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/4d/91986d84b1142f4ae418d03cf896f8/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/91986d84b1142f4ae418d03cf896f8/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/60742acd8016a21773b54e1e7902a4/aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai ==> STAGING COMPLETE (5 inputs) Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bam --METRICS_FILE aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT 20:40:45.452 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 [Wed Jun 03 20:40:45 GMT 2026] MarkDuplicates --INPUT aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-2e5fe9-R1_A23YTGFLT4_1.md.bam --METRICS_FILE aih-tih-sc-2e5fe9-R1_A23YTGFLT4_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 --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 [Wed Jun 03 20:40:45 GMT 2026] Executing as ?@nf-4d91986d84b1142f4ae418d03cf896f8-57c1f-rttdx 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 2026-06-03 20:40:45 MarkDuplicates Start of doWork freeMemory: 105829160; totalMemory: 134217728; maxMemory: 63585648640 INFO 2026-06-03 20:40:45 MarkDuplicates Reading input file and constructing read end information. INFO 2026-06-03 20:40:45 MarkDuplicates Will retain up to 230382784 data points before spilling to disk. INFO 2026-06-03 20:40:49 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:1,204,151 INFO 2026-06-03 20:40:49 MarkDuplicates Tracking 2873 as yet unmatched pairs. 258 records in RAM. INFO 2026-06-03 20:40:51 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 2s. Last read position: chr1:1,752,909 INFO 2026-06-03 20:40:51 MarkDuplicates Tracking 5561 as yet unmatched pairs. 324 records in RAM. INFO 2026-06-03 20:40:53 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: chr1:6,254,605 INFO 2026-06-03 20:40:53 MarkDuplicates Tracking 8265 as yet unmatched pairs. 389 records in RAM. INFO 2026-06-03 20:40:55 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: chr1:8,861,374 INFO 2026-06-03 20:40:55 MarkDuplicates Tracking 14339 as yet unmatched pairs. 4069 records in RAM. INFO 2026-06-03 20:40:57 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: chr1:10,272,295 INFO 2026-06-03 20:40:57 MarkDuplicates Tracking 12705 as yet unmatched pairs. 339 records in RAM. INFO 2026-06-03 20:40:59 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: chr1:11,949,838 INFO 2026-06-03 20:40:59 MarkDuplicates Tracking 15178 as yet unmatched pairs. 742 records in RAM. INFO 2026-06-03 20:41:01 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: chr1:15,774,639 INFO 2026-06-03 20:41:01 MarkDuplicates Tracking 18287 as yet unmatched pairs. 1864 records in RAM. INFO 2026-06-03 20:41:03 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr1:16,938,958 INFO 2026-06-03 20:41:03 MarkDuplicates Tracking 18747 as yet unmatched pairs. 434 records in RAM. INFO 2026-06-03 20:41:05 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 2s. Last read position: chr1:19,199,653 INFO 2026-06-03 20:41:05 MarkDuplicates Tracking 21379 as yet unmatched pairs. 738 records in RAM. INFO 2026-06-03 20:41:07 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: chr1:21,751,601 INFO 2026-06-03 20:41:07 MarkDuplicates Tracking 22876 as yet unmatched pairs. 431 records in RAM. INFO 2026-06-03 20:41:09 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 2s. Last read position: chr1:21,876,348 INFO 2026-06-03 20:41:09 MarkDuplicates Tracking 26240 as yet unmatched pairs. 1408 records in RAM. INFO 2026-06-03 20:41:11 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 2s. Last read position: chr1:23,692,626 INFO 2026-06-03 20:41:11 MarkDuplicates Tracking 32350 as yet unmatched pairs. 5477 records in RAM. INFO 2026-06-03 20:41:13 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 1s. Last read position: chr1:25,984,016 INFO 2026-06-03 20:41:13 MarkDuplicates Tracking 28985 as yet unmatched pairs. 287 records in RAM. INFO 2026-06-03 20:41:14 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 1s. Last read position: chr1:26,863,295 INFO 2026-06-03 20:41:14 MarkDuplicates Tracking 33864 as yet unmatched pairs. 3203 records in RAM. INFO 2026-06-03 20:41:16 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 1s. Last read position: chr1:27,549,014 INFO 2026-06-03 20:41:16 MarkDuplicates Tracking 33312 as yet unmatched pairs. 620 records in RAM. INFO 2026-06-03 20:41:18 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 1s. Last read position: chr1:30,966,176 INFO 2026-06-03 20:41:18 MarkDuplicates Tracking 35679 as yet unmatched pairs. 1099 records in RAM. INFO 2026-06-03 20:41:20 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 1s. Last read position: chr1:32,224,475 INFO 2026-06-03 20:41:20 MarkDuplicates Tracking 38623 as yet unmatched pairs. 1885 records in RAM. INFO 2026-06-03 20:41:21 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 1s. Last read position: chr1:33,328,887 INFO 2026-06-03 20:41:21 MarkDuplicates Tracking 39666 as yet unmatched pairs. 783 records in RAM. INFO 2026-06-03 20:41:24 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 3s. Last read position: chr1:36,282,630 INFO 2026-06-03 20:41:24 MarkDuplicates Tracking 41913 as yet unmatched pairs. 972 records in RAM. INFO 2026-06-03 20:41:27 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 2s. Last read position: chr1:39,353,065 INFO 2026-06-03 20:41:27 MarkDuplicates Tracking 44053 as yet unmatched pairs. 1244 records in RAM. INFO 2026-06-03 20:41:28 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 1s. Last read position: chr1:40,311,135 INFO 2026-06-03 20:41:28 MarkDuplicates Tracking 45634 as yet unmatched pairs. 1014 records in RAM. INFO 2026-06-03 20:41:30 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 1s. Last read position: chr1:42,929,285 INFO 2026-06-03 20:41:30 MarkDuplicates Tracking 62686 as yet unmatched pairs. 15990 records in RAM. INFO 2026-06-03 20:41:32 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 1s. Last read position: chr1:43,438,997 INFO 2026-06-03 20:41:32 MarkDuplicates Tracking 49420 as yet unmatched pairs. 337 records in RAM. INFO 2026-06-03 20:41:34 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 1s. Last read position: chr1:44,220,245 INFO 2026-06-03 20:41:34 MarkDuplicates Tracking 51654 as yet unmatched pairs. 264 records in RAM. INFO 2026-06-03 20:41:35 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 1s. Last read position: chr1:46,281,283 INFO 2026-06-03 20:41:35 MarkDuplicates Tracking 54113 as yet unmatched pairs. 898 records in RAM. INFO 2026-06-03 20:41:37 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 1s. Last read position: chr1:52,606,643 INFO 2026-06-03 20:41:37 MarkDuplicates Tracking 55555 as yet unmatched pairs. 375 records in RAM. INFO 2026-06-03 20:41:38 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 1s. Last read position: chr1:58,576,270 INFO 2026-06-03 20:41:38 MarkDuplicates Tracking 70295 as yet unmatched pairs. 13000 records in RAM. INFO 2026-06-03 20:41:40 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 1s. Last read position: chr1:62,444,986 INFO 2026-06-03 20:41:40 MarkDuplicates Tracking 60524 as yet unmatched pairs. 460 records in RAM. INFO 2026-06-03 20:41:42 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 1s. Last read position: chr1:77,154,513 INFO 2026-06-03 20:41:42 MarkDuplicates Tracking 62115 as yet unmatched pairs. 380 records in RAM. INFO 2026-06-03 20:41:43 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 1s. Last read position: chr1:86,577,902 INFO 2026-06-03 20:41:43 MarkDuplicates Tracking 67322 as yet unmatched pairs. 4110 records in RAM. INFO 2026-06-03 20:41:45 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 1s. Last read position: chr1:89,933,335 INFO 2026-06-03 20:41:45 MarkDuplicates Tracking 65294 as yet unmatched pairs. 481 records in RAM. INFO 2026-06-03 20:41:47 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 1s. Last read position: chr1:99,916,481 INFO 2026-06-03 20:41:47 MarkDuplicates Tracking 66744 as yet unmatched pairs. 297 records in RAM. INFO 2026-06-03 20:41:48 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 1s. Last read position: chr1:109,272,858 INFO 2026-06-03 20:41:48 MarkDuplicates Tracking 68883 as yet unmatched pairs. 609 records in RAM. INFO 2026-06-03 20:41:50 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 1s. Last read position: chr1:112,523,782 INFO 2026-06-03 20:41:50 MarkDuplicates Tracking 70249 as yet unmatched pairs. 197 records in RAM. INFO 2026-06-03 20:41:52 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 1s. Last read position: chr1:114,510,918 INFO 2026-06-03 20:41:52 MarkDuplicates Tracking 72546 as yet unmatched pairs. 707 records in RAM. INFO 2026-06-03 20:41:53 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 1s. Last read position: chr1:116,944,677 INFO 2026-06-03 20:41:53 MarkDuplicates Tracking 75760 as yet unmatched pairs. 2217 records in RAM. INFO 2026-06-03 20:41:55 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 1s. Last read position: chr1:119,963,661 INFO 2026-06-03 20:41:55 MarkDuplicates Tracking 78485 as yet unmatched pairs. 3092 records in RAM. INFO 2026-06-03 20:41:56 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 1s. Last read position: chr1:145,926,124 INFO 2026-06-03 20:41:56 MarkDuplicates Tracking 77218 as yet unmatched pairs. 624 records in RAM. INFO 2026-06-03 20:41:57 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 1s. Last read position: chr1:148,554,350 INFO 2026-06-03 20:41:57 MarkDuplicates Tracking 77606 as yet unmatched pairs. 286 records in RAM. INFO 2026-06-03 20:41:59 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 1s. Last read position: chr1:149,840,814 INFO 2026-06-03 20:41:59 MarkDuplicates Tracking 88050 as yet unmatched pairs. 9637 records in RAM. INFO 2026-06-03 20:42:01 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 2s. Last read position: chr1:150,266,611 INFO 2026-06-03 20:42:01 MarkDuplicates Tracking 80937 as yet unmatched pairs. 1326 records in RAM. INFO 2026-06-03 20:42:04 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 2s. Last read position: chr1:151,234,315 INFO 2026-06-03 20:42:04 MarkDuplicates Tracking 81660 as yet unmatched pairs. 300 records in RAM. INFO 2026-06-03 20:42:05 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 1s. Last read position: chr1:152,910,661 INFO 2026-06-03 20:42:05 MarkDuplicates Tracking 84626 as yet unmatched pairs. 1517 records in RAM. INFO 2026-06-03 20:42:07 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 1s. Last read position: chr1:153,056,370 INFO 2026-06-03 20:42:07 MarkDuplicates Tracking 94444 as yet unmatched pairs. 9904 records in RAM. INFO 2026-06-03 20:42:08 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 1s. Last read position: chr1:153,358,289 INFO 2026-06-03 20:42:08 MarkDuplicates Tracking 144488 as yet unmatched pairs. 59037 records in RAM. INFO 2026-06-03 20:42:10 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 1s. Last read position: chr1:153,390,128 INFO 2026-06-03 20:42:10 MarkDuplicates Tracking 118013 as yet unmatched pairs. 30873 records in RAM. INFO 2026-06-03 20:42:12 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 1s. Last read position: chr1:153,936,090 INFO 2026-06-03 20:42:12 MarkDuplicates Tracking 89473 as yet unmatched pairs. 609 records in RAM. INFO 2026-06-03 20:42:13 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 1s. Last read position: chr1:154,275,153 INFO 2026-06-03 20:42:13 MarkDuplicates Tracking 91484 as yet unmatched pairs. 907 records in RAM. INFO 2026-06-03 20:42:15 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 1s. Last read position: chr1:155,062,280 INFO 2026-06-03 20:42:15 MarkDuplicates Tracking 94863 as yet unmatched pairs. 2215 records in RAM. INFO 2026-06-03 20:42:18 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 2s. Last read position: chr1:155,747,613 INFO 2026-06-03 20:42:18 MarkDuplicates Tracking 94689 as yet unmatched pairs. 304 records in RAM. INFO 2026-06-03 20:42:20 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 2s. Last read position: chr1:156,259,055 INFO 2026-06-03 20:42:20 MarkDuplicates Tracking 97223 as yet unmatched pairs. 646 records in RAM. INFO 2026-06-03 20:42:22 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 2s. Last read position: chr1:159,015,949 INFO 2026-06-03 20:42:22 MarkDuplicates Tracking 100758 as yet unmatched pairs. 2341 records in RAM. INFO 2026-06-03 20:42:24 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 1s. Last read position: chr1:160,999,721 INFO 2026-06-03 20:42:24 MarkDuplicates Tracking 102526 as yet unmatched pairs. 2184 records in RAM. INFO 2026-06-03 20:42:26 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 2s. Last read position: chr1:162,500,155 INFO 2026-06-03 20:42:26 MarkDuplicates Tracking 102634 as yet unmatched pairs. 421 records in RAM. INFO 2026-06-03 20:42:28 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 2s. Last read position: chr1:169,130,070 INFO 2026-06-03 20:42:28 MarkDuplicates Tracking 112345 as yet unmatched pairs. 8351 records in RAM. INFO 2026-06-03 20:42:30 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 1s. Last read position: chr1:173,485,380 INFO 2026-06-03 20:42:30 MarkDuplicates Tracking 106802 as yet unmatched pairs. 1247 records in RAM. INFO 2026-06-03 20:42:31 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 1s. Last read position: chr1:181,089,616 INFO 2026-06-03 20:42:31 MarkDuplicates Tracking 107950 as yet unmatched pairs. 417 records in RAM. INFO 2026-06-03 20:42:33 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 1s. Last read position: chr1:183,566,960 INFO 2026-06-03 20:42:33 MarkDuplicates Tracking 109823 as yet unmatched pairs. 293 records in RAM. INFO 2026-06-03 20:42:35 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 1s. Last read position: chr1:195,142,443 INFO 2026-06-03 20:42:35 MarkDuplicates Tracking 111185 as yet unmatched pairs. 51 records in RAM. INFO 2026-06-03 20:42:37 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 1s. Last read position: chr1:201,386,829 INFO 2026-06-03 20:42:37 MarkDuplicates Tracking 114579 as yet unmatched pairs. 1573 records in RAM. INFO 2026-06-03 20:42:38 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 1s. Last read position: chr1:203,007,412 INFO 2026-06-03 20:42:38 MarkDuplicates Tracking 115422 as yet unmatched pairs. 425 records in RAM. INFO 2026-06-03 20:42:40 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 1s. Last read position: chr1:206,477,779 INFO 2026-06-03 20:42:40 MarkDuplicates Tracking 116820 as yet unmatched pairs. 246 records in RAM. INFO 2026-06-03 20:42:41 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 1s. Last read position: chr1:209,627,456 INFO 2026-06-03 20:42:41 MarkDuplicates Tracking 121231 as yet unmatched pairs. 2607 records in RAM. INFO 2026-06-03 20:42:43 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 1s. Last read position: chr1:219,978,641 INFO 2026-06-03 20:42:43 MarkDuplicates Tracking 120920 as yet unmatched pairs. 361 records in RAM. INFO 2026-06-03 20:42:45 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 1s. Last read position: chr1:225,411,377 INFO 2026-06-03 20:42:45 MarkDuplicates Tracking 122734 as yet unmatched pairs. 430 records in RAM. INFO 2026-06-03 20:42:46 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 1s. Last read position: chr1:228,279,216 INFO 2026-06-03 20:42:46 MarkDuplicates Tracking 124594 as yet unmatched pairs. 306 records in RAM. INFO 2026-06-03 20:42:48 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 1s. Last read position: chr1:234,607,143 INFO 2026-06-03 20:42:48 MarkDuplicates Tracking 128086 as yet unmatched pairs. 1430 records in RAM. INFO 2026-06-03 20:42:49 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 1s. Last read position: chr1:244,856,839 INFO 2026-06-03 20:42:49 MarkDuplicates Tracking 130506 as yet unmatched pairs. 1912 records in RAM. INFO 2026-06-03 20:42:52 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 2s. Last read position: chr2:6,851,577 INFO 2026-06-03 20:42:52 MarkDuplicates Tracking 130835 as yet unmatched pairs. 126942 records in RAM. INFO 2026-06-03 20:42:54 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 1s. Last read position: chr2:10,797,130 INFO 2026-06-03 20:42:54 MarkDuplicates Tracking 134745 as yet unmatched pairs. 130776 records in RAM. INFO 2026-06-03 20:42:56 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 2s. Last read position: chr2:20,202,920 INFO 2026-06-03 20:42:56 MarkDuplicates Tracking 147432 as yet unmatched pairs. 143396 records in RAM. INFO 2026-06-03 20:42:58 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 1s. Last read position: chr2:20,205,383 INFO 2026-06-03 20:42:58 MarkDuplicates Tracking 158541 as yet unmatched pairs. 154471 records in RAM. INFO 2026-06-03 20:43:00 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 1s. Last read position: chr2:26,034,619 INFO 2026-06-03 20:43:00 MarkDuplicates Tracking 140064 as yet unmatched pairs. 135930 records in RAM. INFO 2026-06-03 20:43:01 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 1s. Last read position: chr2:27,576,337 INFO 2026-06-03 20:43:01 MarkDuplicates Tracking 140438 as yet unmatched pairs. 136256 records in RAM. INFO 2026-06-03 20:43:03 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 1s. Last read position: chr2:30,958,431 INFO 2026-06-03 20:43:03 MarkDuplicates Tracking 143133 as yet unmatched pairs. 138896 records in RAM. INFO 2026-06-03 20:43:05 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,257 INFO 2026-06-03 20:43:05 MarkDuplicates Tracking 207585 as yet unmatched pairs. 133687 records in RAM. INFO 2026-06-03 20:43:07 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,264 INFO 2026-06-03 20:43:07 MarkDuplicates Tracking 500205 as yet unmatched pairs. 108876 records in RAM. INFO 2026-06-03 20:43:09 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,406 INFO 2026-06-03 20:43:09 MarkDuplicates Tracking 956057 as yet unmatched pairs. 70176 records in RAM. INFO 2026-06-03 20:43:11 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,407 INFO 2026-06-03 20:43:11 MarkDuplicates Tracking 964909 as yet unmatched pairs. 69524 records in RAM. INFO 2026-06-03 20:43:13 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 2s. Last read position: chr2:38,568,161 INFO 2026-06-03 20:43:13 MarkDuplicates Tracking 1024796 as yet unmatched pairs. 63822 records in RAM. INFO 2026-06-03 20:43:15 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 2s. Last read position: chr2:43,947,331 INFO 2026-06-03 20:43:15 MarkDuplicates Tracking 1023714 as yet unmatched pairs. 62697 records in RAM. INFO 2026-06-03 20:43:17 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 1s. Last read position: chr2:53,927,410 INFO 2026-06-03 20:43:17 MarkDuplicates Tracking 1021990 as yet unmatched pairs. 60901 records in RAM. INFO 2026-06-03 20:43:19 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 1s. Last read position: chr2:55,881,685 INFO 2026-06-03 20:43:19 MarkDuplicates Tracking 1019564 as yet unmatched pairs. 58413 records in RAM. INFO 2026-06-03 20:43:21 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 1s. Last read position: chr2:63,885,708 INFO 2026-06-03 20:43:21 MarkDuplicates Tracking 1018876 as yet unmatched pairs. 57649 records in RAM. INFO 2026-06-03 20:43:23 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 1s. Last read position: chr2:70,087,942 INFO 2026-06-03 20:43:23 MarkDuplicates Tracking 1018062 as yet unmatched pairs. 56771 records in RAM. INFO 2026-06-03 20:43:24 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 1s. Last read position: chr2:74,048,121 INFO 2026-06-03 20:43:24 MarkDuplicates Tracking 1015154 as yet unmatched pairs. 53799 records in RAM. INFO 2026-06-03 20:43:26 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 1s. Last read position: chr2:84,906,590 INFO 2026-06-03 20:43:26 MarkDuplicates Tracking 1012579 as yet unmatched pairs. 51173 records in RAM. INFO 2026-06-03 20:43:28 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 1s. Last read position: chr2:87,519,314 INFO 2026-06-03 20:43:28 MarkDuplicates Tracking 1011039 as yet unmatched pairs. 49575 records in RAM. INFO 2026-06-03 20:43:29 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 1s. Last read position: chr2:96,286,372 INFO 2026-06-03 20:43:29 MarkDuplicates Tracking 1010531 as yet unmatched pairs. 49015 records in RAM. INFO 2026-06-03 20:43:31 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 1s. Last read position: chr2:99,404,635 INFO 2026-06-03 20:43:31 MarkDuplicates Tracking 1008295 as yet unmatched pairs. 46732 records in RAM. INFO 2026-06-03 20:43:32 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 1s. Last read position: chr2:108,751,263 INFO 2026-06-03 20:43:32 MarkDuplicates Tracking 1007843 as yet unmatched pairs. 46233 records in RAM. INFO 2026-06-03 20:43:34 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 1s. Last read position: chr2:110,285,650 INFO 2026-06-03 20:43:34 MarkDuplicates Tracking 1005262 as yet unmatched pairs. 43605 records in RAM. INFO 2026-06-03 20:43:35 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 1s. Last read position: chr2:113,132,891 INFO 2026-06-03 20:43:35 MarkDuplicates Tracking 1012058 as yet unmatched pairs. 50347 records in RAM. INFO 2026-06-03 20:43:37 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 1s. Last read position: chr2:121,347,141 INFO 2026-06-03 20:43:37 MarkDuplicates Tracking 1003198 as yet unmatched pairs. 41439 records in RAM. INFO 2026-06-03 20:43:38 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 1s. Last read position: chr2:131,836,142 INFO 2026-06-03 20:43:38 MarkDuplicates Tracking 1000904 as yet unmatched pairs. 39045 records in RAM. INFO 2026-06-03 20:43:40 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 1s. Last read position: chr2:151,540,349 INFO 2026-06-03 20:43:40 MarkDuplicates Tracking 999797 as yet unmatched pairs. 37869 records in RAM. INFO 2026-06-03 20:43:42 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 1s. Last read position: chr2:158,663,281 INFO 2026-06-03 20:43:42 MarkDuplicates Tracking 998367 as yet unmatched pairs. 36395 records in RAM. INFO 2026-06-03 20:43:44 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 1s. Last read position: chr2:169,607,126 INFO 2026-06-03 20:43:44 MarkDuplicates Tracking 996912 as yet unmatched pairs. 34866 records in RAM. INFO 2026-06-03 20:43:45 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 1s. Last read position: chr2:173,956,011 INFO 2026-06-03 20:43:45 MarkDuplicates Tracking 996029 as yet unmatched pairs. 33906 records in RAM. INFO 2026-06-03 20:43:47 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 1s. Last read position: chr2:178,532,889 INFO 2026-06-03 20:43:47 MarkDuplicates Tracking 993809 as yet unmatched pairs. 31639 records in RAM. INFO 2026-06-03 20:43:49 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 1s. Last read position: chr2:178,618,411 INFO 2026-06-03 20:43:49 MarkDuplicates Tracking 992319 as yet unmatched pairs. 30114 records in RAM. INFO 2026-06-03 20:43:50 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 1s. Last read position: chr2:182,743,649 INFO 2026-06-03 20:43:50 MarkDuplicates Tracking 991475 as yet unmatched pairs. 29246 records in RAM. INFO 2026-06-03 20:43:52 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 1s. Last read position: chr2:189,002,308 INFO 2026-06-03 20:43:52 MarkDuplicates Tracking 992313 as yet unmatched pairs. 30011 records in RAM. INFO 2026-06-03 20:43:55 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 3s. Last read position: chr2:190,974,836 INFO 2026-06-03 20:43:55 MarkDuplicates Tracking 989133 as yet unmatched pairs. 26800 records in RAM. INFO 2026-06-03 20:43:57 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 1s. Last read position: chr2:201,129,839 INFO 2026-06-03 20:43:57 MarkDuplicates Tracking 986681 as yet unmatched pairs. 24293 records in RAM. INFO 2026-06-03 20:43:58 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 1s. Last read position: chr2:206,567,249 INFO 2026-06-03 20:43:58 MarkDuplicates Tracking 984041 as yet unmatched pairs. 21600 records in RAM. INFO 2026-06-03 20:44:00 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 1s. Last read position: chr2:215,365,515 INFO 2026-06-03 20:44:00 MarkDuplicates Tracking 993312 as yet unmatched pairs. 30809 records in RAM. INFO 2026-06-03 20:44:02 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 2s. Last read position: chr2:215,376,522 INFO 2026-06-03 20:44:02 MarkDuplicates Tracking 994957 as yet unmatched pairs. 32426 records in RAM. INFO 2026-06-03 20:44:05 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 2s. Last read position: chr2:215,391,712 INFO 2026-06-03 20:44:05 MarkDuplicates Tracking 985930 as yet unmatched pairs. 23363 records in RAM. INFO 2026-06-03 20:44:06 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 1s. Last read position: chr2:215,409,563 INFO 2026-06-03 20:44:06 MarkDuplicates Tracking 996368 as yet unmatched pairs. 33757 records in RAM. INFO 2026-06-03 20:44:08 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 1s. Last read position: chr2:215,431,849 INFO 2026-06-03 20:44:08 MarkDuplicates Tracking 985020 as yet unmatched pairs. 22386 records in RAM. INFO 2026-06-03 20:44:10 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 1s. Last read position: chr2:217,890,977 INFO 2026-06-03 20:44:10 MarkDuplicates Tracking 974934 as yet unmatched pairs. 12241 records in RAM. INFO 2026-06-03 20:44:12 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 1s. Last read position: chr2:219,250,743 INFO 2026-06-03 20:44:12 MarkDuplicates Tracking 974817 as yet unmatched pairs. 12047 records in RAM. INFO 2026-06-03 20:44:13 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 1s. Last read position: chr2:227,536,913 INFO 2026-06-03 20:44:13 MarkDuplicates Tracking 972058 as yet unmatched pairs. 9228 records in RAM. INFO 2026-06-03 20:44:15 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 1s. Last read position: chr2:231,711,406 INFO 2026-06-03 20:44:15 MarkDuplicates Tracking 971503 as yet unmatched pairs. 8627 records in RAM. INFO 2026-06-03 20:44:17 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 1s. Last read position: chr2:236,580,986 INFO 2026-06-03 20:44:17 MarkDuplicates Tracking 970780 as yet unmatched pairs. 7832 records in RAM. INFO 2026-06-03 20:44:18 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 1s. Last read position: chr2:239,990,087 INFO 2026-06-03 20:44:18 MarkDuplicates Tracking 966581 as yet unmatched pairs. 3567 records in RAM. INFO 2026-06-03 20:44:21 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 2s. Last read position: chr2:241,584,674 INFO 2026-06-03 20:44:21 MarkDuplicates Tracking 964465 as yet unmatched pairs. 1353 records in RAM. INFO 2026-06-03 20:44:24 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 3s. Last read position: chr3:9,793,069 INFO 2026-06-03 20:44:24 MarkDuplicates Tracking 961770 as yet unmatched pairs. 72105 records in RAM. INFO 2026-06-03 20:44:26 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 1s. Last read position: chr3:12,840,208 INFO 2026-06-03 20:44:26 MarkDuplicates Tracking 959848 as yet unmatched pairs. 70136 records in RAM. INFO 2026-06-03 20:44:28 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 1s. Last read position: chr3:20,183,904 INFO 2026-06-03 20:44:28 MarkDuplicates Tracking 958174 as yet unmatched pairs. 68387 records in RAM. INFO 2026-06-03 20:44:29 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 1s. Last read position: chr3:33,855,165 INFO 2026-06-03 20:44:29 MarkDuplicates Tracking 956902 as yet unmatched pairs. 67053 records in RAM. INFO 2026-06-03 20:44:31 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 1s. Last read position: chr3:40,462,032 INFO 2026-06-03 20:44:31 MarkDuplicates Tracking 956905 as yet unmatched pairs. 67009 records in RAM. INFO 2026-06-03 20:44:32 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 1s. Last read position: chr3:45,095,451 INFO 2026-06-03 20:44:32 MarkDuplicates Tracking 955488 as yet unmatched pairs. 65525 records in RAM. INFO 2026-06-03 20:44:34 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 1s. Last read position: chr3:47,006,440 INFO 2026-06-03 20:44:34 MarkDuplicates Tracking 953383 as yet unmatched pairs. 63361 records in RAM. INFO 2026-06-03 20:44:36 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 1s. Last read position: chr3:48,260,886 INFO 2026-06-03 20:44:36 MarkDuplicates Tracking 949410 as yet unmatched pairs. 59328 records in RAM. INFO 2026-06-03 20:44:39 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 3s. Last read position: chr3:48,575,443 INFO 2026-06-03 20:44:39 MarkDuplicates Tracking 948396 as yet unmatched pairs. 58270 records in RAM. INFO 2026-06-03 20:44:41 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 2s. Last read position: chr3:48,694,910 INFO 2026-06-03 20:44:41 MarkDuplicates Tracking 945250 as yet unmatched pairs. 55085 records in RAM. INFO 2026-06-03 20:44:43 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 1s. Last read position: chr3:49,358,089 INFO 2026-06-03 20:44:43 MarkDuplicates Tracking 941815 as yet unmatched pairs. 51620 records in RAM. INFO 2026-06-03 20:44:45 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 2s. Last read position: chr3:50,187,895 INFO 2026-06-03 20:44:45 MarkDuplicates Tracking 940524 as yet unmatched pairs. 50301 records in RAM. INFO 2026-06-03 20:44:47 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 1s. Last read position: chr3:52,232,009 INFO 2026-06-03 20:44:47 MarkDuplicates Tracking 938996 as yet unmatched pairs. 48736 records in RAM. INFO 2026-06-03 20:44:48 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 1s. Last read position: chr3:53,228,056 INFO 2026-06-03 20:44:48 MarkDuplicates Tracking 938506 as yet unmatched pairs. 48190 records in RAM. INFO 2026-06-03 20:44:50 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 1s. Last read position: chr3:58,123,321 INFO 2026-06-03 20:44:50 MarkDuplicates Tracking 935355 as yet unmatched pairs. 44965 records in RAM. INFO 2026-06-03 20:44:51 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 1s. Last read position: chr3:69,180,981 INFO 2026-06-03 20:44:51 MarkDuplicates Tracking 932861 as yet unmatched pairs. 42394 records in RAM. INFO 2026-06-03 20:44:53 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 1s. Last read position: chr3:100,310,524 INFO 2026-06-03 20:44:53 MarkDuplicates Tracking 930948 as yet unmatched pairs. 40385 records in RAM. INFO 2026-06-03 20:44:55 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 2s. Last read position: chr3:111,953,909 INFO 2026-06-03 20:44:55 MarkDuplicates Tracking 929872 as yet unmatched pairs. 39254 records in RAM. INFO 2026-06-03 20:44:57 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 1s. Last read position: chr3:121,691,063 INFO 2026-06-03 20:44:57 MarkDuplicates Tracking 928237 as yet unmatched pairs. 37543 records in RAM. INFO 2026-06-03 20:44:59 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 2s. Last read position: chr3:124,763,593 INFO 2026-06-03 20:44:59 MarkDuplicates Tracking 926503 as yet unmatched pairs. 35765 records in RAM. INFO 2026-06-03 20:45:02 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 2s. Last read position: chr3:128,726,349 INFO 2026-06-03 20:45:02 MarkDuplicates Tracking 926466 as yet unmatched pairs. 35673 records in RAM. INFO 2026-06-03 20:45:03 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 1s. Last read position: chr3:132,666,014 INFO 2026-06-03 20:45:03 MarkDuplicates Tracking 922848 as yet unmatched pairs. 31993 records in RAM. INFO 2026-06-03 20:45:05 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 1s. Last read position: chr3:141,876,905 INFO 2026-06-03 20:45:05 MarkDuplicates Tracking 921923 as yet unmatched pairs. 31023 records in RAM. INFO 2026-06-03 20:45:07 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 1s. Last read position: chr3:150,603,339 INFO 2026-06-03 20:45:07 MarkDuplicates Tracking 919528 as yet unmatched pairs. 28577 records in RAM. INFO 2026-06-03 20:45:08 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 1s. Last read position: chr3:163,026,356 INFO 2026-06-03 20:45:08 MarkDuplicates Tracking 917134 as yet unmatched pairs. 26099 records in RAM. INFO 2026-06-03 20:45:10 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 1s. Last read position: chr3:172,752,058 INFO 2026-06-03 20:45:10 MarkDuplicates Tracking 916716 as yet unmatched pairs. 25612 records in RAM. INFO 2026-06-03 20:45:12 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 1s. Last read position: chr3:180,988,023 INFO 2026-06-03 20:45:12 MarkDuplicates Tracking 915822 as yet unmatched pairs. 24649 records in RAM. INFO 2026-06-03 20:45:14 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 1s. Last read position: chr3:183,987,838 INFO 2026-06-03 20:45:14 MarkDuplicates Tracking 915007 as yet unmatched pairs. 23771 records in RAM. INFO 2026-06-03 20:45:15 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr3:184,315,487 INFO 2026-06-03 20:45:15 MarkDuplicates Tracking 912150 as yet unmatched pairs. 20879 records in RAM. INFO 2026-06-03 20:45:17 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 1s. Last read position: chr3:184,711,631 INFO 2026-06-03 20:45:17 MarkDuplicates Tracking 909355 as yet unmatched pairs. 18048 records in RAM. INFO 2026-06-03 20:45:19 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 2s. Last read position: chr3:187,043,235 INFO 2026-06-03 20:45:19 MarkDuplicates Tracking 907617 as yet unmatched pairs. 16231 records in RAM. INFO 2026-06-03 20:45:21 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 1s. Last read position: chr3:189,867,836 INFO 2026-06-03 20:45:21 MarkDuplicates Tracking 913286 as yet unmatched pairs. 21830 records in RAM. INFO 2026-06-03 20:45:22 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 1s. Last read position: chr3:194,138,118 INFO 2026-06-03 20:45:22 MarkDuplicates Tracking 904675 as yet unmatched pairs. 13173 records in RAM. INFO 2026-06-03 20:45:24 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 1s. Last read position: chr3:195,749,005 INFO 2026-06-03 20:45:24 MarkDuplicates Tracking 903897 as yet unmatched pairs. 12343 records in RAM. INFO 2026-06-03 20:45:25 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 1s. Last read position: chr3:195,779,365 INFO 2026-06-03 20:45:25 MarkDuplicates Tracking 913491 as yet unmatched pairs. 21909 records in RAM. INFO 2026-06-03 20:45:27 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 1s. Last read position: chr3:195,780,738 INFO 2026-06-03 20:45:27 MarkDuplicates Tracking 922729 as yet unmatched pairs. 31136 records in RAM. INFO 2026-06-03 20:45:29 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 1s. Last read position: chr3:195,781,936 INFO 2026-06-03 20:45:29 MarkDuplicates Tracking 925482 as yet unmatched pairs. 33872 records in RAM. INFO 2026-06-03 20:45:32 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 2s. Last read position: chr3:195,783,219 INFO 2026-06-03 20:45:32 MarkDuplicates Tracking 923295 as yet unmatched pairs. 31672 records in RAM. INFO 2026-06-03 20:45:33 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 1s. Last read position: chr3:195,784,784 INFO 2026-06-03 20:45:33 MarkDuplicates Tracking 926296 as yet unmatched pairs. 34661 records in RAM. INFO 2026-06-03 20:45:35 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 1s. Last read position: chr3:195,786,154 INFO 2026-06-03 20:45:35 MarkDuplicates Tracking 915816 as yet unmatched pairs. 24161 records in RAM. INFO 2026-06-03 20:45:36 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 1s. Last read position: chr3:195,788,280 INFO 2026-06-03 20:45:36 MarkDuplicates Tracking 902108 as yet unmatched pairs. 10417 records in RAM. INFO 2026-06-03 20:45:38 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 1s. Last read position: chr3:195,971,323 INFO 2026-06-03 20:45:38 MarkDuplicates Tracking 895695 as yet unmatched pairs. 3959 records in RAM. INFO 2026-06-03 20:45:39 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 1s. Last read position: chr3:196,814,455 INFO 2026-06-03 20:45:39 MarkDuplicates Tracking 894918 as yet unmatched pairs. 3138 records in RAM. INFO 2026-06-03 20:45:41 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 1s. Last read position: chr4:87,331 INFO 2026-06-03 20:45:41 MarkDuplicates Tracking 891916 as yet unmatched pairs. 32544 records in RAM. INFO 2026-06-03 20:45:43 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 1s. Last read position: chr4:1,740,825 INFO 2026-06-03 20:45:43 MarkDuplicates Tracking 890777 as yet unmatched pairs. 31328 records in RAM. INFO 2026-06-03 20:45:45 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 1s. Last read position: chr4:1,806,553 INFO 2026-06-03 20:45:45 MarkDuplicates Tracking 894270 as yet unmatched pairs. 34781 records in RAM. INFO 2026-06-03 20:45:46 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 1s. Last read position: chr4:3,131,682 INFO 2026-06-03 20:45:46 MarkDuplicates Tracking 885507 as yet unmatched pairs. 25954 records in RAM. INFO 2026-06-03 20:45:48 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 1s. Last read position: chr4:8,236,277 INFO 2026-06-03 20:45:48 MarkDuplicates Tracking 883807 as yet unmatched pairs. 24162 records in RAM. INFO 2026-06-03 20:45:49 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 1s. Last read position: chr4:24,556,338 INFO 2026-06-03 20:45:49 MarkDuplicates Tracking 882387 as yet unmatched pairs. 22672 records in RAM. INFO 2026-06-03 20:45:51 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 1s. Last read position: chr4:39,510,511 INFO 2026-06-03 20:45:51 MarkDuplicates Tracking 881488 as yet unmatched pairs. 21701 records in RAM. INFO 2026-06-03 20:45:54 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 2s. Last read position: chr4:53,573,888 INFO 2026-06-03 20:45:54 MarkDuplicates Tracking 878439 as yet unmatched pairs. 18587 records in RAM. INFO 2026-06-03 20:45:56 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 2s. Last read position: chr4:67,717,259 INFO 2026-06-03 20:45:56 MarkDuplicates Tracking 876528 as yet unmatched pairs. 16632 records in RAM. INFO 2026-06-03 20:45:58 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 1s. Last read position: chr4:73,740,683 INFO 2026-06-03 20:45:58 MarkDuplicates Tracking 875239 as yet unmatched pairs. 15283 records in RAM. INFO 2026-06-03 20:46:00 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 1s. Last read position: chr4:82,426,085 INFO 2026-06-03 20:46:00 MarkDuplicates Tracking 874368 as yet unmatched pairs. 14372 records in RAM. INFO 2026-06-03 20:46:02 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 1s. Last read position: chr4:86,732,748 INFO 2026-06-03 20:46:02 MarkDuplicates Tracking 872665 as yet unmatched pairs. 12597 records in RAM. INFO 2026-06-03 20:46:03 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 1s. Last read position: chr4:94,665,930 INFO 2026-06-03 20:46:03 MarkDuplicates Tracking 870242 as yet unmatched pairs. 10128 records in RAM. INFO 2026-06-03 20:46:05 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 1s. Last read position: chr4:105,693,433 INFO 2026-06-03 20:46:05 MarkDuplicates Tracking 868770 as yet unmatched pairs. 8553 records in RAM. INFO 2026-06-03 20:46:06 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:05:20s. Time for last 1,000,000: 1s. Last read position: chr4:121,672,598 INFO 2026-06-03 20:46:06 MarkDuplicates Tracking 867675 as yet unmatched pairs. 7384 records in RAM. INFO 2026-06-03 20:46:08 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 1s. Last read position: chr4:143,195,733 INFO 2026-06-03 20:46:08 MarkDuplicates Tracking 865761 as yet unmatched pairs. 5400 records in RAM. INFO 2026-06-03 20:46:10 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 1s. Last read position: chr4:152,628,468 INFO 2026-06-03 20:46:10 MarkDuplicates Tracking 866317 as yet unmatched pairs. 5874 records in RAM. INFO 2026-06-03 20:46:11 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 1s. Last read position: chr4:169,741,955 INFO 2026-06-03 20:46:11 MarkDuplicates Tracking 862543 as yet unmatched pairs. 2005 records in RAM. INFO 2026-06-03 20:46:13 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 1s. Last read position: chr4:186,628,235 INFO 2026-06-03 20:46:13 MarkDuplicates Tracking 861406 as yet unmatched pairs. 795 records in RAM. INFO 2026-06-03 20:46:15 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 2s. Last read position: chr5:10,394,769 INFO 2026-06-03 20:46:15 MarkDuplicates Tracking 860141 as yet unmatched pairs. 33811 records in RAM. INFO 2026-06-03 20:46:17 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 1s. Last read position: chr5:17,275,396 INFO 2026-06-03 20:46:17 MarkDuplicates Tracking 857132 as yet unmatched pairs. 30738 records in RAM. INFO 2026-06-03 20:46:19 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 1s. Last read position: chr5:38,944,955 INFO 2026-06-03 20:46:19 MarkDuplicates Tracking 855778 as yet unmatched pairs. 29339 records in RAM. INFO 2026-06-03 20:46:21 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 2s. Last read position: chr5:55,941,302 INFO 2026-06-03 20:46:21 MarkDuplicates Tracking 854486 as yet unmatched pairs. 27995 records in RAM. INFO 2026-06-03 20:46:24 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 3s. Last read position: chr5:70,067,114 INFO 2026-06-03 20:46:24 MarkDuplicates Tracking 852576 as yet unmatched pairs. 26032 records in RAM. INFO 2026-06-03 20:46:25 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 1s. Last read position: chr5:78,885,698 INFO 2026-06-03 20:46:25 MarkDuplicates Tracking 851317 as yet unmatched pairs. 24738 records in RAM. INFO 2026-06-03 20:46:27 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 1s. Last read position: chr5:95,898,582 INFO 2026-06-03 20:46:27 MarkDuplicates Tracking 850032 as yet unmatched pairs. 23374 records in RAM. INFO 2026-06-03 20:46:29 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 1s. Last read position: chr5:118,974,092 INFO 2026-06-03 20:46:29 MarkDuplicates Tracking 848403 as yet unmatched pairs. 21687 records in RAM. INFO 2026-06-03 20:46:30 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 1s. Last read position: chr5:134,566,436 INFO 2026-06-03 20:46:30 MarkDuplicates Tracking 847374 as yet unmatched pairs. 20601 records in RAM. INFO 2026-06-03 20:46:32 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 1s. Last read position: chr5:138,783,217 INFO 2026-06-03 20:46:32 MarkDuplicates Tracking 845391 as yet unmatched pairs. 18538 records in RAM. INFO 2026-06-03 20:46:34 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 1s. Last read position: chr5:141,404,509 INFO 2026-06-03 20:46:34 MarkDuplicates Tracking 842849 as yet unmatched pairs. 15944 records in RAM. INFO 2026-06-03 20:46:35 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 1s. Last read position: chr5:149,362,577 INFO 2026-06-03 20:46:35 MarkDuplicates Tracking 841142 as yet unmatched pairs. 14181 records in RAM. INFO 2026-06-03 20:46:37 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 1s. Last read position: chr5:150,402,237 INFO 2026-06-03 20:46:37 MarkDuplicates Tracking 870209 as yet unmatched pairs. 43194 records in RAM. INFO 2026-06-03 20:46:39 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 1s. Last read position: chr5:150,647,991 INFO 2026-06-03 20:46:39 MarkDuplicates Tracking 837725 as yet unmatched pairs. 10676 records in RAM. INFO 2026-06-03 20:46:40 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 1s. Last read position: chr5:151,794,183 INFO 2026-06-03 20:46:40 MarkDuplicates Tracking 836144 as yet unmatched pairs. 9044 records in RAM. INFO 2026-06-03 20:46:42 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 1s. Last read position: chr5:171,387,966 INFO 2026-06-03 20:46:42 MarkDuplicates Tracking 843856 as yet unmatched pairs. 16699 records in RAM. INFO 2026-06-03 20:46:44 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 2s. Last read position: chr5:177,135,138 INFO 2026-06-03 20:46:44 MarkDuplicates Tracking 833037 as yet unmatched pairs. 5833 records in RAM. INFO 2026-06-03 20:46:47 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 2s. Last read position: chr5:179,619,286 INFO 2026-06-03 20:46:47 MarkDuplicates Tracking 830597 as yet unmatched pairs. 3344 records in RAM. INFO 2026-06-03 20:46:49 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 1s. Last read position: chr5:180,567,902 INFO 2026-06-03 20:46:49 MarkDuplicates Tracking 828286 as yet unmatched pairs. 984 records in RAM. INFO 2026-06-03 20:46:51 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 2s. Last read position: chr6:4,943,700 INFO 2026-06-03 20:46:51 MarkDuplicates Tracking 826478 as yet unmatched pairs. 59520 records in RAM. INFO 2026-06-03 20:46:52 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 1s. Last read position: chr6:7,566,448 INFO 2026-06-03 20:46:52 MarkDuplicates Tracking 829002 as yet unmatched pairs. 62007 records in RAM. INFO 2026-06-03 20:46:54 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 1s. Last read position: chr6:7,584,591 INFO 2026-06-03 20:46:54 MarkDuplicates Tracking 823765 as yet unmatched pairs. 56740 records in RAM. INFO 2026-06-03 20:46:56 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:06:09s. Time for last 1,000,000: 1s. Last read position: chr6:17,637,226 INFO 2026-06-03 20:46:56 MarkDuplicates Tracking 820894 as yet unmatched pairs. 53797 records in RAM. INFO 2026-06-03 20:46:57 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 1s. Last read position: chr6:26,103,957 INFO 2026-06-03 20:46:57 MarkDuplicates Tracking 819980 as yet unmatched pairs. 52835 records in RAM. INFO 2026-06-03 20:46:59 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 1s. Last read position: chr6:26,376,815 INFO 2026-06-03 20:46:59 MarkDuplicates Tracking 817042 as yet unmatched pairs. 49864 records in RAM. INFO 2026-06-03 20:47:00 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 1s. Last read position: chr6:27,865,337 INFO 2026-06-03 20:47:00 MarkDuplicates Tracking 815579 as yet unmatched pairs. 48389 records in RAM. INFO 2026-06-03 20:47:02 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 1s. Last read position: chr6:30,186,038 INFO 2026-06-03 20:47:02 MarkDuplicates Tracking 814072 as yet unmatched pairs. 46853 records in RAM. INFO 2026-06-03 20:47:04 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 1s. Last read position: chr6:30,893,414 INFO 2026-06-03 20:47:04 MarkDuplicates Tracking 812669 as yet unmatched pairs. 45401 records in RAM. INFO 2026-06-03 20:47:05 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 1s. Last read position: chr6:31,633,377 INFO 2026-06-03 20:47:05 MarkDuplicates Tracking 810427 as yet unmatched pairs. 43139 records in RAM. INFO 2026-06-03 20:47:07 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 1s. Last read position: chr6:31,828,722 INFO 2026-06-03 20:47:07 MarkDuplicates Tracking 809021 as yet unmatched pairs. 41702 records in RAM. INFO 2026-06-03 20:47:09 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 2s. Last read position: chr6:32,367,924 INFO 2026-06-03 20:47:09 MarkDuplicates Tracking 805902 as yet unmatched pairs. 38540 records in RAM. INFO 2026-06-03 20:47:12 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 3s. Last read position: chr6:33,205,652 INFO 2026-06-03 20:47:12 MarkDuplicates Tracking 804237 as yet unmatched pairs. 36848 records in RAM. INFO 2026-06-03 20:47:14 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 1s. Last read position: chr6:33,671,170 INFO 2026-06-03 20:47:14 MarkDuplicates Tracking 802802 as yet unmatched pairs. 35373 records in RAM. INFO 2026-06-03 20:47:16 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 1s. Last read position: chr6:36,138,377 INFO 2026-06-03 20:47:16 MarkDuplicates Tracking 801807 as yet unmatched pairs. 34320 records in RAM. INFO 2026-06-03 20:47:18 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:06:31s. Time for last 1,000,000: 1s. Last read position: chr6:42,104,570 INFO 2026-06-03 20:47:18 MarkDuplicates Tracking 799312 as yet unmatched pairs. 31757 records in RAM. INFO 2026-06-03 20:47:19 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 1s. Last read position: chr6:43,369,067 INFO 2026-06-03 20:47:19 MarkDuplicates Tracking 796680 as yet unmatched pairs. 29098 records in RAM. INFO 2026-06-03 20:47:21 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 1s. Last read position: chr6:44,310,259 INFO 2026-06-03 20:47:21 MarkDuplicates Tracking 794478 as yet unmatched pairs. 26847 records in RAM. INFO 2026-06-03 20:47:22 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 1s. Last read position: chr6:54,870,190 INFO 2026-06-03 20:47:22 MarkDuplicates Tracking 793264 as yet unmatched pairs. 25418 records in RAM. INFO 2026-06-03 20:47:24 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 1s. Last read position: chr6:56,631,316 INFO 2026-06-03 20:47:24 MarkDuplicates Tracking 794546 as yet unmatched pairs. 26673 records in RAM. INFO 2026-06-03 20:47:26 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 1s. Last read position: chr6:73,792,771 INFO 2026-06-03 20:47:26 MarkDuplicates Tracking 790083 as yet unmatched pairs. 22142 records in RAM. INFO 2026-06-03 20:47:27 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 1s. Last read position: chr6:83,129,153 INFO 2026-06-03 20:47:27 MarkDuplicates Tracking 788604 as yet unmatched pairs. 20622 records in RAM. INFO 2026-06-03 20:47:29 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 1s. Last read position: chr6:89,829,909 INFO 2026-06-03 20:47:29 MarkDuplicates Tracking 786714 as yet unmatched pairs. 18699 records in RAM. INFO 2026-06-03 20:47:31 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:06:44s. Time for last 1,000,000: 1s. Last read position: chr6:107,459,131 INFO 2026-06-03 20:47:31 MarkDuplicates Tracking 785486 as yet unmatched pairs. 17418 records in RAM. INFO 2026-06-03 20:47:32 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:06:46s. Time for last 1,000,000: 1s. Last read position: chr6:113,945,395 INFO 2026-06-03 20:47:32 MarkDuplicates Tracking 784183 as yet unmatched pairs. 16070 records in RAM. INFO 2026-06-03 20:47:35 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 2s. Last read position: chr6:127,280,275 INFO 2026-06-03 20:47:35 MarkDuplicates Tracking 781831 as yet unmatched pairs. 13660 records in RAM. INFO 2026-06-03 20:47:37 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 1s. Last read position: chr6:136,656,305 INFO 2026-06-03 20:47:37 MarkDuplicates Tracking 780070 as yet unmatched pairs. 11849 records in RAM. INFO 2026-06-03 20:47:39 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 1s. Last read position: chr6:139,166,804 INFO 2026-06-03 20:47:39 MarkDuplicates Tracking 778817 as yet unmatched pairs. 10558 records in RAM. INFO 2026-06-03 20:47:40 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 1s. Last read position: chr6:149,946,521 INFO 2026-06-03 20:47:40 MarkDuplicates Tracking 776115 as yet unmatched pairs. 7812 records in RAM. INFO 2026-06-03 20:47:42 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 1s. Last read position: chr6:158,766,892 INFO 2026-06-03 20:47:42 MarkDuplicates Tracking 777118 as yet unmatched pairs. 8754 records in RAM. INFO 2026-06-03 20:47:43 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:06:57s. Time for last 1,000,000: 1s. Last read position: chr6:158,789,293 INFO 2026-06-03 20:47:43 MarkDuplicates Tracking 787177 as yet unmatched pairs. 18788 records in RAM. INFO 2026-06-03 20:47:45 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 1s. Last read position: chr6:160,628,251 INFO 2026-06-03 20:47:45 MarkDuplicates Tracking 770515 as yet unmatched pairs. 2096 records in RAM. INFO 2026-06-03 20:47:47 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:07:00s. Time for last 1,000,000: 1s. Last read position: chr6:170,318,666 INFO 2026-06-03 20:47:47 MarkDuplicates Tracking 769154 as yet unmatched pairs. 685 records in RAM. INFO 2026-06-03 20:47:49 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 2s. Last read position: chr7:5,351,910 INFO 2026-06-03 20:47:49 MarkDuplicates Tracking 766398 as yet unmatched pairs. 48844 records in RAM. INFO 2026-06-03 20:47:51 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:07:04s. Time for last 1,000,000: 1s. Last read position: chr7:5,529,538 INFO 2026-06-03 20:47:51 MarkDuplicates Tracking 771563 as yet unmatched pairs. 53958 records in RAM. INFO 2026-06-03 20:47:52 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 1s. Last read position: chr7:22,150,409 INFO 2026-06-03 20:47:52 MarkDuplicates Tracking 762627 as yet unmatched pairs. 44981 records in RAM. INFO 2026-06-03 20:47:55 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 2s. Last read position: chr7:36,621,709 INFO 2026-06-03 20:47:55 MarkDuplicates Tracking 760945 as yet unmatched pairs. 43235 records in RAM. INFO 2026-06-03 20:47:57 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 2s. Last read position: chr7:44,566,032 INFO 2026-06-03 20:47:57 MarkDuplicates Tracking 759271 as yet unmatched pairs. 41519 records in RAM. INFO 2026-06-03 20:47:59 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:07:12s. Time for last 1,000,000: 2s. Last read position: chr7:55,019,219 INFO 2026-06-03 20:47:59 MarkDuplicates Tracking 758224 as yet unmatched pairs. 40421 records in RAM. INFO 2026-06-03 20:48:01 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:07:14s. Time for last 1,000,000: 1s. Last read position: chr7:67,309,595 INFO 2026-06-03 20:48:01 MarkDuplicates Tracking 754682 as yet unmatched pairs. 36828 records in RAM. INFO 2026-06-03 20:48:02 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:07:15s. Time for last 1,000,000: 1s. Last read position: chr7:73,297,215 INFO 2026-06-03 20:48:02 MarkDuplicates Tracking 753783 as yet unmatched pairs. 35912 records in RAM. INFO 2026-06-03 20:48:03 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:07:16s. Time for last 1,000,000: 1s. Last read position: chr7:74,538,677 INFO 2026-06-03 20:48:03 MarkDuplicates Tracking 752405 as yet unmatched pairs. 34492 records in RAM. INFO 2026-06-03 20:48:05 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:07:18s. Time for last 1,000,000: 1s. Last read position: chr7:75,422,869 INFO 2026-06-03 20:48:05 MarkDuplicates Tracking 750939 as yet unmatched pairs. 32990 records in RAM. INFO 2026-06-03 20:48:06 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:07:19s. Time for last 1,000,000: 1s. Last read position: chr7:76,302,826 INFO 2026-06-03 20:48:06 MarkDuplicates Tracking 797806 as yet unmatched pairs. 79831 records in RAM. INFO 2026-06-03 20:48:08 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:07:21s. Time for last 1,000,000: 1s. Last read position: chr7:76,303,043 INFO 2026-06-03 20:48:08 MarkDuplicates Tracking 801224 as yet unmatched pairs. 83188 records in RAM. INFO 2026-06-03 20:48:10 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:07:23s. Time for last 1,000,000: 1s. Last read position: chr7:76,304,074 INFO 2026-06-03 20:48:10 MarkDuplicates Tracking 767022 as yet unmatched pairs. 48958 records in RAM. INFO 2026-06-03 20:48:11 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:07:24s. Time for last 1,000,000: 1s. Last read position: chr7:77,115,872 INFO 2026-06-03 20:48:11 MarkDuplicates Tracking 742459 as yet unmatched pairs. 24350 records in RAM. INFO 2026-06-03 20:48:13 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:07:26s. Time for last 1,000,000: 1s. Last read position: chr7:92,001,053 INFO 2026-06-03 20:48:13 MarkDuplicates Tracking 741267 as yet unmatched pairs. 23128 records in RAM. INFO 2026-06-03 20:48:14 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 1s. Last read position: chr7:94,407,850 INFO 2026-06-03 20:48:14 MarkDuplicates Tracking 743309 as yet unmatched pairs. 25145 records in RAM. INFO 2026-06-03 20:49:18 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:08:31s. Time for last 1,000,000: 63s. Last read position: chr7:98,320,068 INFO 2026-06-03 20:49:18 MarkDuplicates Tracking 738353 as yet unmatched pairs. 20137 records in RAM. INFO 2026-06-03 20:49:19 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 1s. Last read position: chr7:100,030,330 INFO 2026-06-03 20:49:19 MarkDuplicates Tracking 736187 as yet unmatched pairs. 17923 records in RAM. INFO 2026-06-03 20:49:21 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 1s. Last read position: chr7:100,433,332 INFO 2026-06-03 20:49:21 MarkDuplicates Tracking 734395 as yet unmatched pairs. 16085 records in RAM. INFO 2026-06-03 20:49:22 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:08:36s. Time for last 1,000,000: 1s. Last read position: chr7:101,088,005 INFO 2026-06-03 20:49:22 MarkDuplicates Tracking 731766 as yet unmatched pairs. 13425 records in RAM. INFO 2026-06-03 20:49:24 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 1s. Last read position: chr7:102,566,723 INFO 2026-06-03 20:49:24 MarkDuplicates Tracking 730768 as yet unmatched pairs. 12377 records in RAM. INFO 2026-06-03 20:49:25 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:08:38s. Time for last 1,000,000: 1s. Last read position: chr7:106,253,088 INFO 2026-06-03 20:49:25 MarkDuplicates Tracking 730567 as yet unmatched pairs. 12137 records in RAM. INFO 2026-06-03 20:49:27 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 1s. Last read position: chr7:121,968,062 INFO 2026-06-03 20:49:27 MarkDuplicates Tracking 727137 as yet unmatched pairs. 8668 records in RAM. INFO 2026-06-03 20:49:29 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:08:42s. Time for last 1,000,000: 1s. Last read position: chr7:128,948,286 INFO 2026-06-03 20:49:29 MarkDuplicates Tracking 725331 as yet unmatched pairs. 6838 records in RAM. INFO 2026-06-03 20:49:30 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:08:43s. Time for last 1,000,000: 1s. Last read position: chr7:139,715,941 INFO 2026-06-03 20:49:30 MarkDuplicates Tracking 723752 as yet unmatched pairs. 5199 records in RAM. INFO 2026-06-03 20:49:32 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:08:45s. Time for last 1,000,000: 1s. Last read position: chr7:144,285,738 INFO 2026-06-03 20:49:32 MarkDuplicates Tracking 722188 as yet unmatched pairs. 3579 records in RAM. INFO 2026-06-03 20:49:33 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:08:47s. Time for last 1,000,000: 1s. Last read position: chr7:151,142,407 INFO 2026-06-03 20:49:33 MarkDuplicates Tracking 720499 as yet unmatched pairs. 1846 records in RAM. INFO 2026-06-03 20:49:35 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 1s. Last read position: chr8:8,376,700 INFO 2026-06-03 20:49:35 MarkDuplicates Tracking 718564 as yet unmatched pairs. 41932 records in RAM. INFO 2026-06-03 20:49:37 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:08:50s. Time for last 1,000,000: 1s. Last read position: chr8:15,730,684 INFO 2026-06-03 20:49:37 MarkDuplicates Tracking 717614 as yet unmatched pairs. 40930 records in RAM. INFO 2026-06-03 20:49:39 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:08:52s. Time for last 1,000,000: 1s. Last read position: chr8:22,140,622 INFO 2026-06-03 20:49:39 MarkDuplicates Tracking 715214 as yet unmatched pairs. 38486 records in RAM. INFO 2026-06-03 20:49:40 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 1s. Last read position: chr8:24,384,525 INFO 2026-06-03 20:49:40 MarkDuplicates Tracking 712590 as yet unmatched pairs. 35819 records in RAM. INFO 2026-06-03 20:49:43 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:08:56s. Time for last 1,000,000: 2s. Last read position: chr8:32,647,937 INFO 2026-06-03 20:49:43 MarkDuplicates Tracking 711197 as yet unmatched pairs. 34375 records in RAM. INFO 2026-06-03 20:49:45 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:08:58s. Time for last 1,000,000: 2s. Last read position: chr8:38,337,317 INFO 2026-06-03 20:49:45 MarkDuplicates Tracking 711412 as yet unmatched pairs. 34563 records in RAM. INFO 2026-06-03 20:49:46 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:08:59s. Time for last 1,000,000: 1s. Last read position: chr8:42,318,599 INFO 2026-06-03 20:49:46 MarkDuplicates Tracking 707608 as yet unmatched pairs. 30714 records in RAM. INFO 2026-06-03 20:49:48 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:09:01s. Time for last 1,000,000: 1s. Last read position: chr8:47,927,233 INFO 2026-06-03 20:49:48 MarkDuplicates Tracking 705626 as yet unmatched pairs. 28700 records in RAM. INFO 2026-06-03 20:49:50 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:09:03s. Time for last 1,000,000: 2s. Last read position: chr8:61,526,023 INFO 2026-06-03 20:49:50 MarkDuplicates Tracking 703718 as yet unmatched pairs. 26763 records in RAM. INFO 2026-06-03 20:49:52 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 1s. Last read position: chr8:70,608,077 INFO 2026-06-03 20:49:52 MarkDuplicates Tracking 703083 as yet unmatched pairs. 26082 records in RAM. INFO 2026-06-03 20:49:54 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:09:07s. Time for last 1,000,000: 1s. Last read position: chr8:93,922,169 INFO 2026-06-03 20:49:54 MarkDuplicates Tracking 700573 as yet unmatched pairs. 23521 records in RAM. INFO 2026-06-03 20:49:55 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 1s. Last read position: chr8:100,706,912 INFO 2026-06-03 20:49:55 MarkDuplicates Tracking 701565 as yet unmatched pairs. 24474 records in RAM. INFO 2026-06-03 20:49:57 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:09:10s. Time for last 1,000,000: 1s. Last read position: chr8:103,318,634 INFO 2026-06-03 20:49:57 MarkDuplicates Tracking 697640 as yet unmatched pairs. 20501 records in RAM. INFO 2026-06-03 20:49:59 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:09:12s. Time for last 1,000,000: 1s. Last read position: chr8:119,788,433 INFO 2026-06-03 20:49:59 MarkDuplicates Tracking 695626 as yet unmatched pairs. 18405 records in RAM. INFO 2026-06-03 20:50:00 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:09:13s. Time for last 1,000,000: 1s. Last read position: chr8:127,738,561 INFO 2026-06-03 20:50:00 MarkDuplicates Tracking 697580 as yet unmatched pairs. 20312 records in RAM. INFO 2026-06-03 20:50:02 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:09:15s. Time for last 1,000,000: 1s. Last read position: chr8:133,262,126 INFO 2026-06-03 20:50:02 MarkDuplicates Tracking 698714 as yet unmatched pairs. 21394 records in RAM. INFO 2026-06-03 20:50:03 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 1s. Last read position: chr8:143,576,756 INFO 2026-06-03 20:50:03 MarkDuplicates Tracking 690340 as yet unmatched pairs. 12961 records in RAM. INFO 2026-06-03 20:50:05 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:09:18s. Time for last 1,000,000: 1s. Last read position: chr8:143,858,327 INFO 2026-06-03 20:50:05 MarkDuplicates Tracking 687509 as yet unmatched pairs. 10091 records in RAM. INFO 2026-06-03 20:50:06 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:09:19s. Time for last 1,000,000: 1s. Last read position: chr8:143,861,514 INFO 2026-06-03 20:50:06 MarkDuplicates Tracking 686764 as yet unmatched pairs. 9338 records in RAM. INFO 2026-06-03 20:50:07 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 1s. Last read position: chr8:143,864,634 INFO 2026-06-03 20:50:07 MarkDuplicates Tracking 686732 as yet unmatched pairs. 9293 records in RAM. INFO 2026-06-03 20:50:08 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:09:21s. Time for last 1,000,000: 1s. Last read position: chr8:143,872,503 INFO 2026-06-03 20:50:08 MarkDuplicates Tracking 685625 as yet unmatched pairs. 8177 records in RAM. INFO 2026-06-03 20:50:10 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:09:23s. Time for last 1,000,000: 1s. Last read position: chr8:143,929,818 INFO 2026-06-03 20:50:10 MarkDuplicates Tracking 683486 as yet unmatched pairs. 5996 records in RAM. INFO 2026-06-03 20:50:12 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 1s. Last read position: chr8:144,397,796 INFO 2026-06-03 20:50:12 MarkDuplicates Tracking 679129 as yet unmatched pairs. 1593 records in RAM. INFO 2026-06-03 20:50:14 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:09:27s. Time for last 1,000,000: 1s. Last read position: chr9:2,833,376 INFO 2026-06-03 20:50:14 MarkDuplicates Tracking 677413 as yet unmatched pairs. 48664 records in RAM. INFO 2026-06-03 20:50:15 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:09:28s. Time for last 1,000,000: 1s. Last read position: chr9:18,657,647 INFO 2026-06-03 20:50:15 MarkDuplicates Tracking 675261 as yet unmatched pairs. 46390 records in RAM. INFO 2026-06-03 20:50:17 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:09:30s. Time for last 1,000,000: 1s. Last read position: chr9:32,973,494 INFO 2026-06-03 20:50:17 MarkDuplicates Tracking 673476 as yet unmatched pairs. 44561 records in RAM. INFO 2026-06-03 20:50:18 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:09:32s. Time for last 1,000,000: 1s. Last read position: chr9:35,059,597 INFO 2026-06-03 20:50:18 MarkDuplicates Tracking 674082 as yet unmatched pairs. 45116 records in RAM. INFO 2026-06-03 20:50:20 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:09:33s. Time for last 1,000,000: 1s. Last read position: chr9:35,842,418 INFO 2026-06-03 20:50:20 MarkDuplicates Tracking 668993 as yet unmatched pairs. 39986 records in RAM. INFO 2026-06-03 20:50:21 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:09:34s. Time for last 1,000,000: 1s. Last read position: chr9:69,252,865 INFO 2026-06-03 20:50:21 MarkDuplicates Tracking 668512 as yet unmatched pairs. 39448 records in RAM. INFO 2026-06-03 20:50:24 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 2s. Last read position: chr9:73,162,820 INFO 2026-06-03 20:50:24 MarkDuplicates Tracking 685391 as yet unmatched pairs. 56315 records in RAM. INFO 2026-06-03 20:50:26 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:09:39s. Time for last 1,000,000: 1s. Last read position: chr9:83,663,880 INFO 2026-06-03 20:50:26 MarkDuplicates Tracking 664281 as yet unmatched pairs. 35166 records in RAM. INFO 2026-06-03 20:50:28 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:09:41s. Time for last 1,000,000: 1s. Last read position: chr9:84,727,937 INFO 2026-06-03 20:50:28 MarkDuplicates Tracking 664614 as yet unmatched pairs. 35477 records in RAM. INFO 2026-06-03 20:50:29 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:09:42s. Time for last 1,000,000: 1s. Last read position: chr9:86,323,535 INFO 2026-06-03 20:50:29 MarkDuplicates Tracking 660807 as yet unmatched pairs. 31641 records in RAM. INFO 2026-06-03 20:50:31 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 1s. Last read position: chr9:93,289,561 INFO 2026-06-03 20:50:31 MarkDuplicates Tracking 658916 as yet unmatched pairs. 29714 records in RAM. INFO 2026-06-03 20:50:32 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:09:46s. Time for last 1,000,000: 1s. Last read position: chr9:98,134,803 INFO 2026-06-03 20:50:32 MarkDuplicates Tracking 657608 as yet unmatched pairs. 28343 records in RAM. INFO 2026-06-03 20:50:34 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:09:47s. Time for last 1,000,000: 1s. Last read position: chr9:107,487,444 INFO 2026-06-03 20:50:34 MarkDuplicates Tracking 656435 as yet unmatched pairs. 27141 records in RAM. INFO 2026-06-03 20:50:36 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:09:49s. Time for last 1,000,000: 2s. Last read position: chr9:112,297,878 INFO 2026-06-03 20:50:36 MarkDuplicates Tracking 655493 as yet unmatched pairs. 26163 records in RAM. INFO 2026-06-03 20:50:38 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:09:51s. Time for last 1,000,000: 1s. Last read position: chr9:115,086,455 INFO 2026-06-03 20:50:38 MarkDuplicates Tracking 653763 as yet unmatched pairs. 24398 records in RAM. INFO 2026-06-03 20:50:40 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:09:53s. Time for last 1,000,000: 1s. Last read position: chr9:122,911,279 INFO 2026-06-03 20:50:40 MarkDuplicates Tracking 649359 as yet unmatched pairs. 19956 records in RAM. INFO 2026-06-03 20:50:41 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:09:55s. Time for last 1,000,000: 1s. Last read position: chr9:127,451,280 INFO 2026-06-03 20:50:41 MarkDuplicates Tracking 647455 as yet unmatched pairs. 18017 records in RAM. INFO 2026-06-03 20:50:43 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:09:56s. Time for last 1,000,000: 1s. Last read position: chr9:128,169,094 INFO 2026-06-03 20:50:43 MarkDuplicates Tracking 645601 as yet unmatched pairs. 16129 records in RAM. INFO 2026-06-03 20:50:45 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:09:58s. Time for last 1,000,000: 1s. Last read position: chr9:128,907,464 INFO 2026-06-03 20:50:45 MarkDuplicates Tracking 643970 as yet unmatched pairs. 14465 records in RAM. INFO 2026-06-03 20:50:46 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 1s. Last read position: chr9:130,631,997 INFO 2026-06-03 20:50:46 MarkDuplicates Tracking 641740 as yet unmatched pairs. 12207 records in RAM. INFO 2026-06-03 20:50:48 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:10:01s. Time for last 1,000,000: 1s. Last read position: chr9:132,402,237 INFO 2026-06-03 20:50:48 MarkDuplicates Tracking 639589 as yet unmatched pairs. 10000 records in RAM. INFO 2026-06-03 20:50:49 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:10:03s. Time for last 1,000,000: 1s. Last read position: chr9:134,750,807 INFO 2026-06-03 20:50:49 MarkDuplicates Tracking 639813 as yet unmatched pairs. 10168 records in RAM. INFO 2026-06-03 20:50:51 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:10:04s. Time for last 1,000,000: 1s. Last read position: chr9:136,477,106 INFO 2026-06-03 20:50:51 MarkDuplicates Tracking 636559 as yet unmatched pairs. 6881 records in RAM. INFO 2026-06-03 20:50:53 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 1s. Last read position: chr9:136,897,186 INFO 2026-06-03 20:50:53 MarkDuplicates Tracking 632893 as yet unmatched pairs. 3156 records in RAM. INFO 2026-06-03 20:50:54 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:10:07s. Time for last 1,000,000: 1s. Last read position: chr9:137,613,748 INFO 2026-06-03 20:50:54 MarkDuplicates Tracking 630624 as yet unmatched pairs. 853 records in RAM. INFO 2026-06-03 20:50:56 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 1s. Last read position: chr10:5,446,746 INFO 2026-06-03 20:50:56 MarkDuplicates Tracking 629636 as yet unmatched pairs. 38752 records in RAM. INFO 2026-06-03 20:50:58 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:10:11s. Time for last 1,000,000: 2s. Last read position: chr10:6,216,755 INFO 2026-06-03 20:50:58 MarkDuplicates Tracking 626943 as yet unmatched pairs. 36024 records in RAM. INFO 2026-06-03 20:51:00 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:10:13s. Time for last 1,000,000: 1s. Last read position: chr10:22,318,957 INFO 2026-06-03 20:51:00 MarkDuplicates Tracking 625254 as yet unmatched pairs. 34292 records in RAM. INFO 2026-06-03 20:51:01 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:10:14s. Time for last 1,000,000: 1s. Last read position: chr10:29,462,331 INFO 2026-06-03 20:51:01 MarkDuplicates Tracking 623441 as yet unmatched pairs. 32457 records in RAM. INFO 2026-06-03 20:51:03 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:10:16s. Time for last 1,000,000: 1s. Last read position: chr10:32,901,520 INFO 2026-06-03 20:51:03 MarkDuplicates Tracking 622599 as yet unmatched pairs. 31574 records in RAM. INFO 2026-06-03 20:51:04 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:10:17s. Time for last 1,000,000: 1s. Last read position: chr10:45,699,083 INFO 2026-06-03 20:51:04 MarkDuplicates Tracking 620040 as yet unmatched pairs. 28971 records in RAM. INFO 2026-06-03 20:51:06 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:10:19s. Time for last 1,000,000: 1s. Last read position: chr10:48,010,303 INFO 2026-06-03 20:51:06 MarkDuplicates Tracking 618869 as yet unmatched pairs. 27791 records in RAM. INFO 2026-06-03 20:51:08 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:10:21s. Time for last 1,000,000: 2s. Last read position: chr10:63,207,903 INFO 2026-06-03 20:51:08 MarkDuplicates Tracking 617383 as yet unmatched pairs. 26260 records in RAM. INFO 2026-06-03 20:51:09 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:10:22s. Time for last 1,000,000: 1s. Last read position: chr10:71,293,436 INFO 2026-06-03 20:51:09 MarkDuplicates Tracking 615719 as yet unmatched pairs. 24562 records in RAM. INFO 2026-06-03 20:51:11 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:10:24s. Time for last 1,000,000: 1s. Last read position: chr10:73,793,591 INFO 2026-06-03 20:51:11 MarkDuplicates Tracking 614159 as yet unmatched pairs. 22965 records in RAM. INFO 2026-06-03 20:51:12 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:10:25s. Time for last 1,000,000: 1s. Last read position: chr10:77,821,218 INFO 2026-06-03 20:51:12 MarkDuplicates Tracking 611935 as yet unmatched pairs. 20692 records in RAM. INFO 2026-06-03 20:51:14 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:10:27s. Time for last 1,000,000: 1s. Last read position: chr10:84,150,121 INFO 2026-06-03 20:51:14 MarkDuplicates Tracking 610154 as yet unmatched pairs. 18869 records in RAM. INFO 2026-06-03 20:51:16 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:10:29s. Time for last 1,000,000: 1s. Last read position: chr10:92,018,851 INFO 2026-06-03 20:51:16 MarkDuplicates Tracking 608401 as yet unmatched pairs. 17083 records in RAM. INFO 2026-06-03 20:51:17 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:10:30s. Time for last 1,000,000: 1s. Last read position: chr10:96,551,313 INFO 2026-06-03 20:51:17 MarkDuplicates Tracking 607098 as yet unmatched pairs. 15750 records in RAM. INFO 2026-06-03 20:51:19 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:10:32s. Time for last 1,000,000: 1s. Last read position: chr10:100,347,507 INFO 2026-06-03 20:51:19 MarkDuplicates Tracking 605535 as yet unmatched pairs. 14162 records in RAM. INFO 2026-06-03 20:51:20 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:10:33s. Time for last 1,000,000: 1s. Last read position: chr10:102,379,575 INFO 2026-06-03 20:51:20 MarkDuplicates Tracking 602990 as yet unmatched pairs. 11596 records in RAM. INFO 2026-06-03 20:51:22 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:10:35s. Time for last 1,000,000: 2s. Last read position: chr10:104,003,105 INFO 2026-06-03 20:51:22 MarkDuplicates Tracking 601895 as yet unmatched pairs. 10446 records in RAM. INFO 2026-06-03 20:51:24 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:10:37s. Time for last 1,000,000: 1s. Last read position: chr10:104,070,502 INFO 2026-06-03 20:51:24 MarkDuplicates Tracking 608213 as yet unmatched pairs. 16750 records in RAM. INFO 2026-06-03 20:51:25 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:10:38s. Time for last 1,000,000: 1s. Last read position: chr10:115,120,185 INFO 2026-06-03 20:51:25 MarkDuplicates Tracking 597384 as yet unmatched pairs. 5866 records in RAM. INFO 2026-06-03 20:51:27 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:10:40s. Time for last 1,000,000: 1s. Last read position: chr10:121,503,891 INFO 2026-06-03 20:51:27 MarkDuplicates Tracking 597044 as yet unmatched pairs. 5477 records in RAM. INFO 2026-06-03 20:51:29 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:10:42s. Time for last 1,000,000: 1s. Last read position: chr10:126,008,440 INFO 2026-06-03 20:51:29 MarkDuplicates Tracking 593646 as yet unmatched pairs. 2024 records in RAM. INFO 2026-06-03 20:51:30 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:10:44s. Time for last 1,000,000: 1s. Last read position: chr10:133,558,899 INFO 2026-06-03 20:51:30 MarkDuplicates Tracking 591676 as yet unmatched pairs. 7 records in RAM. INFO 2026-06-03 20:51:33 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 2s. Last read position: chr11:562,605 INFO 2026-06-03 20:51:33 MarkDuplicates Tracking 590392 as yet unmatched pairs. 66483 records in RAM. INFO 2026-06-03 20:51:35 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:10:48s. Time for last 1,000,000: 1s. Last read position: chr11:993,867 INFO 2026-06-03 20:51:35 MarkDuplicates Tracking 587508 as yet unmatched pairs. 63576 records in RAM. INFO 2026-06-03 20:51:37 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:10:50s. Time for last 1,000,000: 1s. Last read position: chr11:3,001,982 INFO 2026-06-03 20:51:37 MarkDuplicates Tracking 584804 as yet unmatched pairs. 60828 records in RAM. INFO 2026-06-03 20:51:38 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:10:51s. Time for last 1,000,000: 1s. Last read position: chr11:7,620,990 INFO 2026-06-03 20:51:38 MarkDuplicates Tracking 583017 as yet unmatched pairs. 59008 records in RAM. INFO 2026-06-03 20:51:40 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:10:53s. Time for last 1,000,000: 1s. Last read position: chr11:10,764,721 INFO 2026-06-03 20:51:40 MarkDuplicates Tracking 580939 as yet unmatched pairs. 56876 records in RAM. INFO 2026-06-03 20:51:42 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:10:55s. Time for last 1,000,000: 1s. Last read position: chr11:15,384,619 INFO 2026-06-03 20:51:42 MarkDuplicates Tracking 579089 as yet unmatched pairs. 54996 records in RAM. INFO 2026-06-03 20:51:43 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:10:57s. Time for last 1,000,000: 1s. Last read position: chr11:20,388,059 INFO 2026-06-03 20:51:43 MarkDuplicates Tracking 577767 as yet unmatched pairs. 53629 records in RAM. INFO 2026-06-03 20:51:45 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 1s. Last read position: chr11:34,651,735 INFO 2026-06-03 20:51:45 MarkDuplicates Tracking 579790 as yet unmatched pairs. 55616 records in RAM. INFO 2026-06-03 20:51:47 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:11:00s. Time for last 1,000,000: 1s. Last read position: chr11:46,378,464 INFO 2026-06-03 20:51:47 MarkDuplicates Tracking 574578 as yet unmatched pairs. 50359 records in RAM. INFO 2026-06-03 20:51:48 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:11:01s. Time for last 1,000,000: 1s. Last read position: chr11:47,723,104 INFO 2026-06-03 20:51:48 MarkDuplicates Tracking 572779 as yet unmatched pairs. 48539 records in RAM. INFO 2026-06-03 20:51:50 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:11:03s. Time for last 1,000,000: 1s. Last read position: chr11:57,795,702 INFO 2026-06-03 20:51:50 MarkDuplicates Tracking 576183 as yet unmatched pairs. 51913 records in RAM. INFO 2026-06-03 20:51:51 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:11:05s. Time for last 1,000,000: 1s. Last read position: chr11:60,902,798 INFO 2026-06-03 20:51:51 MarkDuplicates Tracking 569698 as yet unmatched pairs. 45394 records in RAM. INFO 2026-06-03 20:51:53 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:11:06s. Time for last 1,000,000: 1s. Last read position: chr11:62,146,792 INFO 2026-06-03 20:51:53 MarkDuplicates Tracking 566834 as yet unmatched pairs. 42513 records in RAM. INFO 2026-06-03 20:51:55 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:11:08s. Time for last 1,000,000: 1s. Last read position: chr11:62,525,756 INFO 2026-06-03 20:51:55 MarkDuplicates Tracking 568922 as yet unmatched pairs. 44585 records in RAM. INFO 2026-06-03 20:51:56 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:11:09s. Time for last 1,000,000: 1s. Last read position: chr11:62,559,687 INFO 2026-06-03 20:51:56 MarkDuplicates Tracking 566195 as yet unmatched pairs. 41849 records in RAM. INFO 2026-06-03 20:51:58 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:11:11s. Time for last 1,000,000: 1s. Last read position: chr11:62,824,514 INFO 2026-06-03 20:51:58 MarkDuplicates Tracking 562795 as yet unmatched pairs. 38405 records in RAM. INFO 2026-06-03 20:51:59 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:11:12s. Time for last 1,000,000: 1s. Last read position: chr11:64,286,642 INFO 2026-06-03 20:51:59 MarkDuplicates Tracking 560162 as yet unmatched pairs. 35749 records in RAM. INFO 2026-06-03 20:52:01 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:11:15s. Time for last 1,000,000: 2s. Last read position: chr11:65,110,752 INFO 2026-06-03 20:52:01 MarkDuplicates Tracking 558040 as yet unmatched pairs. 33597 records in RAM. INFO 2026-06-03 20:52:03 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:11:16s. Time for last 1,000,000: 1s. Last read position: chr11:65,579,946 INFO 2026-06-03 20:52:03 MarkDuplicates Tracking 555892 as yet unmatched pairs. 31350 records in RAM. INFO 2026-06-03 20:52:05 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:11:18s. Time for last 1,000,000: 1s. Last read position: chr11:65,856,046 INFO 2026-06-03 20:52:05 MarkDuplicates Tracking 557266 as yet unmatched pairs. 32691 records in RAM. INFO 2026-06-03 20:52:06 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:11:19s. Time for last 1,000,000: 1s. Last read position: chr11:66,643,733 INFO 2026-06-03 20:52:06 MarkDuplicates Tracking 551531 as yet unmatched pairs. 26933 records in RAM. INFO 2026-06-03 20:52:08 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:11:21s. Time for last 1,000,000: 1s. Last read position: chr11:67,435,930 INFO 2026-06-03 20:52:08 MarkDuplicates Tracking 548669 as yet unmatched pairs. 24026 records in RAM. INFO 2026-06-03 20:52:10 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:11:23s. Time for last 1,000,000: 1s. Last read position: chr11:68,411,478 INFO 2026-06-03 20:52:10 MarkDuplicates Tracking 546360 as yet unmatched pairs. 21686 records in RAM. INFO 2026-06-03 20:52:11 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:11:24s. Time for last 1,000,000: 1s. Last read position: chr11:72,015,518 INFO 2026-06-03 20:52:11 MarkDuplicates Tracking 544769 as yet unmatched pairs. 20067 records in RAM. INFO 2026-06-03 20:52:12 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:11:26s. Time for last 1,000,000: 1s. Last read position: chr11:74,949,346 INFO 2026-06-03 20:52:12 MarkDuplicates Tracking 543062 as yet unmatched pairs. 18332 records in RAM. INFO 2026-06-03 20:52:14 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:11:27s. Time for last 1,000,000: 1s. Last read position: chr11:82,850,429 INFO 2026-06-03 20:52:14 MarkDuplicates Tracking 541052 as yet unmatched pairs. 16297 records in RAM. INFO 2026-06-03 20:52:16 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:11:29s. Time for last 1,000,000: 1s. Last read position: chr11:95,184,569 INFO 2026-06-03 20:52:16 MarkDuplicates Tracking 539307 as yet unmatched pairs. 14517 records in RAM. INFO 2026-06-03 20:52:17 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:11:30s. Time for last 1,000,000: 1s. Last read position: chr11:108,052,679 INFO 2026-06-03 20:52:17 MarkDuplicates Tracking 537127 as yet unmatched pairs. 12309 records in RAM. INFO 2026-06-03 20:52:19 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:11:32s. Time for last 1,000,000: 1s. Last read position: chr11:117,229,653 INFO 2026-06-03 20:52:19 MarkDuplicates Tracking 535934 as yet unmatched pairs. 11084 records in RAM. INFO 2026-06-03 20:52:21 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:11:34s. Time for last 1,000,000: 1s. Last read position: chr11:118,627,874 INFO 2026-06-03 20:52:21 MarkDuplicates Tracking 534024 as yet unmatched pairs. 9149 records in RAM. INFO 2026-06-03 20:52:23 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:11:36s. Time for last 1,000,000: 2s. Last read position: chr11:119,664,747 INFO 2026-06-03 20:52:23 MarkDuplicates Tracking 537374 as yet unmatched pairs. 12461 records in RAM. INFO 2026-06-03 20:52:24 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:11:38s. Time for last 1,000,000: 1s. Last read position: chr11:120,137,471 INFO 2026-06-03 20:52:24 MarkDuplicates Tracking 537695 as yet unmatched pairs. 12743 records in RAM. INFO 2026-06-03 20:52:26 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:11:39s. Time for last 1,000,000: 1s. Last read position: chr11:125,595,910 INFO 2026-06-03 20:52:26 MarkDuplicates Tracking 529406 as yet unmatched pairs. 4430 records in RAM. INFO 2026-06-03 20:52:28 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:11:41s. Time for last 1,000,000: 1s. Last read position: chr11:130,189,836 INFO 2026-06-03 20:52:28 MarkDuplicates Tracking 529730 as yet unmatched pairs. 4733 records in RAM. INFO 2026-06-03 20:52:30 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:11:43s. Time for last 1,000,000: 2s. Last read position: chr12:907,922 INFO 2026-06-03 20:52:30 MarkDuplicates Tracking 525412 as yet unmatched pairs. 64835 records in RAM. INFO 2026-06-03 20:52:32 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:11:45s. Time for last 1,000,000: 1s. Last read position: chr12:6,235,490 INFO 2026-06-03 20:52:32 MarkDuplicates Tracking 527457 as yet unmatched pairs. 66843 records in RAM. INFO 2026-06-03 20:52:34 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:11:47s. Time for last 1,000,000: 1s. Last read position: chr12:6,651,141 INFO 2026-06-03 20:52:34 MarkDuplicates Tracking 520313 as yet unmatched pairs. 59683 records in RAM. INFO 2026-06-03 20:52:35 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:11:48s. Time for last 1,000,000: 1s. Last read position: chr12:7,070,336 INFO 2026-06-03 20:52:35 MarkDuplicates Tracking 519005 as yet unmatched pairs. 58362 records in RAM. INFO 2026-06-03 20:52:37 MarkDuplicates Read 368,000,000 records. Elapsed time: 00:11:50s. Time for last 1,000,000: 1s. Last read position: chr12:9,669,721 INFO 2026-06-03 20:52:37 MarkDuplicates Tracking 516759 as yet unmatched pairs. 56094 records in RAM. INFO 2026-06-03 20:52:38 MarkDuplicates Read 369,000,000 records. Elapsed time: 00:11:52s. Time for last 1,000,000: 1s. Last read position: chr12:13,213,532 INFO 2026-06-03 20:52:38 MarkDuplicates Tracking 527104 as yet unmatched pairs. 66416 records in RAM. INFO 2026-06-03 20:52:40 MarkDuplicates Read 370,000,000 records. Elapsed time: 00:11:53s. Time for last 1,000,000: 1s. Last read position: chr12:26,122,717 INFO 2026-06-03 20:52:40 MarkDuplicates Tracking 513516 as yet unmatched pairs. 52792 records in RAM. INFO 2026-06-03 20:52:41 MarkDuplicates Read 371,000,000 records. Elapsed time: 00:11:55s. Time for last 1,000,000: 1s. Last read position: chr12:42,375,045 INFO 2026-06-03 20:52:41 MarkDuplicates Tracking 512154 as yet unmatched pairs. 51398 records in RAM. INFO 2026-06-03 20:52:43 MarkDuplicates Read 372,000,000 records. Elapsed time: 00:11:56s. Time for last 1,000,000: 1s. Last read position: chr12:48,827,771 INFO 2026-06-03 20:52:43 MarkDuplicates Tracking 510133 as yet unmatched pairs. 49343 records in RAM. INFO 2026-06-03 20:52:45 MarkDuplicates Read 373,000,000 records. Elapsed time: 00:11:58s. Time for last 1,000,000: 1s. Last read position: chr12:49,129,549 INFO 2026-06-03 20:52:45 MarkDuplicates Tracking 510406 as yet unmatched pairs. 49596 records in RAM. INFO 2026-06-03 20:52:46 MarkDuplicates Read 374,000,000 records. Elapsed time: 00:12:00s. Time for last 1,000,000: 1s. Last read position: chr12:50,400,916 INFO 2026-06-03 20:52:46 MarkDuplicates Tracking 506607 as yet unmatched pairs. 45766 records in RAM. INFO 2026-06-03 20:52:48 MarkDuplicates Read 375,000,000 records. Elapsed time: 00:12:01s. Time for last 1,000,000: 1s. Last read position: chr12:52,449,776 INFO 2026-06-03 20:52:48 MarkDuplicates Tracking 507906 as yet unmatched pairs. 47045 records in RAM. INFO 2026-06-03 20:52:49 MarkDuplicates Read 376,000,000 records. Elapsed time: 00:12:02s. Time for last 1,000,000: 1s. Last read position: chr12:52,487,922 INFO 2026-06-03 20:52:49 MarkDuplicates Tracking 518343 as yet unmatched pairs. 57465 records in RAM. INFO 2026-06-03 20:52:51 MarkDuplicates Read 377,000,000 records. Elapsed time: 00:12:04s. Time for last 1,000,000: 1s. Last read position: chr12:52,492,976 INFO 2026-06-03 20:52:51 MarkDuplicates Tracking 523269 as yet unmatched pairs. 62354 records in RAM. INFO 2026-06-03 20:52:52 MarkDuplicates Read 378,000,000 records. Elapsed time: 00:12:06s. Time for last 1,000,000: 1s. Last read position: chr12:52,517,956 INFO 2026-06-03 20:52:52 MarkDuplicates Tracking 504846 as yet unmatched pairs. 43895 records in RAM. INFO 2026-06-03 20:52:54 MarkDuplicates Read 379,000,000 records. Elapsed time: 00:12:07s. Time for last 1,000,000: 1s. Last read position: chr12:53,018,863 INFO 2026-06-03 20:52:54 MarkDuplicates Tracking 498879 as yet unmatched pairs. 37888 records in RAM. INFO 2026-06-03 20:52:56 MarkDuplicates Read 380,000,000 records. Elapsed time: 00:12:09s. Time for last 1,000,000: 1s. Last read position: chr12:53,517,167 INFO 2026-06-03 20:52:56 MarkDuplicates Tracking 496650 as yet unmatched pairs. 35639 records in RAM. INFO 2026-06-03 20:52:57 MarkDuplicates Read 381,000,000 records. Elapsed time: 00:12:10s. Time for last 1,000,000: 1s. Last read position: chr12:55,719,149 INFO 2026-06-03 20:52:57 MarkDuplicates Tracking 495495 as yet unmatched pairs. 34463 records in RAM. INFO 2026-06-03 20:52:59 MarkDuplicates Read 382,000,000 records. Elapsed time: 00:12:13s. Time for last 1,000,000: 2s. Last read position: chr12:56,160,069 INFO 2026-06-03 20:52:59 MarkDuplicates Tracking 495803 as yet unmatched pairs. 34752 records in RAM. INFO 2026-06-03 20:53:02 MarkDuplicates Read 383,000,000 records. Elapsed time: 00:12:15s. Time for last 1,000,000: 2s. Last read position: chr12:56,644,825 INFO 2026-06-03 20:53:02 MarkDuplicates Tracking 492919 as yet unmatched pairs. 31858 records in RAM. INFO 2026-06-03 20:53:04 MarkDuplicates Read 384,000,000 records. Elapsed time: 00:12:17s. Time for last 1,000,000: 2s. Last read position: chr12:57,100,003 INFO 2026-06-03 20:53:04 MarkDuplicates Tracking 497963 as yet unmatched pairs. 36895 records in RAM. INFO 2026-06-03 20:53:06 MarkDuplicates Read 385,000,000 records. Elapsed time: 00:12:19s. Time for last 1,000,000: 2s. Last read position: chr12:57,195,015 INFO 2026-06-03 20:53:06 MarkDuplicates Tracking 488716 as yet unmatched pairs. 27618 records in RAM. INFO 2026-06-03 20:53:08 MarkDuplicates Read 386,000,000 records. Elapsed time: 00:12:21s. Time for last 1,000,000: 1s. Last read position: chr12:57,527,863 INFO 2026-06-03 20:53:08 MarkDuplicates Tracking 486419 as yet unmatched pairs. 25287 records in RAM. INFO 2026-06-03 20:53:09 MarkDuplicates Read 387,000,000 records. Elapsed time: 00:12:22s. Time for last 1,000,000: 1s. Last read position: chr12:66,134,419 INFO 2026-06-03 20:53:09 MarkDuplicates Tracking 483652 as yet unmatched pairs. 22495 records in RAM. INFO 2026-06-03 20:53:11 MarkDuplicates Read 388,000,000 records. Elapsed time: 00:12:24s. Time for last 1,000,000: 1s. Last read position: chr12:76,030,715 INFO 2026-06-03 20:53:11 MarkDuplicates Tracking 485969 as yet unmatched pairs. 24792 records in RAM. INFO 2026-06-03 20:53:13 MarkDuplicates Read 389,000,000 records. Elapsed time: 00:12:26s. Time for last 1,000,000: 1s. Last read position: chr12:92,842,545 INFO 2026-06-03 20:53:13 MarkDuplicates Tracking 480865 as yet unmatched pairs. 19654 records in RAM. INFO 2026-06-03 20:53:14 MarkDuplicates Read 390,000,000 records. Elapsed time: 00:12:27s. Time for last 1,000,000: 1s. Last read position: chr12:98,601,379 INFO 2026-06-03 20:53:14 MarkDuplicates Tracking 480267 as yet unmatched pairs. 19037 records in RAM. INFO 2026-06-03 20:53:16 MarkDuplicates Read 391,000,000 records. Elapsed time: 00:12:29s. Time for last 1,000,000: 1s. Last read position: chr12:105,330,881 INFO 2026-06-03 20:53:16 MarkDuplicates Tracking 478203 as yet unmatched pairs. 16951 records in RAM. INFO 2026-06-03 20:53:18 MarkDuplicates Read 392,000,000 records. Elapsed time: 00:12:31s. Time for last 1,000,000: 1s. Last read position: chr12:110,162,951 INFO 2026-06-03 20:53:18 MarkDuplicates Tracking 475510 as yet unmatched pairs. 14239 records in RAM. INFO 2026-06-03 20:53:19 MarkDuplicates Read 393,000,000 records. Elapsed time: 00:12:32s. Time for last 1,000,000: 1s. Last read position: chr12:111,933,825 INFO 2026-06-03 20:53:19 MarkDuplicates Tracking 474049 as yet unmatched pairs. 12767 records in RAM. INFO 2026-06-03 20:53:21 MarkDuplicates Read 394,000,000 records. Elapsed time: 00:12:34s. Time for last 1,000,000: 1s. Last read position: chr12:113,319,005 INFO 2026-06-03 20:53:21 MarkDuplicates Tracking 472081 as yet unmatched pairs. 10764 records in RAM. INFO 2026-06-03 20:53:23 MarkDuplicates Read 395,000,000 records. Elapsed time: 00:12:36s. Time for last 1,000,000: 1s. Last read position: chr12:120,198,958 INFO 2026-06-03 20:53:23 MarkDuplicates Tracking 471923 as yet unmatched pairs. 10561 records in RAM. INFO 2026-06-03 20:53:24 MarkDuplicates Read 396,000,000 records. Elapsed time: 00:12:37s. Time for last 1,000,000: 1s. Last read position: chr12:121,915,899 INFO 2026-06-03 20:53:24 MarkDuplicates Tracking 468216 as yet unmatched pairs. 6819 records in RAM. INFO 2026-06-03 20:53:26 MarkDuplicates Read 397,000,000 records. Elapsed time: 00:12:39s. Time for last 1,000,000: 1s. Last read position: chr12:123,404,918 INFO 2026-06-03 20:53:26 MarkDuplicates Tracking 466872 as yet unmatched pairs. 5453 records in RAM. INFO 2026-06-03 20:53:27 MarkDuplicates Read 398,000,000 records. Elapsed time: 00:12:40s. Time for last 1,000,000: 1s. Last read position: chr12:130,874,567 INFO 2026-06-03 20:53:27 MarkDuplicates Tracking 467192 as yet unmatched pairs. 5730 records in RAM. INFO 2026-06-03 20:53:29 MarkDuplicates Read 399,000,000 records. Elapsed time: 00:12:42s. Time for last 1,000,000: 1s. Last read position: chr12:132,801,824 INFO 2026-06-03 20:53:29 MarkDuplicates Tracking 462735 as yet unmatched pairs. 1243 records in RAM. INFO 2026-06-03 20:53:30 MarkDuplicates Read 400,000,000 records. Elapsed time: 00:12:43s. Time for last 1,000,000: 1s. Last read position: chr13:20,192,767 INFO 2026-06-03 20:53:30 MarkDuplicates Tracking 460896 as yet unmatched pairs. 12487 records in RAM. INFO 2026-06-03 20:53:32 MarkDuplicates Read 401,000,000 records. Elapsed time: 00:12:45s. Time for last 1,000,000: 1s. Last read position: chr13:29,535,992 INFO 2026-06-03 20:53:32 MarkDuplicates Tracking 459176 as yet unmatched pairs. 10749 records in RAM. INFO 2026-06-03 20:53:34 MarkDuplicates Read 402,000,000 records. Elapsed time: 00:12:47s. Time for last 1,000,000: 1s. Last read position: chr13:41,192,709 INFO 2026-06-03 20:53:34 MarkDuplicates Tracking 457047 as yet unmatched pairs. 8591 records in RAM. INFO 2026-06-03 20:53:35 MarkDuplicates Read 403,000,000 records. Elapsed time: 00:12:49s. Time for last 1,000,000: 1s. Last read position: chr13:48,411,994 INFO 2026-06-03 20:53:35 MarkDuplicates Tracking 456363 as yet unmatched pairs. 7875 records in RAM. INFO 2026-06-03 20:53:37 MarkDuplicates Read 404,000,000 records. Elapsed time: 00:12:50s. Time for last 1,000,000: 1s. Last read position: chr13:77,180,283 INFO 2026-06-03 20:53:37 MarkDuplicates Tracking 453668 as yet unmatched pairs. 5155 records in RAM. INFO 2026-06-03 20:53:38 MarkDuplicates Read 405,000,000 records. Elapsed time: 00:12:51s. Time for last 1,000,000: 1s. Last read position: chr13:108,479,882 INFO 2026-06-03 20:53:38 MarkDuplicates Tracking 451772 as yet unmatched pairs. 3217 records in RAM. INFO 2026-06-03 20:53:40 MarkDuplicates Read 406,000,000 records. Elapsed time: 00:12:53s. Time for last 1,000,000: 1s. Last read position: chr13:110,511,980 INFO 2026-06-03 20:53:40 MarkDuplicates Tracking 450443 as yet unmatched pairs. 1875 records in RAM. INFO 2026-06-03 20:53:42 MarkDuplicates Read 407,000,000 records. Elapsed time: 00:12:55s. Time for last 1,000,000: 1s. Last read position: chr14:21,022,877 INFO 2026-06-03 20:53:42 MarkDuplicates Tracking 448981 as yet unmatched pairs. 36509 records in RAM. INFO 2026-06-03 20:53:43 MarkDuplicates Read 408,000,000 records. Elapsed time: 00:12:57s. Time for last 1,000,000: 1s. Last read position: chr14:22,875,557 INFO 2026-06-03 20:53:43 MarkDuplicates Tracking 447638 as yet unmatched pairs. 35147 records in RAM. INFO 2026-06-03 20:53:45 MarkDuplicates Read 409,000,000 records. Elapsed time: 00:12:58s. Time for last 1,000,000: 1s. Last read position: chr14:24,098,479 INFO 2026-06-03 20:53:45 MarkDuplicates Tracking 444311 as yet unmatched pairs. 31803 records in RAM. INFO 2026-06-03 20:53:47 MarkDuplicates Read 410,000,000 records. Elapsed time: 00:13:00s. Time for last 1,000,000: 1s. Last read position: chr14:24,311,195 INFO 2026-06-03 20:53:47 MarkDuplicates Tracking 443827 as yet unmatched pairs. 31292 records in RAM. INFO 2026-06-03 20:53:48 MarkDuplicates Read 411,000,000 records. Elapsed time: 00:13:01s. Time for last 1,000,000: 1s. Last read position: chr14:33,950,451 INFO 2026-06-03 20:53:48 MarkDuplicates Tracking 445011 as yet unmatched pairs. 32454 records in RAM. INFO 2026-06-03 20:53:50 MarkDuplicates Read 412,000,000 records. Elapsed time: 00:13:03s. Time for last 1,000,000: 1s. Last read position: chr14:45,110,140 INFO 2026-06-03 20:53:50 MarkDuplicates Tracking 438440 as yet unmatched pairs. 25866 records in RAM. INFO 2026-06-03 20:53:51 MarkDuplicates Read 413,000,000 records. Elapsed time: 00:13:05s. Time for last 1,000,000: 1s. Last read position: chr14:51,701,125 INFO 2026-06-03 20:53:51 MarkDuplicates Tracking 437026 as yet unmatched pairs. 24281 records in RAM. INFO 2026-06-03 20:53:53 MarkDuplicates Read 414,000,000 records. Elapsed time: 00:13:06s. Time for last 1,000,000: 1s. Last read position: chr14:55,351,434 INFO 2026-06-03 20:53:53 MarkDuplicates Tracking 435728 as yet unmatched pairs. 22963 records in RAM. INFO 2026-06-03 20:53:55 MarkDuplicates Read 415,000,000 records. Elapsed time: 00:13:08s. Time for last 1,000,000: 1s. Last read position: chr14:63,990,414 INFO 2026-06-03 20:53:55 MarkDuplicates Tracking 434325 as yet unmatched pairs. 21547 records in RAM. INFO 2026-06-03 20:53:56 MarkDuplicates Read 416,000,000 records. Elapsed time: 00:13:09s. Time for last 1,000,000: 1s. Last read position: chr14:64,743,055 INFO 2026-06-03 20:53:56 MarkDuplicates Tracking 432232 as yet unmatched pairs. 19444 records in RAM. INFO 2026-06-03 20:53:58 MarkDuplicates Read 417,000,000 records. Elapsed time: 00:13:11s. Time for last 1,000,000: 1s. Last read position: chr14:69,768,162 INFO 2026-06-03 20:53:58 MarkDuplicates Tracking 430558 as yet unmatched pairs. 17747 records in RAM. INFO 2026-06-03 20:53:59 MarkDuplicates Read 418,000,000 records. Elapsed time: 00:13:13s. Time for last 1,000,000: 1s. Last read position: chr14:73,739,117 INFO 2026-06-03 20:53:59 MarkDuplicates Tracking 428107 as yet unmatched pairs. 15276 records in RAM. INFO 2026-06-03 20:54:01 MarkDuplicates Read 419,000,000 records. Elapsed time: 00:13:14s. Time for last 1,000,000: 1s. Last read position: chr14:76,778,945 INFO 2026-06-03 20:54:01 MarkDuplicates Tracking 426394 as yet unmatched pairs. 13538 records in RAM. INFO 2026-06-03 20:54:02 MarkDuplicates Read 420,000,000 records. Elapsed time: 00:13:16s. Time for last 1,000,000: 1s. Last read position: chr14:92,716,211 INFO 2026-06-03 20:54:02 MarkDuplicates Tracking 424578 as yet unmatched pairs. 11697 records in RAM. INFO 2026-06-03 20:54:04 MarkDuplicates Read 421,000,000 records. Elapsed time: 00:13:17s. Time for last 1,000,000: 1s. Last read position: chr14:102,016,843 INFO 2026-06-03 20:54:04 MarkDuplicates Tracking 422677 as yet unmatched pairs. 9780 records in RAM. INFO 2026-06-03 20:54:06 MarkDuplicates Read 422,000,000 records. Elapsed time: 00:13:19s. Time for last 1,000,000: 1s. Last read position: chr14:104,884,273 INFO 2026-06-03 20:54:06 MarkDuplicates Tracking 420588 as yet unmatched pairs. 7676 records in RAM. INFO 2026-06-03 20:54:07 MarkDuplicates Read 423,000,000 records. Elapsed time: 00:13:21s. Time for last 1,000,000: 1s. Last read position: chr14:105,643,359 INFO 2026-06-03 20:54:07 MarkDuplicates Tracking 421750 as yet unmatched pairs. 8826 records in RAM. INFO 2026-06-03 20:54:09 MarkDuplicates Read 424,000,000 records. Elapsed time: 00:13:22s. Time for last 1,000,000: 1s. Last read position: chr14:105,707,462 INFO 2026-06-03 20:54:09 MarkDuplicates Tracking 439920 as yet unmatched pairs. 26976 records in RAM. INFO 2026-06-03 20:54:11 MarkDuplicates Read 425,000,000 records. Elapsed time: 00:13:24s. Time for last 1,000,000: 1s. Last read position: chr14:105,741,614 INFO 2026-06-03 20:54:11 MarkDuplicates Tracking 430107 as yet unmatched pairs. 17138 records in RAM. INFO 2026-06-03 20:54:12 MarkDuplicates Read 426,000,000 records. Elapsed time: 00:13:25s. Time for last 1,000,000: 1s. Last read position: chr14:105,770,293 INFO 2026-06-03 20:54:12 MarkDuplicates Tracking 416202 as yet unmatched pairs. 3215 records in RAM. INFO 2026-06-03 20:54:14 MarkDuplicates Read 427,000,000 records. Elapsed time: 00:13:27s. Time for last 1,000,000: 1s. Last read position: chr15:22,851,765 INFO 2026-06-03 20:54:14 MarkDuplicates Tracking 412956 as yet unmatched pairs. 35045 records in RAM. INFO 2026-06-03 20:54:16 MarkDuplicates Read 428,000,000 records. Elapsed time: 00:13:29s. Time for last 1,000,000: 2s. Last read position: chr15:28,321,431 INFO 2026-06-03 20:54:16 MarkDuplicates Tracking 410792 as yet unmatched pairs. 32858 records in RAM. INFO 2026-06-03 20:54:18 MarkDuplicates Read 429,000,000 records. Elapsed time: 00:13:31s. Time for last 1,000,000: 1s. Last read position: chr15:34,341,967 INFO 2026-06-03 20:54:18 MarkDuplicates Tracking 412257 as yet unmatched pairs. 34305 records in RAM. INFO 2026-06-03 20:54:20 MarkDuplicates Read 430,000,000 records. Elapsed time: 00:13:33s. Time for last 1,000,000: 1s. Last read position: chr15:40,472,065 INFO 2026-06-03 20:54:20 MarkDuplicates Tracking 408106 as yet unmatched pairs. 30120 records in RAM. INFO 2026-06-03 20:54:21 MarkDuplicates Read 431,000,000 records. Elapsed time: 00:13:34s. Time for last 1,000,000: 1s. Last read position: chr15:41,711,224 INFO 2026-06-03 20:54:21 MarkDuplicates Tracking 406176 as yet unmatched pairs. 28174 records in RAM. INFO 2026-06-03 20:54:23 MarkDuplicates Read 432,000,000 records. Elapsed time: 00:13:36s. Time for last 1,000,000: 1s. Last read position: chr15:42,728,688 INFO 2026-06-03 20:54:23 MarkDuplicates Tracking 404059 as yet unmatched pairs. 26040 records in RAM. INFO 2026-06-03 20:54:24 MarkDuplicates Read 433,000,000 records. Elapsed time: 00:13:37s. Time for last 1,000,000: 1s. Last read position: chr15:43,801,730 INFO 2026-06-03 20:54:24 MarkDuplicates Tracking 402467 as yet unmatched pairs. 24433 records in RAM. INFO 2026-06-03 20:54:26 MarkDuplicates Read 434,000,000 records. Elapsed time: 00:13:39s. Time for last 1,000,000: 1s. Last read position: chr15:48,425,739 INFO 2026-06-03 20:54:26 MarkDuplicates Tracking 401180 as yet unmatched pairs. 23132 records in RAM. INFO 2026-06-03 20:54:28 MarkDuplicates Read 435,000,000 records. Elapsed time: 00:13:41s. Time for last 1,000,000: 1s. Last read position: chr15:52,383,174 INFO 2026-06-03 20:54:28 MarkDuplicates Tracking 399114 as yet unmatched pairs. 21045 records in RAM. INFO 2026-06-03 20:54:29 MarkDuplicates Read 436,000,000 records. Elapsed time: 00:13:42s. Time for last 1,000,000: 1s. Last read position: chr15:60,347,546 INFO 2026-06-03 20:54:29 MarkDuplicates Tracking 403230 as yet unmatched pairs. 25141 records in RAM. INFO 2026-06-03 20:54:31 MarkDuplicates Read 437,000,000 records. Elapsed time: 00:13:44s. Time for last 1,000,000: 1s. Last read position: chr15:64,129,994 INFO 2026-06-03 20:54:31 MarkDuplicates Tracking 396212 as yet unmatched pairs. 18094 records in RAM. INFO 2026-06-03 20:54:32 MarkDuplicates Read 438,000,000 records. Elapsed time: 00:13:46s. Time for last 1,000,000: 1s. Last read position: chr15:66,501,841 INFO 2026-06-03 20:54:32 MarkDuplicates Tracking 396040 as yet unmatched pairs. 17903 records in RAM. INFO 2026-06-03 20:54:34 MarkDuplicates Read 439,000,000 records. Elapsed time: 00:13:47s. Time for last 1,000,000: 1s. Last read position: chr15:72,206,854 INFO 2026-06-03 20:54:34 MarkDuplicates Tracking 393643 as yet unmatched pairs. 15483 records in RAM. INFO 2026-06-03 20:54:35 MarkDuplicates Read 440,000,000 records. Elapsed time: 00:13:48s. Time for last 1,000,000: 1s. Last read position: chr15:74,035,168 INFO 2026-06-03 20:54:35 MarkDuplicates Tracking 394654 as yet unmatched pairs. 16474 records in RAM. INFO 2026-06-03 20:54:37 MarkDuplicates Read 441,000,000 records. Elapsed time: 00:13:50s. Time for last 1,000,000: 1s. Last read position: chr15:75,617,527 INFO 2026-06-03 20:54:37 MarkDuplicates Tracking 388250 as yet unmatched pairs. 10043 records in RAM. INFO 2026-06-03 20:54:39 MarkDuplicates Read 442,000,000 records. Elapsed time: 00:13:52s. Time for last 1,000,000: 1s. Last read position: chr15:80,749,636 INFO 2026-06-03 20:54:39 MarkDuplicates Tracking 388819 as yet unmatched pairs. 10589 records in RAM. INFO 2026-06-03 20:54:41 MarkDuplicates Read 443,000,000 records. Elapsed time: 00:13:54s. Time for last 1,000,000: 1s. Last read position: chr15:85,207,028 INFO 2026-06-03 20:54:41 MarkDuplicates Tracking 384268 as yet unmatched pairs. 6013 records in RAM. INFO 2026-06-03 20:54:42 MarkDuplicates Read 444,000,000 records. Elapsed time: 00:13:55s. Time for last 1,000,000: 1s. Last read position: chr15:90,087,148 INFO 2026-06-03 20:54:42 MarkDuplicates Tracking 382914 as yet unmatched pairs. 4645 records in RAM. INFO 2026-06-03 20:54:43 MarkDuplicates Read 445,000,000 records. Elapsed time: 00:13:57s. Time for last 1,000,000: 1s. Last read position: chr15:92,937,603 INFO 2026-06-03 20:54:43 MarkDuplicates Tracking 380475 as yet unmatched pairs. 2184 records in RAM. INFO 2026-06-03 20:54:45 MarkDuplicates Read 446,000,000 records. Elapsed time: 00:13:58s. Time for last 1,000,000: 1s. Last read position: chr16:54,018 INFO 2026-06-03 20:54:45 MarkDuplicates Tracking 378897 as yet unmatched pairs. 58507 records in RAM. INFO 2026-06-03 20:54:47 MarkDuplicates Read 447,000,000 records. Elapsed time: 00:14:00s. Time for last 1,000,000: 1s. Last read position: chr16:1,220,379 INFO 2026-06-03 20:54:47 MarkDuplicates Tracking 375809 as yet unmatched pairs. 55402 records in RAM. INFO 2026-06-03 20:54:49 MarkDuplicates Read 448,000,000 records. Elapsed time: 00:14:02s. Time for last 1,000,000: 1s. Last read position: chr16:2,057,160 INFO 2026-06-03 20:54:49 MarkDuplicates Tracking 373461 as yet unmatched pairs. 53041 records in RAM. INFO 2026-06-03 20:54:50 MarkDuplicates Read 449,000,000 records. Elapsed time: 00:14:03s. Time for last 1,000,000: 1s. Last read position: chr16:2,757,553 INFO 2026-06-03 20:54:50 MarkDuplicates Tracking 372155 as yet unmatched pairs. 51721 records in RAM. INFO 2026-06-03 20:54:52 MarkDuplicates Read 450,000,000 records. Elapsed time: 00:14:05s. Time for last 1,000,000: 1s. Last read position: chr16:2,975,481 INFO 2026-06-03 20:54:52 MarkDuplicates Tracking 369249 as yet unmatched pairs. 48808 records in RAM. INFO 2026-06-03 20:54:53 MarkDuplicates Read 451,000,000 records. Elapsed time: 00:14:07s. Time for last 1,000,000: 1s. Last read position: chr16:4,609,678 INFO 2026-06-03 20:54:53 MarkDuplicates Tracking 366812 as yet unmatched pairs. 46346 records in RAM. INFO 2026-06-03 20:54:55 MarkDuplicates Read 452,000,000 records. Elapsed time: 00:14:08s. Time for last 1,000,000: 1s. Last read position: chr16:4,899,286 INFO 2026-06-03 20:54:55 MarkDuplicates Tracking 367589 as yet unmatched pairs. 47113 records in RAM. INFO 2026-06-03 20:54:57 MarkDuplicates Read 453,000,000 records. Elapsed time: 00:14:10s. Time for last 1,000,000: 1s. Last read position: chr16:14,210,242 INFO 2026-06-03 20:54:57 MarkDuplicates Tracking 363446 as yet unmatched pairs. 42953 records in RAM. INFO 2026-06-03 20:54:58 MarkDuplicates Read 454,000,000 records. Elapsed time: 00:14:11s. Time for last 1,000,000: 1s. Last read position: chr16:15,130,769 INFO 2026-06-03 20:54:58 MarkDuplicates Tracking 361341 as yet unmatched pairs. 40832 records in RAM. INFO 2026-06-03 20:54:59 MarkDuplicates Read 455,000,000 records. Elapsed time: 00:14:12s. Time for last 1,000,000: 1s. Last read position: chr16:16,348,712 INFO 2026-06-03 20:54:59 MarkDuplicates Tracking 360754 as yet unmatched pairs. 40238 records in RAM. INFO 2026-06-03 20:55:01 MarkDuplicates Read 456,000,000 records. Elapsed time: 00:14:14s. Time for last 1,000,000: 1s. Last read position: chr16:18,520,773 INFO 2026-06-03 20:55:01 MarkDuplicates Tracking 360105 as yet unmatched pairs. 39584 records in RAM. INFO 2026-06-03 20:55:02 MarkDuplicates Read 457,000,000 records. Elapsed time: 00:14:15s. Time for last 1,000,000: 1s. Last read position: chr16:21,404,781 INFO 2026-06-03 20:55:02 MarkDuplicates Tracking 359196 as yet unmatched pairs. 38658 records in RAM. INFO 2026-06-03 20:55:03 MarkDuplicates Read 458,000,000 records. Elapsed time: 00:14:16s. Time for last 1,000,000: 1s. Last read position: chr16:21,891,914 INFO 2026-06-03 20:55:03 MarkDuplicates Tracking 357107 as yet unmatched pairs. 36563 records in RAM. INFO 2026-06-03 20:55:05 MarkDuplicates Read 459,000,000 records. Elapsed time: 00:14:18s. Time for last 1,000,000: 1s. Last read position: chr16:23,388,998 INFO 2026-06-03 20:55:05 MarkDuplicates Tracking 356371 as yet unmatched pairs. 35817 records in RAM. INFO 2026-06-03 20:55:07 MarkDuplicates Read 460,000,000 records. Elapsed time: 00:14:20s. Time for last 1,000,000: 2s. Last read position: chr16:28,169,848 INFO 2026-06-03 20:55:07 MarkDuplicates Tracking 354489 as yet unmatched pairs. 33918 records in RAM. INFO 2026-06-03 20:55:09 MarkDuplicates Read 461,000,000 records. Elapsed time: 00:14:22s. Time for last 1,000,000: 2s. Last read position: chr16:29,383,995 INFO 2026-06-03 20:55:09 MarkDuplicates Tracking 353351 as yet unmatched pairs. 32762 records in RAM. INFO 2026-06-03 20:55:10 MarkDuplicates Read 462,000,000 records. Elapsed time: 00:14:24s. Time for last 1,000,000: 1s. Last read position: chr16:29,844,765 INFO 2026-06-03 20:55:10 MarkDuplicates Tracking 352212 as yet unmatched pairs. 31612 records in RAM. INFO 2026-06-03 20:55:12 MarkDuplicates Read 463,000,000 records. Elapsed time: 00:14:25s. Time for last 1,000,000: 1s. Last read position: chr16:30,070,161 INFO 2026-06-03 20:55:12 MarkDuplicates Tracking 357995 as yet unmatched pairs. 37380 records in RAM. INFO 2026-06-03 20:55:14 MarkDuplicates Read 464,000,000 records. Elapsed time: 00:14:27s. Time for last 1,000,000: 1s. Last read position: chr16:30,417,932 INFO 2026-06-03 20:55:14 MarkDuplicates Tracking 348267 as yet unmatched pairs. 27644 records in RAM. INFO 2026-06-03 20:55:16 MarkDuplicates Read 465,000,000 records. Elapsed time: 00:14:29s. Time for last 1,000,000: 1s. Last read position: chr16:30,958,100 INFO 2026-06-03 20:55:16 MarkDuplicates Tracking 346032 as yet unmatched pairs. 25390 records in RAM. INFO 2026-06-03 20:55:17 MarkDuplicates Read 466,000,000 records. Elapsed time: 00:14:30s. Time for last 1,000,000: 1s. Last read position: chr16:31,191,444 INFO 2026-06-03 20:55:17 MarkDuplicates Tracking 344582 as yet unmatched pairs. 23918 records in RAM. INFO 2026-06-03 20:55:19 MarkDuplicates Read 467,000,000 records. Elapsed time: 00:14:32s. Time for last 1,000,000: 1s. Last read position: chr16:51,646,718 INFO 2026-06-03 20:55:19 MarkDuplicates Tracking 342606 as yet unmatched pairs. 21921 records in RAM. INFO 2026-06-03 20:55:20 MarkDuplicates Read 468,000,000 records. Elapsed time: 00:14:33s. Time for last 1,000,000: 1s. Last read position: chr16:57,069,861 INFO 2026-06-03 20:55:20 MarkDuplicates Tracking 341034 as yet unmatched pairs. 20329 records in RAM. INFO 2026-06-03 20:55:22 MarkDuplicates Read 469,000,000 records. Elapsed time: 00:14:35s. Time for last 1,000,000: 1s. Last read position: chr16:58,709,544 INFO 2026-06-03 20:55:22 MarkDuplicates Tracking 339575 as yet unmatched pairs. 18858 records in RAM. INFO 2026-06-03 20:55:23 MarkDuplicates Read 470,000,000 records. Elapsed time: 00:14:36s. Time for last 1,000,000: 1s. Last read position: chr16:67,645,549 INFO 2026-06-03 20:55:23 MarkDuplicates Tracking 336519 as yet unmatched pairs. 15780 records in RAM. INFO 2026-06-03 20:55:25 MarkDuplicates Read 471,000,000 records. Elapsed time: 00:14:38s. Time for last 1,000,000: 1s. Last read position: chr16:68,684,794 INFO 2026-06-03 20:55:25 MarkDuplicates Tracking 336851 as yet unmatched pairs. 16091 records in RAM. INFO 2026-06-03 20:55:27 MarkDuplicates Read 472,000,000 records. Elapsed time: 00:14:40s. Time for last 1,000,000: 1s. Last read position: chr16:69,626,446 INFO 2026-06-03 20:55:27 MarkDuplicates Tracking 332932 as yet unmatched pairs. 12160 records in RAM. INFO 2026-06-03 20:55:28 MarkDuplicates Read 473,000,000 records. Elapsed time: 00:14:41s. Time for last 1,000,000: 1s. Last read position: chr16:71,734,609 INFO 2026-06-03 20:55:28 MarkDuplicates Tracking 331181 as yet unmatched pairs. 10392 records in RAM. INFO 2026-06-03 20:55:30 MarkDuplicates Read 474,000,000 records. Elapsed time: 00:14:43s. Time for last 1,000,000: 1s. Last read position: chr16:75,568,199 INFO 2026-06-03 20:55:30 MarkDuplicates Tracking 329322 as yet unmatched pairs. 8519 records in RAM. INFO 2026-06-03 20:55:31 MarkDuplicates Read 475,000,000 records. Elapsed time: 00:14:44s. Time for last 1,000,000: 1s. Last read position: chr16:85,634,066 INFO 2026-06-03 20:55:31 MarkDuplicates Tracking 326849 as yet unmatched pairs. 5998 records in RAM. INFO 2026-06-03 20:55:33 MarkDuplicates Read 476,000,000 records. Elapsed time: 00:14:46s. Time for last 1,000,000: 1s. Last read position: chr16:88,722,240 INFO 2026-06-03 20:55:33 MarkDuplicates Tracking 325125 as yet unmatched pairs. 4259 records in RAM. INFO 2026-06-03 20:55:34 MarkDuplicates Read 477,000,000 records. Elapsed time: 00:14:47s. Time for last 1,000,000: 1s. Last read position: chr16:89,695,310 INFO 2026-06-03 20:55:34 MarkDuplicates Tracking 322437 as yet unmatched pairs. 1555 records in RAM. INFO 2026-06-03 20:55:37 MarkDuplicates Read 478,000,000 records. Elapsed time: 00:14:50s. Time for last 1,000,000: 2s. Last read position: chr17:1,361,099 INFO 2026-06-03 20:55:37 MarkDuplicates Tracking 326972 as yet unmatched pairs. 108188 records in RAM. INFO 2026-06-03 20:55:38 MarkDuplicates Read 479,000,000 records. Elapsed time: 00:14:51s. Time for last 1,000,000: 1s. Last read position: chr17:1,726,794 INFO 2026-06-03 20:55:38 MarkDuplicates Tracking 318014 as yet unmatched pairs. 99227 records in RAM. INFO 2026-06-03 20:55:40 MarkDuplicates Read 480,000,000 records. Elapsed time: 00:14:53s. Time for last 1,000,000: 1s. Last read position: chr17:3,941,273 INFO 2026-06-03 20:55:40 MarkDuplicates Tracking 316078 as yet unmatched pairs. 97284 records in RAM. INFO 2026-06-03 20:55:42 MarkDuplicates Read 481,000,000 records. Elapsed time: 00:14:55s. Time for last 1,000,000: 1s. Last read position: chr17:4,896,708 INFO 2026-06-03 20:55:42 MarkDuplicates Tracking 315247 as yet unmatched pairs. 96444 records in RAM. INFO 2026-06-03 20:55:43 MarkDuplicates Read 482,000,000 records. Elapsed time: 00:14:56s. Time for last 1,000,000: 1s. Last read position: chr17:7,038,380 INFO 2026-06-03 20:55:43 MarkDuplicates Tracking 311747 as yet unmatched pairs. 92940 records in RAM. INFO 2026-06-03 20:55:45 MarkDuplicates Read 483,000,000 records. Elapsed time: 00:14:58s. Time for last 1,000,000: 1s. Last read position: chr17:7,417,150 INFO 2026-06-03 20:55:45 MarkDuplicates Tracking 309722 as yet unmatched pairs. 90907 records in RAM. INFO 2026-06-03 20:55:47 MarkDuplicates Read 484,000,000 records. Elapsed time: 00:15:00s. Time for last 1,000,000: 1s. Last read position: chr17:7,579,629 INFO 2026-06-03 20:55:47 MarkDuplicates Tracking 308957 as yet unmatched pairs. 90135 records in RAM. INFO 2026-06-03 20:55:48 MarkDuplicates Read 485,000,000 records. Elapsed time: 00:15:01s. Time for last 1,000,000: 1s. Last read position: chr17:8,228,187 INFO 2026-06-03 20:55:48 MarkDuplicates Tracking 306297 as yet unmatched pairs. 87471 records in RAM. INFO 2026-06-03 20:55:50 MarkDuplicates Read 486,000,000 records. Elapsed time: 00:15:03s. Time for last 1,000,000: 1s. Last read position: chr17:15,651,316 INFO 2026-06-03 20:55:50 MarkDuplicates Tracking 308145 as yet unmatched pairs. 89310 records in RAM. INFO 2026-06-03 20:55:52 MarkDuplicates Read 487,000,000 records. Elapsed time: 00:15:05s. Time for last 1,000,000: 2s. Last read position: chr17:17,811,663 INFO 2026-06-03 20:55:52 MarkDuplicates Tracking 302288 as yet unmatched pairs. 83446 records in RAM. INFO 2026-06-03 20:55:54 MarkDuplicates Read 488,000,000 records. Elapsed time: 00:15:07s. Time for last 1,000,000: 1s. Last read position: chr17:18,798,903 INFO 2026-06-03 20:55:54 MarkDuplicates Tracking 302011 as yet unmatched pairs. 83159 records in RAM. INFO 2026-06-03 20:55:56 MarkDuplicates Read 489,000,000 records. Elapsed time: 00:15:09s. Time for last 1,000,000: 1s. Last read position: chr17:27,642,285 INFO 2026-06-03 20:55:56 MarkDuplicates Tracking 302227 as yet unmatched pairs. 83370 records in RAM. INFO 2026-06-03 20:55:57 MarkDuplicates Read 490,000,000 records. Elapsed time: 00:15:11s. Time for last 1,000,000: 1s. Last read position: chr17:28,748,331 INFO 2026-06-03 20:55:57 MarkDuplicates Tracking 297639 as yet unmatched pairs. 78775 records in RAM. INFO 2026-06-03 20:55:59 MarkDuplicates Read 491,000,000 records. Elapsed time: 00:15:12s. Time for last 1,000,000: 1s. Last read position: chr17:30,922,018 INFO 2026-06-03 20:55:59 MarkDuplicates Tracking 294613 as yet unmatched pairs. 75737 records in RAM. INFO 2026-06-03 20:56:01 MarkDuplicates Read 492,000,000 records. Elapsed time: 00:15:14s. Time for last 1,000,000: 1s. Last read position: chr17:35,259,064 INFO 2026-06-03 20:56:01 MarkDuplicates Tracking 293821 as yet unmatched pairs. 74927 records in RAM. INFO 2026-06-03 20:56:02 MarkDuplicates Read 493,000,000 records. Elapsed time: 00:15:15s. Time for last 1,000,000: 1s. Last read position: chr17:36,509,075 INFO 2026-06-03 20:56:02 MarkDuplicates Tracking 291887 as yet unmatched pairs. 72983 records in RAM. INFO 2026-06-03 20:56:04 MarkDuplicates Read 494,000,000 records. Elapsed time: 00:15:17s. Time for last 1,000,000: 1s. Last read position: chr17:38,469,144 INFO 2026-06-03 20:56:04 MarkDuplicates Tracking 291139 as yet unmatched pairs. 72230 records in RAM. INFO 2026-06-03 20:56:05 MarkDuplicates Read 495,000,000 records. Elapsed time: 00:15:18s. Time for last 1,000,000: 1s. Last read position: chr17:39,707,032 INFO 2026-06-03 20:56:05 MarkDuplicates Tracking 290201 as yet unmatched pairs. 71281 records in RAM. INFO 2026-06-03 20:56:07 MarkDuplicates Read 496,000,000 records. Elapsed time: 00:15:20s. Time for last 1,000,000: 1s. Last read position: chr17:40,260,578 INFO 2026-06-03 20:56:07 MarkDuplicates Tracking 286297 as yet unmatched pairs. 67372 records in RAM. INFO 2026-06-03 20:58:06 MarkDuplicates Read 497,000,000 records. Elapsed time: 00:17:20s. Time for last 1,000,000: 119s. Last read position: chr17:41,502,500 INFO 2026-06-03 20:58:06 MarkDuplicates Tracking 303867 as yet unmatched pairs. 84931 records in RAM. INFO 2026-06-03 20:58:09 MarkDuplicates Read 498,000,000 records. Elapsed time: 00:17:22s. Time for last 1,000,000: 2s. Last read position: chr17:41,505,257 INFO 2026-06-03 20:58:09 MarkDuplicates Tracking 295110 as yet unmatched pairs. 76171 records in RAM. INFO 2026-06-03 20:58:11 MarkDuplicates Read 499,000,000 records. Elapsed time: 00:17:24s. Time for last 1,000,000: 2s. Last read position: chr17:41,515,978 INFO 2026-06-03 20:58:11 MarkDuplicates Tracking 299817 as yet unmatched pairs. 80873 records in RAM. INFO 2026-06-03 20:58:12 MarkDuplicates Read 500,000,000 records. Elapsed time: 00:17:25s. Time for last 1,000,000: 1s. Last read position: chr17:41,518,667 INFO 2026-06-03 20:58:12 MarkDuplicates Tracking 286778 as yet unmatched pairs. 67827 records in RAM. INFO 2026-06-03 20:58:14 MarkDuplicates Read 501,000,000 records. Elapsed time: 00:17:27s. Time for last 1,000,000: 1s. Last read position: chr17:41,619,528 INFO 2026-06-03 20:58:14 MarkDuplicates Tracking 289142 as yet unmatched pairs. 70183 records in RAM. INFO 2026-06-03 20:58:15 MarkDuplicates Read 502,000,000 records. Elapsed time: 00:17:28s. Time for last 1,000,000: 1s. Last read position: chr17:41,689,786 INFO 2026-06-03 20:58:15 MarkDuplicates Tracking 274260 as yet unmatched pairs. 55285 records in RAM. INFO 2026-06-03 20:58:17 MarkDuplicates Read 503,000,000 records. Elapsed time: 00:17:30s. Time for last 1,000,000: 1s. Last read position: chr17:41,968,390 INFO 2026-06-03 20:58:17 MarkDuplicates Tracking 271873 as yet unmatched pairs. 52883 records in RAM. INFO 2026-06-03 20:58:19 MarkDuplicates Read 504,000,000 records. Elapsed time: 00:17:32s. Time for last 1,000,000: 1s. Last read position: chr17:42,718,460 INFO 2026-06-03 20:58:19 MarkDuplicates Tracking 268766 as yet unmatched pairs. 49756 records in RAM. INFO 2026-06-03 20:58:20 MarkDuplicates Read 505,000,000 records. Elapsed time: 00:17:33s. Time for last 1,000,000: 1s. Last read position: chr17:44,349,469 INFO 2026-06-03 20:58:20 MarkDuplicates Tracking 269121 as yet unmatched pairs. 50103 records in RAM. INFO 2026-06-03 20:58:22 MarkDuplicates Read 506,000,000 records. Elapsed time: 00:17:35s. Time for last 1,000,000: 1s. Last read position: chr17:45,518,050 INFO 2026-06-03 20:58:22 MarkDuplicates Tracking 264789 as yet unmatched pairs. 45760 records in RAM. INFO 2026-06-03 20:58:23 MarkDuplicates Read 507,000,000 records. Elapsed time: 00:17:37s. Time for last 1,000,000: 1s. Last read position: chr17:47,676,462 INFO 2026-06-03 20:58:23 MarkDuplicates Tracking 263941 as yet unmatched pairs. 44901 records in RAM. INFO 2026-06-03 20:58:25 MarkDuplicates Read 508,000,000 records. Elapsed time: 00:17:38s. Time for last 1,000,000: 1s. Last read position: chr17:50,088,095 INFO 2026-06-03 20:58:25 MarkDuplicates Tracking 262066 as yet unmatched pairs. 43016 records in RAM. INFO 2026-06-03 20:58:27 MarkDuplicates Read 509,000,000 records. Elapsed time: 00:17:40s. Time for last 1,000,000: 2s. Last read position: chr17:50,187,522 INFO 2026-06-03 20:58:27 MarkDuplicates Tracking 295239 as yet unmatched pairs. 76181 records in RAM. INFO 2026-06-03 20:58:29 MarkDuplicates Read 510,000,000 records. Elapsed time: 00:17:42s. Time for last 1,000,000: 1s. Last read position: chr17:50,189,376 INFO 2026-06-03 20:58:29 MarkDuplicates Tracking 275715 as yet unmatched pairs. 56648 records in RAM. INFO 2026-06-03 20:58:31 MarkDuplicates Read 511,000,000 records. Elapsed time: 00:17:44s. Time for last 1,000,000: 1s. Last read position: chr17:50,190,882 INFO 2026-06-03 20:58:31 MarkDuplicates Tracking 275672 as yet unmatched pairs. 56590 records in RAM. INFO 2026-06-03 20:58:33 MarkDuplicates Read 512,000,000 records. Elapsed time: 00:17:46s. Time for last 1,000,000: 1s. Last read position: chr17:50,193,018 INFO 2026-06-03 20:58:33 MarkDuplicates Tracking 294435 as yet unmatched pairs. 75342 records in RAM. INFO 2026-06-03 20:58:34 MarkDuplicates Read 513,000,000 records. Elapsed time: 00:17:47s. Time for last 1,000,000: 1s. Last read position: chr17:50,195,046 INFO 2026-06-03 20:58:34 MarkDuplicates Tracking 289489 as yet unmatched pairs. 70383 records in RAM. INFO 2026-06-03 20:58:36 MarkDuplicates Read 514,000,000 records. Elapsed time: 00:17:49s. Time for last 1,000,000: 1s. Last read position: chr17:50,196,339 INFO 2026-06-03 20:58:36 MarkDuplicates Tracking 287658 as yet unmatched pairs. 68545 records in RAM. INFO 2026-06-03 20:58:38 MarkDuplicates Read 515,000,000 records. Elapsed time: 00:17:51s. Time for last 1,000,000: 1s. Last read position: chr17:50,199,263 INFO 2026-06-03 20:58:38 MarkDuplicates Tracking 270826 as yet unmatched pairs. 51709 records in RAM. INFO 2026-06-03 20:58:39 MarkDuplicates Read 516,000,000 records. Elapsed time: 00:17:52s. Time for last 1,000,000: 1s. Last read position: chr17:51,268,882 INFO 2026-06-03 20:58:39 MarkDuplicates Tracking 243970 as yet unmatched pairs. 24843 records in RAM. INFO 2026-06-03 20:58:41 MarkDuplicates Read 517,000,000 records. Elapsed time: 00:17:54s. Time for last 1,000,000: 1s. Last read position: chr17:59,660,544 INFO 2026-06-03 20:58:41 MarkDuplicates Tracking 245811 as yet unmatched pairs. 26671 records in RAM. INFO 2026-06-03 20:58:42 MarkDuplicates Read 518,000,000 records. Elapsed time: 00:17:55s. Time for last 1,000,000: 1s. Last read position: chr17:61,401,859 INFO 2026-06-03 20:58:42 MarkDuplicates Tracking 240320 as yet unmatched pairs. 21166 records in RAM. INFO 2026-06-03 20:58:44 MarkDuplicates Read 519,000,000 records. Elapsed time: 00:17:57s. Time for last 1,000,000: 1s. Last read position: chr17:64,213,379 INFO 2026-06-03 20:58:44 MarkDuplicates Tracking 238555 as yet unmatched pairs. 19394 records in RAM. INFO 2026-06-03 20:58:45 MarkDuplicates Read 520,000,000 records. Elapsed time: 00:17:58s. Time for last 1,000,000: 1s. Last read position: chr17:68,126,733 INFO 2026-06-03 20:58:45 MarkDuplicates Tracking 236644 as yet unmatched pairs. 17473 records in RAM. INFO 2026-06-03 20:58:47 MarkDuplicates Read 521,000,000 records. Elapsed time: 00:18:00s. Time for last 1,000,000: 1s. Last read position: chr17:75,093,700 INFO 2026-06-03 20:58:47 MarkDuplicates Tracking 234685 as yet unmatched pairs. 15496 records in RAM. INFO 2026-06-03 20:58:48 MarkDuplicates Read 522,000,000 records. Elapsed time: 00:18:01s. Time for last 1,000,000: 1s. Last read position: chr17:75,730,311 INFO 2026-06-03 20:58:48 MarkDuplicates Tracking 236019 as yet unmatched pairs. 16824 records in RAM. INFO 2026-06-03 20:58:50 MarkDuplicates Read 523,000,000 records. Elapsed time: 00:18:03s. Time for last 1,000,000: 1s. Last read position: chr17:75,948,307 INFO 2026-06-03 20:58:50 MarkDuplicates Tracking 230475 as yet unmatched pairs. 11255 records in RAM. INFO 2026-06-03 20:58:52 MarkDuplicates Read 524,000,000 records. Elapsed time: 00:18:05s. Time for last 1,000,000: 1s. Last read position: chr17:76,685,109 INFO 2026-06-03 20:58:52 MarkDuplicates Tracking 228088 as yet unmatched pairs. 8858 records in RAM. INFO 2026-06-03 20:58:54 MarkDuplicates Read 525,000,000 records. Elapsed time: 00:18:07s. Time for last 1,000,000: 2s. Last read position: chr17:80,273,388 INFO 2026-06-03 20:58:54 MarkDuplicates Tracking 226201 as yet unmatched pairs. 6958 records in RAM. INFO 2026-06-03 20:58:56 MarkDuplicates Read 526,000,000 records. Elapsed time: 00:18:09s. Time for last 1,000,000: 2s. Last read position: chr17:81,565,531 INFO 2026-06-03 20:58:56 MarkDuplicates Tracking 224707 as yet unmatched pairs. 5448 records in RAM. INFO 2026-06-03 20:58:58 MarkDuplicates Read 527,000,000 records. Elapsed time: 00:18:11s. Time for last 1,000,000: 1s. Last read position: chr17:82,089,125 INFO 2026-06-03 20:58:58 MarkDuplicates Tracking 221678 as yet unmatched pairs. 2404 records in RAM. INFO 2026-06-03 20:59:00 MarkDuplicates Read 528,000,000 records. Elapsed time: 00:18:13s. Time for last 1,000,000: 1s. Last read position: chr18:2,694,543 INFO 2026-06-03 20:59:00 MarkDuplicates Tracking 219037 as yet unmatched pairs. 15642 records in RAM. INFO 2026-06-03 20:59:01 MarkDuplicates Read 529,000,000 records. Elapsed time: 00:18:14s. Time for last 1,000,000: 1s. Last read position: chr18:12,325,647 INFO 2026-06-03 20:59:01 MarkDuplicates Tracking 219538 as yet unmatched pairs. 16130 records in RAM. INFO 2026-06-03 20:59:03 MarkDuplicates Read 530,000,000 records. Elapsed time: 00:18:16s. Time for last 1,000,000: 1s. Last read position: chr18:26,035,062 INFO 2026-06-03 20:59:03 MarkDuplicates Tracking 215904 as yet unmatched pairs. 12480 records in RAM. INFO 2026-06-03 20:59:04 MarkDuplicates Read 531,000,000 records. Elapsed time: 00:18:17s. Time for last 1,000,000: 1s. Last read position: chr18:31,458,571 INFO 2026-06-03 20:59:04 MarkDuplicates Tracking 219494 as yet unmatched pairs. 16063 records in RAM. INFO 2026-06-03 20:59:06 MarkDuplicates Read 532,000,000 records. Elapsed time: 00:18:19s. Time for last 1,000,000: 1s. Last read position: chr18:35,683,459 INFO 2026-06-03 20:59:06 MarkDuplicates Tracking 212604 as yet unmatched pairs. 9165 records in RAM. INFO 2026-06-03 20:59:07 MarkDuplicates Read 533,000,000 records. Elapsed time: 00:18:20s. Time for last 1,000,000: 1s. Last read position: chr18:49,878,965 INFO 2026-06-03 20:59:07 MarkDuplicates Tracking 210973 as yet unmatched pairs. 7520 records in RAM. INFO 2026-06-03 20:59:09 MarkDuplicates Read 534,000,000 records. Elapsed time: 00:18:22s. Time for last 1,000,000: 1s. Last read position: chr18:58,366,190 INFO 2026-06-03 20:59:09 MarkDuplicates Tracking 208688 as yet unmatched pairs. 5218 records in RAM. INFO 2026-06-03 20:59:10 MarkDuplicates Read 535,000,000 records. Elapsed time: 00:18:23s. Time for last 1,000,000: 1s. Last read position: chr18:63,344,419 INFO 2026-06-03 20:59:10 MarkDuplicates Tracking 207346 as yet unmatched pairs. 3865 records in RAM. INFO 2026-06-03 20:59:12 MarkDuplicates Read 536,000,000 records. Elapsed time: 00:18:25s. Time for last 1,000,000: 1s. Last read position: chr18:63,903,081 INFO 2026-06-03 20:59:12 MarkDuplicates Tracking 210362 as yet unmatched pairs. 6872 records in RAM. INFO 2026-06-03 20:59:14 MarkDuplicates Read 537,000,000 records. Elapsed time: 00:18:27s. Time for last 1,000,000: 2s. Last read position: chr19:580,647 INFO 2026-06-03 20:59:14 MarkDuplicates Tracking 205670 as yet unmatched pairs. 91721 records in RAM. INFO 2026-06-03 20:59:16 MarkDuplicates Read 538,000,000 records. Elapsed time: 00:18:29s. Time for last 1,000,000: 1s. Last read position: chr19:1,084,279 INFO 2026-06-03 20:59:16 MarkDuplicates Tracking 200754 as yet unmatched pairs. 86796 records in RAM. INFO 2026-06-03 20:59:17 MarkDuplicates Read 539,000,000 records. Elapsed time: 00:18:30s. Time for last 1,000,000: 1s. Last read position: chr19:1,475,005 INFO 2026-06-03 20:59:17 MarkDuplicates Tracking 198473 as yet unmatched pairs. 84496 records in RAM. INFO 2026-06-03 20:59:19 MarkDuplicates Read 540,000,000 records. Elapsed time: 00:18:32s. Time for last 1,000,000: 1s. Last read position: chr19:2,123,852 INFO 2026-06-03 20:59:19 MarkDuplicates Tracking 196404 as yet unmatched pairs. 82415 records in RAM. INFO 2026-06-03 20:59:21 MarkDuplicates Read 541,000,000 records. Elapsed time: 00:18:34s. Time for last 1,000,000: 1s. Last read position: chr19:3,453,819 INFO 2026-06-03 20:59:21 MarkDuplicates Tracking 193760 as yet unmatched pairs. 79762 records in RAM. INFO 2026-06-03 20:59:23 MarkDuplicates Read 542,000,000 records. Elapsed time: 00:18:36s. Time for last 1,000,000: 2s. Last read position: chr19:4,499,595 INFO 2026-06-03 20:59:23 MarkDuplicates Tracking 190666 as yet unmatched pairs. 76659 records in RAM. INFO 2026-06-03 20:59:25 MarkDuplicates Read 543,000,000 records. Elapsed time: 00:18:38s. Time for last 1,000,000: 2s. Last read position: chr19:5,679,367 INFO 2026-06-03 20:59:25 MarkDuplicates Tracking 188603 as yet unmatched pairs. 74592 records in RAM. INFO 2026-06-03 20:59:27 MarkDuplicates Read 544,000,000 records. Elapsed time: 00:18:40s. Time for last 1,000,000: 1s. Last read position: chr19:5,923,222 INFO 2026-06-03 20:59:27 MarkDuplicates Tracking 186634 as yet unmatched pairs. 72620 records in RAM. INFO 2026-06-03 20:59:28 MarkDuplicates Read 545,000,000 records. Elapsed time: 00:18:42s. Time for last 1,000,000: 1s. Last read position: chr19:7,612,141 INFO 2026-06-03 20:59:28 MarkDuplicates Tracking 184153 as yet unmatched pairs. 70136 records in RAM. INFO 2026-06-03 20:59:30 MarkDuplicates Read 546,000,000 records. Elapsed time: 00:18:43s. Time for last 1,000,000: 1s. Last read position: chr19:8,939,033 INFO 2026-06-03 20:59:30 MarkDuplicates Tracking 181758 as yet unmatched pairs. 67740 records in RAM. INFO 2026-06-03 20:59:31 MarkDuplicates Read 547,000,000 records. Elapsed time: 00:18:45s. Time for last 1,000,000: 1s. Last read position: chr19:10,284,198 INFO 2026-06-03 20:59:31 MarkDuplicates Tracking 180495 as yet unmatched pairs. 66471 records in RAM. INFO 2026-06-03 20:59:33 MarkDuplicates Read 548,000,000 records. Elapsed time: 00:18:46s. Time for last 1,000,000: 1s. Last read position: chr19:10,908,053 INFO 2026-06-03 20:59:33 MarkDuplicates Tracking 178197 as yet unmatched pairs. 64170 records in RAM. INFO 2026-06-03 20:59:35 MarkDuplicates Read 549,000,000 records. Elapsed time: 00:18:48s. Time for last 1,000,000: 1s. Last read position: chr19:11,925,134 INFO 2026-06-03 20:59:35 MarkDuplicates Tracking 175884 as yet unmatched pairs. 61856 records in RAM. INFO 2026-06-03 20:59:36 MarkDuplicates Read 550,000,000 records. Elapsed time: 00:18:49s. Time for last 1,000,000: 1s. Last read position: chr19:12,940,620 INFO 2026-06-03 20:59:36 MarkDuplicates Tracking 174863 as yet unmatched pairs. 60826 records in RAM. INFO 2026-06-03 20:59:38 MarkDuplicates Read 551,000,000 records. Elapsed time: 00:18:51s. Time for last 1,000,000: 1s. Last read position: chr19:14,159,510 INFO 2026-06-03 20:59:38 MarkDuplicates Tracking 171103 as yet unmatched pairs. 57060 records in RAM. INFO 2026-06-03 20:59:39 MarkDuplicates Read 552,000,000 records. Elapsed time: 00:18:52s. Time for last 1,000,000: 1s. Last read position: chr19:15,161,371 INFO 2026-06-03 20:59:39 MarkDuplicates Tracking 170981 as yet unmatched pairs. 56938 records in RAM. INFO 2026-06-03 20:59:41 MarkDuplicates Read 553,000,000 records. Elapsed time: 00:18:54s. Time for last 1,000,000: 1s. Last read position: chr19:15,254,152 INFO 2026-06-03 20:59:41 MarkDuplicates Tracking 172083 as yet unmatched pairs. 58038 records in RAM. INFO 2026-06-03 20:59:42 MarkDuplicates Read 554,000,000 records. Elapsed time: 00:18:56s. Time for last 1,000,000: 1s. Last read position: chr19:16,525,561 INFO 2026-06-03 20:59:42 MarkDuplicates Tracking 164366 as yet unmatched pairs. 50321 records in RAM. INFO 2026-06-03 20:59:44 MarkDuplicates Read 555,000,000 records. Elapsed time: 00:18:57s. Time for last 1,000,000: 1s. Last read position: chr19:17,861,313 INFO 2026-06-03 20:59:44 MarkDuplicates Tracking 163949 as yet unmatched pairs. 49889 records in RAM. INFO 2026-06-03 20:59:45 MarkDuplicates Read 556,000,000 records. Elapsed time: 00:18:59s. Time for last 1,000,000: 1s. Last read position: chr19:18,856,032 INFO 2026-06-03 20:59:45 MarkDuplicates Tracking 159865 as yet unmatched pairs. 45798 records in RAM. INFO 2026-06-03 20:59:47 MarkDuplicates Read 557,000,000 records. Elapsed time: 00:19:00s. Time for last 1,000,000: 1s. Last read position: chr19:31,276,498 INFO 2026-06-03 20:59:47 MarkDuplicates Tracking 157257 as yet unmatched pairs. 43183 records in RAM. INFO 2026-06-03 20:59:49 MarkDuplicates Read 558,000,000 records. Elapsed time: 00:19:02s. Time for last 1,000,000: 1s. Last read position: chr19:35,116,234 INFO 2026-06-03 20:59:49 MarkDuplicates Tracking 155691 as yet unmatched pairs. 41602 records in RAM. INFO 2026-06-03 20:59:50 MarkDuplicates Read 559,000,000 records. Elapsed time: 00:19:03s. Time for last 1,000,000: 1s. Last read position: chr19:35,637,162 INFO 2026-06-03 20:59:50 MarkDuplicates Tracking 153403 as yet unmatched pairs. 39307 records in RAM. INFO 2026-06-03 20:59:52 MarkDuplicates Read 560,000,000 records. Elapsed time: 00:19:05s. Time for last 1,000,000: 2s. Last read position: chr19:38,283,649 INFO 2026-06-03 20:59:52 MarkDuplicates Tracking 153470 as yet unmatched pairs. 39369 records in RAM. INFO 2026-06-03 20:59:54 MarkDuplicates Read 561,000,000 records. Elapsed time: 00:19:08s. Time for last 1,000,000: 2s. Last read position: chr19:38,845,910 INFO 2026-06-03 20:59:54 MarkDuplicates Tracking 150374 as yet unmatched pairs. 36261 records in RAM. INFO 2026-06-03 20:59:56 MarkDuplicates Read 562,000,000 records. Elapsed time: 00:19:09s. Time for last 1,000,000: 1s. Last read position: chr19:39,879,749 INFO 2026-06-03 20:59:56 MarkDuplicates Tracking 146944 as yet unmatched pairs. 32825 records in RAM. INFO 2026-06-03 20:59:58 MarkDuplicates Read 563,000,000 records. Elapsed time: 00:19:11s. Time for last 1,000,000: 1s. Last read position: chr19:40,717,974 INFO 2026-06-03 20:59:58 MarkDuplicates Tracking 145386 as yet unmatched pairs. 31263 records in RAM. INFO 2026-06-03 20:59:59 MarkDuplicates Read 564,000,000 records. Elapsed time: 00:19:12s. Time for last 1,000,000: 1s. Last read position: chr19:41,762,088 INFO 2026-06-03 20:59:59 MarkDuplicates Tracking 142821 as yet unmatched pairs. 28695 records in RAM. INFO 2026-06-03 21:00:01 MarkDuplicates Read 565,000,000 records. Elapsed time: 00:19:14s. Time for last 1,000,000: 1s. Last read position: chr19:42,290,311 INFO 2026-06-03 21:00:01 MarkDuplicates Tracking 141905 as yet unmatched pairs. 27776 records in RAM. INFO 2026-06-03 21:00:02 MarkDuplicates Read 566,000,000 records. Elapsed time: 00:19:15s. Time for last 1,000,000: 1s. Last read position: chr19:43,464,407 INFO 2026-06-03 21:00:02 MarkDuplicates Tracking 143942 as yet unmatched pairs. 29803 records in RAM. INFO 2026-06-03 21:00:04 MarkDuplicates Read 567,000,000 records. Elapsed time: 00:19:17s. Time for last 1,000,000: 1s. Last read position: chr19:45,069,066 INFO 2026-06-03 21:00:04 MarkDuplicates Tracking 136067 as yet unmatched pairs. 21925 records in RAM. INFO 2026-06-03 21:00:05 MarkDuplicates Read 568,000,000 records. Elapsed time: 00:19:18s. Time for last 1,000,000: 1s. Last read position: chr19:45,885,176 INFO 2026-06-03 21:00:05 MarkDuplicates Tracking 133574 as yet unmatched pairs. 19429 records in RAM. INFO 2026-06-03 21:00:07 MarkDuplicates Read 569,000,000 records. Elapsed time: 00:19:20s. Time for last 1,000,000: 1s. Last read position: chr19:47,680,523 INFO 2026-06-03 21:00:07 MarkDuplicates Tracking 131029 as yet unmatched pairs. 16882 records in RAM. INFO 2026-06-03 21:00:08 MarkDuplicates Read 570,000,000 records. Elapsed time: 00:19:21s. Time for last 1,000,000: 1s. Last read position: chr19:48,873,299 INFO 2026-06-03 21:00:08 MarkDuplicates Tracking 128904 as yet unmatched pairs. 14754 records in RAM. INFO 2026-06-03 21:00:10 MarkDuplicates Read 571,000,000 records. Elapsed time: 00:19:23s. Time for last 1,000,000: 1s. Last read position: chr19:49,489,860 INFO 2026-06-03 21:00:10 MarkDuplicates Tracking 132664 as yet unmatched pairs. 18511 records in RAM. INFO 2026-06-03 21:00:11 MarkDuplicates Read 572,000,000 records. Elapsed time: 00:19:25s. Time for last 1,000,000: 1s. Last read position: chr19:49,806,122 INFO 2026-06-03 21:00:11 MarkDuplicates Tracking 124238 as yet unmatched pairs. 10081 records in RAM. INFO 2026-06-03 21:00:13 MarkDuplicates Read 573,000,000 records. Elapsed time: 00:19:26s. Time for last 1,000,000: 1s. Last read position: chr19:51,341,895 INFO 2026-06-03 21:00:13 MarkDuplicates Tracking 121586 as yet unmatched pairs. 7416 records in RAM. INFO 2026-06-03 21:00:14 MarkDuplicates Read 574,000,000 records. Elapsed time: 00:19:27s. Time for last 1,000,000: 1s. Last read position: chr19:54,206,399 INFO 2026-06-03 21:00:14 MarkDuplicates Tracking 123643 as yet unmatched pairs. 9460 records in RAM. INFO 2026-06-03 21:00:16 MarkDuplicates Read 575,000,000 records. Elapsed time: 00:19:29s. Time for last 1,000,000: 1s. Last read position: chr19:55,486,996 INFO 2026-06-03 21:00:16 MarkDuplicates Tracking 117312 as yet unmatched pairs. 3123 records in RAM. INFO 2026-06-03 21:00:17 MarkDuplicates Read 576,000,000 records. Elapsed time: 00:19:31s. Time for last 1,000,000: 1s. Last read position: chr19:58,387,287 INFO 2026-06-03 21:00:17 MarkDuplicates Tracking 116166 as yet unmatched pairs. 1970 records in RAM. INFO 2026-06-03 21:00:19 MarkDuplicates Read 577,000,000 records. Elapsed time: 00:19:32s. Time for last 1,000,000: 1s. Last read position: chr20:2,462,740 INFO 2026-06-03 21:00:19 MarkDuplicates Tracking 113990 as yet unmatched pairs. 27987 records in RAM. INFO 2026-06-03 21:00:21 MarkDuplicates Read 578,000,000 records. Elapsed time: 00:19:34s. Time for last 1,000,000: 1s. Last read position: chr20:5,115,452 INFO 2026-06-03 21:00:21 MarkDuplicates Tracking 112044 as yet unmatched pairs. 26035 records in RAM. INFO 2026-06-03 21:00:23 MarkDuplicates Read 579,000,000 records. Elapsed time: 00:19:36s. Time for last 1,000,000: 2s. Last read position: chr20:17,968,221 INFO 2026-06-03 21:00:23 MarkDuplicates Tracking 109533 as yet unmatched pairs. 23516 records in RAM. INFO 2026-06-03 21:00:24 MarkDuplicates Read 580,000,000 records. Elapsed time: 00:19:37s. Time for last 1,000,000: 1s. Last read position: chr20:31,554,747 INFO 2026-06-03 21:00:24 MarkDuplicates Tracking 108677 as yet unmatched pairs. 22655 records in RAM. INFO 2026-06-03 21:00:26 MarkDuplicates Read 581,000,000 records. Elapsed time: 00:19:39s. Time for last 1,000,000: 1s. Last read position: chr20:34,741,617 INFO 2026-06-03 21:00:26 MarkDuplicates Tracking 105245 as yet unmatched pairs. 19221 records in RAM. INFO 2026-06-03 21:00:28 MarkDuplicates Read 582,000,000 records. Elapsed time: 00:19:41s. Time for last 1,000,000: 1s. Last read position: chr20:36,188,414 INFO 2026-06-03 21:00:28 MarkDuplicates Tracking 103306 as yet unmatched pairs. 17274 records in RAM. INFO 2026-06-03 21:00:29 MarkDuplicates Read 583,000,000 records. Elapsed time: 00:19:42s. Time for last 1,000,000: 1s. Last read position: chr20:39,028,486 INFO 2026-06-03 21:00:29 MarkDuplicates Tracking 101098 as yet unmatched pairs. 15062 records in RAM. INFO 2026-06-03 21:00:31 MarkDuplicates Read 584,000,000 records. Elapsed time: 00:19:44s. Time for last 1,000,000: 1s. Last read position: chr20:45,253,113 INFO 2026-06-03 21:00:31 MarkDuplicates Tracking 105321 as yet unmatched pairs. 19279 records in RAM. INFO 2026-06-03 21:00:32 MarkDuplicates Read 585,000,000 records. Elapsed time: 00:19:45s. Time for last 1,000,000: 1s. Last read position: chr20:47,210,767 INFO 2026-06-03 21:00:32 MarkDuplicates Tracking 97903 as yet unmatched pairs. 11852 records in RAM. INFO 2026-06-03 21:00:34 MarkDuplicates Read 586,000,000 records. Elapsed time: 00:19:47s. Time for last 1,000,000: 1s. Last read position: chr20:50,891,365 INFO 2026-06-03 21:00:34 MarkDuplicates Tracking 96294 as yet unmatched pairs. 10237 records in RAM. INFO 2026-06-03 21:00:35 MarkDuplicates Read 587,000,000 records. Elapsed time: 00:19:48s. Time for last 1,000,000: 1s. Last read position: chr20:58,891,854 INFO 2026-06-03 21:00:35 MarkDuplicates Tracking 98120 as yet unmatched pairs. 12058 records in RAM. INFO 2026-06-03 21:00:37 MarkDuplicates Read 588,000,000 records. Elapsed time: 00:19:50s. Time for last 1,000,000: 1s. Last read position: chr20:62,315,115 INFO 2026-06-03 21:00:37 MarkDuplicates Tracking 92559 as yet unmatched pairs. 6494 records in RAM. INFO 2026-06-03 21:00:38 MarkDuplicates Read 589,000,000 records. Elapsed time: 00:19:51s. Time for last 1,000,000: 1s. Last read position: chr20:62,910,917 INFO 2026-06-03 21:00:38 MarkDuplicates Tracking 89142 as yet unmatched pairs. 3070 records in RAM. INFO 2026-06-03 21:00:40 MarkDuplicates Read 590,000,000 records. Elapsed time: 00:19:53s. Time for last 1,000,000: 1s. Last read position: chr21:5,034,001 INFO 2026-06-03 21:00:40 MarkDuplicates Tracking 86637 as yet unmatched pairs. 17197 records in RAM. INFO 2026-06-03 21:00:41 MarkDuplicates Read 591,000,000 records. Elapsed time: 00:19:54s. Time for last 1,000,000: 1s. Last read position: chr21:8,258,912 INFO 2026-06-03 21:00:41 MarkDuplicates Tracking 84886 as yet unmatched pairs. 15440 records in RAM. INFO 2026-06-03 21:00:42 MarkDuplicates Read 592,000,000 records. Elapsed time: 00:19:55s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,570 INFO 2026-06-03 21:00:42 MarkDuplicates Tracking 85013 as yet unmatched pairs. 15565 records in RAM. INFO 2026-06-03 21:00:44 MarkDuplicates Read 593,000,000 records. Elapsed time: 00:19:57s. Time for last 1,000,000: 1s. Last read position: chr21:29,042,058 INFO 2026-06-03 21:00:44 MarkDuplicates Tracking 82282 as yet unmatched pairs. 12825 records in RAM. INFO 2026-06-03 21:00:45 MarkDuplicates Read 594,000,000 records. Elapsed time: 00:19:58s. Time for last 1,000,000: 1s. Last read position: chr21:33,552,345 INFO 2026-06-03 21:00:45 MarkDuplicates Tracking 81736 as yet unmatched pairs. 12275 records in RAM. INFO 2026-06-03 21:00:46 MarkDuplicates Read 595,000,000 records. Elapsed time: 00:20:00s. Time for last 1,000,000: 1s. Last read position: chr21:38,299,373 INFO 2026-06-03 21:00:46 MarkDuplicates Tracking 78070 as yet unmatched pairs. 8605 records in RAM. INFO 2026-06-03 21:00:48 MarkDuplicates Read 596,000,000 records. Elapsed time: 00:20:01s. Time for last 1,000,000: 1s. Last read position: chr21:43,066,278 INFO 2026-06-03 21:00:48 MarkDuplicates Tracking 76065 as yet unmatched pairs. 6596 records in RAM. INFO 2026-06-03 21:00:50 MarkDuplicates Read 597,000,000 records. Elapsed time: 00:20:03s. Time for last 1,000,000: 1s. Last read position: chr21:44,234,200 INFO 2026-06-03 21:00:50 MarkDuplicates Tracking 75427 as yet unmatched pairs. 5953 records in RAM. INFO 2026-06-03 21:00:52 MarkDuplicates Read 598,000,000 records. Elapsed time: 00:20:05s. Time for last 1,000,000: 2s. Last read position: chr21:45,992,012 INFO 2026-06-03 21:00:52 MarkDuplicates Tracking 72965 as yet unmatched pairs. 3488 records in RAM. INFO 2026-06-03 21:00:53 MarkDuplicates Read 599,000,000 records. Elapsed time: 00:20:07s. Time for last 1,000,000: 1s. Last read position: chr21:46,644,338 INFO 2026-06-03 21:00:53 MarkDuplicates Tracking 70043 as yet unmatched pairs. 562 records in RAM. INFO 2026-06-03 21:00:55 MarkDuplicates Read 600,000,000 records. Elapsed time: 00:20:08s. Time for last 1,000,000: 1s. Last read position: chr22:20,141,332 INFO 2026-06-03 21:00:55 MarkDuplicates Tracking 67783 as yet unmatched pairs. 34187 records in RAM. INFO 2026-06-03 21:00:57 MarkDuplicates Read 601,000,000 records. Elapsed time: 00:20:10s. Time for last 1,000,000: 1s. Last read position: chr22:22,921,418 INFO 2026-06-03 21:00:57 MarkDuplicates Tracking 65599 as yet unmatched pairs. 32002 records in RAM. INFO 2026-06-03 21:00:58 MarkDuplicates Read 602,000,000 records. Elapsed time: 00:20:11s. Time for last 1,000,000: 1s. Last read position: chr22:24,091,651 INFO 2026-06-03 21:00:58 MarkDuplicates Tracking 63346 as yet unmatched pairs. 29748 records in RAM. INFO 2026-06-03 21:01:00 MarkDuplicates Read 603,000,000 records. Elapsed time: 00:20:13s. Time for last 1,000,000: 1s. Last read position: chr22:29,278,003 INFO 2026-06-03 21:01:00 MarkDuplicates Tracking 65036 as yet unmatched pairs. 31435 records in RAM. INFO 2026-06-03 21:01:01 MarkDuplicates Read 604,000,000 records. Elapsed time: 00:20:14s. Time for last 1,000,000: 1s. Last read position: chr22:30,013,439 INFO 2026-06-03 21:01:01 MarkDuplicates Tracking 59843 as yet unmatched pairs. 26242 records in RAM. INFO 2026-06-03 21:01:03 MarkDuplicates Read 605,000,000 records. Elapsed time: 00:20:16s. Time for last 1,000,000: 1s. Last read position: chr22:32,498,315 INFO 2026-06-03 21:01:03 MarkDuplicates Tracking 57304 as yet unmatched pairs. 23701 records in RAM. INFO 2026-06-03 21:01:04 MarkDuplicates Read 606,000,000 records. Elapsed time: 00:20:18s. Time for last 1,000,000: 1s. Last read position: chr22:36,288,786 INFO 2026-06-03 21:01:04 MarkDuplicates Tracking 57852 as yet unmatched pairs. 24245 records in RAM. INFO 2026-06-03 21:01:06 MarkDuplicates Read 607,000,000 records. Elapsed time: 00:20:19s. Time for last 1,000,000: 1s. Last read position: chr22:37,296,010 INFO 2026-06-03 21:01:06 MarkDuplicates Tracking 53025 as yet unmatched pairs. 19409 records in RAM. INFO 2026-06-03 21:01:07 MarkDuplicates Read 608,000,000 records. Elapsed time: 00:20:20s. Time for last 1,000,000: 1s. Last read position: chr22:37,944,422 INFO 2026-06-03 21:01:07 MarkDuplicates Tracking 50673 as yet unmatched pairs. 17050 records in RAM. INFO 2026-06-03 21:01:09 MarkDuplicates Read 609,000,000 records. Elapsed time: 00:20:22s. Time for last 1,000,000: 1s. Last read position: chr22:38,962,133 INFO 2026-06-03 21:01:09 MarkDuplicates Tracking 58835 as yet unmatched pairs. 25212 records in RAM. INFO 2026-06-03 21:01:11 MarkDuplicates Read 610,000,000 records. Elapsed time: 00:20:24s. Time for last 1,000,000: 1s. Last read position: chr22:41,117,727 INFO 2026-06-03 21:01:11 MarkDuplicates Tracking 47258 as yet unmatched pairs. 13633 records in RAM. INFO 2026-06-03 21:01:12 MarkDuplicates Read 611,000,000 records. Elapsed time: 00:20:25s. Time for last 1,000,000: 1s. Last read position: chr22:41,870,941 INFO 2026-06-03 21:01:12 MarkDuplicates Tracking 44944 as yet unmatched pairs. 11314 records in RAM. INFO 2026-06-03 21:01:13 MarkDuplicates Read 612,000,000 records. Elapsed time: 00:20:27s. Time for last 1,000,000: 1s. Last read position: chr22:43,168,116 INFO 2026-06-03 21:01:13 MarkDuplicates Tracking 43611 as yet unmatched pairs. 9980 records in RAM. INFO 2026-06-03 21:01:15 MarkDuplicates Read 613,000,000 records. Elapsed time: 00:20:28s. Time for last 1,000,000: 1s. Last read position: chr22:46,658,184 INFO 2026-06-03 21:01:15 MarkDuplicates Tracking 40530 as yet unmatched pairs. 6899 records in RAM. INFO 2026-06-03 21:01:17 MarkDuplicates Read 614,000,000 records. Elapsed time: 00:20:30s. Time for last 1,000,000: 1s. Last read position: chr22:50,447,223 INFO 2026-06-03 21:01:17 MarkDuplicates Tracking 38179 as yet unmatched pairs. 4546 records in RAM. INFO 2026-06-03 21:01:18 MarkDuplicates Read 615,000,000 records. Elapsed time: 00:20:31s. Time for last 1,000,000: 1s. Last read position: chr22:50,579,170 INFO 2026-06-03 21:01:18 MarkDuplicates Tracking 34716 as yet unmatched pairs. 1080 records in RAM. INFO 2026-06-03 21:01:20 MarkDuplicates Read 616,000,000 records. Elapsed time: 00:20:34s. Time for last 1,000,000: 2s. Last read position: chrX:9,688,036 INFO 2026-06-03 21:01:20 MarkDuplicates Tracking 32017 as yet unmatched pairs. 26029 records in RAM. INFO 2026-06-03 21:01:22 MarkDuplicates Read 617,000,000 records. Elapsed time: 00:20:35s. Time for last 1,000,000: 1s. Last read position: chrX:23,783,864 INFO 2026-06-03 21:01:22 MarkDuplicates Tracking 34083 as yet unmatched pairs. 28094 records in RAM. INFO 2026-06-03 21:01:23 MarkDuplicates Read 618,000,000 records. Elapsed time: 00:20:36s. Time for last 1,000,000: 1s. Last read position: chrX:41,170,157 INFO 2026-06-03 21:01:23 MarkDuplicates Tracking 28860 as yet unmatched pairs. 22870 records in RAM. INFO 2026-06-03 21:01:25 MarkDuplicates Read 619,000,000 records. Elapsed time: 00:20:38s. Time for last 1,000,000: 1s. Last read position: chrX:47,242,471 INFO 2026-06-03 21:01:25 MarkDuplicates Tracking 27441 as yet unmatched pairs. 21451 records in RAM. INFO 2026-06-03 21:01:27 MarkDuplicates Read 620,000,000 records. Elapsed time: 00:20:40s. Time for last 1,000,000: 1s. Last read position: chrX:49,067,510 INFO 2026-06-03 21:01:27 MarkDuplicates Tracking 25110 as yet unmatched pairs. 19120 records in RAM. INFO 2026-06-03 21:01:28 MarkDuplicates Read 621,000,000 records. Elapsed time: 00:20:41s. Time for last 1,000,000: 1s. Last read position: chrX:53,552,638 INFO 2026-06-03 21:01:28 MarkDuplicates Tracking 24275 as yet unmatched pairs. 18284 records in RAM. INFO 2026-06-03 21:01:29 MarkDuplicates Read 622,000,000 records. Elapsed time: 00:20:43s. Time for last 1,000,000: 1s. Last read position: chrX:68,063,962 INFO 2026-06-03 21:01:29 MarkDuplicates Tracking 21469 as yet unmatched pairs. 15478 records in RAM. INFO 2026-06-03 21:01:31 MarkDuplicates Read 623,000,000 records. Elapsed time: 00:20:44s. Time for last 1,000,000: 1s. Last read position: chrX:74,594,372 INFO 2026-06-03 21:01:31 MarkDuplicates Tracking 19963 as yet unmatched pairs. 13971 records in RAM. INFO 2026-06-03 21:01:33 MarkDuplicates Read 624,000,000 records. Elapsed time: 00:20:46s. Time for last 1,000,000: 1s. Last read position: chrX:100,676,058 INFO 2026-06-03 21:01:33 MarkDuplicates Tracking 18248 as yet unmatched pairs. 12254 records in RAM. INFO 2026-06-03 21:01:34 MarkDuplicates Read 625,000,000 records. Elapsed time: 00:20:47s. Time for last 1,000,000: 1s. Last read position: chrX:118,580,097 INFO 2026-06-03 21:01:34 MarkDuplicates Tracking 16735 as yet unmatched pairs. 10741 records in RAM. INFO 2026-06-03 21:01:36 MarkDuplicates Read 626,000,000 records. Elapsed time: 00:20:49s. Time for last 1,000,000: 1s. Last read position: chrX:130,402,000 INFO 2026-06-03 21:01:36 MarkDuplicates Tracking 14942 as yet unmatched pairs. 8946 records in RAM. INFO 2026-06-03 21:01:37 MarkDuplicates Read 627,000,000 records. Elapsed time: 00:20:50s. Time for last 1,000,000: 1s. Last read position: chrX:152,700,897 INFO 2026-06-03 21:01:37 MarkDuplicates Tracking 14871 as yet unmatched pairs. 8875 records in RAM. INFO 2026-06-03 21:01:39 MarkDuplicates Read 628,000,000 records. Elapsed time: 00:20:52s. Time for last 1,000,000: 1s. Last read position: chrX:153,951,623 INFO 2026-06-03 21:01:39 MarkDuplicates Tracking 12137 as yet unmatched pairs. 6138 records in RAM. INFO 2026-06-03 21:01:40 MarkDuplicates Read 629,000,000 records. Elapsed time: 00:20:53s. Time for last 1,000,000: 1s. Last read position: chrX:154,360,559 INFO 2026-06-03 21:01:40 MarkDuplicates Tracking 12993 as yet unmatched pairs. 6994 records in RAM. INFO 2026-06-03 21:01:42 MarkDuplicates Read 630,000,000 records. Elapsed time: 00:20:55s. Time for last 1,000,000: 1s. Last read position: chrX:154,562,855 INFO 2026-06-03 21:01:42 MarkDuplicates Tracking 6525 as yet unmatched pairs. 522 records in RAM. INFO 2026-06-03 21:01:43 MarkDuplicates Read 631,000,000 records. Elapsed time: 00:20:56s. Time for last 1,000,000: 1s. Last read position: GL000220.1:114,153 INFO 2026-06-03 21:01:43 MarkDuplicates Tracking 4926 as yet unmatched pairs. 1766 records in RAM. INFO 2026-06-03 21:01:44 MarkDuplicates Read 632,000,000 records. Elapsed time: 00:20:57s. Time for last 1,000,000: 1s. Last read position: KI270733.1:129,677 INFO 2026-06-03 21:01:44 MarkDuplicates Tracking 3057 as yet unmatched pairs. 3025 records in RAM. INFO 2026-06-03 21:01:45 MarkDuplicates Read 632883332 records. 0 pairs never matched. INFO 2026-06-03 21:02:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 204141576; totalMemory: 234881024; maxMemory: 63585648640 INFO 2026-06-03 21:02:31 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk. INFO 2026-06-03 21:02:33 MarkDuplicates Traversing read pair information and detecting duplicates. WARNING 2026-06-03 21:02:33 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered. INFO 2026-06-03 21:02:38 OpticalDuplicateFinder Large duplicate set. size = 1159 INFO 2026-06-03 21:02:38 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,863 INFO 2026-06-03 21:02:48 OpticalDuplicateFinder Large duplicate set. size = 1171 INFO 2026-06-03 21:02:48 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,729 INFO 2026-06-03 21:02:57 OpticalDuplicateFinder Large duplicate set. size = 1192 INFO 2026-06-03 21:02:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,503 INFO 2026-06-03 21:02:57 OpticalDuplicateFinder Large duplicate set. size = 1270 INFO 2026-06-03 21:02:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:2,537 INFO 2026-06-03 21:02:57 OpticalDuplicateFinder Large duplicate set. size = 1190 INFO 2026-06-03 21:02:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,269 INFO 2026-06-03 21:02:58 OpticalDuplicateFinder Large duplicate set. size = 1283 INFO 2026-06-03 21:02:58 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-27,783 INFO 2026-06-03 21:02:58 OpticalDuplicateFinder Large duplicate set. size = 1275 INFO 2026-06-03 21:02:58 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,755 INFO 2026-06-03 21:02:58 OpticalDuplicateFinder Large duplicate set. size = 1085 INFO 2026-06-03 21:02:58 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,774 INFO 2026-06-03 21:02:58 OpticalDuplicateFinder Large duplicate set. size = 1060 INFO 2026-06-03 21:02:58 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:6,995 INFO 2026-06-03 21:02:58 OpticalDuplicateFinder Large duplicate set. size = 1185 INFO 2026-06-03 21:02:58 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,456 INFO 2026-06-03 21:02:58 OpticalDuplicateFinder Large duplicate set. size = 1098 INFO 2026-06-03 21:02:58 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,066 INFO 2026-06-03 21:03:23 OpticalDuplicateFinder Large duplicate set. size = 1056 INFO 2026-06-03 21:03:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,441 INFO 2026-06-03 21:03:35 MarkDuplicates Traversing fragment information and detecting duplicates. WARNING 2026-06-03 21:03:35 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered. INFO 2026-06-03 21:04:38 MarkDuplicates Sorting list of duplicate records. INFO 2026-06-03 21:04:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 10792685656; totalMemory: 26742882304; maxMemory: 63585648640 INFO 2026-06-03 21:04:48 MarkDuplicates Marking 253481949 records as duplicates. INFO 2026-06-03 21:04:48 MarkDuplicates Found 22259295 optical duplicate clusters. INFO 2026-06-03 21:04:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2026-06-03 21:05:05 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:16s. Time for last 10,000,000: 16s. Last read position: chr1:21,751,601 INFO 2026-06-03 21:05:23 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:34s. Time for last 10,000,000: 18s. Last read position: chr1:39,353,065 INFO 2026-06-03 21:05:40 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:52s. Time for last 10,000,000: 17s. Last read position: chr1:86,577,902 INFO 2026-06-03 21:05:58 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:09s. Time for last 10,000,000: 17s. Last read position: chr1:149,840,814 INFO 2026-06-03 21:06:15 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:26s. Time for last 10,000,000: 17s. Last read position: chr1:155,747,613 INFO 2026-06-03 21:06:33 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:44s. Time for last 10,000,000: 18s. Last read position: chr1:201,386,829 INFO 2026-06-03 21:06:52 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:03s. Time for last 10,000,000: 18s. Last read position: chr2:10,797,130 INFO 2026-06-03 21:07:09 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:20s. Time for last 10,000,000: 17s. Last read position: chr2:38,568,161 INFO 2026-06-03 21:07:26 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:38s. Time for last 10,000,000: 17s. Last read position: chr2:99,404,635 INFO 2026-06-03 21:07:43 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:54s. Time for last 10,000,000: 16s. Last read position: chr2:178,532,889 INFO 2026-06-03 21:08:00 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:03:11s. Time for last 10,000,000: 16s. Last read position: chr2:215,409,563 INFO 2026-06-03 21:08:17 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:28s. Time for last 10,000,000: 16s. Last read position: chr3:12,840,208 INFO 2026-06-03 21:08:33 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:45s. Time for last 10,000,000: 16s. Last read position: chr3:50,187,895 INFO 2026-06-03 21:08:50 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:04:01s. Time for last 10,000,000: 16s. Last read position: chr3:132,666,014 INFO 2026-06-03 21:09:07 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:04:18s. Time for last 10,000,000: 16s. Last read position: chr3:189,867,836 INFO 2026-06-03 21:09:24 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:35s. Time for last 10,000,000: 16s. Last read position: chr3:195,971,323 INFO 2026-06-03 21:09:40 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:04:51s. Time for last 10,000,000: 16s. Last read position: chr4:67,717,259 INFO 2026-06-03 21:09:57 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:05:08s. Time for last 10,000,000: 16s. Last read position: chr4:186,628,235 INFO 2026-06-03 21:10:14 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:05:25s. Time for last 10,000,000: 16s. Last read position: chr5:138,783,217 INFO 2026-06-03 21:10:30 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:05:41s. Time for last 10,000,000: 16s. Last read position: chr6:4,943,700 INFO 2026-06-03 21:10:46 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:05:57s. Time for last 10,000,000: 16s. Last read position: chr6:31,828,722 INFO 2026-06-03 21:11:03 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:06:14s. Time for last 10,000,000: 16s. Last read position: chr6:73,792,771 INFO 2026-06-03 21:11:19 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:06:31s. Time for last 10,000,000: 16s. Last read position: chr6:158,789,293 INFO 2026-06-03 21:11:36 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:06:47s. Time for last 10,000,000: 16s. Last read position: chr7:73,297,215 INFO 2026-06-03 21:11:52 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:07:03s. Time for last 10,000,000: 16s. Last read position: chr7:100,030,330 INFO 2026-06-03 21:12:09 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:07:20s. Time for last 10,000,000: 16s. Last read position: chr8:8,376,700 INFO 2026-06-03 21:12:26 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:07:37s. Time for last 10,000,000: 16s. Last read position: chr8:93,922,169 INFO 2026-06-03 21:12:42 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:07:53s. Time for last 10,000,000: 16s. Last read position: chr8:143,872,503 INFO 2026-06-03 21:12:59 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:08:10s. Time for last 10,000,000: 16s. Last read position: chr9:83,663,880 INFO 2026-06-03 21:13:15 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:08:26s. Time for last 10,000,000: 16s. Last read position: chr9:128,169,094 INFO 2026-06-03 21:13:32 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:08:43s. Time for last 10,000,000: 16s. Last read position: chr10:22,318,957 INFO 2026-06-03 21:13:48 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:08:59s. Time for last 10,000,000: 16s. Last read position: chr10:92,018,851 INFO 2026-06-03 21:14:05 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:09:16s. Time for last 10,000,000: 16s. Last read position: chr11:562,605 INFO 2026-06-03 21:14:21 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:09:32s. Time for last 10,000,000: 16s. Last read position: chr11:57,795,702 INFO 2026-06-03 21:14:38 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:09:49s. Time for last 10,000,000: 16s. Last read position: chr11:66,643,733 INFO 2026-06-03 21:14:55 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:10:06s. Time for last 10,000,000: 16s. Last read position: chr11:119,664,747 INFO 2026-06-03 21:15:11 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:10:22s. Time for last 10,000,000: 16s. Last read position: chr12:26,122,717 INFO 2026-06-03 21:15:27 MarkDuplicates Written 380,000,000 records. Elapsed time: 00:10:38s. Time for last 10,000,000: 16s. Last read position: chr12:53,517,167 INFO 2026-06-03 21:15:43 MarkDuplicates Written 390,000,000 records. Elapsed time: 00:10:55s. Time for last 10,000,000: 16s. Last read position: chr12:98,601,379 INFO 2026-06-03 21:16:00 MarkDuplicates Written 400,000,000 records. Elapsed time: 00:11:11s. Time for last 10,000,000: 16s. Last read position: chr13:20,192,767 INFO 2026-06-03 21:16:18 MarkDuplicates Written 410,000,000 records. Elapsed time: 00:11:29s. Time for last 10,000,000: 17s. Last read position: chr14:24,311,195 INFO 2026-06-03 21:16:34 MarkDuplicates Written 420,000,000 records. Elapsed time: 00:11:45s. Time for last 10,000,000: 16s. Last read position: chr14:92,716,211 INFO 2026-06-03 21:16:52 MarkDuplicates Written 430,000,000 records. Elapsed time: 00:12:03s. Time for last 10,000,000: 17s. Last read position: chr15:40,472,065 INFO 2026-06-03 21:17:09 MarkDuplicates Written 440,000,000 records. Elapsed time: 00:12:20s. Time for last 10,000,000: 17s. Last read position: chr15:74,035,168 INFO 2026-06-03 21:17:27 MarkDuplicates Written 450,000,000 records. Elapsed time: 00:12:38s. Time for last 10,000,000: 17s. Last read position: chr16:2,975,481 INFO 2026-06-03 21:17:43 MarkDuplicates Written 460,000,000 records. Elapsed time: 00:12:54s. Time for last 10,000,000: 16s. Last read position: chr16:28,169,848 INFO 2026-06-03 21:18:01 MarkDuplicates Written 470,000,000 records. Elapsed time: 00:13:12s. Time for last 10,000,000: 17s. Last read position: chr16:67,645,549 INFO 2026-06-03 21:18:19 MarkDuplicates Written 480,000,000 records. Elapsed time: 00:13:30s. Time for last 10,000,000: 18s. Last read position: chr17:3,941,273 INFO 2026-06-03 21:18:37 MarkDuplicates Written 490,000,000 records. Elapsed time: 00:13:48s. Time for last 10,000,000: 18s. Last read position: chr17:28,748,331 INFO 2026-06-03 21:18:57 MarkDuplicates Written 500,000,000 records. Elapsed time: 00:14:08s. Time for last 10,000,000: 19s. Last read position: chr17:41,518,667 INFO 2026-06-03 21:19:18 MarkDuplicates Written 510,000,000 records. Elapsed time: 00:14:29s. Time for last 10,000,000: 21s. Last read position: chr17:50,189,376 INFO 2026-06-03 21:19:40 MarkDuplicates Written 520,000,000 records. Elapsed time: 00:14:52s. Time for last 10,000,000: 22s. Last read position: chr17:68,126,733 INFO 2026-06-03 21:20:03 MarkDuplicates Written 530,000,000 records. Elapsed time: 00:15:14s. Time for last 10,000,000: 22s. Last read position: chr18:26,035,062 INFO 2026-06-03 21:20:26 MarkDuplicates Written 540,000,000 records. Elapsed time: 00:15:37s. Time for last 10,000,000: 22s. Last read position: chr19:2,123,852 INFO 2026-06-03 21:20:50 MarkDuplicates Written 550,000,000 records. Elapsed time: 00:16:01s. Time for last 10,000,000: 23s. Last read position: chr19:12,940,620 INFO 2026-06-03 21:21:12 MarkDuplicates Written 560,000,000 records. Elapsed time: 00:16:23s. Time for last 10,000,000: 21s. Last read position: chr19:38,283,649 INFO 2026-06-03 21:21:34 MarkDuplicates Written 570,000,000 records. Elapsed time: 00:16:45s. Time for last 10,000,000: 21s. Last read position: chr19:48,873,299 INFO 2026-06-03 21:21:56 MarkDuplicates Written 580,000,000 records. Elapsed time: 00:17:07s. Time for last 10,000,000: 22s. Last read position: chr20:31,554,747 INFO 2026-06-03 21:22:18 MarkDuplicates Written 590,000,000 records. Elapsed time: 00:17:29s. Time for last 10,000,000: 22s. Last read position: chr21:5,034,001 INFO 2026-06-03 21:22:41 MarkDuplicates Written 600,000,000 records. Elapsed time: 00:17:52s. Time for last 10,000,000: 22s. Last read position: chr22:20,141,332 INFO 2026-06-03 21:23:05 MarkDuplicates Written 610,000,000 records. Elapsed time: 00:18:16s. Time for last 10,000,000: 23s. Last read position: chr22:41,117,727 INFO 2026-06-03 21:23:28 MarkDuplicates Written 620,000,000 records. Elapsed time: 00:18:39s. Time for last 10,000,000: 22s. Last read position: chrX:49,067,510 INFO 2026-06-03 21:23:52 MarkDuplicates Written 630,000,000 records. Elapsed time: 00:19:03s. Time for last 10,000,000: 24s. Last read position: chrX:154,562,855 INFO 2026-06-03 21:24:11 MarkDuplicates Writing complete. Closing input iterator. INFO 2026-06-03 21:24:11 MarkDuplicates Duplicate Index cleanup. INFO 2026-06-03 21:24:11 MarkDuplicates Getting Memory Stats. INFO 2026-06-03 21:24:11 MarkDuplicates Before output close freeMemory: 201364792; totalMemory: 234881024; maxMemory: 63585648640 INFO 2026-06-03 21:24:11 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2026-06-03 21:24:11 MarkDuplicates After output close freeMemory: 104163680; totalMemory: 134217728; maxMemory: 63585648640 [Wed Jun 03 21:24:11 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 43.43 minutes. Runtime.totalMemory()=134217728 Tool returned: 0 ls: *cram: No such file or directory ls: *.crai: No such file or directory