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/83/0f8be5e36f003b5dd877ca3e3052fd/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/0f8be5e36f003b5dd877ca3e3052fd/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/e88c47953a7f0cd33d14ed88aae2c6/aih-tih-sc-00d05f-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai ==> STAGING COMPLETE (5 inputs) Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT aih-tih-sc-00d05f-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bam --METRICS_FILE aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT 08:35:08.288 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Mon Jun 08 08:35:08 GMT 2026] MarkDuplicates --INPUT aih-tih-sc-00d05f-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bam --METRICS_FILE aih-tih-sc-00d05f-R1_A23WJ53LT4_1.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Mon Jun 08 08:35:08 GMT 2026] Executing as ?@nf-830f8be5e36f003b5dd877ca3e3052fd-ebab9-pk8gl on Linux 6.12.88 amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0 INFO 2026-06-08 08:35:08 MarkDuplicates Start of doWork freeMemory: 105828544; totalMemory: 134217728; maxMemory: 63585648640 INFO 2026-06-08 08:35:08 MarkDuplicates Reading input file and constructing read end information. INFO 2026-06-08 08:35:08 MarkDuplicates Will retain up to 230382784 data points before spilling to disk. INFO 2026-06-08 08:35:12 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:1,355,304 INFO 2026-06-08 08:35:12 MarkDuplicates Tracking 3027 as yet unmatched pairs. 989 records in RAM. INFO 2026-06-08 08:35:14 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 2s. Last read position: chr1:3,515,350 INFO 2026-06-08 08:35:14 MarkDuplicates Tracking 4716 as yet unmatched pairs. 382 records in RAM. INFO 2026-06-08 08:35:16 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: chr1:8,832,424 INFO 2026-06-08 08:35:16 MarkDuplicates Tracking 6479 as yet unmatched pairs. 14 records in RAM. INFO 2026-06-08 08:35:18 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: chr1:12,283,467 INFO 2026-06-08 08:35:18 MarkDuplicates Tracking 8487 as yet unmatched pairs. 185 records in RAM. INFO 2026-06-08 08:35:19 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: chr1:16,975,708 INFO 2026-06-08 08:35:19 MarkDuplicates Tracking 10244 as yet unmatched pairs. 404 records in RAM. INFO 2026-06-08 08:35:21 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: chr1:21,272,723 INFO 2026-06-08 08:35:21 MarkDuplicates Tracking 12335 as yet unmatched pairs. 752 records in RAM. INFO 2026-06-08 08:35:24 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: chr1:21,875,888 INFO 2026-06-08 08:35:24 MarkDuplicates Tracking 14581 as yet unmatched pairs. 1137 records in RAM. INFO 2026-06-08 08:35:25 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: chr1:24,814,095 INFO 2026-06-08 08:35:25 MarkDuplicates Tracking 15383 as yet unmatched pairs. 73 records in RAM. INFO 2026-06-08 08:35:27 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: chr1:27,548,441 INFO 2026-06-08 08:35:27 MarkDuplicates Tracking 17245 as yet unmatched pairs. 215 records in RAM. INFO 2026-06-08 08:35:28 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: chr1:31,684,197 INFO 2026-06-08 08:35:28 MarkDuplicates Tracking 19401 as yet unmatched pairs. 534 records in RAM. INFO 2026-06-08 08:35:30 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 2s. Last read position: chr1:35,184,467 INFO 2026-06-08 08:35:30 MarkDuplicates Tracking 20682 as yet unmatched pairs. 41 records in RAM. INFO 2026-06-08 08:35:33 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 2s. Last read position: chr1:39,284,333 INFO 2026-06-08 08:35:33 MarkDuplicates Tracking 22543 as yet unmatched pairs. 194 records in RAM. INFO 2026-06-08 08:35:34 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: chr1:40,861,850 INFO 2026-06-08 08:35:34 MarkDuplicates Tracking 24059 as yet unmatched pairs. 93 records in RAM. INFO 2026-06-08 08:35:36 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 1s. Last read position: chr1:44,739,961 INFO 2026-06-08 08:35:36 MarkDuplicates Tracking 25907 as yet unmatched pairs. 62 records in RAM. INFO 2026-06-08 08:35:39 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 3s. Last read position: chr1:51,834,108 INFO 2026-06-08 08:35:39 MarkDuplicates Tracking 27922 as yet unmatched pairs. 327 records in RAM. INFO 2026-06-08 08:35:42 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 3s. Last read position: chr1:63,454,901 INFO 2026-06-08 08:35:42 MarkDuplicates Tracking 29360 as yet unmatched pairs. 50 records in RAM. INFO 2026-06-08 08:35:44 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 1s. Last read position: chr1:86,356,413 INFO 2026-06-08 08:35:44 MarkDuplicates Tracking 31104 as yet unmatched pairs. 119 records in RAM. INFO 2026-06-08 08:35:46 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 1s. Last read position: chr1:108,136,671 INFO 2026-06-08 08:35:46 MarkDuplicates Tracking 32609 as yet unmatched pairs. 72 records in RAM. INFO 2026-06-08 08:35:48 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 1s. Last read position: chr1:113,585,417 INFO 2026-06-08 08:35:48 MarkDuplicates Tracking 34662 as yet unmatched pairs. 433 records in RAM. INFO 2026-06-08 08:35:50 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 2s. Last read position: chr1:119,916,286 INFO 2026-06-08 08:35:50 MarkDuplicates Tracking 37880 as yet unmatched pairs. 2016 records in RAM. INFO 2026-06-08 08:35:52 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chr1:120,807,666 INFO 2026-06-08 08:35:52 MarkDuplicates Tracking 37416 as yet unmatched pairs. 291 records in RAM. INFO 2026-06-08 08:35:54 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 1s. Last read position: chr1:145,996,170 INFO 2026-06-08 08:35:54 MarkDuplicates Tracking 38494 as yet unmatched pairs. 353 records in RAM. INFO 2026-06-08 08:35:55 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 1s. Last read position: chr1:148,117,681 INFO 2026-06-08 08:35:55 MarkDuplicates Tracking 39415 as yet unmatched pairs. 431 records in RAM. INFO 2026-06-08 08:35:57 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 1s. Last read position: chr1:149,430,950 INFO 2026-06-08 08:35:57 MarkDuplicates Tracking 40508 as yet unmatched pairs. 816 records in RAM. INFO 2026-06-08 08:35:58 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 1s. Last read position: chr1:150,159,292 INFO 2026-06-08 08:35:58 MarkDuplicates Tracking 41468 as yet unmatched pairs. 814 records in RAM. INFO 2026-06-08 08:36:00 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 1s. Last read position: chr1:150,807,245 INFO 2026-06-08 08:36:00 MarkDuplicates Tracking 42300 as yet unmatched pairs. 57 records in RAM. INFO 2026-06-08 08:36:03 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 2s. Last read position: chr1:151,540,319 INFO 2026-06-08 08:36:03 MarkDuplicates Tracking 44040 as yet unmatched pairs. 101 records in RAM. INFO 2026-06-08 08:36:05 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 2s. Last read position: chr1:153,982,080 INFO 2026-06-08 08:36:05 MarkDuplicates Tracking 45722 as yet unmatched pairs. 227 records in RAM. INFO 2026-06-08 08:36:06 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 1s. Last read position: chr1:154,343,893 INFO 2026-06-08 08:36:06 MarkDuplicates Tracking 46864 as yet unmatched pairs. 44 records in RAM. INFO 2026-06-08 08:36:08 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 1s. Last read position: chr1:155,188,319 INFO 2026-06-08 08:36:08 MarkDuplicates Tracking 48824 as yet unmatched pairs. 184 records in RAM. INFO 2026-06-08 08:36:10 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 1s. Last read position: chr1:155,689,108 INFO 2026-06-08 08:36:10 MarkDuplicates Tracking 50648 as yet unmatched pairs. 575 records in RAM. INFO 2026-06-08 08:36:12 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 1s. Last read position: chr1:156,135,242 INFO 2026-06-08 08:36:12 MarkDuplicates Tracking 60676 as yet unmatched pairs. 8497 records in RAM. INFO 2026-06-08 08:36:14 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 1s. Last read position: chr1:156,550,273 INFO 2026-06-08 08:36:14 MarkDuplicates Tracking 54250 as yet unmatched pairs. 160 records in RAM. INFO 2026-06-08 08:36:16 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 2s. Last read position: chr1:160,092,953 INFO 2026-06-08 08:36:16 MarkDuplicates Tracking 56103 as yet unmatched pairs. 277 records in RAM. INFO 2026-06-08 08:36:18 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 1s. Last read position: chr1:161,589,562 INFO 2026-06-08 08:36:18 MarkDuplicates Tracking 60400 as yet unmatched pairs. 2802 records in RAM. INFO 2026-06-08 08:36:20 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 1s. Last read position: chr1:168,696,587 INFO 2026-06-08 08:36:20 MarkDuplicates Tracking 59547 as yet unmatched pairs. 342 records in RAM. INFO 2026-06-08 08:36:21 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 1s. Last read position: chr1:174,231,224 INFO 2026-06-08 08:36:21 MarkDuplicates Tracking 60768 as yet unmatched pairs. 94 records in RAM. INFO 2026-06-08 08:36:23 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 1s. Last read position: chr1:182,887,105 INFO 2026-06-08 08:36:23 MarkDuplicates Tracking 62620 as yet unmatched pairs. 381 records in RAM. INFO 2026-06-08 08:36:25 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 1s. Last read position: chr1:186,350,221 INFO 2026-06-08 08:36:25 MarkDuplicates Tracking 64407 as yet unmatched pairs. 619 records in RAM. INFO 2026-06-08 08:36:26 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 1s. Last read position: chr1:201,782,610 INFO 2026-06-08 08:36:26 MarkDuplicates Tracking 65739 as yet unmatched pairs. 438 records in RAM. INFO 2026-06-08 08:36:28 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 1s. Last read position: chr1:203,802,003 INFO 2026-06-08 08:36:28 MarkDuplicates Tracking 67231 as yet unmatched pairs. 375 records in RAM. INFO 2026-06-08 08:36:30 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 1s. Last read position: chr1:206,685,378 INFO 2026-06-08 08:36:30 MarkDuplicates Tracking 69370 as yet unmatched pairs. 807 records in RAM. INFO 2026-06-08 08:36:31 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 1s. Last read position: chr1:215,601,920 INFO 2026-06-08 08:36:31 MarkDuplicates Tracking 70703 as yet unmatched pairs. 445 records in RAM. INFO 2026-06-08 08:36:33 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 1s. Last read position: chr1:226,495,926 INFO 2026-06-08 08:36:33 MarkDuplicates Tracking 71776 as yet unmatched pairs. 1 records in RAM. INFO 2026-06-08 08:36:34 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 1s. Last read position: chr1:233,258,505 INFO 2026-06-08 08:36:34 MarkDuplicates Tracking 74006 as yet unmatched pairs. 185 records in RAM. INFO 2026-06-08 08:36:36 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 2s. Last read position: chr1:244,855,526 INFO 2026-06-08 08:36:36 MarkDuplicates Tracking 75971 as yet unmatched pairs. 85 records in RAM. INFO 2026-06-08 08:36:39 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 2s. Last read position: chr2:9,585,308 INFO 2026-06-08 08:36:39 MarkDuplicates Tracking 78064 as yet unmatched pairs. 77810 records in RAM. INFO 2026-06-08 08:36:41 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 1s. Last read position: chr2:24,082,949 INFO 2026-06-08 08:36:41 MarkDuplicates Tracking 79688 as yet unmatched pairs. 79427 records in RAM. INFO 2026-06-08 08:36:43 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 1s. Last read position: chr2:27,226,847 INFO 2026-06-08 08:36:43 MarkDuplicates Tracking 81371 as yet unmatched pairs. 81105 records in RAM. INFO 2026-06-08 08:36:44 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 1s. Last read position: chr2:32,617,818 INFO 2026-06-08 08:36:44 MarkDuplicates Tracking 83124 as yet unmatched pairs. 82852 records in RAM. INFO 2026-06-08 08:36:46 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,264 INFO 2026-06-08 08:36:46 MarkDuplicates Tracking 530613 as yet unmatched pairs. 62485 records in RAM. INFO 2026-06-08 08:36:48 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,406 INFO 2026-06-08 08:36:48 MarkDuplicates Tracking 708676 as yet unmatched pairs. 54748 records in RAM. INFO 2026-06-08 08:36:49 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 1s. Last read position: chr2:40,115,311 INFO 2026-06-08 08:36:49 MarkDuplicates Tracking 750454 as yet unmatched pairs. 51778 records in RAM. INFO 2026-06-08 08:36:51 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 2s. Last read position: chr2:47,162,287 INFO 2026-06-08 08:36:51 MarkDuplicates Tracking 750107 as yet unmatched pairs. 51423 records in RAM. INFO 2026-06-08 08:36:53 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 1s. Last read position: chr2:58,198,487 INFO 2026-06-08 08:36:53 MarkDuplicates Tracking 747117 as yet unmatched pairs. 48431 records in RAM. INFO 2026-06-08 08:36:55 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 1s. Last read position: chr2:70,088,081 INFO 2026-06-08 08:36:55 MarkDuplicates Tracking 746372 as yet unmatched pairs. 47685 records in RAM. INFO 2026-06-08 08:36:57 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 1s. Last read position: chr2:74,460,323 INFO 2026-06-08 08:36:57 MarkDuplicates Tracking 743862 as yet unmatched pairs. 45172 records in RAM. INFO 2026-06-08 08:36:59 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 2s. Last read position: chr2:86,987,532 INFO 2026-06-08 08:36:59 MarkDuplicates Tracking 741940 as yet unmatched pairs. 43249 records in RAM. INFO 2026-06-08 08:37:01 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 1s. Last read position: chr2:97,084,137 INFO 2026-06-08 08:37:01 MarkDuplicates Tracking 740605 as yet unmatched pairs. 41912 records in RAM. INFO 2026-06-08 08:37:02 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 1s. Last read position: chr2:105,275,562 INFO 2026-06-08 08:37:02 MarkDuplicates Tracking 738896 as yet unmatched pairs. 40186 records in RAM. INFO 2026-06-08 08:37:04 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 1s. Last read position: chr2:109,836,618 INFO 2026-06-08 08:37:04 MarkDuplicates Tracking 738102 as yet unmatched pairs. 39392 records in RAM. INFO 2026-06-08 08:37:05 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 1s. Last read position: chr2:113,443,816 INFO 2026-06-08 08:37:05 MarkDuplicates Tracking 736790 as yet unmatched pairs. 38078 records in RAM. INFO 2026-06-08 08:37:07 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 1s. Last read position: chr2:130,370,055 INFO 2026-06-08 08:37:07 MarkDuplicates Tracking 735740 as yet unmatched pairs. 36999 records in RAM. INFO 2026-06-08 08:37:08 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 1s. Last read position: chr2:131,626,581 INFO 2026-06-08 08:37:08 MarkDuplicates Tracking 735335 as yet unmatched pairs. 36584 records in RAM. INFO 2026-06-08 08:37:10 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 1s. Last read position: chr2:140,867,633 INFO 2026-06-08 08:37:10 MarkDuplicates Tracking 733894 as yet unmatched pairs. 35140 records in RAM. INFO 2026-06-08 08:37:11 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 1s. Last read position: chr2:152,384,219 INFO 2026-06-08 08:37:11 MarkDuplicates Tracking 731234 as yet unmatched pairs. 32463 records in RAM. INFO 2026-06-08 08:37:13 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 1s. Last read position: chr2:165,888,374 INFO 2026-06-08 08:37:13 MarkDuplicates Tracking 729403 as yet unmatched pairs. 30617 records in RAM. INFO 2026-06-08 08:37:14 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 1s. Last read position: chr2:178,542,394 INFO 2026-06-08 08:37:14 MarkDuplicates Tracking 727988 as yet unmatched pairs. 29195 records in RAM. INFO 2026-06-08 08:37:16 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 1s. Last read position: chr2:188,994,233 INFO 2026-06-08 08:37:16 MarkDuplicates Tracking 730438 as yet unmatched pairs. 31644 records in RAM. INFO 2026-06-08 08:37:18 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 1s. Last read position: chr2:189,006,426 INFO 2026-06-08 08:37:18 MarkDuplicates Tracking 728623 as yet unmatched pairs. 29826 records in RAM. INFO 2026-06-08 08:37:19 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 1s. Last read position: chr2:190,436,644 INFO 2026-06-08 08:37:19 MarkDuplicates Tracking 722791 as yet unmatched pairs. 23993 records in RAM. INFO 2026-06-08 08:37:22 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 2s. Last read position: chr2:202,035,167 INFO 2026-06-08 08:37:22 MarkDuplicates Tracking 721223 as yet unmatched pairs. 22422 records in RAM. INFO 2026-06-08 08:37:24 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 1s. Last read position: chr2:215,361,395 INFO 2026-06-08 08:37:24 MarkDuplicates Tracking 724554 as yet unmatched pairs. 25749 records in RAM. INFO 2026-06-08 08:37:25 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 1s. Last read position: chr2:215,371,950 INFO 2026-06-08 08:37:25 MarkDuplicates Tracking 727691 as yet unmatched pairs. 28886 records in RAM. INFO 2026-06-08 08:37:27 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 1s. Last read position: chr2:215,376,496 INFO 2026-06-08 08:37:27 MarkDuplicates Tracking 728428 as yet unmatched pairs. 29621 records in RAM. INFO 2026-06-08 08:37:29 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 1s. Last read position: chr2:215,384,109 INFO 2026-06-08 08:37:29 MarkDuplicates Tracking 722134 as yet unmatched pairs. 23327 records in RAM. INFO 2026-06-08 08:37:31 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 1s. Last read position: chr2:215,404,444 INFO 2026-06-08 08:37:31 MarkDuplicates Tracking 720060 as yet unmatched pairs. 21253 records in RAM. INFO 2026-06-08 08:37:32 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr2:215,410,064 INFO 2026-06-08 08:37:32 MarkDuplicates Tracking 719420 as yet unmatched pairs. 20613 records in RAM. INFO 2026-06-08 08:37:34 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 1s. Last read position: chr2:215,430,727 INFO 2026-06-08 08:37:34 MarkDuplicates Tracking 716863 as yet unmatched pairs. 18056 records in RAM. INFO 2026-06-08 08:37:36 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 1s. Last read position: chr2:217,818,385 INFO 2026-06-08 08:37:36 MarkDuplicates Tracking 711368 as yet unmatched pairs. 12559 records in RAM. INFO 2026-06-08 08:37:37 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 1s. Last read position: chr2:219,540,139 INFO 2026-06-08 08:37:37 MarkDuplicates Tracking 708150 as yet unmatched pairs. 9341 records in RAM. INFO 2026-06-08 08:37:39 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 1s. Last read position: chr2:231,455,188 INFO 2026-06-08 08:37:39 MarkDuplicates Tracking 706025 as yet unmatched pairs. 7210 records in RAM. INFO 2026-06-08 08:37:40 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 1s. Last read position: chr2:237,341,029 INFO 2026-06-08 08:37:40 MarkDuplicates Tracking 706300 as yet unmatched pairs. 7485 records in RAM. INFO 2026-06-08 08:37:42 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 1s. Last read position: chr2:237,376,772 INFO 2026-06-08 08:37:42 MarkDuplicates Tracking 704292 as yet unmatched pairs. 5477 records in RAM. INFO 2026-06-08 08:37:44 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 1s. Last read position: chr2:239,176,453 INFO 2026-06-08 08:37:44 MarkDuplicates Tracking 701115 as yet unmatched pairs. 2298 records in RAM. INFO 2026-06-08 08:37:45 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 1s. Last read position: chr2:241,735,267 INFO 2026-06-08 08:37:45 MarkDuplicates Tracking 701600 as yet unmatched pairs. 2766 records in RAM. INFO 2026-06-08 08:37:47 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 2s. Last read position: chr3:9,946,766 INFO 2026-06-08 08:37:47 MarkDuplicates Tracking 697408 as yet unmatched pairs. 33564 records in RAM. INFO 2026-06-08 08:37:49 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 1s. Last read position: chr3:13,637,733 INFO 2026-06-08 08:37:49 MarkDuplicates Tracking 696412 as yet unmatched pairs. 32567 records in RAM. INFO 2026-06-08 08:37:50 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 1s. Last read position: chr3:31,830,161 INFO 2026-06-08 08:37:50 MarkDuplicates Tracking 694126 as yet unmatched pairs. 30276 records in RAM. INFO 2026-06-08 08:37:53 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 2s. Last read position: chr3:40,170,006 INFO 2026-06-08 08:37:53 MarkDuplicates Tracking 692419 as yet unmatched pairs. 28567 records in RAM. INFO 2026-06-08 08:37:54 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 1s. Last read position: chr3:46,441,415 INFO 2026-06-08 08:37:54 MarkDuplicates Tracking 690920 as yet unmatched pairs. 27068 records in RAM. INFO 2026-06-08 08:37:55 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 1s. Last read position: chr3:47,916,265 INFO 2026-06-08 08:37:55 MarkDuplicates Tracking 689510 as yet unmatched pairs. 25658 records in RAM. INFO 2026-06-08 08:37:57 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 1s. Last read position: chr3:49,012,983 INFO 2026-06-08 08:37:57 MarkDuplicates Tracking 688214 as yet unmatched pairs. 24358 records in RAM. INFO 2026-06-08 08:37:59 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 1s. Last read position: chr3:49,678,895 INFO 2026-06-08 08:37:59 MarkDuplicates Tracking 685744 as yet unmatched pairs. 21886 records in RAM. INFO 2026-06-08 08:38:00 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 1s. Last read position: chr3:51,590,474 INFO 2026-06-08 08:38:00 MarkDuplicates Tracking 683502 as yet unmatched pairs. 19643 records in RAM. INFO 2026-06-08 08:38:03 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 2s. Last read position: chr3:52,707,725 INFO 2026-06-08 08:38:03 MarkDuplicates Tracking 681607 as yet unmatched pairs. 17748 records in RAM. INFO 2026-06-08 08:38:04 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 1s. Last read position: chr3:64,018,909 INFO 2026-06-08 08:38:04 MarkDuplicates Tracking 680005 as yet unmatched pairs. 16133 records in RAM. INFO 2026-06-08 08:38:06 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 1s. Last read position: chr3:99,849,003 INFO 2026-06-08 08:38:06 MarkDuplicates Tracking 679172 as yet unmatched pairs. 15286 records in RAM. INFO 2026-06-08 08:38:08 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 2s. Last read position: chr3:112,639,070 INFO 2026-06-08 08:38:08 MarkDuplicates Tracking 677436 as yet unmatched pairs. 13549 records in RAM. INFO 2026-06-08 08:38:10 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 1s. Last read position: chr3:123,614,290 INFO 2026-06-08 08:38:10 MarkDuplicates Tracking 675851 as yet unmatched pairs. 11963 records in RAM. INFO 2026-06-08 08:38:12 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 1s. Last read position: chr3:129,499,939 INFO 2026-06-08 08:38:12 MarkDuplicates Tracking 673861 as yet unmatched pairs. 9963 records in RAM. INFO 2026-06-08 08:38:13 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 1s. Last read position: chr3:141,743,523 INFO 2026-06-08 08:38:13 MarkDuplicates Tracking 672628 as yet unmatched pairs. 8723 records in RAM. INFO 2026-06-08 08:38:15 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 1s. Last read position: chr3:152,835,895 INFO 2026-06-08 08:38:15 MarkDuplicates Tracking 670273 as yet unmatched pairs. 6364 records in RAM. INFO 2026-06-08 08:38:16 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 1s. Last read position: chr3:179,229,367 INFO 2026-06-08 08:38:16 MarkDuplicates Tracking 669013 as yet unmatched pairs. 5094 records in RAM. INFO 2026-06-08 08:38:18 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 1s. Last read position: chr3:184,383,621 INFO 2026-06-08 08:38:18 MarkDuplicates Tracking 667143 as yet unmatched pairs. 3218 records in RAM. INFO 2026-06-08 08:38:19 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 1s. Last read position: chr3:195,516,803 INFO 2026-06-08 08:38:19 MarkDuplicates Tracking 665784 as yet unmatched pairs. 1857 records in RAM. INFO 2026-06-08 08:38:21 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 1s. Last read position: chr4:744,629 INFO 2026-06-08 08:38:21 MarkDuplicates Tracking 663974 as yet unmatched pairs. 22041 records in RAM. INFO 2026-06-08 08:38:23 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 1s. Last read position: chr4:1,737,284 INFO 2026-06-08 08:38:23 MarkDuplicates Tracking 662066 as yet unmatched pairs. 20131 records in RAM. INFO 2026-06-08 08:38:24 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 1s. Last read position: chr4:3,235,730 INFO 2026-06-08 08:38:24 MarkDuplicates Tracking 659552 as yet unmatched pairs. 17617 records in RAM. INFO 2026-06-08 08:38:26 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 1s. Last read position: chr4:10,083,039 INFO 2026-06-08 08:38:26 MarkDuplicates Tracking 657690 as yet unmatched pairs. 15750 records in RAM. INFO 2026-06-08 08:38:28 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 1s. Last read position: chr4:39,457,672 INFO 2026-06-08 08:38:28 MarkDuplicates Tracking 656442 as yet unmatched pairs. 14493 records in RAM. INFO 2026-06-08 08:38:29 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 1s. Last read position: chr4:56,435,450 INFO 2026-06-08 08:38:29 MarkDuplicates Tracking 654335 as yet unmatched pairs. 12384 records in RAM. INFO 2026-06-08 08:38:30 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 1s. Last read position: chr4:76,740,073 INFO 2026-06-08 08:38:30 MarkDuplicates Tracking 652863 as yet unmatched pairs. 10909 records in RAM. INFO 2026-06-08 08:38:32 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: chr4:87,105,628 INFO 2026-06-08 08:38:32 MarkDuplicates Tracking 651292 as yet unmatched pairs. 9337 records in RAM. INFO 2026-06-08 08:38:34 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 2s. Last read position: chr4:97,962,204 INFO 2026-06-08 08:38:34 MarkDuplicates Tracking 649471 as yet unmatched pairs. 7509 records in RAM. INFO 2026-06-08 08:38:36 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 1s. Last read position: chr4:119,027,172 INFO 2026-06-08 08:38:36 MarkDuplicates Tracking 648222 as yet unmatched pairs. 6253 records in RAM. INFO 2026-06-08 08:38:37 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 1s. Last read position: chr4:139,730,637 INFO 2026-06-08 08:38:37 MarkDuplicates Tracking 646446 as yet unmatched pairs. 4473 records in RAM. INFO 2026-06-08 08:38:39 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 1s. Last read position: chr4:151,101,130 INFO 2026-06-08 08:38:39 MarkDuplicates Tracking 646397 as yet unmatched pairs. 4413 records in RAM. INFO 2026-06-08 08:38:41 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 1s. Last read position: chr4:168,711,728 INFO 2026-06-08 08:38:41 MarkDuplicates Tracking 643393 as yet unmatched pairs. 1403 records in RAM. INFO 2026-06-08 08:38:43 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 1s. Last read position: chr5:465,733 INFO 2026-06-08 08:38:43 MarkDuplicates Tracking 642103 as yet unmatched pairs. 33972 records in RAM. INFO 2026-06-08 08:38:45 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 1s. Last read position: chr5:14,359,470 INFO 2026-06-08 08:38:45 MarkDuplicates Tracking 641661 as yet unmatched pairs. 33530 records in RAM. INFO 2026-06-08 08:38:47 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 2s. Last read position: chr5:21,503,167 INFO 2026-06-08 08:38:47 MarkDuplicates Tracking 638154 as yet unmatched pairs. 30015 records in RAM. INFO 2026-06-08 08:38:48 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 1s. Last read position: chr5:42,800,899 INFO 2026-06-08 08:38:48 MarkDuplicates Tracking 638188 as yet unmatched pairs. 30042 records in RAM. INFO 2026-06-08 08:38:50 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 1s. Last read position: chr5:67,164,277 INFO 2026-06-08 08:38:50 MarkDuplicates Tracking 635466 as yet unmatched pairs. 27314 records in RAM. INFO 2026-06-08 08:38:51 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 1s. Last read position: chr5:72,186,663 INFO 2026-06-08 08:38:51 MarkDuplicates Tracking 634443 as yet unmatched pairs. 26286 records in RAM. INFO 2026-06-08 08:38:53 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 1s. Last read position: chr5:80,076,885 INFO 2026-06-08 08:38:53 MarkDuplicates Tracking 633076 as yet unmatched pairs. 24918 records in RAM. INFO 2026-06-08 08:38:54 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 1s. Last read position: chr5:93,784,327 INFO 2026-06-08 08:38:54 MarkDuplicates Tracking 631378 as yet unmatched pairs. 23206 records in RAM. INFO 2026-06-08 08:38:56 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 1s. Last read position: chr5:115,458,545 INFO 2026-06-08 08:38:56 MarkDuplicates Tracking 629821 as yet unmatched pairs. 21649 records in RAM. INFO 2026-06-08 08:38:58 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 1s. Last read position: chr5:132,897,093 INFO 2026-06-08 08:38:58 MarkDuplicates Tracking 628846 as yet unmatched pairs. 20670 records in RAM. INFO 2026-06-08 08:38:59 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 1s. Last read position: chr5:138,467,485 INFO 2026-06-08 08:38:59 MarkDuplicates Tracking 627572 as yet unmatched pairs. 19391 records in RAM. INFO 2026-06-08 08:39:01 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 1s. Last read position: chr5:140,671,549 INFO 2026-06-08 08:39:01 MarkDuplicates Tracking 624975 as yet unmatched pairs. 16761 records in RAM. INFO 2026-06-08 08:39:02 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 1s. Last read position: chr5:141,864,884 INFO 2026-06-08 08:39:02 MarkDuplicates Tracking 623865 as yet unmatched pairs. 15651 records in RAM. INFO 2026-06-08 08:39:04 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 1s. Last read position: chr5:150,118,765 INFO 2026-06-08 08:39:04 MarkDuplicates Tracking 625012 as yet unmatched pairs. 16779 records in RAM. INFO 2026-06-08 08:39:06 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 1s. Last read position: chr5:150,402,215 INFO 2026-06-08 08:39:06 MarkDuplicates Tracking 638952 as yet unmatched pairs. 30701 records in RAM. INFO 2026-06-08 08:39:07 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 1s. Last read position: chr5:150,649,221 INFO 2026-06-08 08:39:07 MarkDuplicates Tracking 618335 as yet unmatched pairs. 10084 records in RAM. INFO 2026-06-08 08:39:09 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 1s. Last read position: chr5:157,481,824 INFO 2026-06-08 08:39:09 MarkDuplicates Tracking 616444 as yet unmatched pairs. 8188 records in RAM. INFO 2026-06-08 08:39:11 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 1s. Last read position: chr5:171,864,058 INFO 2026-06-08 08:39:11 MarkDuplicates Tracking 614667 as yet unmatched pairs. 6400 records in RAM. INFO 2026-06-08 08:39:12 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 1s. Last read position: chr5:177,367,515 INFO 2026-06-08 08:39:12 MarkDuplicates Tracking 612858 as yet unmatched pairs. 4591 records in RAM. INFO 2026-06-08 08:39:14 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 1s. Last read position: chr5:179,623,015 INFO 2026-06-08 08:39:14 MarkDuplicates Tracking 611230 as yet unmatched pairs. 2958 records in RAM. INFO 2026-06-08 08:39:15 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 1s. Last read position: chr5:179,899,231 INFO 2026-06-08 08:39:15 MarkDuplicates Tracking 609750 as yet unmatched pairs. 1476 records in RAM. INFO 2026-06-08 08:39:17 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 1s. Last read position: chr6:7,211,666 INFO 2026-06-08 08:39:17 MarkDuplicates Tracking 607979 as yet unmatched pairs. 37515 records in RAM. INFO 2026-06-08 08:39:20 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 2s. Last read position: chr6:17,130,734 INFO 2026-06-08 08:39:20 MarkDuplicates Tracking 605767 as yet unmatched pairs. 35302 records in RAM. INFO 2026-06-08 08:39:21 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 1s. Last read position: chr6:27,814,369 INFO 2026-06-08 08:39:21 MarkDuplicates Tracking 604797 as yet unmatched pairs. 34331 records in RAM. INFO 2026-06-08 08:39:22 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 1s. Last read position: chr6:30,730,964 INFO 2026-06-08 08:39:22 MarkDuplicates Tracking 602755 as yet unmatched pairs. 32288 records in RAM. INFO 2026-06-08 08:39:24 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 2s. Last read position: chr6:31,635,719 INFO 2026-06-08 08:39:24 MarkDuplicates Tracking 601044 as yet unmatched pairs. 30576 records in RAM. INFO 2026-06-08 08:39:26 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 1s. Last read position: chr6:31,862,634 INFO 2026-06-08 08:39:26 MarkDuplicates Tracking 599472 as yet unmatched pairs. 29003 records in RAM. INFO 2026-06-08 08:39:27 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 1s. Last read position: chr6:32,043,124 INFO 2026-06-08 08:39:27 MarkDuplicates Tracking 598424 as yet unmatched pairs. 27955 records in RAM. INFO 2026-06-08 08:39:29 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 1s. Last read position: chr6:32,096,893 INFO 2026-06-08 08:39:29 MarkDuplicates Tracking 597296 as yet unmatched pairs. 26822 records in RAM. INFO 2026-06-08 08:39:31 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 1s. Last read position: chr6:33,085,214 INFO 2026-06-08 08:39:31 MarkDuplicates Tracking 594841 as yet unmatched pairs. 24367 records in RAM. INFO 2026-06-08 08:39:33 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 1s. Last read position: chr6:33,655,820 INFO 2026-06-08 08:39:33 MarkDuplicates Tracking 592716 as yet unmatched pairs. 22242 records in RAM. INFO 2026-06-08 08:39:35 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 1s. Last read position: chr6:36,985,876 INFO 2026-06-08 08:39:35 MarkDuplicates Tracking 592315 as yet unmatched pairs. 21839 records in RAM. INFO 2026-06-08 08:39:36 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr6:43,203,153 INFO 2026-06-08 08:39:36 MarkDuplicates Tracking 589264 as yet unmatched pairs. 18787 records in RAM. INFO 2026-06-08 08:39:38 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr6:53,005,154 INFO 2026-06-08 08:39:38 MarkDuplicates Tracking 587745 as yet unmatched pairs. 17262 records in RAM. INFO 2026-06-08 08:39:39 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 1s. Last read position: chr6:75,121,286 INFO 2026-06-08 08:39:39 MarkDuplicates Tracking 586321 as yet unmatched pairs. 15838 records in RAM. INFO 2026-06-08 08:39:41 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 1s. Last read position: chr6:89,081,110 INFO 2026-06-08 08:39:41 MarkDuplicates Tracking 585035 as yet unmatched pairs. 14545 records in RAM. INFO 2026-06-08 08:39:42 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 1s. Last read position: chr6:109,446,262 INFO 2026-06-08 08:39:42 MarkDuplicates Tracking 583317 as yet unmatched pairs. 12818 records in RAM. INFO 2026-06-08 08:39:44 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 1s. Last read position: chr6:122,458,548 INFO 2026-06-08 08:39:44 MarkDuplicates Tracking 581599 as yet unmatched pairs. 11094 records in RAM. INFO 2026-06-08 08:39:46 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 1s. Last read position: chr6:135,187,885 INFO 2026-06-08 08:39:46 MarkDuplicates Tracking 579611 as yet unmatched pairs. 9103 records in RAM. INFO 2026-06-08 08:39:47 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 1s. Last read position: chr6:144,523,034 INFO 2026-06-08 08:39:47 MarkDuplicates Tracking 577959 as yet unmatched pairs. 7451 records in RAM. INFO 2026-06-08 08:39:49 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 1s. Last read position: chr6:151,808,063 INFO 2026-06-08 08:39:49 MarkDuplicates Tracking 583356 as yet unmatched pairs. 12843 records in RAM. INFO 2026-06-08 08:39:50 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 1s. Last read position: chr6:157,207,442 INFO 2026-06-08 08:39:50 MarkDuplicates Tracking 574171 as yet unmatched pairs. 3642 records in RAM. INFO 2026-06-08 08:39:52 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 1s. Last read position: chr6:160,048,521 INFO 2026-06-08 08:39:52 MarkDuplicates Tracking 572472 as yet unmatched pairs. 1943 records in RAM. INFO 2026-06-08 08:39:54 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 1s. Last read position: chr7:195,699 INFO 2026-06-08 08:39:54 MarkDuplicates Tracking 570730 as yet unmatched pairs. 41187 records in RAM. INFO 2026-06-08 08:39:55 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 1s. Last read position: chr7:2,658,369 INFO 2026-06-08 08:39:55 MarkDuplicates Tracking 568493 as yet unmatched pairs. 38950 records in RAM. INFO 2026-06-08 08:39:57 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 2s. Last read position: chr7:5,421,081 INFO 2026-06-08 08:39:57 MarkDuplicates Tracking 567966 as yet unmatched pairs. 38413 records in RAM. INFO 2026-06-08 08:39:59 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 1s. Last read position: chr7:5,711,740 INFO 2026-06-08 08:39:59 MarkDuplicates Tracking 564408 as yet unmatched pairs. 34850 records in RAM. INFO 2026-06-08 08:40:01 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 1s. Last read position: chr7:23,260,601 INFO 2026-06-08 08:40:01 MarkDuplicates Tracking 562952 as yet unmatched pairs. 33382 records in RAM. INFO 2026-06-08 08:40:03 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 1s. Last read position: chr7:38,789,831 INFO 2026-06-08 08:40:03 MarkDuplicates Tracking 560990 as yet unmatched pairs. 31413 records in RAM. INFO 2026-06-08 08:40:04 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 1s. Last read position: chr7:44,112,845 INFO 2026-06-08 08:40:04 MarkDuplicates Tracking 559889 as yet unmatched pairs. 30311 records in RAM. INFO 2026-06-08 08:40:06 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 1s. Last read position: chr7:54,544,689 INFO 2026-06-08 08:40:06 MarkDuplicates Tracking 559222 as yet unmatched pairs. 29638 records in RAM. INFO 2026-06-08 08:40:08 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 1s. Last read position: chr7:70,790,012 INFO 2026-06-08 08:40:08 MarkDuplicates Tracking 557453 as yet unmatched pairs. 27868 records in RAM. INFO 2026-06-08 08:40:09 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 1s. Last read position: chr7:73,769,434 INFO 2026-06-08 08:40:09 MarkDuplicates Tracking 556034 as yet unmatched pairs. 26449 records in RAM. INFO 2026-06-08 08:40:11 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 1s. Last read position: chr7:75,209,474 INFO 2026-06-08 08:40:11 MarkDuplicates Tracking 553912 as yet unmatched pairs. 24325 records in RAM. INFO 2026-06-08 08:40:12 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 1s. Last read position: chr7:76,303,815 INFO 2026-06-08 08:40:12 MarkDuplicates Tracking 559980 as yet unmatched pairs. 30393 records in RAM. INFO 2026-06-08 08:40:14 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 1s. Last read position: chr7:90,726,551 INFO 2026-06-08 08:40:14 MarkDuplicates Tracking 550651 as yet unmatched pairs. 21064 records in RAM. INFO 2026-06-08 08:40:15 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 1s. Last read position: chr7:94,406,265 INFO 2026-06-08 08:40:15 MarkDuplicates Tracking 551721 as yet unmatched pairs. 22133 records in RAM. INFO 2026-06-08 08:40:17 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 1s. Last read position: chr7:94,425,833 INFO 2026-06-08 08:40:17 MarkDuplicates Tracking 549828 as yet unmatched pairs. 20239 records in RAM. INFO 2026-06-08 08:40:18 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr7:99,573,245 INFO 2026-06-08 08:40:18 MarkDuplicates Tracking 545811 as yet unmatched pairs. 16221 records in RAM. INFO 2026-06-08 08:40:20 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 1s. Last read position: chr7:100,582,358 INFO 2026-06-08 08:40:20 MarkDuplicates Tracking 544374 as yet unmatched pairs. 14783 records in RAM. INFO 2026-06-08 08:40:22 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 1s. Last read position: chr7:101,237,407 INFO 2026-06-08 08:40:22 MarkDuplicates Tracking 542047 as yet unmatched pairs. 12455 records in RAM. INFO 2026-06-08 08:40:23 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 1s. Last read position: chr7:102,637,556 INFO 2026-06-08 08:40:23 MarkDuplicates Tracking 541955 as yet unmatched pairs. 12362 records in RAM. INFO 2026-06-08 08:40:24 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 1s. Last read position: chr7:107,961,643 INFO 2026-06-08 08:40:24 MarkDuplicates Tracking 539986 as yet unmatched pairs. 10390 records in RAM. INFO 2026-06-08 08:40:26 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 1s. Last read position: chr7:128,091,865 INFO 2026-06-08 08:40:26 MarkDuplicates Tracking 540136 as yet unmatched pairs. 10524 records in RAM. INFO 2026-06-08 08:40:28 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 1s. Last read position: chr7:137,577,281 INFO 2026-06-08 08:40:28 MarkDuplicates Tracking 536885 as yet unmatched pairs. 7268 records in RAM. INFO 2026-06-08 08:40:29 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 1s. Last read position: chr7:141,551,407 INFO 2026-06-08 08:40:29 MarkDuplicates Tracking 535189 as yet unmatched pairs. 5571 records in RAM. INFO 2026-06-08 08:40:30 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 1s. Last read position: chr7:148,811,620 INFO 2026-06-08 08:40:30 MarkDuplicates Tracking 534004 as yet unmatched pairs. 4386 records in RAM. INFO 2026-06-08 08:40:32 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 1s. Last read position: chr7:151,081,391 INFO 2026-06-08 08:40:32 MarkDuplicates Tracking 532135 as yet unmatched pairs. 2516 records in RAM. INFO 2026-06-08 08:40:34 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 1s. Last read position: chr7:158,110,828 INFO 2026-06-08 08:40:34 MarkDuplicates Tracking 530715 as yet unmatched pairs. 1095 records in RAM. INFO 2026-06-08 08:40:36 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 1s. Last read position: chr8:17,548,762 INFO 2026-06-08 08:40:36 MarkDuplicates Tracking 528445 as yet unmatched pairs. 38213 records in RAM. INFO 2026-06-08 08:40:37 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 1s. Last read position: chr8:22,618,478 INFO 2026-06-08 08:40:37 MarkDuplicates Tracking 528507 as yet unmatched pairs. 38275 records in RAM. INFO 2026-06-08 08:40:39 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 1s. Last read position: chr8:32,760,349 INFO 2026-06-08 08:40:39 MarkDuplicates Tracking 524689 as yet unmatched pairs. 34455 records in RAM. INFO 2026-06-08 08:40:40 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 1s. Last read position: chr8:38,290,553 INFO 2026-06-08 08:40:40 MarkDuplicates Tracking 523049 as yet unmatched pairs. 32814 records in RAM. INFO 2026-06-08 08:40:43 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 2s. Last read position: chr8:38,842,304 INFO 2026-06-08 08:40:43 MarkDuplicates Tracking 522490 as yet unmatched pairs. 32238 records in RAM. INFO 2026-06-08 08:40:44 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 1s. Last read position: chr8:47,831,747 INFO 2026-06-08 08:40:44 MarkDuplicates Tracking 519471 as yet unmatched pairs. 29212 records in RAM. INFO 2026-06-08 08:40:46 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 2s. Last read position: chr8:67,059,243 INFO 2026-06-08 08:40:46 MarkDuplicates Tracking 518209 as yet unmatched pairs. 27950 records in RAM. INFO 2026-06-08 08:40:48 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 1s. Last read position: chr8:80,499,592 INFO 2026-06-08 08:40:48 MarkDuplicates Tracking 516420 as yet unmatched pairs. 26152 records in RAM. INFO 2026-06-08 08:40:49 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 1s. Last read position: chr8:98,042,660 INFO 2026-06-08 08:40:49 MarkDuplicates Tracking 517228 as yet unmatched pairs. 26960 records in RAM. INFO 2026-06-08 08:40:51 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 1s. Last read position: chr8:102,651,259 INFO 2026-06-08 08:40:51 MarkDuplicates Tracking 513630 as yet unmatched pairs. 23361 records in RAM. INFO 2026-06-08 08:40:53 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:05:43s. Time for last 1,000,000: 1s. Last read position: chr8:120,125,245 INFO 2026-06-08 08:40:53 MarkDuplicates Tracking 512162 as yet unmatched pairs. 21892 records in RAM. INFO 2026-06-08 08:40:54 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 1s. Last read position: chr8:127,738,900 INFO 2026-06-08 08:40:54 MarkDuplicates Tracking 512952 as yet unmatched pairs. 22682 records in RAM. INFO 2026-06-08 08:40:56 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 1s. Last read position: chr8:143,296,455 INFO 2026-06-08 08:40:56 MarkDuplicates Tracking 508566 as yet unmatched pairs. 18292 records in RAM. INFO 2026-06-08 08:40:58 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 1s. Last read position: chr8:143,803,894 INFO 2026-06-08 08:40:58 MarkDuplicates Tracking 506947 as yet unmatched pairs. 16672 records in RAM. INFO 2026-06-08 08:40:59 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 1s. Last read position: chr8:143,858,787 INFO 2026-06-08 08:40:59 MarkDuplicates Tracking 508008 as yet unmatched pairs. 17729 records in RAM. INFO 2026-06-08 08:41:00 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 1s. Last read position: chr8:143,860,147 INFO 2026-06-08 08:41:00 MarkDuplicates Tracking 508020 as yet unmatched pairs. 17741 records in RAM. INFO 2026-06-08 08:41:01 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 1s. Last read position: chr8:143,861,146 INFO 2026-06-08 08:41:01 MarkDuplicates Tracking 504830 as yet unmatched pairs. 14551 records in RAM. INFO 2026-06-08 08:41:02 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 1s. Last read position: chr8:143,862,184 INFO 2026-06-08 08:41:02 MarkDuplicates Tracking 503830 as yet unmatched pairs. 13551 records in RAM. INFO 2026-06-08 08:41:03 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 1s. Last read position: chr8:143,863,086 INFO 2026-06-08 08:41:03 MarkDuplicates Tracking 507185 as yet unmatched pairs. 16906 records in RAM. INFO 2026-06-08 08:41:04 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 1s. Last read position: chr8:143,863,955 INFO 2026-06-08 08:41:04 MarkDuplicates Tracking 501791 as yet unmatched pairs. 11512 records in RAM. INFO 2026-06-08 08:41:06 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 1s. Last read position: chr8:143,865,203 INFO 2026-06-08 08:41:06 MarkDuplicates Tracking 501271 as yet unmatched pairs. 10992 records in RAM. INFO 2026-06-08 08:41:07 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 0s. Last read position: chr8:143,866,204 INFO 2026-06-08 08:41:07 MarkDuplicates Tracking 499919 as yet unmatched pairs. 9640 records in RAM. INFO 2026-06-08 08:41:08 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 1s. Last read position: chr8:143,871,857 INFO 2026-06-08 08:41:08 MarkDuplicates Tracking 501407 as yet unmatched pairs. 11128 records in RAM. INFO 2026-06-08 08:41:09 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 1s. Last read position: chr8:143,924,259 INFO 2026-06-08 08:41:09 MarkDuplicates Tracking 496807 as yet unmatched pairs. 6525 records in RAM. INFO 2026-06-08 08:41:11 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 1s. Last read position: chr8:144,106,441 INFO 2026-06-08 08:41:11 MarkDuplicates Tracking 494020 as yet unmatched pairs. 3732 records in RAM. INFO 2026-06-08 08:41:13 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 1s. Last read position: chr8:144,473,382 INFO 2026-06-08 08:41:13 MarkDuplicates Tracking 492829 as yet unmatched pairs. 2539 records in RAM. INFO 2026-06-08 08:41:14 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 1s. Last read position: chr9:5,787,200 INFO 2026-06-08 08:41:14 MarkDuplicates Tracking 489832 as yet unmatched pairs. 31696 records in RAM. INFO 2026-06-08 08:41:16 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 1s. Last read position: chr9:25,677,853 INFO 2026-06-08 08:41:16 MarkDuplicates Tracking 488445 as yet unmatched pairs. 30300 records in RAM. INFO 2026-06-08 08:41:18 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 1s. Last read position: chr9:35,546,493 INFO 2026-06-08 08:41:18 MarkDuplicates Tracking 486820 as yet unmatched pairs. 28673 records in RAM. INFO 2026-06-08 08:41:21 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 2s. Last read position: chr9:39,288,018 INFO 2026-06-08 08:41:21 MarkDuplicates Tracking 484676 as yet unmatched pairs. 26524 records in RAM. INFO 2026-06-08 08:41:22 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 1s. Last read position: chr9:83,975,469 INFO 2026-06-08 08:41:22 MarkDuplicates Tracking 485236 as yet unmatched pairs. 27081 records in RAM. INFO 2026-06-08 08:41:24 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 1s. Last read position: chr9:93,293,096 INFO 2026-06-08 08:41:24 MarkDuplicates Tracking 481688 as yet unmatched pairs. 23520 records in RAM. INFO 2026-06-08 08:41:25 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:06:16s. Time for last 1,000,000: 1s. Last read position: chr9:100,302,291 INFO 2026-06-08 08:41:25 MarkDuplicates Tracking 479964 as yet unmatched pairs. 21789 records in RAM. INFO 2026-06-08 08:41:27 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 1s. Last read position: chr9:113,267,389 INFO 2026-06-08 08:41:27 MarkDuplicates Tracking 478356 as yet unmatched pairs. 20175 records in RAM. INFO 2026-06-08 08:41:29 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 1s. Last read position: chr9:120,471,757 INFO 2026-06-08 08:41:29 MarkDuplicates Tracking 476457 as yet unmatched pairs. 18274 records in RAM. INFO 2026-06-08 08:41:30 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 1s. Last read position: chr9:125,171,121 INFO 2026-06-08 08:41:30 MarkDuplicates Tracking 474734 as yet unmatched pairs. 16548 records in RAM. INFO 2026-06-08 08:41:32 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 1s. Last read position: chr9:128,107,311 INFO 2026-06-08 08:41:32 MarkDuplicates Tracking 472794 as yet unmatched pairs. 14608 records in RAM. INFO 2026-06-08 08:41:34 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 1s. Last read position: chr9:128,907,332 INFO 2026-06-08 08:41:34 MarkDuplicates Tracking 470871 as yet unmatched pairs. 12677 records in RAM. INFO 2026-06-08 08:41:35 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 1s. Last read position: chr9:130,885,401 INFO 2026-06-08 08:41:35 MarkDuplicates Tracking 469999 as yet unmatched pairs. 11803 records in RAM. INFO 2026-06-08 08:41:37 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 1s. Last read position: chr9:133,349,601 INFO 2026-06-08 08:41:37 MarkDuplicates Tracking 468691 as yet unmatched pairs. 10495 records in RAM. INFO 2026-06-08 08:41:38 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 1s. Last read position: chr9:134,798,417 INFO 2026-06-08 08:41:38 MarkDuplicates Tracking 467335 as yet unmatched pairs. 9135 records in RAM. INFO 2026-06-08 08:41:40 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:06:30s. Time for last 1,000,000: 1s. Last read position: chr9:136,475,290 INFO 2026-06-08 08:41:40 MarkDuplicates Tracking 464745 as yet unmatched pairs. 6544 records in RAM. INFO 2026-06-08 08:41:42 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 1s. Last read position: chr9:137,014,220 INFO 2026-06-08 08:41:42 MarkDuplicates Tracking 462409 as yet unmatched pairs. 4203 records in RAM. INFO 2026-06-08 08:41:43 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 1s. Last read position: chr9:137,457,635 INFO 2026-06-08 08:41:43 MarkDuplicates Tracking 459537 as yet unmatched pairs. 1324 records in RAM. INFO 2026-06-08 08:41:45 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:06:35s. Time for last 1,000,000: 1s. Last read position: chr10:5,924,356 INFO 2026-06-08 08:41:45 MarkDuplicates Tracking 457205 as yet unmatched pairs. 23169 records in RAM. INFO 2026-06-08 08:41:47 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 1s. Last read position: chr10:17,235,186 INFO 2026-06-08 08:41:47 MarkDuplicates Tracking 456151 as yet unmatched pairs. 22110 records in RAM. INFO 2026-06-08 08:41:48 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 1s. Last read position: chr10:30,849,262 INFO 2026-06-08 08:41:48 MarkDuplicates Tracking 453925 as yet unmatched pairs. 19881 records in RAM. INFO 2026-06-08 08:41:50 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 1s. Last read position: chr10:38,055,958 INFO 2026-06-08 08:41:50 MarkDuplicates Tracking 452583 as yet unmatched pairs. 18537 records in RAM. INFO 2026-06-08 08:41:51 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 1s. Last read position: chr10:45,727,456 INFO 2026-06-08 08:41:51 MarkDuplicates Tracking 451878 as yet unmatched pairs. 17831 records in RAM. INFO 2026-06-08 08:41:53 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 1s. Last read position: chr10:58,715,757 INFO 2026-06-08 08:41:53 MarkDuplicates Tracking 449398 as yet unmatched pairs. 15350 records in RAM. INFO 2026-06-08 08:41:55 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 1s. Last read position: chr10:70,152,428 INFO 2026-06-08 08:41:55 MarkDuplicates Tracking 447732 as yet unmatched pairs. 13681 records in RAM. INFO 2026-06-08 08:41:57 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:06:47s. Time for last 1,000,000: 1s. Last read position: chr10:73,914,782 INFO 2026-06-08 08:41:57 MarkDuplicates Tracking 445832 as yet unmatched pairs. 11779 records in RAM. INFO 2026-06-08 08:41:59 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 1s. Last read position: chr10:84,152,388 INFO 2026-06-08 08:41:59 MarkDuplicates Tracking 444252 as yet unmatched pairs. 10188 records in RAM. INFO 2026-06-08 08:42:00 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 1s. Last read position: chr10:93,396,197 INFO 2026-06-08 08:42:00 MarkDuplicates Tracking 442868 as yet unmatched pairs. 8803 records in RAM. INFO 2026-06-08 08:42:02 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 1s. Last read position: chr10:100,913,170 INFO 2026-06-08 08:42:02 MarkDuplicates Tracking 441272 as yet unmatched pairs. 7206 records in RAM. INFO 2026-06-08 08:42:03 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 1s. Last read position: chr10:103,570,883 INFO 2026-06-08 08:42:03 MarkDuplicates Tracking 439124 as yet unmatched pairs. 5056 records in RAM. INFO 2026-06-08 08:42:05 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 1s. Last read position: chr10:116,951,934 INFO 2026-06-08 08:42:05 MarkDuplicates Tracking 437684 as yet unmatched pairs. 3604 records in RAM. INFO 2026-06-08 08:42:07 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:06:57s. Time for last 1,000,000: 1s. Last read position: chr10:123,799,115 INFO 2026-06-08 08:42:07 MarkDuplicates Tracking 435751 as yet unmatched pairs. 1655 records in RAM. INFO 2026-06-08 08:42:09 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 2s. Last read position: chr11:213,260 INFO 2026-06-08 08:42:09 MarkDuplicates Tracking 434074 as yet unmatched pairs. 51586 records in RAM. INFO 2026-06-08 08:42:10 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:07:00s. Time for last 1,000,000: 1s. Last read position: chr11:490,519 INFO 2026-06-08 08:42:10 MarkDuplicates Tracking 432238 as yet unmatched pairs. 49750 records in RAM. INFO 2026-06-08 08:42:12 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 1s. Last read position: chr11:850,291 INFO 2026-06-08 08:42:12 MarkDuplicates Tracking 430444 as yet unmatched pairs. 47955 records in RAM. INFO 2026-06-08 08:42:13 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:07:03s. Time for last 1,000,000: 1s. Last read position: chr11:1,761,339 INFO 2026-06-08 08:42:13 MarkDuplicates Tracking 431086 as yet unmatched pairs. 48597 records in RAM. INFO 2026-06-08 08:42:15 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 1s. Last read position: chr11:6,456,586 INFO 2026-06-08 08:42:15 MarkDuplicates Tracking 426991 as yet unmatched pairs. 44499 records in RAM. INFO 2026-06-08 08:42:16 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:07:07s. Time for last 1,000,000: 1s. Last read position: chr11:9,832,254 INFO 2026-06-08 08:42:16 MarkDuplicates Tracking 424524 as yet unmatched pairs. 42026 records in RAM. INFO 2026-06-08 08:43:15 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:08:06s. Time for last 1,000,000: 58s. Last read position: chr11:17,788,178 INFO 2026-06-08 08:43:15 MarkDuplicates Tracking 423183 as yet unmatched pairs. 40676 records in RAM. INFO 2026-06-08 08:43:17 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:08:08s. Time for last 1,000,000: 2s. Last read position: chr11:36,036,133 INFO 2026-06-08 08:43:17 MarkDuplicates Tracking 421499 as yet unmatched pairs. 38987 records in RAM. INFO 2026-06-08 08:43:20 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:08:10s. Time for last 1,000,000: 2s. Last read position: chr11:46,680,701 INFO 2026-06-08 08:43:20 MarkDuplicates Tracking 419950 as yet unmatched pairs. 37437 records in RAM. INFO 2026-06-08 08:43:22 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:08:12s. Time for last 1,000,000: 2s. Last read position: chr11:57,597,697 INFO 2026-06-08 08:43:22 MarkDuplicates Tracking 418039 as yet unmatched pairs. 35526 records in RAM. INFO 2026-06-08 08:43:24 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:08:14s. Time for last 1,000,000: 2s. Last read position: chr11:61,331,660 INFO 2026-06-08 08:43:24 MarkDuplicates Tracking 416640 as yet unmatched pairs. 34124 records in RAM. INFO 2026-06-08 08:43:26 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 1s. Last read position: chr11:62,519,005 INFO 2026-06-08 08:43:26 MarkDuplicates Tracking 415108 as yet unmatched pairs. 32589 records in RAM. INFO 2026-06-08 08:43:27 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:08:17s. Time for last 1,000,000: 1s. Last read position: chr11:62,531,655 INFO 2026-06-08 08:43:27 MarkDuplicates Tracking 414393 as yet unmatched pairs. 31874 records in RAM. INFO 2026-06-08 08:43:29 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 1s. Last read position: chr11:63,974,663 INFO 2026-06-08 08:43:29 MarkDuplicates Tracking 411887 as yet unmatched pairs. 29368 records in RAM. INFO 2026-06-08 08:43:31 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 1s. Last read position: chr11:65,131,315 INFO 2026-06-08 08:43:31 MarkDuplicates Tracking 409483 as yet unmatched pairs. 26964 records in RAM. INFO 2026-06-08 08:43:32 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:08:22s. Time for last 1,000,000: 1s. Last read position: chr11:65,659,786 INFO 2026-06-08 08:43:32 MarkDuplicates Tracking 408609 as yet unmatched pairs. 26081 records in RAM. INFO 2026-06-08 08:43:34 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:08:24s. Time for last 1,000,000: 1s. Last read position: chr11:66,693,305 INFO 2026-06-08 08:43:34 MarkDuplicates Tracking 405511 as yet unmatched pairs. 22980 records in RAM. INFO 2026-06-08 08:43:35 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 1s. Last read position: chr11:67,490,964 INFO 2026-06-08 08:43:35 MarkDuplicates Tracking 403282 as yet unmatched pairs. 20743 records in RAM. INFO 2026-06-08 08:43:37 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:08:27s. Time for last 1,000,000: 1s. Last read position: chr11:69,641,347 INFO 2026-06-08 08:43:37 MarkDuplicates Tracking 426873 as yet unmatched pairs. 44334 records in RAM. INFO 2026-06-08 08:43:39 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 1s. Last read position: chr11:69,643,939 INFO 2026-06-08 08:43:39 MarkDuplicates Tracking 419027 as yet unmatched pairs. 36488 records in RAM. INFO 2026-06-08 08:43:40 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:08:30s. Time for last 1,000,000: 1s. Last read position: chr11:69,653,209 INFO 2026-06-08 08:43:40 MarkDuplicates Tracking 402796 as yet unmatched pairs. 20257 records in RAM. INFO 2026-06-08 08:43:42 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 1s. Last read position: chr11:71,481,971 INFO 2026-06-08 08:43:42 MarkDuplicates Tracking 396812 as yet unmatched pairs. 14273 records in RAM. INFO 2026-06-08 08:43:44 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 1s. Last read position: chr11:72,229,932 INFO 2026-06-08 08:43:44 MarkDuplicates Tracking 393882 as yet unmatched pairs. 11342 records in RAM. INFO 2026-06-08 08:43:45 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 1s. Last read position: chr11:74,090,819 INFO 2026-06-08 08:43:45 MarkDuplicates Tracking 391601 as yet unmatched pairs. 9061 records in RAM. INFO 2026-06-08 08:43:47 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 1s. Last read position: chr11:85,990,363 INFO 2026-06-08 08:43:47 MarkDuplicates Tracking 390390 as yet unmatched pairs. 7846 records in RAM. INFO 2026-06-08 08:43:49 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:08:39s. Time for last 1,000,000: 1s. Last read position: chr11:108,343,252 INFO 2026-06-08 08:43:49 MarkDuplicates Tracking 388626 as yet unmatched pairs. 6077 records in RAM. INFO 2026-06-08 08:43:50 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 1s. Last read position: chr11:118,386,506 INFO 2026-06-08 08:43:50 MarkDuplicates Tracking 386941 as yet unmatched pairs. 4392 records in RAM. INFO 2026-06-08 08:43:52 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:08:42s. Time for last 1,000,000: 1s. Last read position: chr11:119,339,743 INFO 2026-06-08 08:43:52 MarkDuplicates Tracking 385329 as yet unmatched pairs. 2777 records in RAM. INFO 2026-06-08 08:43:54 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:08:44s. Time for last 1,000,000: 1s. Last read position: chr11:128,972,391 INFO 2026-06-08 08:43:54 MarkDuplicates Tracking 383261 as yet unmatched pairs. 706 records in RAM. INFO 2026-06-08 08:43:56 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:08:46s. Time for last 1,000,000: 2s. Last read position: chr12:1,780,579 INFO 2026-06-08 08:43:56 MarkDuplicates Tracking 382029 as yet unmatched pairs. 39270 records in RAM. INFO 2026-06-08 08:43:58 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 1s. Last read position: chr12:6,464,885 INFO 2026-06-08 08:43:58 MarkDuplicates Tracking 379963 as yet unmatched pairs. 37204 records in RAM. INFO 2026-06-08 08:43:59 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 1s. Last read position: chr12:6,941,426 INFO 2026-06-08 08:43:59 MarkDuplicates Tracking 379179 as yet unmatched pairs. 36412 records in RAM. INFO 2026-06-08 08:44:01 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 1s. Last read position: chr12:9,098,702 INFO 2026-06-08 08:44:01 MarkDuplicates Tracking 377080 as yet unmatched pairs. 34313 records in RAM. INFO 2026-06-08 08:44:02 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:08:52s. Time for last 1,000,000: 1s. Last read position: chr12:14,882,080 INFO 2026-06-08 08:44:02 MarkDuplicates Tracking 375827 as yet unmatched pairs. 33056 records in RAM. INFO 2026-06-08 08:44:04 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 1s. Last read position: chr12:32,216,268 INFO 2026-06-08 08:44:04 MarkDuplicates Tracking 373553 as yet unmatched pairs. 30781 records in RAM. INFO 2026-06-08 08:44:06 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:08:56s. Time for last 1,000,000: 1s. Last read position: chr12:47,802,223 INFO 2026-06-08 08:44:06 MarkDuplicates Tracking 372635 as yet unmatched pairs. 29863 records in RAM. INFO 2026-06-08 08:44:07 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:08:57s. Time for last 1,000,000: 1s. Last read position: chr12:49,040,924 INFO 2026-06-08 08:44:07 MarkDuplicates Tracking 370257 as yet unmatched pairs. 27484 records in RAM. INFO 2026-06-08 08:44:09 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:08:59s. Time for last 1,000,000: 1s. Last read position: chr12:50,177,568 INFO 2026-06-08 08:44:09 MarkDuplicates Tracking 368823 as yet unmatched pairs. 26048 records in RAM. INFO 2026-06-08 08:44:10 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:09:00s. Time for last 1,000,000: 1s. Last read position: chr12:52,952,244 INFO 2026-06-08 08:44:10 MarkDuplicates Tracking 367810 as yet unmatched pairs. 25035 records in RAM. INFO 2026-06-08 08:44:12 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:09:02s. Time for last 1,000,000: 1s. Last read position: chr12:53,486,058 INFO 2026-06-08 08:44:12 MarkDuplicates Tracking 365498 as yet unmatched pairs. 22723 records in RAM. INFO 2026-06-08 08:44:14 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:09:04s. Time for last 1,000,000: 1s. Last read position: chr12:55,796,025 INFO 2026-06-08 08:44:14 MarkDuplicates Tracking 363930 as yet unmatched pairs. 21147 records in RAM. INFO 2026-06-08 08:44:15 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 1s. Last read position: chr12:56,581,351 INFO 2026-06-08 08:44:15 MarkDuplicates Tracking 362387 as yet unmatched pairs. 19604 records in RAM. INFO 2026-06-08 08:44:17 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:09:07s. Time for last 1,000,000: 1s. Last read position: chr12:57,107,638 INFO 2026-06-08 08:44:17 MarkDuplicates Tracking 361130 as yet unmatched pairs. 18346 records in RAM. INFO 2026-06-08 08:44:18 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 1s. Last read position: chr12:57,526,597 INFO 2026-06-08 08:44:18 MarkDuplicates Tracking 359819 as yet unmatched pairs. 17034 records in RAM. INFO 2026-06-08 08:44:20 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:09:10s. Time for last 1,000,000: 1s. Last read position: chr12:68,824,558 INFO 2026-06-08 08:44:20 MarkDuplicates Tracking 357691 as yet unmatched pairs. 14906 records in RAM. INFO 2026-06-08 08:44:22 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:09:12s. Time for last 1,000,000: 1s. Last read position: chr12:91,108,850 INFO 2026-06-08 08:44:22 MarkDuplicates Tracking 356440 as yet unmatched pairs. 13633 records in RAM. INFO 2026-06-08 08:44:23 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:09:13s. Time for last 1,000,000: 1s. Last read position: chr12:102,475,668 INFO 2026-06-08 08:44:23 MarkDuplicates Tracking 354433 as yet unmatched pairs. 11625 records in RAM. INFO 2026-06-08 08:44:25 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:09:15s. Time for last 1,000,000: 1s. Last read position: chr12:110,326,437 INFO 2026-06-08 08:44:25 MarkDuplicates Tracking 352777 as yet unmatched pairs. 9969 records in RAM. INFO 2026-06-08 08:44:27 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:09:17s. Time for last 1,000,000: 2s. Last read position: chr12:113,358,732 INFO 2026-06-08 08:44:27 MarkDuplicates Tracking 350900 as yet unmatched pairs. 8090 records in RAM. INFO 2026-06-08 08:44:29 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:09:19s. Time for last 1,000,000: 1s. Last read position: chr12:120,463,968 INFO 2026-06-08 08:44:29 MarkDuplicates Tracking 349190 as yet unmatched pairs. 6367 records in RAM. INFO 2026-06-08 08:44:31 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:09:21s. Time for last 1,000,000: 1s. Last read position: chr12:122,981,810 INFO 2026-06-08 08:44:31 MarkDuplicates Tracking 347930 as yet unmatched pairs. 5105 records in RAM. INFO 2026-06-08 08:44:32 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 1s. Last read position: chr12:124,402,513 INFO 2026-06-08 08:44:32 MarkDuplicates Tracking 345749 as yet unmatched pairs. 2923 records in RAM. INFO 2026-06-08 08:44:34 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:09:24s. Time for last 1,000,000: 1s. Last read position: chr12:132,583,432 INFO 2026-06-08 08:44:34 MarkDuplicates Tracking 343867 as yet unmatched pairs. 1031 records in RAM. INFO 2026-06-08 08:44:35 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 1s. Last read position: chr13:21,496,128 INFO 2026-06-08 08:44:35 MarkDuplicates Tracking 341969 as yet unmatched pairs. 10556 records in RAM. INFO 2026-06-08 08:44:37 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:09:27s. Time for last 1,000,000: 1s. Last read position: chr13:35,159,460 INFO 2026-06-08 08:44:37 MarkDuplicates Tracking 340596 as yet unmatched pairs. 9183 records in RAM. INFO 2026-06-08 08:44:38 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:09:29s. Time for last 1,000,000: 1s. Last read position: chr13:43,968,686 INFO 2026-06-08 08:44:38 MarkDuplicates Tracking 338863 as yet unmatched pairs. 7450 records in RAM. INFO 2026-06-08 08:44:40 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:09:30s. Time for last 1,000,000: 1s. Last read position: chr13:73,846,103 INFO 2026-06-08 08:44:40 MarkDuplicates Tracking 337370 as yet unmatched pairs. 5956 records in RAM. INFO 2026-06-08 08:44:42 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:09:32s. Time for last 1,000,000: 1s. Last read position: chr13:100,112,042 INFO 2026-06-08 08:44:42 MarkDuplicates Tracking 335706 as yet unmatched pairs. 4276 records in RAM. INFO 2026-06-08 08:44:43 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:09:33s. Time for last 1,000,000: 1s. Last read position: chr13:110,428,573 INFO 2026-06-08 08:44:43 MarkDuplicates Tracking 334206 as yet unmatched pairs. 2776 records in RAM. INFO 2026-06-08 08:44:45 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 1s. Last read position: chr13:113,310,760 INFO 2026-06-08 08:44:45 MarkDuplicates Tracking 332240 as yet unmatched pairs. 810 records in RAM. INFO 2026-06-08 08:44:47 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 1s. Last read position: chr14:21,431,273 INFO 2026-06-08 08:44:47 MarkDuplicates Tracking 330499 as yet unmatched pairs. 23446 records in RAM. INFO 2026-06-08 08:44:48 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:09:38s. Time for last 1,000,000: 1s. Last read position: chr14:24,102,721 INFO 2026-06-08 08:44:48 MarkDuplicates Tracking 328742 as yet unmatched pairs. 21684 records in RAM. INFO 2026-06-08 08:44:50 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:09:40s. Time for last 1,000,000: 1s. Last read position: chr14:30,638,233 INFO 2026-06-08 08:44:50 MarkDuplicates Tracking 326710 as yet unmatched pairs. 19652 records in RAM. INFO 2026-06-08 08:44:51 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:09:42s. Time for last 1,000,000: 1s. Last read position: chr14:49,586,609 INFO 2026-06-08 08:44:51 MarkDuplicates Tracking 325630 as yet unmatched pairs. 18569 records in RAM. INFO 2026-06-08 08:44:53 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:09:43s. Time for last 1,000,000: 1s. Last read position: chr14:55,667,239 INFO 2026-06-08 08:44:53 MarkDuplicates Tracking 324141 as yet unmatched pairs. 17076 records in RAM. INFO 2026-06-08 08:44:54 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 1s. Last read position: chr14:64,741,299 INFO 2026-06-08 08:44:54 MarkDuplicates Tracking 322340 as yet unmatched pairs. 15275 records in RAM. INFO 2026-06-08 08:44:56 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:09:46s. Time for last 1,000,000: 1s. Last read position: chr14:71,105,302 INFO 2026-06-08 08:44:56 MarkDuplicates Tracking 320344 as yet unmatched pairs. 13276 records in RAM. INFO 2026-06-08 08:44:58 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:09:48s. Time for last 1,000,000: 2s. Last read position: chr14:74,816,585 INFO 2026-06-08 08:44:58 MarkDuplicates Tracking 318452 as yet unmatched pairs. 11383 records in RAM. INFO 2026-06-08 08:45:00 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:09:50s. Time for last 1,000,000: 1s. Last read position: chr14:81,068,243 INFO 2026-06-08 08:45:00 MarkDuplicates Tracking 316529 as yet unmatched pairs. 9460 records in RAM. INFO 2026-06-08 08:45:02 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:09:52s. Time for last 1,000,000: 2s. Last read position: chr14:94,079,510 INFO 2026-06-08 08:45:02 MarkDuplicates Tracking 315083 as yet unmatched pairs. 8009 records in RAM. INFO 2026-06-08 08:45:05 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:09:55s. Time for last 1,000,000: 2s. Last read position: chr14:100,146,934 INFO 2026-06-08 08:45:05 MarkDuplicates Tracking 313209 as yet unmatched pairs. 6131 records in RAM. INFO 2026-06-08 08:45:07 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:09:57s. Time for last 1,000,000: 2s. Last read position: chr14:103,475,042 INFO 2026-06-08 08:45:07 MarkDuplicates Tracking 311638 as yet unmatched pairs. 4560 records in RAM. INFO 2026-06-08 08:45:09 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 1s. Last read position: chr14:104,946,437 INFO 2026-06-08 08:45:09 MarkDuplicates Tracking 310330 as yet unmatched pairs. 3252 records in RAM. INFO 2026-06-08 08:45:11 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:10:01s. Time for last 1,000,000: 1s. Last read position: chr14:105,640,995 INFO 2026-06-08 08:45:11 MarkDuplicates Tracking 308026 as yet unmatched pairs. 948 records in RAM. INFO 2026-06-08 08:45:12 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:10:03s. Time for last 1,000,000: 1s. Last read position: chr15:30,908,167 INFO 2026-06-08 08:45:12 MarkDuplicates Tracking 306199 as yet unmatched pairs. 20863 records in RAM. INFO 2026-06-08 08:45:14 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:10:04s. Time for last 1,000,000: 1s. Last read position: chr15:39,594,173 INFO 2026-06-08 08:45:14 MarkDuplicates Tracking 306110 as yet unmatched pairs. 20773 records in RAM. INFO 2026-06-08 08:45:15 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 1s. Last read position: chr15:42,211,653 INFO 2026-06-08 08:45:15 MarkDuplicates Tracking 303131 as yet unmatched pairs. 17794 records in RAM. INFO 2026-06-08 08:45:17 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:10:07s. Time for last 1,000,000: 1s. Last read position: chr15:44,565,827 INFO 2026-06-08 08:45:17 MarkDuplicates Tracking 301527 as yet unmatched pairs. 16190 records in RAM. INFO 2026-06-08 08:45:19 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 1s. Last read position: chr15:52,050,115 INFO 2026-06-08 08:45:19 MarkDuplicates Tracking 299814 as yet unmatched pairs. 14477 records in RAM. INFO 2026-06-08 08:45:20 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:10:10s. Time for last 1,000,000: 1s. Last read position: chr15:61,962,374 INFO 2026-06-08 08:45:20 MarkDuplicates Tracking 298690 as yet unmatched pairs. 13352 records in RAM. INFO 2026-06-08 08:45:22 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 1s. Last read position: chr15:65,197,958 INFO 2026-06-08 08:45:22 MarkDuplicates Tracking 296857 as yet unmatched pairs. 11519 records in RAM. INFO 2026-06-08 08:45:24 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:10:14s. Time for last 1,000,000: 1s. Last read position: chr15:71,242,832 INFO 2026-06-08 08:45:24 MarkDuplicates Tracking 296188 as yet unmatched pairs. 10836 records in RAM. INFO 2026-06-08 08:45:25 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:10:15s. Time for last 1,000,000: 1s. Last read position: chr15:74,176,058 INFO 2026-06-08 08:45:25 MarkDuplicates Tracking 292764 as yet unmatched pairs. 7394 records in RAM. INFO 2026-06-08 08:45:27 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:10:17s. Time for last 1,000,000: 1s. Last read position: chr15:77,745,818 INFO 2026-06-08 08:45:27 MarkDuplicates Tracking 290643 as yet unmatched pairs. 5273 records in RAM. INFO 2026-06-08 08:45:29 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:10:19s. Time for last 1,000,000: 2s. Last read position: chr15:85,579,417 INFO 2026-06-08 08:45:29 MarkDuplicates Tracking 289562 as yet unmatched pairs. 4190 records in RAM. INFO 2026-06-08 08:45:31 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:10:21s. Time for last 1,000,000: 1s. Last read position: chr15:90,629,274 INFO 2026-06-08 08:45:31 MarkDuplicates Tracking 287663 as yet unmatched pairs. 2291 records in RAM. INFO 2026-06-08 08:45:32 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:10:22s. Time for last 1,000,000: 1s. Last read position: chr15:100,898,083 INFO 2026-06-08 08:45:32 MarkDuplicates Tracking 285958 as yet unmatched pairs. 584 records in RAM. INFO 2026-06-08 08:45:34 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:10:25s. Time for last 1,000,000: 2s. Last read position: chr16:579,149 INFO 2026-06-08 08:45:34 MarkDuplicates Tracking 284071 as yet unmatched pairs. 44199 records in RAM. INFO 2026-06-08 08:45:36 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 1s. Last read position: chr16:1,204,065 INFO 2026-06-08 08:45:36 MarkDuplicates Tracking 283656 as yet unmatched pairs. 43784 records in RAM. INFO 2026-06-08 08:45:38 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:10:28s. Time for last 1,000,000: 1s. Last read position: chr16:1,523,612 INFO 2026-06-08 08:45:38 MarkDuplicates Tracking 279403 as yet unmatched pairs. 39531 records in RAM. INFO 2026-06-08 08:45:39 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:10:30s. Time for last 1,000,000: 1s. Last read position: chr16:2,080,274 INFO 2026-06-08 08:45:39 MarkDuplicates Tracking 277565 as yet unmatched pairs. 37693 records in RAM. INFO 2026-06-08 08:45:41 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:10:31s. Time for last 1,000,000: 1s. Last read position: chr16:2,243,340 INFO 2026-06-08 08:45:41 MarkDuplicates Tracking 275175 as yet unmatched pairs. 35303 records in RAM. INFO 2026-06-08 08:45:43 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:10:33s. Time for last 1,000,000: 1s. Last read position: chr16:2,767,033 INFO 2026-06-08 08:45:43 MarkDuplicates Tracking 275595 as yet unmatched pairs. 35719 records in RAM. INFO 2026-06-08 08:45:44 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:10:34s. Time for last 1,000,000: 1s. Last read position: chr16:3,736,116 INFO 2026-06-08 08:45:44 MarkDuplicates Tracking 271418 as yet unmatched pairs. 31542 records in RAM. INFO 2026-06-08 08:45:46 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:10:36s. Time for last 1,000,000: 1s. Last read position: chr16:9,156,363 INFO 2026-06-08 08:45:46 MarkDuplicates Tracking 269310 as yet unmatched pairs. 29433 records in RAM. INFO 2026-06-08 08:45:47 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:10:38s. Time for last 1,000,000: 1s. Last read position: chr16:14,895,054 INFO 2026-06-08 08:45:47 MarkDuplicates Tracking 267983 as yet unmatched pairs. 28106 records in RAM. INFO 2026-06-08 08:45:49 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:10:39s. Time for last 1,000,000: 1s. Last read position: chr16:15,127,879 INFO 2026-06-08 08:45:49 MarkDuplicates Tracking 267374 as yet unmatched pairs. 27497 records in RAM. INFO 2026-06-08 08:45:50 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:10:40s. Time for last 1,000,000: 1s. Last read position: chr16:16,319,982 INFO 2026-06-08 08:45:50 MarkDuplicates Tracking 266552 as yet unmatched pairs. 26675 records in RAM. INFO 2026-06-08 08:45:52 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:10:42s. Time for last 1,000,000: 1s. Last read position: chr16:16,369,480 INFO 2026-06-08 08:45:52 MarkDuplicates Tracking 266065 as yet unmatched pairs. 26187 records in RAM. INFO 2026-06-08 08:45:53 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:10:43s. Time for last 1,000,000: 1s. Last read position: chr16:18,351,793 INFO 2026-06-08 08:45:53 MarkDuplicates Tracking 266110 as yet unmatched pairs. 26232 records in RAM. INFO 2026-06-08 08:45:54 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:10:45s. Time for last 1,000,000: 1s. Last read position: chr16:18,819,618 INFO 2026-06-08 08:45:54 MarkDuplicates Tracking 263603 as yet unmatched pairs. 23725 records in RAM. INFO 2026-06-08 08:45:56 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 1s. Last read position: chr16:21,467,153 INFO 2026-06-08 08:45:56 MarkDuplicates Tracking 262895 as yet unmatched pairs. 23017 records in RAM. INFO 2026-06-08 08:45:57 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:10:48s. Time for last 1,000,000: 1s. Last read position: chr16:22,519,245 INFO 2026-06-08 08:45:57 MarkDuplicates Tracking 261694 as yet unmatched pairs. 21816 records in RAM. INFO 2026-06-08 08:45:59 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:10:49s. Time for last 1,000,000: 1s. Last read position: chr16:27,461,542 INFO 2026-06-08 08:45:59 MarkDuplicates Tracking 261125 as yet unmatched pairs. 21246 records in RAM. INFO 2026-06-08 08:46:01 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:10:51s. Time for last 1,000,000: 2s. Last read position: chr16:28,983,235 INFO 2026-06-08 08:46:01 MarkDuplicates Tracking 259621 as yet unmatched pairs. 19742 records in RAM. INFO 2026-06-08 08:46:03 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:10:53s. Time for last 1,000,000: 1s. Last read position: chr16:29,812,291 INFO 2026-06-08 08:46:03 MarkDuplicates Tracking 258601 as yet unmatched pairs. 18722 records in RAM. INFO 2026-06-08 08:46:04 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:10:54s. Time for last 1,000,000: 1s. Last read position: chr16:30,225,356 INFO 2026-06-08 08:46:04 MarkDuplicates Tracking 256641 as yet unmatched pairs. 16762 records in RAM. INFO 2026-06-08 08:46:06 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:10:56s. Time for last 1,000,000: 1s. Last read position: chr16:30,748,814 INFO 2026-06-08 08:46:06 MarkDuplicates Tracking 255510 as yet unmatched pairs. 15631 records in RAM. INFO 2026-06-08 08:46:07 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 1s. Last read position: chr16:31,357,469 INFO 2026-06-08 08:46:07 MarkDuplicates Tracking 253569 as yet unmatched pairs. 13690 records in RAM. INFO 2026-06-08 08:46:09 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:10:59s. Time for last 1,000,000: 1s. Last read position: chr16:55,482,965 INFO 2026-06-08 08:46:09 MarkDuplicates Tracking 253607 as yet unmatched pairs. 13728 records in RAM. INFO 2026-06-08 08:46:11 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:11:01s. Time for last 1,000,000: 1s. Last read position: chr16:58,723,891 INFO 2026-06-08 08:46:11 MarkDuplicates Tracking 250171 as yet unmatched pairs. 10291 records in RAM. INFO 2026-06-08 08:46:12 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:11:02s. Time for last 1,000,000: 1s. Last read position: chr16:67,947,753 INFO 2026-06-08 08:46:12 MarkDuplicates Tracking 248525 as yet unmatched pairs. 8642 records in RAM. INFO 2026-06-08 08:46:14 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:11:04s. Time for last 1,000,000: 1s. Last read position: chr16:71,915,628 INFO 2026-06-08 08:46:14 MarkDuplicates Tracking 246780 as yet unmatched pairs. 6897 records in RAM. INFO 2026-06-08 08:46:16 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:11:06s. Time for last 1,000,000: 1s. Last read position: chr16:84,422,560 INFO 2026-06-08 08:46:16 MarkDuplicates Tracking 244553 as yet unmatched pairs. 4667 records in RAM. INFO 2026-06-08 08:46:17 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:11:07s. Time for last 1,000,000: 1s. Last read position: chr16:88,437,583 INFO 2026-06-08 08:46:17 MarkDuplicates Tracking 242704 as yet unmatched pairs. 2818 records in RAM. INFO 2026-06-08 08:46:19 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:11:09s. Time for last 1,000,000: 1s. Last read position: chr16:89,649,441 INFO 2026-06-08 08:46:19 MarkDuplicates Tracking 241139 as yet unmatched pairs. 1245 records in RAM. INFO 2026-06-08 08:46:21 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:11:12s. Time for last 1,000,000: 2s. Last read position: chr17:1,471,136 INFO 2026-06-08 08:46:21 MarkDuplicates Tracking 239244 as yet unmatched pairs. 90652 records in RAM. INFO 2026-06-08 08:46:24 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:11:14s. Time for last 1,000,000: 2s. Last read position: chr17:2,667,120 INFO 2026-06-08 08:46:24 MarkDuplicates Tracking 237470 as yet unmatched pairs. 88878 records in RAM. INFO 2026-06-08 08:46:26 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:11:16s. Time for last 1,000,000: 1s. Last read position: chr17:4,941,131 INFO 2026-06-08 08:46:26 MarkDuplicates Tracking 235546 as yet unmatched pairs. 86954 records in RAM. INFO 2026-06-08 08:46:27 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:11:18s. Time for last 1,000,000: 1s. Last read position: chr17:7,256,700 INFO 2026-06-08 08:46:27 MarkDuplicates Tracking 233673 as yet unmatched pairs. 85079 records in RAM. INFO 2026-06-08 08:46:29 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:11:19s. Time for last 1,000,000: 1s. Last read position: chr17:7,578,397 INFO 2026-06-08 08:46:29 MarkDuplicates Tracking 232061 as yet unmatched pairs. 83467 records in RAM. INFO 2026-06-08 08:46:31 MarkDuplicates Read 368,000,000 records. Elapsed time: 00:11:21s. Time for last 1,000,000: 1s. Last read position: chr17:8,147,493 INFO 2026-06-08 08:46:31 MarkDuplicates Tracking 230649 as yet unmatched pairs. 82055 records in RAM. INFO 2026-06-08 08:46:32 MarkDuplicates Read 369,000,000 records. Elapsed time: 00:11:23s. Time for last 1,000,000: 1s. Last read position: chr17:16,139,096 INFO 2026-06-08 08:46:32 MarkDuplicates Tracking 229053 as yet unmatched pairs. 80459 records in RAM. INFO 2026-06-08 08:46:34 MarkDuplicates Read 370,000,000 records. Elapsed time: 00:11:24s. Time for last 1,000,000: 1s. Last read position: chr17:17,819,242 INFO 2026-06-08 08:46:34 MarkDuplicates Tracking 227515 as yet unmatched pairs. 78921 records in RAM. INFO 2026-06-08 08:46:36 MarkDuplicates Read 371,000,000 records. Elapsed time: 00:11:26s. Time for last 1,000,000: 1s. Last read position: chr17:27,643,531 INFO 2026-06-08 08:46:36 MarkDuplicates Tracking 225256 as yet unmatched pairs. 76662 records in RAM. INFO 2026-06-08 08:46:37 MarkDuplicates Read 372,000,000 records. Elapsed time: 00:11:27s. Time for last 1,000,000: 1s. Last read position: chr17:29,575,448 INFO 2026-06-08 08:46:37 MarkDuplicates Tracking 223570 as yet unmatched pairs. 74975 records in RAM. INFO 2026-06-08 08:46:39 MarkDuplicates Read 373,000,000 records. Elapsed time: 00:11:29s. Time for last 1,000,000: 1s. Last read position: chr17:35,650,595 INFO 2026-06-08 08:46:39 MarkDuplicates Tracking 221816 as yet unmatched pairs. 73221 records in RAM. INFO 2026-06-08 08:46:40 MarkDuplicates Read 374,000,000 records. Elapsed time: 00:11:31s. Time for last 1,000,000: 1s. Last read position: chr17:38,563,377 INFO 2026-06-08 08:46:40 MarkDuplicates Tracking 220453 as yet unmatched pairs. 71852 records in RAM. INFO 2026-06-08 08:46:42 MarkDuplicates Read 375,000,000 records. Elapsed time: 00:11:32s. Time for last 1,000,000: 1s. Last read position: chr17:39,700,186 INFO 2026-06-08 08:46:42 MarkDuplicates Tracking 220769 as yet unmatched pairs. 72168 records in RAM. INFO 2026-06-08 08:46:44 MarkDuplicates Read 376,000,000 records. Elapsed time: 00:11:34s. Time for last 1,000,000: 1s. Last read position: chr17:39,994,953 INFO 2026-06-08 08:46:44 MarkDuplicates Tracking 216858 as yet unmatched pairs. 68257 records in RAM. INFO 2026-06-08 08:46:45 MarkDuplicates Read 377,000,000 records. Elapsed time: 00:11:36s. Time for last 1,000,000: 1s. Last read position: chr17:41,515,596 INFO 2026-06-08 08:46:45 MarkDuplicates Tracking 215446 as yet unmatched pairs. 66845 records in RAM. INFO 2026-06-08 08:46:47 MarkDuplicates Read 378,000,000 records. Elapsed time: 00:11:37s. Time for last 1,000,000: 1s. Last read position: chr17:42,292,053 INFO 2026-06-08 08:46:47 MarkDuplicates Tracking 212936 as yet unmatched pairs. 64334 records in RAM. INFO 2026-06-08 08:46:49 MarkDuplicates Read 379,000,000 records. Elapsed time: 00:11:39s. Time for last 1,000,000: 1s. Last read position: chr17:44,071,124 INFO 2026-06-08 08:46:49 MarkDuplicates Tracking 211330 as yet unmatched pairs. 62728 records in RAM. INFO 2026-06-08 08:46:51 MarkDuplicates Read 380,000,000 records. Elapsed time: 00:11:41s. Time for last 1,000,000: 1s. Last read position: chr17:45,586,857 INFO 2026-06-08 08:46:51 MarkDuplicates Tracking 209880 as yet unmatched pairs. 61277 records in RAM. INFO 2026-06-08 08:46:53 MarkDuplicates Read 381,000,000 records. Elapsed time: 00:11:43s. Time for last 1,000,000: 1s. Last read position: chr17:47,973,573 INFO 2026-06-08 08:46:53 MarkDuplicates Tracking 208792 as yet unmatched pairs. 60186 records in RAM. INFO 2026-06-08 08:46:55 MarkDuplicates Read 382,000,000 records. Elapsed time: 00:11:45s. Time for last 1,000,000: 2s. Last read position: chr17:50,185,610 INFO 2026-06-08 08:46:55 MarkDuplicates Tracking 222521 as yet unmatched pairs. 73909 records in RAM. INFO 2026-06-08 08:46:57 MarkDuplicates Read 383,000,000 records. Elapsed time: 00:11:47s. Time for last 1,000,000: 1s. Last read position: chr17:50,186,783 INFO 2026-06-08 08:46:57 MarkDuplicates Tracking 215172 as yet unmatched pairs. 66556 records in RAM. INFO 2026-06-08 08:46:59 MarkDuplicates Read 384,000,000 records. Elapsed time: 00:11:49s. Time for last 1,000,000: 1s. Last read position: chr17:50,187,515 INFO 2026-06-08 08:46:59 MarkDuplicates Tracking 257368 as yet unmatched pairs. 108752 records in RAM. INFO 2026-06-08 08:47:00 MarkDuplicates Read 385,000,000 records. Elapsed time: 00:11:51s. Time for last 1,000,000: 1s. Last read position: chr17:50,188,097 INFO 2026-06-08 08:47:00 MarkDuplicates Tracking 279206 as yet unmatched pairs. 130590 records in RAM. INFO 2026-06-08 08:47:02 MarkDuplicates Read 386,000,000 records. Elapsed time: 00:11:52s. Time for last 1,000,000: 1s. Last read position: chr17:50,188,771 INFO 2026-06-08 08:47:02 MarkDuplicates Tracking 247088 as yet unmatched pairs. 98472 records in RAM. INFO 2026-06-08 08:47:04 MarkDuplicates Read 387,000,000 records. Elapsed time: 00:11:54s. Time for last 1,000,000: 1s. Last read position: chr17:50,189,378 INFO 2026-06-08 08:47:04 MarkDuplicates Tracking 232717 as yet unmatched pairs. 84101 records in RAM. INFO 2026-06-08 08:47:06 MarkDuplicates Read 388,000,000 records. Elapsed time: 00:11:56s. Time for last 1,000,000: 1s. Last read position: chr17:50,189,685 INFO 2026-06-08 08:47:06 MarkDuplicates Tracking 269429 as yet unmatched pairs. 120812 records in RAM. INFO 2026-06-08 08:47:09 MarkDuplicates Read 389,000,000 records. Elapsed time: 00:11:59s. Time for last 1,000,000: 2s. Last read position: chr17:50,190,043 INFO 2026-06-08 08:47:09 MarkDuplicates Tracking 277338 as yet unmatched pairs. 128721 records in RAM. INFO 2026-06-08 08:47:10 MarkDuplicates Read 390,000,000 records. Elapsed time: 00:12:01s. Time for last 1,000,000: 1s. Last read position: chr17:50,190,828 INFO 2026-06-08 08:47:10 MarkDuplicates Tracking 210862 as yet unmatched pairs. 62245 records in RAM. INFO 2026-06-08 08:47:12 MarkDuplicates Read 391,000,000 records. Elapsed time: 00:12:02s. Time for last 1,000,000: 1s. Last read position: chr17:50,191,803 INFO 2026-06-08 08:47:12 MarkDuplicates Tracking 236548 as yet unmatched pairs. 87931 records in RAM. INFO 2026-06-08 08:47:14 MarkDuplicates Read 392,000,000 records. Elapsed time: 00:12:04s. Time for last 1,000,000: 2s. Last read position: chr17:50,192,650 INFO 2026-06-08 08:47:14 MarkDuplicates Tracking 235720 as yet unmatched pairs. 87103 records in RAM. INFO 2026-06-08 08:47:17 MarkDuplicates Read 393,000,000 records. Elapsed time: 00:12:07s. Time for last 1,000,000: 2s. Last read position: chr17:50,193,022 INFO 2026-06-08 08:47:17 MarkDuplicates Tracking 256474 as yet unmatched pairs. 107857 records in RAM. INFO 2026-06-08 08:47:19 MarkDuplicates Read 394,000,000 records. Elapsed time: 00:12:10s. Time for last 1,000,000: 2s. Last read position: chr17:50,194,143 INFO 2026-06-08 08:47:19 MarkDuplicates Tracking 273108 as yet unmatched pairs. 124491 records in RAM. INFO 2026-06-08 08:47:22 MarkDuplicates Read 395,000,000 records. Elapsed time: 00:12:12s. Time for last 1,000,000: 2s. Last read position: chr17:50,194,602 INFO 2026-06-08 08:47:22 MarkDuplicates Tracking 231259 as yet unmatched pairs. 82634 records in RAM. INFO 2026-06-08 08:47:24 MarkDuplicates Read 396,000,000 records. Elapsed time: 00:12:14s. Time for last 1,000,000: 1s. Last read position: chr17:50,195,232 INFO 2026-06-08 08:47:24 MarkDuplicates Tracking 237159 as yet unmatched pairs. 88533 records in RAM. INFO 2026-06-08 08:47:26 MarkDuplicates Read 397,000,000 records. Elapsed time: 00:12:16s. Time for last 1,000,000: 1s. Last read position: chr17:50,195,597 INFO 2026-06-08 08:47:26 MarkDuplicates Tracking 247446 as yet unmatched pairs. 98820 records in RAM. INFO 2026-06-08 08:47:28 MarkDuplicates Read 398,000,000 records. Elapsed time: 00:12:18s. Time for last 1,000,000: 1s. Last read position: chr17:50,196,160 INFO 2026-06-08 08:47:28 MarkDuplicates Tracking 264655 as yet unmatched pairs. 116028 records in RAM. INFO 2026-06-08 08:47:29 MarkDuplicates Read 399,000,000 records. Elapsed time: 00:12:19s. Time for last 1,000,000: 1s. Last read position: chr17:50,196,496 INFO 2026-06-08 08:47:29 MarkDuplicates Tracking 223319 as yet unmatched pairs. 74680 records in RAM. INFO 2026-06-08 08:47:31 MarkDuplicates Read 400,000,000 records. Elapsed time: 00:12:21s. Time for last 1,000,000: 1s. Last read position: chr17:50,197,029 INFO 2026-06-08 08:47:31 MarkDuplicates Tracking 257742 as yet unmatched pairs. 109103 records in RAM. INFO 2026-06-08 08:47:33 MarkDuplicates Read 401,000,000 records. Elapsed time: 00:12:23s. Time for last 1,000,000: 1s. Last read position: chr17:50,197,983 INFO 2026-06-08 08:47:33 MarkDuplicates Tracking 203404 as yet unmatched pairs. 54765 records in RAM. INFO 2026-06-08 08:47:35 MarkDuplicates Read 402,000,000 records. Elapsed time: 00:12:25s. Time for last 1,000,000: 1s. Last read position: chr17:50,199,274 INFO 2026-06-08 08:47:35 MarkDuplicates Tracking 220401 as yet unmatched pairs. 71762 records in RAM. INFO 2026-06-08 08:47:36 MarkDuplicates Read 403,000,000 records. Elapsed time: 00:12:27s. Time for last 1,000,000: 1s. Last read position: chr17:50,201,411 INFO 2026-06-08 08:47:36 MarkDuplicates Tracking 183101 as yet unmatched pairs. 34462 records in RAM. INFO 2026-06-08 08:47:38 MarkDuplicates Read 404,000,000 records. Elapsed time: 00:12:28s. Time for last 1,000,000: 1s. Last read position: chr17:58,494,953 INFO 2026-06-08 08:47:38 MarkDuplicates Tracking 167286 as yet unmatched pairs. 18646 records in RAM. INFO 2026-06-08 08:47:40 MarkDuplicates Read 405,000,000 records. Elapsed time: 00:12:31s. Time for last 1,000,000: 2s. Last read position: chr17:62,029,958 INFO 2026-06-08 08:47:40 MarkDuplicates Tracking 166015 as yet unmatched pairs. 17375 records in RAM. INFO 2026-06-08 08:47:42 MarkDuplicates Read 406,000,000 records. Elapsed time: 00:12:33s. Time for last 1,000,000: 2s. Last read position: chr17:64,531,013 INFO 2026-06-08 08:47:42 MarkDuplicates Tracking 163760 as yet unmatched pairs. 15116 records in RAM. INFO 2026-06-08 08:47:44 MarkDuplicates Read 407,000,000 records. Elapsed time: 00:12:34s. Time for last 1,000,000: 1s. Last read position: chr17:68,530,292 INFO 2026-06-08 08:47:44 MarkDuplicates Tracking 165815 as yet unmatched pairs. 17170 records in RAM. INFO 2026-06-08 08:47:45 MarkDuplicates Read 408,000,000 records. Elapsed time: 00:12:36s. Time for last 1,000,000: 1s. Last read position: chr17:75,498,999 INFO 2026-06-08 08:47:45 MarkDuplicates Tracking 160923 as yet unmatched pairs. 12270 records in RAM. INFO 2026-06-08 08:47:47 MarkDuplicates Read 409,000,000 records. Elapsed time: 00:12:37s. Time for last 1,000,000: 1s. Last read position: chr17:76,046,058 INFO 2026-06-08 08:47:47 MarkDuplicates Tracking 158667 as yet unmatched pairs. 10014 records in RAM. INFO 2026-06-08 08:47:49 MarkDuplicates Read 410,000,000 records. Elapsed time: 00:12:39s. Time for last 1,000,000: 1s. Last read position: chr17:78,171,861 INFO 2026-06-08 08:47:49 MarkDuplicates Tracking 157847 as yet unmatched pairs. 9194 records in RAM. INFO 2026-06-08 08:47:50 MarkDuplicates Read 411,000,000 records. Elapsed time: 00:12:41s. Time for last 1,000,000: 1s. Last read position: chr17:80,340,162 INFO 2026-06-08 08:47:50 MarkDuplicates Tracking 155065 as yet unmatched pairs. 6411 records in RAM. INFO 2026-06-08 08:47:52 MarkDuplicates Read 412,000,000 records. Elapsed time: 00:12:42s. Time for last 1,000,000: 1s. Last read position: chr17:81,547,217 INFO 2026-06-08 08:47:52 MarkDuplicates Tracking 153082 as yet unmatched pairs. 4427 records in RAM. INFO 2026-06-08 08:47:54 MarkDuplicates Read 413,000,000 records. Elapsed time: 00:12:44s. Time for last 1,000,000: 1s. Last read position: chr17:82,080,724 INFO 2026-06-08 08:47:54 MarkDuplicates Tracking 151775 as yet unmatched pairs. 3119 records in RAM. INFO 2026-06-08 08:47:56 MarkDuplicates Read 414,000,000 records. Elapsed time: 00:12:46s. Time for last 1,000,000: 1s. Last read position: chr17:83,084,977 INFO 2026-06-08 08:47:56 MarkDuplicates Tracking 148903 as yet unmatched pairs. 244 records in RAM. INFO 2026-06-08 08:47:57 MarkDuplicates Read 415,000,000 records. Elapsed time: 00:12:47s. Time for last 1,000,000: 1s. Last read position: chr18:13,621,173 INFO 2026-06-08 08:47:57 MarkDuplicates Tracking 148522 as yet unmatched pairs. 7335 records in RAM. INFO 2026-06-08 08:47:59 MarkDuplicates Read 416,000,000 records. Elapsed time: 00:12:49s. Time for last 1,000,000: 1s. Last read position: chr18:36,114,271 INFO 2026-06-08 08:47:59 MarkDuplicates Tracking 147726 as yet unmatched pairs. 6537 records in RAM. INFO 2026-06-08 08:48:00 MarkDuplicates Read 417,000,000 records. Elapsed time: 00:12:51s. Time for last 1,000,000: 1s. Last read position: chr18:50,273,664 INFO 2026-06-08 08:48:00 MarkDuplicates Tracking 144346 as yet unmatched pairs. 3156 records in RAM. INFO 2026-06-08 08:48:02 MarkDuplicates Read 418,000,000 records. Elapsed time: 00:12:52s. Time for last 1,000,000: 1s. Last read position: chr18:69,010,966 INFO 2026-06-08 08:48:02 MarkDuplicates Tracking 142251 as yet unmatched pairs. 1052 records in RAM. INFO 2026-06-08 08:48:05 MarkDuplicates Read 419,000,000 records. Elapsed time: 00:12:55s. Time for last 1,000,000: 2s. Last read position: chr19:810,788 INFO 2026-06-08 08:48:05 MarkDuplicates Tracking 140321 as yet unmatched pairs. 61786 records in RAM. INFO 2026-06-08 08:48:07 MarkDuplicates Read 420,000,000 records. Elapsed time: 00:12:57s. Time for last 1,000,000: 2s. Last read position: chr19:1,271,549 INFO 2026-06-08 08:48:07 MarkDuplicates Tracking 138745 as yet unmatched pairs. 60210 records in RAM. INFO 2026-06-08 08:48:09 MarkDuplicates Read 421,000,000 records. Elapsed time: 00:12:59s. Time for last 1,000,000: 1s. Last read position: chr19:2,226,605 INFO 2026-06-08 08:48:09 MarkDuplicates Tracking 135970 as yet unmatched pairs. 57428 records in RAM. INFO 2026-06-08 08:48:10 MarkDuplicates Read 422,000,000 records. Elapsed time: 00:13:01s. Time for last 1,000,000: 1s. Last read position: chr19:3,964,802 INFO 2026-06-08 08:48:10 MarkDuplicates Tracking 133878 as yet unmatched pairs. 55336 records in RAM. INFO 2026-06-08 08:48:12 MarkDuplicates Read 423,000,000 records. Elapsed time: 00:13:02s. Time for last 1,000,000: 1s. Last read position: chr19:5,616,454 INFO 2026-06-08 08:48:12 MarkDuplicates Tracking 131718 as yet unmatched pairs. 53176 records in RAM. INFO 2026-06-08 08:48:14 MarkDuplicates Read 424,000,000 records. Elapsed time: 00:13:04s. Time for last 1,000,000: 1s. Last read position: chr19:7,467,484 INFO 2026-06-08 08:48:14 MarkDuplicates Tracking 129933 as yet unmatched pairs. 51390 records in RAM. INFO 2026-06-08 08:48:16 MarkDuplicates Read 425,000,000 records. Elapsed time: 00:13:06s. Time for last 1,000,000: 1s. Last read position: chr19:9,296,717 INFO 2026-06-08 08:48:16 MarkDuplicates Tracking 127942 as yet unmatched pairs. 49399 records in RAM. INFO 2026-06-08 08:48:18 MarkDuplicates Read 426,000,000 records. Elapsed time: 00:13:08s. Time for last 1,000,000: 1s. Last read position: chr19:10,687,695 INFO 2026-06-08 08:48:18 MarkDuplicates Tracking 126048 as yet unmatched pairs. 47505 records in RAM. INFO 2026-06-08 08:48:19 MarkDuplicates Read 427,000,000 records. Elapsed time: 00:13:09s. Time for last 1,000,000: 1s. Last read position: chr19:12,629,146 INFO 2026-06-08 08:48:19 MarkDuplicates Tracking 124173 as yet unmatched pairs. 45630 records in RAM. INFO 2026-06-08 08:48:21 MarkDuplicates Read 428,000,000 records. Elapsed time: 00:13:11s. Time for last 1,000,000: 1s. Last read position: chr19:13,993,562 INFO 2026-06-08 08:48:21 MarkDuplicates Tracking 122209 as yet unmatched pairs. 43666 records in RAM. INFO 2026-06-08 08:48:23 MarkDuplicates Read 429,000,000 records. Elapsed time: 00:13:13s. Time for last 1,000,000: 1s. Last read position: chr19:15,184,415 INFO 2026-06-08 08:48:23 MarkDuplicates Tracking 120906 as yet unmatched pairs. 42363 records in RAM. INFO 2026-06-08 08:48:24 MarkDuplicates Read 430,000,000 records. Elapsed time: 00:13:14s. Time for last 1,000,000: 1s. Last read position: chr19:16,089,090 INFO 2026-06-08 08:48:24 MarkDuplicates Tracking 118616 as yet unmatched pairs. 40073 records in RAM. INFO 2026-06-08 08:48:26 MarkDuplicates Read 431,000,000 records. Elapsed time: 00:13:16s. Time for last 1,000,000: 1s. Last read position: chr19:17,580,883 INFO 2026-06-08 08:48:26 MarkDuplicates Tracking 116149 as yet unmatched pairs. 37606 records in RAM. INFO 2026-06-08 08:48:27 MarkDuplicates Read 432,000,000 records. Elapsed time: 00:13:18s. Time for last 1,000,000: 1s. Last read position: chr19:18,749,843 INFO 2026-06-08 08:48:27 MarkDuplicates Tracking 114620 as yet unmatched pairs. 36072 records in RAM. INFO 2026-06-08 08:48:29 MarkDuplicates Read 433,000,000 records. Elapsed time: 00:13:19s. Time for last 1,000,000: 1s. Last read position: chr19:32,581,293 INFO 2026-06-08 08:48:29 MarkDuplicates Tracking 112408 as yet unmatched pairs. 33859 records in RAM. INFO 2026-06-08 08:48:30 MarkDuplicates Read 434,000,000 records. Elapsed time: 00:13:21s. Time for last 1,000,000: 1s. Last read position: chr19:35,633,792 INFO 2026-06-08 08:48:30 MarkDuplicates Tracking 110463 as yet unmatched pairs. 31914 records in RAM. INFO 2026-06-08 08:48:32 MarkDuplicates Read 435,000,000 records. Elapsed time: 00:13:22s. Time for last 1,000,000: 1s. Last read position: chr19:38,081,850 INFO 2026-06-08 08:48:32 MarkDuplicates Tracking 107846 as yet unmatched pairs. 29297 records in RAM. INFO 2026-06-08 08:48:34 MarkDuplicates Read 436,000,000 records. Elapsed time: 00:13:24s. Time for last 1,000,000: 1s. Last read position: chr19:39,393,628 INFO 2026-06-08 08:48:34 MarkDuplicates Tracking 105976 as yet unmatched pairs. 27427 records in RAM. INFO 2026-06-08 08:48:35 MarkDuplicates Read 437,000,000 records. Elapsed time: 00:13:25s. Time for last 1,000,000: 1s. Last read position: chr19:40,224,739 INFO 2026-06-08 08:48:35 MarkDuplicates Tracking 104690 as yet unmatched pairs. 26141 records in RAM. INFO 2026-06-08 08:48:37 MarkDuplicates Read 438,000,000 records. Elapsed time: 00:13:27s. Time for last 1,000,000: 2s. Last read position: chr19:40,942,065 INFO 2026-06-08 08:48:37 MarkDuplicates Tracking 102511 as yet unmatched pairs. 23962 records in RAM. INFO 2026-06-08 08:48:39 MarkDuplicates Read 439,000,000 records. Elapsed time: 00:13:30s. Time for last 1,000,000: 2s. Last read position: chr19:42,269,359 INFO 2026-06-08 08:48:39 MarkDuplicates Tracking 100720 as yet unmatched pairs. 22171 records in RAM. INFO 2026-06-08 08:48:41 MarkDuplicates Read 440,000,000 records. Elapsed time: 00:13:31s. Time for last 1,000,000: 1s. Last read position: chr19:42,293,922 INFO 2026-06-08 08:48:41 MarkDuplicates Tracking 100425 as yet unmatched pairs. 21876 records in RAM. INFO 2026-06-08 08:48:43 MarkDuplicates Read 441,000,000 records. Elapsed time: 00:13:33s. Time for last 1,000,000: 1s. Last read position: chr19:44,820,934 INFO 2026-06-08 08:48:43 MarkDuplicates Tracking 98354 as yet unmatched pairs. 19800 records in RAM. INFO 2026-06-08 08:48:44 MarkDuplicates Read 442,000,000 records. Elapsed time: 00:13:34s. Time for last 1,000,000: 1s. Last read position: chr19:45,617,677 INFO 2026-06-08 08:48:44 MarkDuplicates Tracking 94384 as yet unmatched pairs. 15830 records in RAM. INFO 2026-06-08 08:48:46 MarkDuplicates Read 443,000,000 records. Elapsed time: 00:13:36s. Time for last 1,000,000: 1s. Last read position: chr19:47,169,846 INFO 2026-06-08 08:48:46 MarkDuplicates Tracking 92361 as yet unmatched pairs. 13807 records in RAM. INFO 2026-06-08 08:48:47 MarkDuplicates Read 444,000,000 records. Elapsed time: 00:13:38s. Time for last 1,000,000: 1s. Last read position: chr19:48,617,389 INFO 2026-06-08 08:48:47 MarkDuplicates Tracking 90129 as yet unmatched pairs. 11575 records in RAM. INFO 2026-06-08 08:48:49 MarkDuplicates Read 445,000,000 records. Elapsed time: 00:13:39s. Time for last 1,000,000: 1s. Last read position: chr19:49,497,916 INFO 2026-06-08 08:48:49 MarkDuplicates Tracking 89799 as yet unmatched pairs. 11245 records in RAM. INFO 2026-06-08 08:48:51 MarkDuplicates Read 446,000,000 records. Elapsed time: 00:13:41s. Time for last 1,000,000: 1s. Last read position: chr19:49,861,265 INFO 2026-06-08 08:48:51 MarkDuplicates Tracking 86660 as yet unmatched pairs. 8106 records in RAM. INFO 2026-06-08 08:48:52 MarkDuplicates Read 447,000,000 records. Elapsed time: 00:13:42s. Time for last 1,000,000: 1s. Last read position: chr19:53,873,538 INFO 2026-06-08 08:48:52 MarkDuplicates Tracking 85254 as yet unmatched pairs. 6700 records in RAM. INFO 2026-06-08 08:48:54 MarkDuplicates Read 448,000,000 records. Elapsed time: 00:13:44s. Time for last 1,000,000: 1s. Last read position: chr19:55,230,774 INFO 2026-06-08 08:48:54 MarkDuplicates Tracking 83479 as yet unmatched pairs. 4925 records in RAM. INFO 2026-06-08 08:48:55 MarkDuplicates Read 449,000,000 records. Elapsed time: 00:13:46s. Time for last 1,000,000: 1s. Last read position: chr19:57,291,270 INFO 2026-06-08 08:48:55 MarkDuplicates Tracking 80718 as yet unmatched pairs. 2164 records in RAM. INFO 2026-06-08 08:48:57 MarkDuplicates Read 450,000,000 records. Elapsed time: 00:13:47s. Time for last 1,000,000: 1s. Last read position: chr19:58,548,031 INFO 2026-06-08 08:48:57 MarkDuplicates Tracking 79658 as yet unmatched pairs. 1104 records in RAM. INFO 2026-06-08 08:48:59 MarkDuplicates Read 451,000,000 records. Elapsed time: 00:13:49s. Time for last 1,000,000: 1s. Last read position: chr20:2,965,192 INFO 2026-06-08 08:48:59 MarkDuplicates Tracking 77666 as yet unmatched pairs. 23152 records in RAM. INFO 2026-06-08 08:49:00 MarkDuplicates Read 452,000,000 records. Elapsed time: 00:13:50s. Time for last 1,000,000: 1s. Last read position: chr20:8,729,096 INFO 2026-06-08 08:49:00 MarkDuplicates Tracking 75047 as yet unmatched pairs. 20533 records in RAM. INFO 2026-06-08 08:49:02 MarkDuplicates Read 453,000,000 records. Elapsed time: 00:13:52s. Time for last 1,000,000: 1s. Last read position: chr20:21,328,651 INFO 2026-06-08 08:49:02 MarkDuplicates Tracking 73805 as yet unmatched pairs. 19291 records in RAM. INFO 2026-06-08 08:49:03 MarkDuplicates Read 454,000,000 records. Elapsed time: 00:13:54s. Time for last 1,000,000: 1s. Last read position: chr20:32,456,332 INFO 2026-06-08 08:49:03 MarkDuplicates Tracking 72118 as yet unmatched pairs. 17604 records in RAM. INFO 2026-06-08 08:49:05 MarkDuplicates Read 455,000,000 records. Elapsed time: 00:13:55s. Time for last 1,000,000: 1s. Last read position: chr20:35,653,910 INFO 2026-06-08 08:49:05 MarkDuplicates Tracking 70109 as yet unmatched pairs. 15587 records in RAM. INFO 2026-06-08 08:49:07 MarkDuplicates Read 456,000,000 records. Elapsed time: 00:13:57s. Time for last 1,000,000: 1s. Last read position: chr20:38,574,821 INFO 2026-06-08 08:49:07 MarkDuplicates Tracking 68152 as yet unmatched pairs. 13630 records in RAM. INFO 2026-06-08 08:49:08 MarkDuplicates Read 457,000,000 records. Elapsed time: 00:13:58s. Time for last 1,000,000: 1s. Last read position: chr20:45,327,305 INFO 2026-06-08 08:49:08 MarkDuplicates Tracking 68567 as yet unmatched pairs. 14044 records in RAM. INFO 2026-06-08 08:49:10 MarkDuplicates Read 458,000,000 records. Elapsed time: 00:14:00s. Time for last 1,000,000: 2s. Last read position: chr20:48,655,318 INFO 2026-06-08 08:49:10 MarkDuplicates Tracking 64845 as yet unmatched pairs. 10322 records in RAM. INFO 2026-06-08 08:49:12 MarkDuplicates Read 459,000,000 records. Elapsed time: 00:14:03s. Time for last 1,000,000: 2s. Last read position: chr20:53,576,195 INFO 2026-06-08 08:49:12 MarkDuplicates Tracking 63512 as yet unmatched pairs. 8989 records in RAM. INFO 2026-06-08 08:49:14 MarkDuplicates Read 460,000,000 records. Elapsed time: 00:14:04s. Time for last 1,000,000: 1s. Last read position: chr20:62,273,314 INFO 2026-06-08 08:49:14 MarkDuplicates Tracking 61119 as yet unmatched pairs. 6596 records in RAM. INFO 2026-06-08 08:49:16 MarkDuplicates Read 461,000,000 records. Elapsed time: 00:14:06s. Time for last 1,000,000: 2s. Last read position: chr20:62,367,088 INFO 2026-06-08 08:49:16 MarkDuplicates Tracking 58876 as yet unmatched pairs. 4353 records in RAM. INFO 2026-06-08 08:49:18 MarkDuplicates Read 462,000,000 records. Elapsed time: 00:14:08s. Time for last 1,000,000: 1s. Last read position: chr20:63,590,493 INFO 2026-06-08 08:49:18 MarkDuplicates Tracking 56818 as yet unmatched pairs. 2295 records in RAM. INFO 2026-06-08 08:49:20 MarkDuplicates Read 463,000,000 records. Elapsed time: 00:14:10s. Time for last 1,000,000: 1s. Last read position: chr21:6,116,998 INFO 2026-06-08 08:49:20 MarkDuplicates Tracking 54495 as yet unmatched pairs. 12686 records in RAM. INFO 2026-06-08 08:49:21 MarkDuplicates Read 464,000,000 records. Elapsed time: 00:14:11s. Time for last 1,000,000: 1s. Last read position: chr21:8,259,011 INFO 2026-06-08 08:49:21 MarkDuplicates Tracking 53755 as yet unmatched pairs. 11941 records in RAM. INFO 2026-06-08 08:49:22 MarkDuplicates Read 465,000,000 records. Elapsed time: 00:14:12s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,193 INFO 2026-06-08 08:49:22 MarkDuplicates Tracking 52922 as yet unmatched pairs. 11108 records in RAM. INFO 2026-06-08 08:49:23 MarkDuplicates Read 466,000,000 records. Elapsed time: 00:14:13s. Time for last 1,000,000: 1s. Last read position: chr21:33,504,120 INFO 2026-06-08 08:49:23 MarkDuplicates Tracking 51573 as yet unmatched pairs. 9759 records in RAM. INFO 2026-06-08 08:49:25 MarkDuplicates Read 467,000,000 records. Elapsed time: 00:14:15s. Time for last 1,000,000: 1s. Last read position: chr21:38,817,036 INFO 2026-06-08 08:49:25 MarkDuplicates Tracking 49951 as yet unmatched pairs. 8127 records in RAM. INFO 2026-06-08 08:49:26 MarkDuplicates Read 468,000,000 records. Elapsed time: 00:14:16s. Time for last 1,000,000: 1s. Last read position: chr21:44,851,401 INFO 2026-06-08 08:49:26 MarkDuplicates Tracking 49061 as yet unmatched pairs. 7237 records in RAM. INFO 2026-06-08 08:49:28 MarkDuplicates Read 469,000,000 records. Elapsed time: 00:14:18s. Time for last 1,000,000: 1s. Last read position: chr21:45,987,166 INFO 2026-06-08 08:49:28 MarkDuplicates Tracking 47543 as yet unmatched pairs. 5719 records in RAM. INFO 2026-06-08 08:49:29 MarkDuplicates Read 470,000,000 records. Elapsed time: 00:14:19s. Time for last 1,000,000: 1s. Last read position: chr21:46,112,259 INFO 2026-06-08 08:49:29 MarkDuplicates Tracking 46178 as yet unmatched pairs. 4354 records in RAM. INFO 2026-06-08 08:49:31 MarkDuplicates Read 471,000,000 records. Elapsed time: 00:14:21s. Time for last 1,000,000: 1s. Last read position: chr21:46,280,503 INFO 2026-06-08 08:49:31 MarkDuplicates Tracking 42519 as yet unmatched pairs. 695 records in RAM. INFO 2026-06-08 08:49:32 MarkDuplicates Read 472,000,000 records. Elapsed time: 00:14:23s. Time for last 1,000,000: 1s. Last read position: chr22:20,668,164 INFO 2026-06-08 08:49:32 MarkDuplicates Tracking 40348 as yet unmatched pairs. 18072 records in RAM. INFO 2026-06-08 08:49:34 MarkDuplicates Read 473,000,000 records. Elapsed time: 00:14:24s. Time for last 1,000,000: 1s. Last read position: chr22:24,055,111 INFO 2026-06-08 08:49:34 MarkDuplicates Tracking 38520 as yet unmatched pairs. 16244 records in RAM. INFO 2026-06-08 08:49:36 MarkDuplicates Read 474,000,000 records. Elapsed time: 00:14:26s. Time for last 1,000,000: 1s. Last read position: chr22:29,286,978 INFO 2026-06-08 08:49:36 MarkDuplicates Tracking 39484 as yet unmatched pairs. 17208 records in RAM. INFO 2026-06-08 08:49:37 MarkDuplicates Read 475,000,000 records. Elapsed time: 00:14:27s. Time for last 1,000,000: 1s. Last read position: chr22:31,283,035 INFO 2026-06-08 08:49:37 MarkDuplicates Tracking 35291 as yet unmatched pairs. 13015 records in RAM. INFO 2026-06-08 08:49:39 MarkDuplicates Read 476,000,000 records. Elapsed time: 00:14:29s. Time for last 1,000,000: 1s. Last read position: chr22:36,305,077 INFO 2026-06-08 08:49:39 MarkDuplicates Tracking 34152 as yet unmatched pairs. 11876 records in RAM. INFO 2026-06-08 08:49:40 MarkDuplicates Read 477,000,000 records. Elapsed time: 00:14:31s. Time for last 1,000,000: 1s. Last read position: chr22:38,482,512 INFO 2026-06-08 08:49:40 MarkDuplicates Tracking 31334 as yet unmatched pairs. 9058 records in RAM. INFO 2026-06-08 08:49:42 MarkDuplicates Read 478,000,000 records. Elapsed time: 00:14:32s. Time for last 1,000,000: 1s. Last read position: chr22:41,149,761 INFO 2026-06-08 08:49:42 MarkDuplicates Tracking 29768 as yet unmatched pairs. 7492 records in RAM. INFO 2026-06-08 08:49:43 MarkDuplicates Read 479,000,000 records. Elapsed time: 00:14:33s. Time for last 1,000,000: 1s. Last read position: chr22:45,178,578 INFO 2026-06-08 08:49:43 MarkDuplicates Tracking 28014 as yet unmatched pairs. 5738 records in RAM. INFO 2026-06-08 08:49:45 MarkDuplicates Read 480,000,000 records. Elapsed time: 00:14:35s. Time for last 1,000,000: 1s. Last read position: chr22:49,794,214 INFO 2026-06-08 08:49:45 MarkDuplicates Tracking 25911 as yet unmatched pairs. 3635 records in RAM. INFO 2026-06-08 08:49:47 MarkDuplicates Read 481,000,000 records. Elapsed time: 00:14:37s. Time for last 1,000,000: 1s. Last read position: chr22:50,526,099 INFO 2026-06-08 08:49:47 MarkDuplicates Tracking 24462 as yet unmatched pairs. 2186 records in RAM. INFO 2026-06-08 08:49:48 MarkDuplicates Read 482,000,000 records. Elapsed time: 00:14:38s. Time for last 1,000,000: 1s. Last read position: chrX:3,310,760 INFO 2026-06-08 08:49:48 MarkDuplicates Tracking 22081 as yet unmatched pairs. 18245 records in RAM. INFO 2026-06-08 08:49:50 MarkDuplicates Read 483,000,000 records. Elapsed time: 00:14:40s. Time for last 1,000,000: 1s. Last read position: chrX:17,376,284 INFO 2026-06-08 08:49:50 MarkDuplicates Tracking 19772 as yet unmatched pairs. 15936 records in RAM. INFO 2026-06-08 08:49:51 MarkDuplicates Read 484,000,000 records. Elapsed time: 00:14:41s. Time for last 1,000,000: 1s. Last read position: chrX:41,343,307 INFO 2026-06-08 08:49:51 MarkDuplicates Tracking 18766 as yet unmatched pairs. 14928 records in RAM. INFO 2026-06-08 08:49:53 MarkDuplicates Read 485,000,000 records. Elapsed time: 00:14:43s. Time for last 1,000,000: 1s. Last read position: chrX:48,831,952 INFO 2026-06-08 08:49:53 MarkDuplicates Tracking 16793 as yet unmatched pairs. 12954 records in RAM. INFO 2026-06-08 08:49:55 MarkDuplicates Read 486,000,000 records. Elapsed time: 00:14:45s. Time for last 1,000,000: 1s. Last read position: chrX:53,431,991 INFO 2026-06-08 08:49:55 MarkDuplicates Tracking 14961 as yet unmatched pairs. 11122 records in RAM. INFO 2026-06-08 08:49:56 MarkDuplicates Read 487,000,000 records. Elapsed time: 00:14:46s. Time for last 1,000,000: 1s. Last read position: chrX:65,716,863 INFO 2026-06-08 08:49:56 MarkDuplicates Tracking 14179 as yet unmatched pairs. 10340 records in RAM. INFO 2026-06-08 08:49:58 MarkDuplicates Read 488,000,000 records. Elapsed time: 00:14:48s. Time for last 1,000,000: 1s. Last read position: chrX:74,594,353 INFO 2026-06-08 08:49:58 MarkDuplicates Tracking 11726 as yet unmatched pairs. 7885 records in RAM. INFO 2026-06-08 08:50:00 MarkDuplicates Read 489,000,000 records. Elapsed time: 00:14:50s. Time for last 1,000,000: 2s. Last read position: chrX:104,166,868 INFO 2026-06-08 08:50:00 MarkDuplicates Tracking 10253 as yet unmatched pairs. 6412 records in RAM. INFO 2026-06-08 08:50:02 MarkDuplicates Read 490,000,000 records. Elapsed time: 00:14:52s. Time for last 1,000,000: 1s. Last read position: chrX:130,165,438 INFO 2026-06-08 08:50:02 MarkDuplicates Tracking 8773 as yet unmatched pairs. 4932 records in RAM. INFO 2026-06-08 08:50:03 MarkDuplicates Read 491,000,000 records. Elapsed time: 00:14:54s. Time for last 1,000,000: 1s. Last read position: chrX:153,798,336 INFO 2026-06-08 08:50:03 MarkDuplicates Tracking 7307 as yet unmatched pairs. 3465 records in RAM. INFO 2026-06-08 08:50:05 MarkDuplicates Read 492,000,000 records. Elapsed time: 00:14:55s. Time for last 1,000,000: 1s. Last read position: chrX:154,364,144 INFO 2026-06-08 08:50:05 MarkDuplicates Tracking 6045 as yet unmatched pairs. 2203 records in RAM. INFO 2026-06-08 08:50:07 MarkDuplicates Read 493,000,000 records. Elapsed time: 00:14:57s. Time for last 1,000,000: 1s. Last read position: chrM:10,227 INFO 2026-06-08 08:50:07 MarkDuplicates Tracking 3804 as yet unmatched pairs. 15 records in RAM. INFO 2026-06-08 08:50:08 MarkDuplicates Read 494,000,000 records. Elapsed time: 00:14:58s. Time for last 1,000,000: 0s. Last read position: GL000220.1:160,700 INFO 2026-06-08 08:50:08 MarkDuplicates Tracking 3185 as yet unmatched pairs. 2 records in RAM. INFO 2026-06-08 08:50:09 MarkDuplicates Read 495,000,000 records. Elapsed time: 00:14:59s. Time for last 1,000,000: 1s. Last read position: KI270733.1:176,096 INFO 2026-06-08 08:50:09 MarkDuplicates Tracking 63 as yet unmatched pairs. 60 records in RAM. INFO 2026-06-08 08:50:09 MarkDuplicates Read 495408873 records. 0 pairs never matched. INFO 2026-06-08 08:51:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 42676049152; totalMemory: 60968402944; maxMemory: 63585648640 INFO 2026-06-08 08:51:12 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk. INFO 2026-06-08 08:51:28 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2026-06-08 08:52:05 OpticalDuplicateFinder Large duplicate set. size = 1044 INFO 2026-06-08 08:52:05 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:10,182 INFO 2026-06-08 08:52:16 OpticalDuplicateFinder Large duplicate set. size = 1090 INFO 2026-06-08 08:52:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:6,445 INFO 2026-06-08 08:52:16 OpticalDuplicateFinder Large duplicate set. size = 1254 INFO 2026-06-08 08:52:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,235 INFO 2026-06-08 08:52:16 OpticalDuplicateFinder Large duplicate set. size = 1527 INFO 2026-06-08 08:52:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-18,698 INFO 2026-06-08 08:52:16 OpticalDuplicateFinder Large duplicate set. size = 1190 INFO 2026-06-08 08:52:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:23,458 INFO 2026-06-08 08:52:16 OpticalDuplicateFinder Large duplicate set. size = 1876 INFO 2026-06-08 08:52:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,092 INFO 2026-06-08 08:52:16 OpticalDuplicateFinder Large duplicate set. size = 1246 INFO 2026-06-08 08:52:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-21,764 INFO 2026-06-08 08:52:16 OpticalDuplicateFinder Large duplicate set. size = 1252 INFO 2026-06-08 08:52:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,654 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder Large duplicate set. size = 1172 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:7,197 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder Large duplicate set. size = 1236 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-19,434 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder Large duplicate set. size = 1127 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,756 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder Large duplicate set. size = 1238 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,158 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder Large duplicate set. size = 1537 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,547 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder Large duplicate set. size = 1134 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,078 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder Large duplicate set. size = 1351 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,908 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder Large duplicate set. size = 1164 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,887 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder Large duplicate set. size = 1474 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,381 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder Large duplicate set. size = 1200 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:23,870 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder Large duplicate set. size = 1083 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,785 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder Large duplicate set. size = 1057 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,159 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder Large duplicate set. size = 1534 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,126 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder Large duplicate set. size = 1191 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:10,805 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder Large duplicate set. size = 1301 INFO 2026-06-08 08:52:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,380 INFO 2026-06-08 08:52:18 OpticalDuplicateFinder Large duplicate set. size = 1074 INFO 2026-06-08 08:52:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,088 INFO 2026-06-08 08:52:18 OpticalDuplicateFinder Large duplicate set. size = 1118 INFO 2026-06-08 08:52:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-14,119 INFO 2026-06-08 08:52:18 OpticalDuplicateFinder Large duplicate set. size = 1105 INFO 2026-06-08 08:52:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-14,240 INFO 2026-06-08 08:52:18 OpticalDuplicateFinder Large duplicate set. size = 1040 INFO 2026-06-08 08:52:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:5,320 INFO 2026-06-08 08:52:18 OpticalDuplicateFinder Large duplicate set. size = 1172 INFO 2026-06-08 08:52:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,026 INFO 2026-06-08 08:52:18 OpticalDuplicateFinder Large duplicate set. size = 1018 INFO 2026-06-08 08:52:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,123 INFO 2026-06-08 08:52:18 OpticalDuplicateFinder Large duplicate set. size = 1122 INFO 2026-06-08 08:52:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,540 INFO 2026-06-08 08:52:18 OpticalDuplicateFinder Large duplicate set. size = 1372 INFO 2026-06-08 08:52:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:10,514 INFO 2026-06-08 08:52:18 OpticalDuplicateFinder Large duplicate set. size = 1380 INFO 2026-06-08 08:52:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,535 INFO 2026-06-08 08:52:18 OpticalDuplicateFinder Large duplicate set. size = 1438 INFO 2026-06-08 08:52:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,495 INFO 2026-06-08 08:52:18 OpticalDuplicateFinder Large duplicate set. size = 1875 INFO 2026-06-08 08:52:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,469 INFO 2026-06-08 08:52:18 OpticalDuplicateFinder Large duplicate set. size = 1917 INFO 2026-06-08 08:52:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,051 INFO 2026-06-08 08:52:19 OpticalDuplicateFinder Large duplicate set. size = 1140 INFO 2026-06-08 08:52:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,118 INFO 2026-06-08 08:52:19 OpticalDuplicateFinder Large duplicate set. size = 1198 INFO 2026-06-08 08:52:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,530 INFO 2026-06-08 08:52:19 OpticalDuplicateFinder Large duplicate set. size = 1339 INFO 2026-06-08 08:52:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,226 INFO 2026-06-08 08:52:19 OpticalDuplicateFinder Large duplicate set. size = 1077 INFO 2026-06-08 08:52:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,309 INFO 2026-06-08 08:52:19 OpticalDuplicateFinder Large duplicate set. size = 1421 INFO 2026-06-08 08:52:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,439 INFO 2026-06-08 08:52:19 OpticalDuplicateFinder Large duplicate set. size = 1703 INFO 2026-06-08 08:52:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,187 INFO 2026-06-08 08:52:19 OpticalDuplicateFinder Large duplicate set. size = 1424 INFO 2026-06-08 08:52:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,893 INFO 2026-06-08 08:52:19 OpticalDuplicateFinder Large duplicate set. size = 2511 INFO 2026-06-08 08:52:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:15,133 INFO 2026-06-08 08:52:19 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:4,487 INFO 2026-06-08 08:52:19 OpticalDuplicateFinder Large duplicate set. size = 1369 INFO 2026-06-08 08:52:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,321 INFO 2026-06-08 08:52:19 OpticalDuplicateFinder Large duplicate set. size = 1059 INFO 2026-06-08 08:52:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,536 INFO 2026-06-08 08:52:35 OpticalDuplicateFinder Large duplicate set. size = 1164 INFO 2026-06-08 08:52:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:23,409 INFO 2026-06-08 08:52:35 OpticalDuplicateFinder Large duplicate set. size = 1097 INFO 2026-06-08 08:52:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:17,034 INFO 2026-06-08 08:52:35 OpticalDuplicateFinder Large duplicate set. size = 1707 INFO 2026-06-08 08:52:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,826 INFO 2026-06-08 08:52:35 OpticalDuplicateFinder Large duplicate set. size = 2772 INFO 2026-06-08 08:52:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:5,716 INFO 2026-06-08 08:52:35 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:21,007 INFO 2026-06-08 08:52:35 OpticalDuplicateFinder Large duplicate set. size = 1055 INFO 2026-06-08 08:52:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-21,748 INFO 2026-06-08 08:52:35 OpticalDuplicateFinder Large duplicate set. size = 1250 INFO 2026-06-08 08:52:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:2,375 INFO 2026-06-08 08:52:35 OpticalDuplicateFinder Large duplicate set. size = 1644 INFO 2026-06-08 08:52:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,000 INFO 2026-06-08 08:52:35 OpticalDuplicateFinder Large duplicate set. size = 1507 INFO 2026-06-08 08:52:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,492 INFO 2026-06-08 08:52:35 OpticalDuplicateFinder Large duplicate set. size = 1218 INFO 2026-06-08 08:52:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:4,285 INFO 2026-06-08 08:52:35 OpticalDuplicateFinder Large duplicate set. size = 1235 INFO 2026-06-08 08:52:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,090 INFO 2026-06-08 08:52:35 OpticalDuplicateFinder Large duplicate set. size = 1069 INFO 2026-06-08 08:52:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,102 INFO 2026-06-08 08:52:35 OpticalDuplicateFinder Large duplicate set. size = 1513 INFO 2026-06-08 08:52:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:4,406 INFO 2026-06-08 08:52:36 OpticalDuplicateFinder Large duplicate set. size = 1038 INFO 2026-06-08 08:52:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:8,872 INFO 2026-06-08 08:52:36 OpticalDuplicateFinder Large duplicate set. size = 1030 INFO 2026-06-08 08:52:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,879 INFO 2026-06-08 08:52:36 OpticalDuplicateFinder Large duplicate set. size = 1626 INFO 2026-06-08 08:52:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,237 INFO 2026-06-08 08:52:36 OpticalDuplicateFinder Large duplicate set. size = 1040 INFO 2026-06-08 08:52:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,953 INFO 2026-06-08 08:52:36 OpticalDuplicateFinder Large duplicate set. size = 1014 INFO 2026-06-08 08:52:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,401 INFO 2026-06-08 08:52:36 OpticalDuplicateFinder Large duplicate set. size = 1203 INFO 2026-06-08 08:52:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:1,364 INFO 2026-06-08 08:52:36 OpticalDuplicateFinder Large duplicate set. size = 1135 INFO 2026-06-08 08:52:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,448 INFO 2026-06-08 08:52:36 OpticalDuplicateFinder Large duplicate set. size = 1572 INFO 2026-06-08 08:52:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,605 INFO 2026-06-08 08:52:36 OpticalDuplicateFinder Large duplicate set. size = 1675 INFO 2026-06-08 08:52:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,575 INFO 2026-06-08 08:52:36 OpticalDuplicateFinder Large duplicate set. size = 1013 INFO 2026-06-08 08:52:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,232 INFO 2026-06-08 08:52:36 OpticalDuplicateFinder Large duplicate set. size = 1459 INFO 2026-06-08 08:52:36 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 2026-06-08 08:52:47 MarkDuplicates Traversing fragment information and detecting duplicates. WARNING 2026-06-08 08:52:48 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered. INFO 2026-06-08 08:53:40 MarkDuplicates Sorting list of duplicate records. INFO 2026-06-08 08:53:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 204596664; totalMemory: 234881024; maxMemory: 63585648640 INFO 2026-06-08 08:53:44 MarkDuplicates Marking 334128888 records as duplicates. INFO 2026-06-08 08:53:44 MarkDuplicates Found 14922832 optical duplicate clusters. INFO 2026-06-08 08:53:44 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2026-06-08 08:54:03 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:18s. Time for last 10,000,000: 18s. Last read position: chr1:31,684,197 INFO 2026-06-08 08:54:20 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:35s. Time for last 10,000,000: 17s. Last read position: chr1:119,916,286 INFO 2026-06-08 08:54:37 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:52s. Time for last 10,000,000: 16s. Last read position: chr1:155,188,319 INFO 2026-06-08 08:54:55 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:10s. Time for last 10,000,000: 17s. Last read position: chr1:201,782,610 INFO 2026-06-08 08:55:11 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:27s. Time for last 10,000,000: 16s. Last read position: chr2:32,617,818 INFO 2026-06-08 08:55:28 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:43s. Time for last 10,000,000: 16s. Last read position: chr2:105,275,562 INFO 2026-06-08 08:55:46 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:01s. Time for last 10,000,000: 17s. Last read position: chr2:189,006,426 INFO 2026-06-08 08:56:03 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:18s. Time for last 10,000,000: 16s. Last read position: chr2:217,818,385 INFO 2026-06-08 08:56:19 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:35s. Time for last 10,000,000: 16s. Last read position: chr3:40,170,006 INFO 2026-06-08 08:56:37 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:52s. Time for last 10,000,000: 17s. Last read position: chr3:123,614,290 INFO 2026-06-08 08:56:54 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:03:09s. Time for last 10,000,000: 17s. Last read position: chr4:10,083,039 INFO 2026-06-08 08:57:11 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:26s. Time for last 10,000,000: 17s. Last read position: chr5:465,733 INFO 2026-06-08 08:57:28 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:43s. Time for last 10,000,000: 17s. Last read position: chr5:138,467,485 INFO 2026-06-08 08:57:45 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:04:00s. Time for last 10,000,000: 16s. Last read position: chr5:179,899,231 INFO 2026-06-08 08:58:01 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:04:16s. Time for last 10,000,000: 16s. Last read position: chr6:33,655,820 INFO 2026-06-08 08:58:18 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:33s. Time for last 10,000,000: 16s. Last read position: chr6:151,808,063 INFO 2026-06-08 08:58:34 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:04:49s. Time for last 10,000,000: 16s. Last read position: chr7:54,544,689 INFO 2026-06-08 08:58:51 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:05:06s. Time for last 10,000,000: 16s. Last read position: chr7:101,237,407 INFO 2026-06-08 08:59:07 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:05:22s. Time for last 10,000,000: 16s. Last read position: chr8:22,618,478 INFO 2026-06-08 08:59:24 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:05:40s. Time for last 10,000,000: 17s. Last read position: chr8:127,738,900 INFO 2026-06-08 08:59:40 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:05:56s. Time for last 10,000,000: 16s. Last read position: chr8:143,866,204 INFO 2026-06-08 08:59:57 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:06:12s. Time for last 10,000,000: 16s. Last read position: chr9:93,293,096 INFO 2026-06-08 09:00:14 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:06:29s. Time for last 10,000,000: 16s. Last read position: chr9:136,475,290 INFO 2026-06-08 09:00:30 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:06:45s. Time for last 10,000,000: 16s. Last read position: chr10:73,914,782 INFO 2026-06-08 09:00:47 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:07:02s. Time for last 10,000,000: 16s. Last read position: chr11:1,761,339 INFO 2026-06-08 09:01:04 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:07:19s. Time for last 10,000,000: 16s. Last read position: chr11:63,974,663 INFO 2026-06-08 09:01:20 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:07:35s. Time for last 10,000,000: 16s. Last read position: chr11:74,090,819 INFO 2026-06-08 09:01:37 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:07:52s. Time for last 10,000,000: 16s. Last read position: chr12:14,882,080 INFO 2026-06-08 09:01:53 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:08:08s. Time for last 10,000,000: 16s. Last read position: chr12:57,526,597 INFO 2026-06-08 09:02:10 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:08:25s. Time for last 10,000,000: 16s. Last read position: chr13:21,496,128 INFO 2026-06-08 09:02:26 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:08:41s. Time for last 10,000,000: 16s. Last read position: chr14:49,586,609 INFO 2026-06-08 09:02:43 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:08:58s. Time for last 10,000,000: 16s. Last read position: chr14:105,640,995 INFO 2026-06-08 09:02:59 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:09:14s. Time for last 10,000,000: 16s. Last read position: chr15:77,745,818 INFO 2026-06-08 09:03:16 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:09:31s. Time for last 10,000,000: 16s. Last read position: chr16:3,736,116 INFO 2026-06-08 09:03:32 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:09:47s. Time for last 10,000,000: 16s. Last read position: chr16:27,461,542 INFO 2026-06-08 09:03:48 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:10:04s. Time for last 10,000,000: 16s. Last read position: chr16:84,422,560 INFO 2026-06-08 09:04:05 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:10:20s. Time for last 10,000,000: 16s. Last read position: chr17:17,819,242 INFO 2026-06-08 09:04:21 MarkDuplicates Written 380,000,000 records. Elapsed time: 00:10:36s. Time for last 10,000,000: 16s. Last read position: chr17:45,586,857 INFO 2026-06-08 09:04:37 MarkDuplicates Written 390,000,000 records. Elapsed time: 00:10:53s. Time for last 10,000,000: 16s. Last read position: chr17:50,190,828 INFO 2026-06-08 09:04:54 MarkDuplicates Written 400,000,000 records. Elapsed time: 00:11:09s. Time for last 10,000,000: 16s. Last read position: chr17:50,197,029 INFO 2026-06-08 09:05:10 MarkDuplicates Written 410,000,000 records. Elapsed time: 00:11:25s. Time for last 10,000,000: 16s. Last read position: chr17:78,171,861 INFO 2026-06-08 09:05:27 MarkDuplicates Written 420,000,000 records. Elapsed time: 00:11:42s. Time for last 10,000,000: 16s. Last read position: chr19:1,271,549 INFO 2026-06-08 09:05:43 MarkDuplicates Written 430,000,000 records. Elapsed time: 00:11:58s. Time for last 10,000,000: 15s. Last read position: chr19:16,089,090 INFO 2026-06-08 09:05:59 MarkDuplicates Written 440,000,000 records. Elapsed time: 00:12:14s. Time for last 10,000,000: 16s. Last read position: chr19:42,293,922 INFO 2026-06-08 09:06:15 MarkDuplicates Written 450,000,000 records. Elapsed time: 00:12:30s. Time for last 10,000,000: 15s. Last read position: chr19:58,548,031 INFO 2026-06-08 09:06:31 MarkDuplicates Written 460,000,000 records. Elapsed time: 00:12:46s. Time for last 10,000,000: 16s. Last read position: chr20:62,273,314 INFO 2026-06-08 09:06:46 MarkDuplicates Written 470,000,000 records. Elapsed time: 00:13:01s. Time for last 10,000,000: 15s. Last read position: chr21:46,112,259 INFO 2026-06-08 09:07:03 MarkDuplicates Written 480,000,000 records. Elapsed time: 00:13:18s. Time for last 10,000,000: 16s. Last read position: chr22:49,794,214 INFO 2026-06-08 09:07:20 MarkDuplicates Written 490,000,000 records. Elapsed time: 00:13:35s. Time for last 10,000,000: 16s. Last read position: chrX:130,165,438 INFO 2026-06-08 09:07:34 MarkDuplicates Writing complete. Closing input iterator. INFO 2026-06-08 09:07:34 MarkDuplicates Duplicate Index cleanup. INFO 2026-06-08 09:07:34 MarkDuplicates Getting Memory Stats. INFO 2026-06-08 09:07:34 MarkDuplicates Before output close freeMemory: 204531592; totalMemory: 234881024; maxMemory: 63585648640 INFO 2026-06-08 09:07:34 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2026-06-08 09:07:35 MarkDuplicates After output close freeMemory: 104793880; totalMemory: 134217728; maxMemory: 63585648640 [Mon Jun 08 09:07:35 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 32.45 minutes. Runtime.totalMemory()=134217728 Tool returned: 0 ls: *cram: No such file or directory ls: *.crai: No such file or directory