138,360
INFO 2026-06-08 08:28:15 MarkDuplicates Tracking 431806 as yet unmatched pairs. 27224 records in RAM.
INFO 2026-06-08 08:28:17 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 1s. Last read position: chr8:27,598,148
INFO 2026-06-08 08:28:17 MarkDuplicates Tracking 431821 as yet unmatched pairs. 27238 records in RAM.
INFO 2026-06-08 08:28:18 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 1s. Last read position: chr8:29,337,255
INFO 2026-06-08 08:28:18 MarkDuplicates Tracking 428433 as yet unmatched pairs. 23849 records in RAM.
INFO 2026-06-08 08:28:20 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 1s. Last read position: chr8:38,416,043
INFO 2026-06-08 08:28:20 MarkDuplicates Tracking 426710 as yet unmatched pairs. 22113 records in RAM.
INFO 2026-06-08 08:28:21 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 1s. Last read position: chr8:47,737,657
INFO 2026-06-08 08:28:21 MarkDuplicates Tracking 425172 as yet unmatched pairs. 20572 records in RAM.
INFO 2026-06-08 08:28:23 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 1s. Last read position: chr8:61,684,063
INFO 2026-06-08 08:28:23 MarkDuplicates Tracking 423713 as yet unmatched pairs. 19112 records in RAM.
INFO 2026-06-08 08:28:24 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 1s. Last read position: chr8:80,643,059
INFO 2026-06-08 08:28:24 MarkDuplicates Tracking 421809 as yet unmatched pairs. 17207 records in RAM.
INFO 2026-06-08 08:28:27 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 2s. Last read position: chr8:100,703,331
INFO 2026-06-08 08:28:27 MarkDuplicates Tracking 422879 as yet unmatched pairs. 18277 records in RAM.
INFO 2026-06-08 08:28:29 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 2s. Last read position: chr8:103,400,453
INFO 2026-06-08 08:28:29 MarkDuplicates Tracking 418655 as yet unmatched pairs. 14052 records in RAM.
INFO 2026-06-08 08:28:31 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 1s. Last read position: chr8:127,738,448
INFO 2026-06-08 08:28:31 MarkDuplicates Tracking 417281 as yet unmatched pairs. 12677 records in RAM.
INFO 2026-06-08 08:28:32 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr8:143,580,508
INFO 2026-06-08 08:28:32 MarkDuplicates Tracking 415213 as yet unmatched pairs. 10580 records in RAM.
INFO 2026-06-08 08:28:33 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 1s. Last read position: chr8:143,858,552
INFO 2026-06-08 08:28:33 MarkDuplicates Tracking 413849 as yet unmatched pairs. 9216 records in RAM.
INFO 2026-06-08 08:28:35 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 1s. Last read position: chr8:143,860,633
INFO 2026-06-08 08:28:35 MarkDuplicates Tracking 414632 as yet unmatched pairs. 9997 records in RAM.
INFO 2026-06-08 08:28:36 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 0s. Last read position: chr8:143,862,278
INFO 2026-06-08 08:28:36 MarkDuplicates Tracking 412982 as yet unmatched pairs. 8347 records in RAM.
INFO 2026-06-08 08:28:37 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 1s. Last read position: chr8:143,863,997
INFO 2026-06-08 08:28:37 MarkDuplicates Tracking 411413 as yet unmatched pairs. 6778 records in RAM.
INFO 2026-06-08 08:28:38 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 0s. Last read position: chr8:143,866,087
INFO 2026-06-08 08:28:38 MarkDuplicates Tracking 410922 as yet unmatched pairs. 6287 records in RAM.
INFO 2026-06-08 08:28:39 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 1s. Last read position: chr8:143,919,186
INFO 2026-06-08 08:28:39 MarkDuplicates Tracking 409930 as yet unmatched pairs. 5295 records in RAM.
INFO 2026-06-08 08:28:41 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 1s. Last read position: chr8:144,085,330
INFO 2026-06-08 08:28:41 MarkDuplicates Tracking 407338 as yet unmatched pairs. 2703 records in RAM.
INFO 2026-06-08 08:28:42 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 1s. Last read position: chr8:144,522,899
INFO 2026-06-08 08:28:42 MarkDuplicates Tracking 405120 as yet unmatched pairs. 485 records in RAM.
INFO 2026-06-08 08:28:44 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 1s. Last read position: chr9:14,150,216
INFO 2026-06-08 08:28:44 MarkDuplicates Tracking 404822 as yet unmatched pairs. 24365 records in RAM.
INFO 2026-06-08 08:28:45 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 1s. Last read position: chr9:33,922,929
INFO 2026-06-08 08:28:45 MarkDuplicates Tracking 401836 as yet unmatched pairs. 21378 records in RAM.
INFO 2026-06-08 08:28:47 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 1s. Last read position: chr9:38,067,674
INFO 2026-06-08 08:28:47 MarkDuplicates Tracking 399876 as yet unmatched pairs. 19407 records in RAM.
INFO 2026-06-08 08:28:48 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 1s. Last read position: chr9:83,971,684
INFO 2026-06-08 08:28:48 MarkDuplicates Tracking 398892 as yet unmatched pairs. 18423 records in RAM.
INFO 2026-06-08 08:28:51 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 2s. Last read position: chr9:95,972,182
INFO 2026-06-08 08:28:51 MarkDuplicates Tracking 397007 as yet unmatched pairs. 16529 records in RAM.
INFO 2026-06-08 08:28:53 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 2s. Last read position: chr9:110,244,178
INFO 2026-06-08 08:28:53 MarkDuplicates Tracking 395736 as yet unmatched pairs. 15255 records in RAM.
INFO 2026-06-08 08:28:54 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 1s. Last read position: chr9:120,713,910
INFO 2026-06-08 08:28:54 MarkDuplicates Tracking 393785 as yet unmatched pairs. 13302 records in RAM.
INFO 2026-06-08 08:28:56 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 1s. Last read position: chr9:125,355,702
INFO 2026-06-08 08:28:56 MarkDuplicates Tracking 391911 as yet unmatched pairs. 11427 records in RAM.
INFO 2026-06-08 08:28:57 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 1s. Last read position: chr9:128,598,474
INFO 2026-06-08 08:28:57 MarkDuplicates Tracking 390249 as yet unmatched pairs. 9763 records in RAM.
INFO 2026-06-08 08:28:59 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 1s. Last read position: chr9:130,681,610
INFO 2026-06-08 08:28:59 MarkDuplicates Tracking 388384 as yet unmatched pairs. 7898 records in RAM.
INFO 2026-06-08 08:29:00 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 1s. Last read position: chr9:133,352,517
INFO 2026-06-08 08:29:00 MarkDuplicates Tracking 386854 as yet unmatched pairs. 6366 records in RAM.
INFO 2026-06-08 08:29:02 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 1s. Last read position: chr9:136,475,649
INFO 2026-06-08 08:29:02 MarkDuplicates Tracking 385102 as yet unmatched pairs. 4614 records in RAM.
INFO 2026-06-08 08:29:03 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 1s. Last read position: chr9:137,108,855
INFO 2026-06-08 08:29:03 MarkDuplicates Tracking 382910 as yet unmatched pairs. 2421 records in RAM.
INFO 2026-06-08 08:29:05 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 1s. Last read position: chr10:1,015,602
INFO 2026-06-08 08:29:05 MarkDuplicates Tracking 380291 as yet unmatched pairs. 19173 records in RAM.
INFO 2026-06-08 08:29:07 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 1s. Last read position: chr10:8,069,514
INFO 2026-06-08 08:29:07 MarkDuplicates Tracking 378630 as yet unmatched pairs. 17512 records in RAM.
INFO 2026-06-08 08:29:09 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 1s. Last read position: chr10:27,526,852
INFO 2026-06-08 08:29:09 MarkDuplicates Tracking 377017 as yet unmatched pairs. 15896 records in RAM.
INFO 2026-06-08 08:29:10 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 1s. Last read position: chr10:42,831,016
INFO 2026-06-08 08:29:10 MarkDuplicates Tracking 375550 as yet unmatched pairs. 14428 records in RAM.
INFO 2026-06-08 08:29:12 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 1s. Last read position: chr10:50,008,862
INFO 2026-06-08 08:29:12 MarkDuplicates Tracking 374289 as yet unmatched pairs. 13167 records in RAM.
INFO 2026-06-08 08:29:13 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr10:70,204,892
INFO 2026-06-08 08:29:13 MarkDuplicates Tracking 372885 as yet unmatched pairs. 11760 records in RAM.
INFO 2026-06-08 08:29:14 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 1s. Last read position: chr10:75,028,585
INFO 2026-06-08 08:29:14 MarkDuplicates Tracking 371016 as yet unmatched pairs. 9891 records in RAM.
INFO 2026-06-08 08:29:16 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 1s. Last read position: chr10:87,094,413
INFO 2026-06-08 08:29:16 MarkDuplicates Tracking 369628 as yet unmatched pairs. 8503 records in RAM.
INFO 2026-06-08 08:29:18 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 1s. Last read position: chr10:95,866,845
INFO 2026-06-08 08:29:18 MarkDuplicates Tracking 368155 as yet unmatched pairs. 7030 records in RAM.
INFO 2026-06-08 08:29:19 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 1s. Last read position: chr10:100,356,742
INFO 2026-06-08 08:29:19 MarkDuplicates Tracking 367214 as yet unmatched pairs. 6088 records in RAM.
INFO 2026-06-08 08:29:21 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 1s. Last read position: chr10:104,315,950
INFO 2026-06-08 08:29:21 MarkDuplicates Tracking 364533 as yet unmatched pairs. 3407 records in RAM.
INFO 2026-06-08 08:29:22 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 1s. Last read position: chr10:119,842,503
INFO 2026-06-08 08:29:22 MarkDuplicates Tracking 363039 as yet unmatched pairs. 1912 records in RAM.
INFO 2026-06-08 08:29:24 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 2s. Last read position: chr10:133,380,466
INFO 2026-06-08 08:29:24 MarkDuplicates Tracking 361326 as yet unmatched pairs. 197 records in RAM.
INFO 2026-06-08 08:29:27 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 2s. Last read position: chr11:613,012
INFO 2026-06-08 08:29:27 MarkDuplicates Tracking 359486 as yet unmatched pairs. 46150 records in RAM.
INFO 2026-06-08 08:29:28 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 1s. Last read position: chr11:865,948
INFO 2026-06-08 08:29:28 MarkDuplicates Tracking 357146 as yet unmatched pairs. 43798 records in RAM.
INFO 2026-06-08 08:29:30 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 1s. Last read position: chr11:2,396,806
INFO 2026-06-08 08:29:30 MarkDuplicates Tracking 355774 as yet unmatched pairs. 42424 records in RAM.
INFO 2026-06-08 08:29:31 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 1s. Last read position: chr11:6,615,256
INFO 2026-06-08 08:29:31 MarkDuplicates Tracking 353255 as yet unmatched pairs. 39905 records in RAM.
INFO 2026-06-08 08:29:32 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 1s. Last read position: chr11:11,332,715
INFO 2026-06-08 08:29:32 MarkDuplicates Tracking 351491 as yet unmatched pairs. 38140 records in RAM.
INFO 2026-06-08 08:29:34 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 1s. Last read position: chr11:18,701,724
INFO 2026-06-08 08:29:34 MarkDuplicates Tracking 350548 as yet unmatched pairs. 37197 records in RAM.
INFO 2026-06-08 08:29:35 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 1s. Last read position: chr11:44,107,858
INFO 2026-06-08 08:29:35 MarkDuplicates Tracking 348763 as yet unmatched pairs. 35411 records in RAM.
INFO 2026-06-08 08:29:37 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 1s. Last read position: chr11:47,259,939
INFO 2026-06-08 08:29:37 MarkDuplicates Tracking 346934 as yet unmatched pairs. 33581 records in RAM.
INFO 2026-06-08 08:29:38 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 1s. Last read position: chr11:57,741,593
INFO 2026-06-08 08:29:38 MarkDuplicates Tracking 345144 as yet unmatched pairs. 31791 records in RAM.
INFO 2026-06-08 08:29:40 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 1s. Last read position: chr11:61,303,987
INFO 2026-06-08 08:29:40 MarkDuplicates Tracking 343437 as yet unmatched pairs. 30082 records in RAM.
INFO 2026-06-08 08:29:41 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 1s. Last read position: chr11:62,518,633
INFO 2026-06-08 08:29:41 MarkDuplicates Tracking 342079 as yet unmatched pairs. 28720 records in RAM.
INFO 2026-06-08 08:29:43 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 1s. Last read position: chr11:62,528,850
INFO 2026-06-08 08:29:43 MarkDuplicates Tracking 340991 as yet unmatched pairs. 27632 records in RAM.
INFO 2026-06-08 08:29:45 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 1s. Last read position: chr11:62,634,901
INFO 2026-06-08 08:29:45 MarkDuplicates Tracking 338907 as yet unmatched pairs. 25548 records in RAM.
INFO 2026-06-08 08:29:47 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:05:43s. Time for last 1,000,000: 1s. Last read position: chr11:64,224,148
INFO 2026-06-08 08:29:47 MarkDuplicates Tracking 337193 as yet unmatched pairs. 23834 records in RAM.
INFO 2026-06-08 08:29:49 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 2s. Last read position: chr11:65,112,574
INFO 2026-06-08 08:29:49 MarkDuplicates Tracking 334753 as yet unmatched pairs. 21394 records in RAM.
INFO 2026-06-08 08:29:50 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 1s. Last read position: chr11:65,625,978
INFO 2026-06-08 08:29:50 MarkDuplicates Tracking 332837 as yet unmatched pairs. 19478 records in RAM.
INFO 2026-06-08 08:29:52 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 1s. Last read position: chr11:66,495,450
INFO 2026-06-08 08:29:52 MarkDuplicates Tracking 330757 as yet unmatched pairs. 17398 records in RAM.
INFO 2026-06-08 08:29:53 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 1s. Last read position: chr11:67,435,863
INFO 2026-06-08 08:29:53 MarkDuplicates Tracking 328836 as yet unmatched pairs. 15468 records in RAM.
INFO 2026-06-08 08:29:55 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 1s. Last read position: chr11:68,120,866
INFO 2026-06-08 08:29:55 MarkDuplicates Tracking 326822 as yet unmatched pairs. 13452 records in RAM.
INFO 2026-06-08 08:29:57 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 1s. Last read position: chr11:71,444,888
INFO 2026-06-08 08:29:57 MarkDuplicates Tracking 325336 as yet unmatched pairs. 11966 records in RAM.
INFO 2026-06-08 08:29:59 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 2s. Last read position: chr11:73,978,269
INFO 2026-06-08 08:29:59 MarkDuplicates Tracking 323806 as yet unmatched pairs. 10436 records in RAM.
INFO 2026-06-08 08:30:01 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 1s. Last read position: chr11:78,225,147
INFO 2026-06-08 08:30:01 MarkDuplicates Tracking 321623 as yet unmatched pairs. 8251 records in RAM.
INFO 2026-06-08 08:30:02 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 1s. Last read position: chr11:108,161,595
INFO 2026-06-08 08:30:02 MarkDuplicates Tracking 320004 as yet unmatched pairs. 6632 records in RAM.
INFO 2026-06-08 08:30:04 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 1s. Last read position: chr11:118,382,671
INFO 2026-06-08 08:30:04 MarkDuplicates Tracking 318257 as yet unmatched pairs. 4866 records in RAM.
INFO 2026-06-08 08:30:05 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 1s. Last read position: chr11:119,728,481
INFO 2026-06-08 08:30:05 MarkDuplicates Tracking 316898 as yet unmatched pairs. 3507 records in RAM.
INFO 2026-06-08 08:30:06 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 1s. Last read position: chr11:128,807,212
INFO 2026-06-08 08:30:06 MarkDuplicates Tracking 315030 as yet unmatched pairs. 1639 records in RAM.
INFO 2026-06-08 08:30:08 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 1s. Last read position: chr12:830,001
INFO 2026-06-08 08:30:08 MarkDuplicates Tracking 313301 as yet unmatched pairs. 35568 records in RAM.
INFO 2026-06-08 08:30:10 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 1s. Last read position: chr12:6,354,801
INFO 2026-06-08 08:30:10 MarkDuplicates Tracking 311475 as yet unmatched pairs. 33736 records in RAM.
INFO 2026-06-08 08:30:11 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 1s. Last read position: chr12:7,069,999
INFO 2026-06-08 08:30:11 MarkDuplicates Tracking 310073 as yet unmatched pairs. 32334 records in RAM.
INFO 2026-06-08 08:30:14 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 2s. Last read position: chr12:12,165,283
INFO 2026-06-08 08:30:14 MarkDuplicates Tracking 308070 as yet unmatched pairs. 30331 records in RAM.
INFO 2026-06-08 08:30:15 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 1s. Last read position: chr12:26,427,968
INFO 2026-06-08 08:30:15 MarkDuplicates Tracking 306468 as yet unmatched pairs. 28729 records in RAM.
INFO 2026-06-08 08:30:17 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 1s. Last read position: chr12:46,201,166
INFO 2026-06-08 08:30:17 MarkDuplicates Tracking 305414 as yet unmatched pairs. 27674 records in RAM.
INFO 2026-06-08 08:30:18 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 1s. Last read position: chr12:49,128,462
INFO 2026-06-08 08:30:18 MarkDuplicates Tracking 303654 as yet unmatched pairs. 25914 records in RAM.
INFO 2026-06-08 08:30:20 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:06:16s. Time for last 1,000,000: 1s. Last read position: chr12:52,054,637
INFO 2026-06-08 08:30:20 MarkDuplicates Tracking 302198 as yet unmatched pairs. 24458 records in RAM.
INFO 2026-06-08 08:30:21 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 1s. Last read position: chr12:53,383,330
INFO 2026-06-08 08:30:21 MarkDuplicates Tracking 300181 as yet unmatched pairs. 22440 records in RAM.
INFO 2026-06-08 08:30:23 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 1s. Last read position: chr12:54,855,123
INFO 2026-06-08 08:30:23 MarkDuplicates Tracking 306191 as yet unmatched pairs. 28450 records in RAM.
INFO 2026-06-08 08:30:25 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 1s. Last read position: chr12:56,107,032
INFO 2026-06-08 08:30:25 MarkDuplicates Tracking 296982 as yet unmatched pairs. 19241 records in RAM.
INFO 2026-06-08 08:30:26 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 1s. Last read position: chr12:57,094,688
INFO 2026-06-08 08:30:26 MarkDuplicates Tracking 295526 as yet unmatched pairs. 17785 records in RAM.
INFO 2026-06-08 08:30:28 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 1s. Last read position: chr12:57,205,037
INFO 2026-06-08 08:30:28 MarkDuplicates Tracking 293801 as yet unmatched pairs. 16060 records in RAM.
INFO 2026-06-08 08:30:30 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 1s. Last read position: chr12:64,434,884
INFO 2026-06-08 08:30:30 MarkDuplicates Tracking 291961 as yet unmatched pairs. 14220 records in RAM.
INFO 2026-06-08 08:30:32 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 2s. Last read position: chr12:89,351,813
INFO 2026-06-08 08:30:32 MarkDuplicates Tracking 290536 as yet unmatched pairs. 12794 records in RAM.
INFO 2026-06-08 08:30:34 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:06:30s. Time for last 1,000,000: 1s. Last read position: chr12:102,400,056
INFO 2026-06-08 08:30:34 MarkDuplicates Tracking 288946 as yet unmatched pairs. 11199 records in RAM.
INFO 2026-06-08 08:30:35 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 1s. Last read position: chr12:109,245,716
INFO 2026-06-08 08:30:35 MarkDuplicates Tracking 287456 as yet unmatched pairs. 9709 records in RAM.
INFO 2026-06-08 08:30:37 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:06:33s. Time for last 1,000,000: 1s. Last read position: chr12:112,228,167
INFO 2026-06-08 08:30:37 MarkDuplicates Tracking 285649 as yet unmatched pairs. 7902 records in RAM.
INFO 2026-06-08 08:30:38 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:06:35s. Time for last 1,000,000: 1s. Last read position: chr12:120,130,646
INFO 2026-06-08 08:30:38 MarkDuplicates Tracking 284094 as yet unmatched pairs. 6347 records in RAM.
INFO 2026-06-08 08:30:40 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 1s. Last read position: chr12:121,817,539
INFO 2026-06-08 08:30:40 MarkDuplicates Tracking 282404 as yet unmatched pairs. 4657 records in RAM.
INFO 2026-06-08 08:30:41 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 1s. Last read position: chr12:124,354,930
INFO 2026-06-08 08:30:41 MarkDuplicates Tracking 280675 as yet unmatched pairs. 2926 records in RAM.
INFO 2026-06-08 08:30:43 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 1s. Last read position: chr12:132,583,148
INFO 2026-06-08 08:30:43 MarkDuplicates Tracking 278704 as yet unmatched pairs. 954 records in RAM.
INFO 2026-06-08 08:32:00 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:07:56s. Time for last 1,000,000: 76s. Last read position: chr13:24,249,703
INFO 2026-06-08 08:32:00 MarkDuplicates Tracking 277155 as yet unmatched pairs. 8258 records in RAM.
INFO 2026-06-08 08:32:01 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:07:57s. Time for last 1,000,000: 1s. Last read position: chr13:40,665,952
INFO 2026-06-08 08:32:01 MarkDuplicates Tracking 275721 as yet unmatched pairs. 6823 records in RAM.
INFO 2026-06-08 08:32:03 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:07:59s. Time for last 1,000,000: 1s. Last read position: chr13:49,549,490
INFO 2026-06-08 08:32:03 MarkDuplicates Tracking 274119 as yet unmatched pairs. 5220 records in RAM.
INFO 2026-06-08 08:32:05 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:08:01s. Time for last 1,000,000: 1s. Last read position: chr13:95,763,859
INFO 2026-06-08 08:32:05 MarkDuplicates Tracking 272573 as yet unmatched pairs. 3668 records in RAM.
INFO 2026-06-08 08:32:06 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:08:03s. Time for last 1,000,000: 1s. Last read position: chr13:110,210,164
INFO 2026-06-08 08:32:06 MarkDuplicates Tracking 270900 as yet unmatched pairs. 1994 records in RAM.
INFO 2026-06-08 08:32:08 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:08:04s. Time for last 1,000,000: 1s. Last read position: chr14:20,311,596
INFO 2026-06-08 08:32:08 MarkDuplicates Tracking 268973 as yet unmatched pairs. 18983 records in RAM.
INFO 2026-06-08 08:32:10 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:08:06s. Time for last 1,000,000: 1s. Last read position: chr14:23,034,724
INFO 2026-06-08 08:32:10 MarkDuplicates Tracking 267340 as yet unmatched pairs. 17350 records in RAM.
INFO 2026-06-08 08:32:12 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:08:08s. Time for last 1,000,000: 1s. Last read position: chr14:24,143,432
INFO 2026-06-08 08:32:12 MarkDuplicates Tracking 265829 as yet unmatched pairs. 15837 records in RAM.
INFO 2026-06-08 08:32:13 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:08:10s. Time for last 1,000,000: 1s. Last read position: chr14:35,403,695
INFO 2026-06-08 08:32:13 MarkDuplicates Tracking 264550 as yet unmatched pairs. 14549 records in RAM.
INFO 2026-06-08 08:32:15 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:08:11s. Time for last 1,000,000: 1s. Last read position: chr14:54,436,369
INFO 2026-06-08 08:32:15 MarkDuplicates Tracking 262636 as yet unmatched pairs. 12628 records in RAM.
INFO 2026-06-08 08:32:17 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:08:14s. Time for last 1,000,000: 2s. Last read position: chr14:64,704,664
INFO 2026-06-08 08:32:17 MarkDuplicates Tracking 261019 as yet unmatched pairs. 11007 records in RAM.
INFO 2026-06-08 08:32:20 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 2s. Last read position: chr14:73,287,239
INFO 2026-06-08 08:32:20 MarkDuplicates Tracking 259329 as yet unmatched pairs. 9315 records in RAM.
INFO 2026-06-08 08:32:21 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:08:18s. Time for last 1,000,000: 1s. Last read position: chr14:75,280,975
INFO 2026-06-08 08:32:21 MarkDuplicates Tracking 258648 as yet unmatched pairs. 8632 records in RAM.
INFO 2026-06-08 08:32:23 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 1s. Last read position: chr14:91,792,407
INFO 2026-06-08 08:32:23 MarkDuplicates Tracking 256272 as yet unmatched pairs. 6254 records in RAM.
INFO 2026-06-08 08:32:24 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 1s. Last read position: chr14:101,983,555
INFO 2026-06-08 08:32:24 MarkDuplicates Tracking 254455 as yet unmatched pairs. 4434 records in RAM.
INFO 2026-06-08 08:32:26 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:08:22s. Time for last 1,000,000: 1s. Last read position: chr14:104,587,816
INFO 2026-06-08 08:32:26 MarkDuplicates Tracking 252509 as yet unmatched pairs. 2488 records in RAM.
INFO 2026-06-08 08:32:27 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:08:24s. Time for last 1,000,000: 1s. Last read position: chr14:105,624,617
INFO 2026-06-08 08:32:27 MarkDuplicates Tracking 250999 as yet unmatched pairs. 978 records in RAM.
INFO 2026-06-08 08:32:29 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 1s. Last read position: chr15:22,914,738
INFO 2026-06-08 08:32:29 MarkDuplicates Tracking 249813 as yet unmatched pairs. 19365 records in RAM.
INFO 2026-06-08 08:32:31 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:08:27s. Time for last 1,000,000: 1s. Last read position: chr15:34,381,365
INFO 2026-06-08 08:32:31 MarkDuplicates Tracking 248519 as yet unmatched pairs. 18071 records in RAM.
INFO 2026-06-08 08:32:32 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 1s. Last read position: chr15:41,055,268
INFO 2026-06-08 08:32:32 MarkDuplicates Tracking 246775 as yet unmatched pairs. 16326 records in RAM.
INFO 2026-06-08 08:32:34 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:08:30s. Time for last 1,000,000: 1s. Last read position: chr15:43,184,484
INFO 2026-06-08 08:32:34 MarkDuplicates Tracking 245481 as yet unmatched pairs. 15032 records in RAM.
INFO 2026-06-08 08:32:35 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 1s. Last read position: chr15:44,711,538
INFO 2026-06-08 08:32:35 MarkDuplicates Tracking 243958 as yet unmatched pairs. 13509 records in RAM.
INFO 2026-06-08 08:32:37 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:08:33s. Time for last 1,000,000: 1s. Last read position: chr15:52,582,220
INFO 2026-06-08 08:32:37 MarkDuplicates Tracking 242319 as yet unmatched pairs. 11870 records in RAM.
INFO 2026-06-08 08:32:39 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 1s. Last read position: chr15:62,835,902
INFO 2026-06-08 08:32:39 MarkDuplicates Tracking 240793 as yet unmatched pairs. 10344 records in RAM.
INFO 2026-06-08 08:32:40 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 1s. Last read position: chr15:66,703,341
INFO 2026-06-08 08:32:40 MarkDuplicates Tracking 239166 as yet unmatched pairs. 8717 records in RAM.
INFO 2026-06-08 08:32:42 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:08:38s. Time for last 1,000,000: 1s. Last read position: chr15:74,033,251
INFO 2026-06-08 08:32:42 MarkDuplicates Tracking 238070 as yet unmatched pairs. 7616 records in RAM.
INFO 2026-06-08 08:32:43 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 1s. Last read position: chr15:77,179,340
INFO 2026-06-08 08:32:43 MarkDuplicates Tracking 235417 as yet unmatched pairs. 4963 records in RAM.
INFO 2026-06-08 08:32:45 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:08:41s. Time for last 1,000,000: 1s. Last read position: chr15:85,582,047
INFO 2026-06-08 08:32:45 MarkDuplicates Tracking 234051 as yet unmatched pairs. 3596 records in RAM.
INFO 2026-06-08 08:32:46 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:08:43s. Time for last 1,000,000: 1s. Last read position: chr15:90,467,491
INFO 2026-06-08 08:32:46 MarkDuplicates Tracking 232214 as yet unmatched pairs. 1759 records in RAM.
INFO 2026-06-08 08:32:49 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:08:45s. Time for last 1,000,000: 2s. Last read position: chr16:18,703
INFO 2026-06-08 08:32:49 MarkDuplicates Tracking 230455 as yet unmatched pairs. 36850 records in RAM.
INFO 2026-06-08 08:32:51 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 2s. Last read position: chr16:1,153,737
INFO 2026-06-08 08:32:51 MarkDuplicates Tracking 228274 as yet unmatched pairs. 34669 records in RAM.
INFO 2026-06-08 08:32:53 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 1s. Last read position: chr16:2,036,790
INFO 2026-06-08 08:32:53 MarkDuplicates Tracking 226411 as yet unmatched pairs. 32806 records in RAM.
INFO 2026-06-08 08:32:55 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 1s. Last read position: chr16:2,439,413
INFO 2026-06-08 08:32:55 MarkDuplicates Tracking 223867 as yet unmatched pairs. 30262 records in RAM.
INFO 2026-06-08 08:32:56 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:08:53s. Time for last 1,000,000: 1s. Last read position: chr16:3,023,319
INFO 2026-06-08 08:32:56 MarkDuplicates Tracking 222350 as yet unmatched pairs. 28745 records in RAM.
INFO 2026-06-08 08:32:58 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 1s. Last read position: chr16:9,156,492
INFO 2026-06-08 08:32:58 MarkDuplicates Tracking 220346 as yet unmatched pairs. 26741 records in RAM.
INFO 2026-06-08 08:32:59 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:08:56s. Time for last 1,000,000: 1s. Last read position: chr16:14,924,570
INFO 2026-06-08 08:32:59 MarkDuplicates Tracking 219219 as yet unmatched pairs. 25614 records in RAM.
INFO 2026-06-08 08:33:01 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:08:57s. Time for last 1,000,000: 1s. Last read position: chr16:16,275,087
INFO 2026-06-08 08:33:01 MarkDuplicates Tracking 217823 as yet unmatched pairs. 24218 records in RAM.
INFO 2026-06-08 08:33:02 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:08:58s. Time for last 1,000,000: 1s. Last read position: chr16:18,376,816
INFO 2026-06-08 08:33:02 MarkDuplicates Tracking 217649 as yet unmatched pairs. 24044 records in RAM.
INFO 2026-06-08 08:33:03 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:09:00s. Time for last 1,000,000: 1s. Last read position: chr16:20,625,440
INFO 2026-06-08 08:33:03 MarkDuplicates Tracking 216392 as yet unmatched pairs. 22787 records in RAM.
INFO 2026-06-08 08:33:05 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:09:01s. Time for last 1,000,000: 1s. Last read position: chr16:21,599,782
INFO 2026-06-08 08:33:05 MarkDuplicates Tracking 215596 as yet unmatched pairs. 21991 records in RAM.
INFO 2026-06-08 08:33:06 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:09:03s. Time for last 1,000,000: 1s. Last read position: chr16:22,533,780
INFO 2026-06-08 08:33:06 MarkDuplicates Tracking 214677 as yet unmatched pairs. 21072 records in RAM.
INFO 2026-06-08 08:33:08 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:09:04s. Time for last 1,000,000: 1s. Last read position: chr16:28,486,597
INFO 2026-06-08 08:33:08 MarkDuplicates Tracking 213982 as yet unmatched pairs. 20377 records in RAM.
INFO 2026-06-08 08:33:09 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 1s. Last read position: chr16:29,485,097
INFO 2026-06-08 08:33:09 MarkDuplicates Tracking 212499 as yet unmatched pairs. 18893 records in RAM.
INFO 2026-06-08 08:33:11 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 2s. Last read position: chr16:30,193,219
INFO 2026-06-08 08:33:11 MarkDuplicates Tracking 210712 as yet unmatched pairs. 17106 records in RAM.
INFO 2026-06-08 08:33:13 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:09:09s. Time for last 1,000,000: 1s. Last read position: chr16:30,930,218
INFO 2026-06-08 08:33:13 MarkDuplicates Tracking 209332 as yet unmatched pairs. 15724 records in RAM.
INFO 2026-06-08 08:33:14 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:09:11s. Time for last 1,000,000: 1s. Last read position: chr16:48,175,344
INFO 2026-06-08 08:33:14 MarkDuplicates Tracking 208123 as yet unmatched pairs. 14515 records in RAM.
INFO 2026-06-08 08:33:16 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:09:12s. Time for last 1,000,000: 1s. Last read position: chr16:53,470,445
INFO 2026-06-08 08:33:16 MarkDuplicates Tracking 206294 as yet unmatched pairs. 12686 records in RAM.
INFO 2026-06-08 08:33:18 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:09:15s. Time for last 1,000,000: 2s. Last read position: chr16:58,002,519
INFO 2026-06-08 08:33:18 MarkDuplicates Tracking 204157 as yet unmatched pairs. 10549 records in RAM.
INFO 2026-06-08 08:33:20 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 1s. Last read position: chr16:67,666,141
INFO 2026-06-08 08:33:20 MarkDuplicates Tracking 201840 as yet unmatched pairs. 8232 records in RAM.
INFO 2026-06-08 08:33:22 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:09:18s. Time for last 1,000,000: 2s. Last read position: chr16:70,024,640
INFO 2026-06-08 08:33:22 MarkDuplicates Tracking 200338 as yet unmatched pairs. 6730 records in RAM.
INFO 2026-06-08 08:33:24 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 2s. Last read position: chr16:75,617,184
INFO 2026-06-08 08:33:24 MarkDuplicates Tracking 198487 as yet unmatched pairs. 4878 records in RAM.
INFO 2026-06-08 08:33:26 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 1s. Last read position: chr16:87,411,993
INFO 2026-06-08 08:33:26 MarkDuplicates Tracking 196642 as yet unmatched pairs. 3031 records in RAM.
INFO 2026-06-08 08:33:27 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:09:24s. Time for last 1,000,000: 1s. Last read position: chr16:89,561,283
INFO 2026-06-08 08:33:27 MarkDuplicates Tracking 196320 as yet unmatched pairs. 2708 records in RAM.
INFO 2026-06-08 08:33:29 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:09:26s. Time for last 1,000,000: 2s. Last read position: chr17:1,593,203
INFO 2026-06-08 08:33:29 MarkDuplicates Tracking 192760 as yet unmatched pairs. 53555 records in RAM.
INFO 2026-06-08 08:33:31 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:09:27s. Time for last 1,000,000: 1s. Last read position: chr17:4,539,664
INFO 2026-06-08 08:33:31 MarkDuplicates Tracking 190946 as yet unmatched pairs. 51738 records in RAM.
INFO 2026-06-08 08:33:33 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:09:29s. Time for last 1,000,000: 1s. Last read position: chr17:7,309,702
INFO 2026-06-08 08:33:33 MarkDuplicates Tracking 189411 as yet unmatched pairs. 50202 records in RAM.
INFO 2026-06-08 08:33:34 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:09:30s. Time for last 1,000,000: 1s. Last read position: chr17:8,039,578
INFO 2026-06-08 08:33:34 MarkDuplicates Tracking 188656 as yet unmatched pairs. 49447 records in RAM.
INFO 2026-06-08 08:33:36 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:09:32s. Time for last 1,000,000: 1s. Last read position: chr17:16,101,408
INFO 2026-06-08 08:33:36 MarkDuplicates Tracking 185947 as yet unmatched pairs. 46737 records in RAM.
INFO 2026-06-08 08:33:37 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:09:34s. Time for last 1,000,000: 1s. Last read position: chr17:18,248,683
INFO 2026-06-08 08:33:37 MarkDuplicates Tracking 183921 as yet unmatched pairs. 44711 records in RAM.
INFO 2026-06-08 08:33:39 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 1s. Last read position: chr17:28,881,991
INFO 2026-06-08 08:33:39 MarkDuplicates Tracking 182512 as yet unmatched pairs. 43302 records in RAM.
INFO 2026-06-08 08:33:41 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 1s. Last read position: chr17:35,834,577
INFO 2026-06-08 08:33:41 MarkDuplicates Tracking 180900 as yet unmatched pairs. 41689 records in RAM.
INFO 2026-06-08 08:33:42 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:09:38s. Time for last 1,000,000: 1s. Last read position: chr17:38,724,933
INFO 2026-06-08 08:33:42 MarkDuplicates Tracking 179669 as yet unmatched pairs. 40458 records in RAM.
INFO 2026-06-08 08:33:44 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:09:40s. Time for last 1,000,000: 1s. Last read position: chr17:39,715,294
INFO 2026-06-08 08:33:44 MarkDuplicates Tracking 179987 as yet unmatched pairs. 40775 records in RAM.
INFO 2026-06-08 08:33:46 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:09:43s. Time for last 1,000,000: 2s. Last read position: chr17:40,163,784
INFO 2026-06-08 08:33:46 MarkDuplicates Tracking 175983 as yet unmatched pairs. 36771 records in RAM.
INFO 2026-06-08 08:33:48 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:09:45s. Time for last 1,000,000: 1s. Last read position: chr17:42,216,039
INFO 2026-06-08 08:33:48 MarkDuplicates Tracking 174075 as yet unmatched pairs. 34863 records in RAM.
INFO 2026-06-08 08:33:50 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:09:46s. Time for last 1,000,000: 1s. Last read position: chr17:44,189,270
INFO 2026-06-08 08:33:50 MarkDuplicates Tracking 172231 as yet unmatched pairs. 33015 records in RAM.
INFO 2026-06-08 08:33:51 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:09:48s. Time for last 1,000,000: 1s. Last read position: chr17:47,590,777
INFO 2026-06-08 08:33:51 MarkDuplicates Tracking 170670 as yet unmatched pairs. 31452 records in RAM.
INFO 2026-06-08 08:33:53 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:09:49s. Time for last 1,000,000: 1s. Last read position: chr17:50,186,425
INFO 2026-06-08 08:33:53 MarkDuplicates Tracking 169399 as yet unmatched pairs. 30180 records in RAM.
INFO 2026-06-08 08:33:54 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:09:51s. Time for last 1,000,000: 1s. Last read position: chr17:50,189,520
INFO 2026-06-08 08:33:54 MarkDuplicates Tracking 171634 as yet unmatched pairs. 32414 records in RAM.
INFO 2026-06-08 08:33:56 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:09:52s. Time for last 1,000,000: 1s. Last read position: chr17:50,193,012
INFO 2026-06-08 08:33:56 MarkDuplicates Tracking 171200 as yet unmatched pairs. 31980 records in RAM.
INFO 2026-06-08 08:33:58 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:09:54s. Time for last 1,000,000: 1s. Last read position: chr17:50,196,170
INFO 2026-06-08 08:33:58 MarkDuplicates Tracking 169062 as yet unmatched pairs. 29842 records in RAM.
INFO 2026-06-08 08:33:59 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:09:56s. Time for last 1,000,000: 1s. Last read position: chr17:50,463,834
INFO 2026-06-08 08:33:59 MarkDuplicates Tracking 161519 as yet unmatched pairs. 22299 records in RAM.
INFO 2026-06-08 08:34:01 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:09:57s. Time for last 1,000,000: 1s. Last read position: chr17:59,660,388
INFO 2026-06-08 08:34:01 MarkDuplicates Tracking 160519 as yet unmatched pairs. 21299 records in RAM.
INFO 2026-06-08 08:34:03 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 1s. Last read position: chr17:63,433,322
INFO 2026-06-08 08:34:03 MarkDuplicates Tracking 158200 as yet unmatched pairs. 18980 records in RAM.
INFO 2026-06-08 08:34:04 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:10:01s. Time for last 1,000,000: 1s. Last read position: chr17:67,945,493
INFO 2026-06-08 08:34:04 MarkDuplicates Tracking 156490 as yet unmatched pairs. 17270 records in RAM.
INFO 2026-06-08 08:34:06 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:10:02s. Time for last 1,000,000: 1s. Last read position: chr17:75,231,615
INFO 2026-06-08 08:34:06 MarkDuplicates Tracking 154737 as yet unmatched pairs. 15516 records in RAM.
INFO 2026-06-08 08:34:07 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:10:04s. Time for last 1,000,000: 1s. Last read position: chr17:76,387,440
INFO 2026-06-08 08:34:07 MarkDuplicates Tracking 152737 as yet unmatched pairs. 13515 records in RAM.
INFO 2026-06-08 08:34:09 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:10:05s. Time for last 1,000,000: 1s. Last read position: chr17:79,085,766
INFO 2026-06-08 08:34:09 MarkDuplicates Tracking 151095 as yet unmatched pairs. 11873 records in RAM.
INFO 2026-06-08 08:34:11 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:10:07s. Time for last 1,000,000: 1s. Last read position: chr17:81,461,502
INFO 2026-06-08 08:34:11 MarkDuplicates Tracking 149144 as yet unmatched pairs. 9922 records in RAM.
INFO 2026-06-08 08:34:12 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 1s. Last read position: chr17:81,934,674
INFO 2026-06-08 08:34:12 MarkDuplicates Tracking 147387 as yet unmatched pairs. 8165 records in RAM.
INFO 2026-06-08 08:34:15 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 2s. Last read position: chr17:82,082,606
INFO 2026-06-08 08:34:15 MarkDuplicates Tracking 146398 as yet unmatched pairs. 7176 records in RAM.
INFO 2026-06-08 08:34:17 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:10:14s. Time for last 1,000,000: 1s. Last read position: chr17:82,086,475
INFO 2026-06-08 08:34:17 MarkDuplicates Tracking 145315 as yet unmatched pairs. 6093 records in RAM.
INFO 2026-06-08 08:34:19 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:10:15s. Time for last 1,000,000: 1s. Last read position: chr17:82,092,459
INFO 2026-06-08 08:34:19 MarkDuplicates Tracking 142307 as yet unmatched pairs. 3085 records in RAM.
INFO 2026-06-08 08:34:21 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:10:17s. Time for last 1,000,000: 1s. Last read position: chr18:706,488
INFO 2026-06-08 08:34:21 MarkDuplicates Tracking 139467 as yet unmatched pairs. 6516 records in RAM.
INFO 2026-06-08 08:34:22 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:10:19s. Time for last 1,000,000: 1s. Last read position: chr18:13,621,130
INFO 2026-06-08 08:34:22 MarkDuplicates Tracking 137574 as yet unmatched pairs. 4623 records in RAM.
INFO 2026-06-08 08:34:24 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:10:20s. Time for last 1,000,000: 1s. Last read position: chr18:45,908,014
INFO 2026-06-08 08:34:24 MarkDuplicates Tracking 135896 as yet unmatched pairs. 2944 records in RAM.
INFO 2026-06-08 08:34:26 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:10:22s. Time for last 1,000,000: 1s. Last read position: chr18:62,716,644
INFO 2026-06-08 08:34:26 MarkDuplicates Tracking 134287 as yet unmatched pairs. 1331 records in RAM.
INFO 2026-06-08 08:34:28 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:10:24s. Time for last 1,000,000: 2s. Last read position: chr19:582,569
INFO 2026-06-08 08:34:28 MarkDuplicates Tracking 133124 as yet unmatched pairs. 60804 records in RAM.
INFO 2026-06-08 08:34:29 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 1s. Last read position: chr19:1,108,633
INFO 2026-06-08 08:34:29 MarkDuplicates Tracking 130473 as yet unmatched pairs. 58153 records in RAM.
INFO 2026-06-08 08:34:31 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:10:27s. Time for last 1,000,000: 1s. Last read position: chr19:1,615,415
INFO 2026-06-08 08:34:31 MarkDuplicates Tracking 128272 as yet unmatched pairs. 55952 records in RAM.
INFO 2026-06-08 08:34:33 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:10:29s. Time for last 1,000,000: 1s. Last read position: chr19:2,422,041
INFO 2026-06-08 08:34:33 MarkDuplicates Tracking 126127 as yet unmatched pairs. 53807 records in RAM.
INFO 2026-06-08 08:34:34 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:10:31s. Time for last 1,000,000: 1s. Last read position: chr19:4,054,413
INFO 2026-06-08 08:34:34 MarkDuplicates Tracking 124269 as yet unmatched pairs. 51949 records in RAM.
INFO 2026-06-08 08:34:36 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:10:33s. Time for last 1,000,000: 1s. Last read position: chr19:4,512,802
INFO 2026-06-08 08:34:36 MarkDuplicates Tracking 123703 as yet unmatched pairs. 51383 records in RAM.
INFO 2026-06-08 08:34:39 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:10:35s. Time for last 1,000,000: 2s. Last read position: chr19:5,641,900
INFO 2026-06-08 08:34:39 MarkDuplicates Tracking 120753 as yet unmatched pairs. 48433 records in RAM.
INFO 2026-06-08 08:34:41 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:10:37s. Time for last 1,000,000: 1s. Last read position: chr19:7,440,392
INFO 2026-06-08 08:34:41 MarkDuplicates Tracking 119010 as yet unmatched pairs. 46690 records in RAM.
INFO 2026-06-08 08:34:42 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:10:39s. Time for last 1,000,000: 1s. Last read position: chr19:8,812,636
INFO 2026-06-08 08:34:42 MarkDuplicates Tracking 116804 as yet unmatched pairs. 44484 records in RAM.
INFO 2026-06-08 08:34:44 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:10:40s. Time for last 1,000,000: 1s. Last read position: chr19:10,707,370
INFO 2026-06-08 08:34:44 MarkDuplicates Tracking 115170 as yet unmatched pairs. 42850 records in RAM.
INFO 2026-06-08 08:34:46 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:10:42s. Time for last 1,000,000: 1s. Last read position: chr19:11,576,832
INFO 2026-06-08 08:34:46 MarkDuplicates Tracking 113702 as yet unmatched pairs. 41382 records in RAM.
INFO 2026-06-08 08:34:47 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:10:43s. Time for last 1,000,000: 1s. Last read position: chr19:12,954,425
INFO 2026-06-08 08:34:47 MarkDuplicates Tracking 111602 as yet unmatched pairs. 39279 records in RAM.
INFO 2026-06-08 08:34:49 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:10:45s. Time for last 1,000,000: 1s. Last read position: chr19:14,571,920
INFO 2026-06-08 08:34:49 MarkDuplicates Tracking 109710 as yet unmatched pairs. 37375 records in RAM.
INFO 2026-06-08 08:34:51 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:10:47s. Time for last 1,000,000: 1s. Last read position: chr19:16,088,025
INFO 2026-06-08 08:34:51 MarkDuplicates Tracking 107772 as yet unmatched pairs. 35437 records in RAM.
INFO 2026-06-08 08:34:52 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:10:49s. Time for last 1,000,000: 1s. Last read position: chr19:17,832,591
INFO 2026-06-08 08:34:52 MarkDuplicates Tracking 105312 as yet unmatched pairs. 32975 records in RAM.
INFO 2026-06-08 08:34:54 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:10:50s. Time for last 1,000,000: 1s. Last read position: chr19:18,855,122
INFO 2026-06-08 08:34:54 MarkDuplicates Tracking 103645 as yet unmatched pairs. 31308 records in RAM.
INFO 2026-06-08 08:34:55 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:10:52s. Time for last 1,000,000: 1s. Last read position: chr19:29,942,557
INFO 2026-06-08 08:34:55 MarkDuplicates Tracking 102009 as yet unmatched pairs. 29671 records in RAM.
INFO 2026-06-08 08:34:57 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:10:53s. Time for last 1,000,000: 1s. Last read position: chr19:35,267,617
INFO 2026-06-08 08:34:57 MarkDuplicates Tracking 100255 as yet unmatched pairs. 27916 records in RAM.
INFO 2026-06-08 08:34:59 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:10:55s. Time for last 1,000,000: 1s. Last read position: chr19:38,142,640
INFO 2026-06-08 08:34:59 MarkDuplicates Tracking 97781 as yet unmatched pairs. 25438 records in RAM.
INFO 2026-06-08 08:35:00 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:10:57s. Time for last 1,000,000: 1s. Last read position: chr19:39,380,720
INFO 2026-06-08 08:35:00 MarkDuplicates Tracking 96129 as yet unmatched pairs. 23786 records in RAM.
INFO 2026-06-08 08:35:02 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 1s. Last read position: chr19:40,242,548
INFO 2026-06-08 08:35:02 MarkDuplicates Tracking 95441 as yet unmatched pairs. 23092 records in RAM.
INFO 2026-06-08 08:35:04 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:11:00s. Time for last 1,000,000: 2s. Last read position: chr19:41,320,347
INFO 2026-06-08 08:35:04 MarkDuplicates Tracking 92273 as yet unmatched pairs. 19923 records in RAM.
INFO 2026-06-08 08:35:06 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:11:03s. Time for last 1,000,000: 2s. Last read position: chr19:42,291,652
INFO 2026-06-08 08:35:06 MarkDuplicates Tracking 90641 as yet unmatched pairs. 18291 records in RAM.
INFO 2026-06-08 08:35:08 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:11:04s. Time for last 1,000,000: 1s. Last read position: chr19:44,892,834
INFO 2026-06-08 08:35:08 MarkDuplicates Tracking 88396 as yet unmatched pairs. 16045 records in RAM.
INFO 2026-06-08 08:35:10 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:11:06s. Time for last 1,000,000: 1s. Last read position: chr19:45,766,374
INFO 2026-06-08 08:35:10 MarkDuplicates Tracking 86415 as yet unmatched pairs. 14062 records in RAM.
INFO 2026-06-08 08:35:11 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:11:07s. Time for last 1,000,000: 1s. Last read position: chr19:47,694,555
INFO 2026-06-08 08:35:11 MarkDuplicates Tracking 84353 as yet unmatched pairs. 12000 records in RAM.
INFO 2026-06-08 08:35:13 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:11:09s. Time for last 1,000,000: 1s. Last read position: chr19:49,086,511
INFO 2026-06-08 08:35:13 MarkDuplicates Tracking 83245 as yet unmatched pairs. 10892 records in RAM.
INFO 2026-06-08 08:35:14 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:11:11s. Time for last 1,000,000: 1s. Last read position: chr19:49,651,446
INFO 2026-06-08 08:35:14 MarkDuplicates Tracking 80829 as yet unmatched pairs. 8476 records in RAM.
INFO 2026-06-08 08:35:16 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:11:12s. Time for last 1,000,000: 1s. Last read position: chr19:51,872,486
INFO 2026-06-08 08:35:16 MarkDuplicates Tracking 78920 as yet unmatched pairs. 6567 records in RAM.
INFO 2026-06-08 08:35:17 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:11:14s. Time for last 1,000,000: 1s. Last read position: chr19:54,207,428
INFO 2026-06-08 08:35:17 MarkDuplicates Tracking 77340 as yet unmatched pairs. 4987 records in RAM.
INFO 2026-06-08 08:35:19 MarkDuplicates Read 368,000,000 records. Elapsed time: 00:11:15s. Time for last 1,000,000: 1s. Last read position: chr19:55,579,050
INFO 2026-06-08 08:35:19 MarkDuplicates Tracking 75195 as yet unmatched pairs. 2842 records in RAM.
INFO 2026-06-08 08:35:20 MarkDuplicates Read 369,000,000 records. Elapsed time: 00:11:17s. Time for last 1,000,000: 1s. Last read position: chr19:58,084,619
INFO 2026-06-08 08:35:20 MarkDuplicates Tracking 73547 as yet unmatched pairs. 1194 records in RAM.
INFO 2026-06-08 08:35:22 MarkDuplicates Read 370,000,000 records. Elapsed time: 00:11:18s. Time for last 1,000,000: 1s. Last read position: chr20:1,922,520
INFO 2026-06-08 08:35:22 MarkDuplicates Tracking 71639 as yet unmatched pairs. 18599 records in RAM.
INFO 2026-06-08 08:35:24 MarkDuplicates Read 371,000,000 records. Elapsed time: 00:11:20s. Time for last 1,000,000: 1s. Last read position: chr20:5,943,557
INFO 2026-06-08 08:35:24 MarkDuplicates Tracking 69564 as yet unmatched pairs. 16524 records in RAM.
INFO 2026-06-08 08:35:25 MarkDuplicates Read 372,000,000 records. Elapsed time: 00:11:21s. Time for last 1,000,000: 1s. Last read position: chr20:18,535,681
INFO 2026-06-08 08:35:25 MarkDuplicates Tracking 68071 as yet unmatched pairs. 15031 records in RAM.
INFO 2026-06-08 08:35:28 MarkDuplicates Read 373,000,000 records. Elapsed time: 00:11:24s. Time for last 1,000,000: 2s. Last read position: chr20:25,504,989
INFO 2026-06-08 08:35:28 MarkDuplicates Tracking 66300 as yet unmatched pairs. 13260 records in RAM.
INFO 2026-06-08 08:35:29 MarkDuplicates Read 374,000,000 records. Elapsed time: 00:11:26s. Time for last 1,000,000: 1s. Last read position: chr20:34,926,133
INFO 2026-06-08 08:35:29 MarkDuplicates Tracking 64742 as yet unmatched pairs. 11702 records in RAM.
INFO 2026-06-08 08:35:31 MarkDuplicates Read 375,000,000 records. Elapsed time: 00:11:27s. Time for last 1,000,000: 1s. Last read position: chr20:37,199,209
INFO 2026-06-08 08:35:31 MarkDuplicates Tracking 63137 as yet unmatched pairs. 10097 records in RAM.
INFO 2026-06-08 08:35:32 MarkDuplicates Read 376,000,000 records. Elapsed time: 00:11:29s. Time for last 1,000,000: 1s. Last read position: chr20:44,116,189
INFO 2026-06-08 08:35:32 MarkDuplicates Tracking 61102 as yet unmatched pairs. 8061 records in RAM.
INFO 2026-06-08 08:35:34 MarkDuplicates Read 377,000,000 records. Elapsed time: 00:11:30s. Time for last 1,000,000: 1s. Last read position: chr20:47,652,961
INFO 2026-06-08 08:35:34 MarkDuplicates Tracking 59595 as yet unmatched pairs. 6554 records in RAM.
INFO 2026-06-08 08:35:36 MarkDuplicates Read 378,000,000 records. Elapsed time: 00:11:32s. Time for last 1,000,000: 1s. Last read position: chr20:57,611,791
INFO 2026-06-08 08:35:36 MarkDuplicates Tracking 57683 as yet unmatched pairs. 4634 records in RAM.
INFO 2026-06-08 08:35:37 MarkDuplicates Read 379,000,000 records. Elapsed time: 00:11:33s. Time for last 1,000,000: 1s. Last read position: chr20:62,328,372
INFO 2026-06-08 08:35:37 MarkDuplicates Tracking 55942 as yet unmatched pairs. 2893 records in RAM.
INFO 2026-06-08 08:35:39 MarkDuplicates Read 380,000,000 records. Elapsed time: 00:11:35s. Time for last 1,000,000: 1s. Last read position: chr20:63,742,595
INFO 2026-06-08 08:35:39 MarkDuplicates Tracking 54206 as yet unmatched pairs. 1157 records in RAM.
INFO 2026-06-08 08:35:40 MarkDuplicates Read 381,000,000 records. Elapsed time: 00:11:36s. Time for last 1,000,000: 1s. Last read position: chr21:8,258,958
INFO 2026-06-08 08:35:40 MarkDuplicates Tracking 52331 as yet unmatched pairs. 9271 records in RAM.
INFO 2026-06-08 08:35:41 MarkDuplicates Read 382,000,000 records. Elapsed time: 00:11:38s. Time for last 1,000,000: 1s. Last read position: chr21:25,955,635
INFO 2026-06-08 08:35:41 MarkDuplicates Tracking 51450 as yet unmatched pairs. 8389 records in RAM.
INFO 2026-06-08 08:35:43 MarkDuplicates Read 383,000,000 records. Elapsed time: 00:11:39s. Time for last 1,000,000: 1s. Last read position: chr21:33,553,118
INFO 2026-06-08 08:35:43 MarkDuplicates Tracking 49722 as yet unmatched pairs. 6661 records in RAM.
INFO 2026-06-08 08:35:44 MarkDuplicates Read 384,000,000 records. Elapsed time: 00:11:41s. Time for last 1,000,000: 1s. Last read position: chr21:39,180,433
INFO 2026-06-08 08:35:44 MarkDuplicates Tracking 47819 as yet unmatched pairs. 4758 records in RAM.
INFO 2026-06-08 08:35:46 MarkDuplicates Read 385,000,000 records. Elapsed time: 00:11:42s. Time for last 1,000,000: 1s. Last read position: chr21:44,240,825
INFO 2026-06-08 08:35:46 MarkDuplicates Tracking 46115 as yet unmatched pairs. 3054 records in RAM.
INFO 2026-06-08 08:35:47 MarkDuplicates Read 386,000,000 records. Elapsed time: 00:11:44s. Time for last 1,000,000: 1s. Last read position: chr21:46,125,295
INFO 2026-06-08 08:35:47 MarkDuplicates Tracking 44313 as yet unmatched pairs. 1252 records in RAM.
INFO 2026-06-08 08:35:49 MarkDuplicates Read 387,000,000 records. Elapsed time: 00:11:46s. Time for last 1,000,000: 1s. Last read position: chr22:19,029,570
INFO 2026-06-08 08:35:49 MarkDuplicates Tracking 42358 as yet unmatched pairs. 22509 records in RAM.
INFO 2026-06-08 08:35:51 MarkDuplicates Read 388,000,000 records. Elapsed time: 00:11:47s. Time for last 1,000,000: 1s. Last read position: chr22:21,208,201
INFO 2026-06-08 08:35:51 MarkDuplicates Tracking 40440 as yet unmatched pairs. 20591 records in RAM.
INFO 2026-06-08 08:35:52 MarkDuplicates Read 389,000,000 records. Elapsed time: 00:11:49s. Time for last 1,000,000: 1s. Last read position: chr22:23,790,793
INFO 2026-06-08 08:35:52 MarkDuplicates Tracking 38833 as yet unmatched pairs. 18984 records in RAM.
INFO 2026-06-08 08:35:54 MarkDuplicates Read 390,000,000 records. Elapsed time: 00:11:50s. Time for last 1,000,000: 1s. Last read position: chr22:24,627,906
INFO 2026-06-08 08:35:54 MarkDuplicates Tracking 39637 as yet unmatched pairs. 19788 records in RAM.
INFO 2026-06-08 08:35:57 MarkDuplicates Read 391,000,000 records. Elapsed time: 00:11:53s. Time for last 1,000,000: 2s. Last read position: chr22:29,287,020
INFO 2026-06-08 08:35:57 MarkDuplicates Tracking 36378 as yet unmatched pairs. 16529 records in RAM.
INFO 2026-06-08 08:35:59 MarkDuplicates Read 392,000,000 records. Elapsed time: 00:11:55s. Time for last 1,000,000: 1s. Last read position: chr22:31,088,026
INFO 2026-06-08 08:35:59 MarkDuplicates Tracking 33918 as yet unmatched pairs. 14069 records in RAM.
INFO 2026-06-08 08:36:00 MarkDuplicates Read 393,000,000 records. Elapsed time: 00:11:57s. Time for last 1,000,000: 1s. Last read position: chr22:36,312,117
INFO 2026-06-08 08:36:00 MarkDuplicates Tracking 32265 as yet unmatched pairs. 12416 records in RAM.
INFO 2026-06-08 08:36:02 MarkDuplicates Read 394,000,000 records. Elapsed time: 00:11:58s. Time for last 1,000,000: 1s. Last read position: chr22:38,486,410
INFO 2026-06-08 08:36:02 MarkDuplicates Tracking 30131 as yet unmatched pairs. 10281 records in RAM.
INFO 2026-06-08 08:36:04 MarkDuplicates Read 395,000,000 records. Elapsed time: 00:12:00s. Time for last 1,000,000: 1s. Last read position: chr22:40,744,111
INFO 2026-06-08 08:36:04 MarkDuplicates Tracking 28314 as yet unmatched pairs. 8464 records in RAM.
INFO 2026-06-08 08:36:05 MarkDuplicates Read 396,000,000 records. Elapsed time: 00:12:02s. Time for last 1,000,000: 1s. Last read position: chr22:42,501,672
INFO 2026-06-08 08:36:05 MarkDuplicates Tracking 28583 as yet unmatched pairs. 8733 records in RAM.
INFO 2026-06-08 08:36:07 MarkDuplicates Read 397,000,000 records. Elapsed time: 00:12:03s. Time for last 1,000,000: 1s. Last read position: chr22:42,619,849
INFO 2026-06-08 08:36:07 MarkDuplicates Tracking 25867 as yet unmatched pairs. 6017 records in RAM.
INFO 2026-06-08 08:36:09 MarkDuplicates Read 398,000,000 records. Elapsed time: 00:12:05s. Time for last 1,000,000: 1s. Last read position: chr22:49,920,169
INFO 2026-06-08 08:36:09 MarkDuplicates Tracking 23276 as yet unmatched pairs. 3426 records in RAM.
INFO 2026-06-08 08:36:10 MarkDuplicates Read 399,000,000 records. Elapsed time: 00:12:07s. Time for last 1,000,000: 1s. Last read position: chr22:50,465,036
INFO 2026-06-08 08:36:10 MarkDuplicates Tracking 21350 as yet unmatched pairs. 1500 records in RAM.
INFO 2026-06-08 08:36:12 MarkDuplicates Read 400,000,000 records. Elapsed time: 00:12:08s. Time for last 1,000,000: 1s. Last read position: chrX:2,917,827
INFO 2026-06-08 08:36:12 MarkDuplicates Tracking 19158 as yet unmatched pairs. 16477 records in RAM.
INFO 2026-06-08 08:36:14 MarkDuplicates Read 401,000,000 records. Elapsed time: 00:12:10s. Time for last 1,000,000: 1s. Last read position: chrX:23,837,237
INFO 2026-06-08 08:36:14 MarkDuplicates Tracking 17513 as yet unmatched pairs. 14825 records in RAM.
INFO 2026-06-08 08:36:16 MarkDuplicates Read 402,000,000 records. Elapsed time: 00:12:12s. Time for last 1,000,000: 2s. Last read position: chrX:46,679,678
INFO 2026-06-08 08:36:16 MarkDuplicates Tracking 16103 as yet unmatched pairs. 13415 records in RAM.
INFO 2026-06-08 08:36:18 MarkDuplicates Read 403,000,000 records. Elapsed time: 00:12:14s. Time for last 1,000,000: 2s. Last read position: chrX:49,173,172
INFO 2026-06-08 08:36:18 MarkDuplicates Tracking 14264 as yet unmatched pairs. 11576 records in RAM.
INFO 2026-06-08 08:36:20 MarkDuplicates Read 404,000,000 records. Elapsed time: 00:12:16s. Time for last 1,000,000: 1s. Last read position: chrX:54,444,562
INFO 2026-06-08 08:36:20 MarkDuplicates Tracking 12549 as yet unmatched pairs. 9861 records in RAM.
INFO 2026-06-08 08:36:21 MarkDuplicates Read 405,000,000 records. Elapsed time: 00:12:17s. Time for last 1,000,000: 1s. Last read position: chrX:71,382,836
INFO 2026-06-08 08:36:21 MarkDuplicates Tracking 11042 as yet unmatched pairs. 8354 records in RAM.
INFO 2026-06-08 08:36:23 MarkDuplicates Read 406,000,000 records. Elapsed time: 00:12:19s. Time for last 1,000,000: 1s. Last read position: chrX:101,395,335
INFO 2026-06-08 08:36:23 MarkDuplicates Tracking 9729 as yet unmatched pairs. 7041 records in RAM.
INFO 2026-06-08 08:36:24 MarkDuplicates Read 407,000,000 records. Elapsed time: 00:12:20s. Time for last 1,000,000: 1s. Last read position: chrX:119,663,615
INFO 2026-06-08 08:36:24 MarkDuplicates Tracking 8162 as yet unmatched pairs. 5474 records in RAM.
INFO 2026-06-08 08:36:26 MarkDuplicates Read 408,000,000 records. Elapsed time: 00:12:22s. Time for last 1,000,000: 1s. Last read position: chrX:150,232,178
INFO 2026-06-08 08:36:26 MarkDuplicates Tracking 6598 as yet unmatched pairs. 3910 records in RAM.
INFO 2026-06-08 08:36:27 MarkDuplicates Read 409,000,000 records. Elapsed time: 00:12:24s. Time for last 1,000,000: 1s. Last read position: chrX:154,019,509
INFO 2026-06-08 08:36:27 MarkDuplicates Tracking 5987 as yet unmatched pairs. 3299 records in RAM.
INFO 2026-06-08 08:36:29 MarkDuplicates Read 410,000,000 records. Elapsed time: 00:12:25s. Time for last 1,000,000: 1s. Last read position: chrX:154,558,500
INFO 2026-06-08 08:36:29 MarkDuplicates Tracking 2969 as yet unmatched pairs. 281 records in RAM.
INFO 2026-06-08 08:36:30 MarkDuplicates Read 411,000,000 records. Elapsed time: 00:12:27s. Time for last 1,000,000: 1s. Last read position: GL000220.1:160,614
INFO 2026-06-08 08:36:30 MarkDuplicates Tracking 1562 as yet unmatched pairs. 0 records in RAM.
INFO 2026-06-08 08:36:31 MarkDuplicates Read 412,000,000 records. Elapsed time: 00:12:28s. Time for last 1,000,000: 1s. Last read position: KI270734.1:156,331
INFO 2026-06-08 08:36:31 MarkDuplicates Tracking 12 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 08:36:31 MarkDuplicates Read 412013281 records. 0 pairs never matched.
INFO 2026-06-08 08:37:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 36287937816; totalMemory: 51808043008; maxMemory: 63585648640
INFO 2026-06-08 08:37:18 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:37:36 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:37:55 OpticalDuplicateFinder Large duplicate set. size = 1206
INFO 2026-06-08 08:37:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,098
INFO 2026-06-08 08:37:55 OpticalDuplicateFinder Large duplicate set. size = 1172
INFO 2026-06-08 08:37:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,327
INFO 2026-06-08 08:37:55 OpticalDuplicateFinder Large duplicate set. size = 1168
INFO 2026-06-08 08:37:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,482
INFO 2026-06-08 08:38:39 MarkDuplicates Traversing fragment information and detecting duplicates.
WARNING 2026-06-08 08:38:39 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
INFO 2026-06-08 08:39:15 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:39:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 204692824; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:39:16 MarkDuplicates Marking 279413443 records as duplicates.
INFO 2026-06-08 08:39:16 MarkDuplicates Found 8072843 optical duplicate clusters.
INFO 2026-06-08 08:39:16 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 08:39:33 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:17s. Time for last 10,000,000: 17s. Last read position: chr1:37,885,667
INFO 2026-06-08 08:39:48 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:32s. Time for last 10,000,000: 15s. Last read position: chr1:119,929,025
INFO 2026-06-08 08:40:04 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:47s. Time for last 10,000,000: 15s. Last read position: chr1:169,106,800
INFO 2026-06-08 08:40:19 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:03s. Time for last 10,000,000: 15s. Last read position: chr2:28,793,875
INFO 2026-06-08 08:40:34 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:18s. Time for last 10,000,000: 15s. Last read position: chr2:108,258,967
INFO 2026-06-08 08:40:50 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:33s. Time for last 10,000,000: 15s. Last read position: chr2:216,119,052
INFO 2026-06-08 08:41:05 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:01:48s. Time for last 10,000,000: 14s. Last read position: chr3:48,440,619
INFO 2026-06-08 08:41:20 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:03s. Time for last 10,000,000: 15s. Last read position: chr3:155,147,206
INFO 2026-06-08 08:41:35 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:18s. Time for last 10,000,000: 14s. Last read position: chr4:77,055,332
INFO 2026-06-08 08:41:50 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:33s. Time for last 10,000,000: 15s. Last read position: chr5:72,893,157
INFO 2026-06-08 08:42:04 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:02:48s. Time for last 10,000,000: 14s. Last read position: chr5:170,106,127
INFO 2026-06-08 08:42:19 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:03s. Time for last 10,000,000: 14s. Last read position: chr6:31,983,917
INFO 2026-06-08 08:42:35 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:18s. Time for last 10,000,000: 15s. Last read position: chr6:130,869,755
INFO 2026-06-08 08:42:50 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:03:33s. Time for last 10,000,000: 14s. Last read position: chr7:65,967,758
INFO 2026-06-08 08:43:05 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:03:48s. Time for last 10,000,000: 14s. Last read position: chr7:127,703,232
INFO 2026-06-08 08:43:19 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:03s. Time for last 10,000,000: 14s. Last read position: chr8:29,337,255
INFO 2026-06-08 08:43:34 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:04:18s. Time for last 10,000,000: 14s. Last read position: chr8:143,860,633
INFO 2026-06-08 08:43:49 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:04:33s. Time for last 10,000,000: 15s. Last read position: chr9:83,971,684
INFO 2026-06-08 08:44:04 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:04:48s. Time for last 10,000,000: 14s. Last read position: chr10:1,015,602
INFO 2026-06-08 08:44:20 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:05:04s. Time for last 10,000,000: 16s. Last read position: chr10:104,315,950
INFO 2026-06-08 08:44:35 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:05:19s. Time for last 10,000,000: 14s. Last read position: chr11:47,259,939
INFO 2026-06-08 08:44:50 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:05:34s. Time for last 10,000,000: 14s. Last read position: chr11:67,435,863
INFO 2026-06-08 08:45:05 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:05:48s. Time for last 10,000,000: 14s. Last read position: chr12:6,354,801
INFO 2026-06-08 08:45:19 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:06:03s. Time for last 10,000,000: 14s. Last read position: chr12:57,094,688
INFO 2026-06-08 08:45:34 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:06:18s. Time for last 10,000,000: 14s. Last read position: chr12:132,583,148
INFO 2026-06-08 08:45:49 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:06:33s. Time for last 10,000,000: 14s. Last read position: chr14:54,436,369
INFO 2026-06-08 08:46:03 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:06:47s. Time for last 10,000,000: 14s. Last read position: chr15:41,055,268
INFO 2026-06-08 08:46:18 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:07:02s. Time for last 10,000,000: 14s. Last read position: chr16:18,703
INFO 2026-06-08 08:46:33 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:07:17s. Time for last 10,000,000: 14s. Last read position: chr16:21,599,782
INFO 2026-06-08 08:46:48 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:07:32s. Time for last 10,000,000: 14s. Last read position: chr16:70,024,640
INFO 2026-06-08 08:47:03 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:07:47s. Time for last 10,000,000: 14s. Last read position: chr17:28,881,991
INFO 2026-06-08 08:47:19 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:08:02s. Time for last 10,000,000: 15s. Last read position: chr17:50,193,012
INFO 2026-06-08 08:47:34 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:08:17s. Time for last 10,000,000: 14s. Last read position: chr17:81,934,674
INFO 2026-06-08 08:47:50 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:08:33s. Time for last 10,000,000: 16s. Last read position: chr19:1,615,415
INFO 2026-06-08 08:48:06 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:08:49s. Time for last 10,000,000: 15s. Last read position: chr19:14,571,920
INFO 2026-06-08 08:48:20 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:09:04s. Time for last 10,000,000: 14s. Last read position: chr19:42,291,652
INFO 2026-06-08 08:48:35 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:09:19s. Time for last 10,000,000: 14s. Last read position: chr20:1,922,520
INFO 2026-06-08 08:48:50 MarkDuplicates Written 380,000,000 records. Elapsed time: 00:09:34s. Time for last 10,000,000: 15s. Last read position: chr20:63,742,595
INFO 2026-06-08 08:49:09 MarkDuplicates Written 390,000,000 records. Elapsed time: 00:09:53s. Time for last 10,000,000: 19s. Last read position: chr22:24,627,906
INFO 2026-06-08 08:49:25 MarkDuplicates Written 400,000,000 records. Elapsed time: 00:10:08s. Time for last 10,000,000: 15s. Last read position: chrX:2,917,827
INFO 2026-06-08 08:49:40 MarkDuplicates Written 410,000,000 records. Elapsed time: 00:10:23s. Time for last 10,000,000: 14s. Last read position: chrX:154,558,500
INFO 2026-06-08 08:49:47 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:49:47 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:49:47 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:49:47 MarkDuplicates Before output close freeMemory: 204664424; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:49:47 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:49:47 MarkDuplicates After output close freeMemory: 104904488; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 08:49:47 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 25.76 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory