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 BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.md.bam --METRICS_FILE BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT 08:23:31.197 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 08:23:31 GMT 2026] MarkDuplicates --INPUT BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.md.bam --METRICS_FILE BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.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 08:23:31 GMT 2026] Executing as ?@nf-3e95e31d544769aeef17fd5093ad85d9-6c0d8-tpf4b 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 08:23:31 MarkDuplicates Start of doWork freeMemory: 105828872; totalMemory: 134217728; maxMemory: 63585648640 INFO 2026-06-08 08:23:31 MarkDuplicates Reading input file and constructing read end information. INFO 2026-06-08 08:23:31 MarkDuplicates Will retain up to 230382784 data points before spilling to disk. INFO 2026-06-08 08:23:35 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:1,787,006 INFO 2026-06-08 08:23:35 MarkDuplicates Tracking 2522 as yet unmatched pairs. 237 records in RAM. INFO 2026-06-08 08:23:37 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 2s. Last read position: chr1:9,596,923 INFO 2026-06-08 08:23:37 MarkDuplicates Tracking 4716 as yet unmatched pairs. 2 records in RAM. INFO 2026-06-08 08:23:39 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: chr1:15,719,889 INFO 2026-06-08 08:23:39 MarkDuplicates Tracking 7033 as yet unmatched pairs. 76 records in RAM. INFO 2026-06-08 08:23:41 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: chr1:19,311,914 INFO 2026-06-08 08:23:41 MarkDuplicates Tracking 9178 as yet unmatched pairs. 5 records in RAM. INFO 2026-06-08 08:23:42 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: chr1:22,638,896 INFO 2026-06-08 08:23:42 MarkDuplicates Tracking 11777 as yet unmatched pairs. 216 records in RAM. INFO 2026-06-08 08:23:44 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: chr1:25,805,110 INFO 2026-06-08 08:23:44 MarkDuplicates Tracking 13719 as yet unmatched pairs. 38 records in RAM. INFO 2026-06-08 08:23:47 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: chr1:28,768,950 INFO 2026-06-08 08:23:47 MarkDuplicates Tracking 16120 as yet unmatched pairs. 81 records in RAM. INFO 2026-06-08 08:23:49 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: chr1:32,771,191 INFO 2026-06-08 08:23:49 MarkDuplicates Tracking 18658 as yet unmatched pairs. 194 records in RAM. INFO 2026-06-08 08:23:51 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 2s. Last read position: chr1:37,569,108 INFO 2026-06-08 08:23:51 MarkDuplicates Tracking 20875 as yet unmatched pairs. 24 records in RAM. INFO 2026-06-08 08:23:53 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: chr1:42,459,600 INFO 2026-06-08 08:23:53 MarkDuplicates Tracking 23185 as yet unmatched pairs. 68 records in RAM. INFO 2026-06-08 08:23:55 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: chr1:45,633,536 INFO 2026-06-08 08:23:55 MarkDuplicates Tracking 25493 as yet unmatched pairs. 52 records in RAM. INFO 2026-06-08 08:23:57 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 2s. Last read position: chr1:54,257,127 INFO 2026-06-08 08:23:57 MarkDuplicates Tracking 27634 as yet unmatched pairs. 16 records in RAM. INFO 2026-06-08 08:23:59 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 1s. Last read position: chr1:77,632,177 INFO 2026-06-08 08:23:59 MarkDuplicates Tracking 29797 as yet unmatched pairs. 19 records in RAM. INFO 2026-06-08 08:24:01 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 1s. Last read position: chr1:96,678,827 INFO 2026-06-08 08:24:01 MarkDuplicates Tracking 31992 as yet unmatched pairs. 12 records in RAM. INFO 2026-06-08 08:24:03 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 2s. Last read position: chr1:109,325,031 INFO 2026-06-08 08:24:03 MarkDuplicates Tracking 34167 as yet unmatched pairs. 25 records in RAM. INFO 2026-06-08 08:24:05 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 1s. Last read position: chr1:113,940,639 INFO 2026-06-08 08:24:05 MarkDuplicates Tracking 36626 as yet unmatched pairs. 120 records in RAM. INFO 2026-06-08 08:24:08 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 2s. Last read position: chr1:119,916,047 INFO 2026-06-08 08:24:08 MarkDuplicates Tracking 39072 as yet unmatched pairs. 432 records in RAM. INFO 2026-06-08 08:24:10 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 1s. Last read position: chr1:119,967,494 INFO 2026-06-08 08:24:10 MarkDuplicates Tracking 41572 as yet unmatched pairs. 590 records in RAM. INFO 2026-06-08 08:24:12 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 1s. Last read position: chr1:144,438,037 INFO 2026-06-08 08:24:12 MarkDuplicates Tracking 42373 as yet unmatched pairs. 110 records in RAM. INFO 2026-06-08 08:24:13 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 1s. Last read position: chr1:146,142,657 INFO 2026-06-08 08:24:13 MarkDuplicates Tracking 43532 as yet unmatched pairs. 145 records in RAM. INFO 2026-06-08 08:24:14 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 1s. Last read position: chr1:148,569,222 INFO 2026-06-08 08:24:14 MarkDuplicates Tracking 44236 as yet unmatched pairs. 32 records in RAM. INFO 2026-06-08 08:24:16 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 1s. Last read position: chr1:149,480,685 INFO 2026-06-08 08:24:16 MarkDuplicates Tracking 45239 as yet unmatched pairs. 88 records in RAM. INFO 2026-06-08 08:24:18 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: chr1:150,268,821 INFO 2026-06-08 08:24:18 MarkDuplicates Tracking 47011 as yet unmatched pairs. 23 records in RAM. INFO 2026-06-08 08:24:20 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 2s. Last read position: chr1:151,132,520 INFO 2026-06-08 08:24:20 MarkDuplicates Tracking 49241 as yet unmatched pairs. 40 records in RAM. INFO 2026-06-08 08:24:22 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 1s. Last read position: chr1:153,614,984 INFO 2026-06-08 08:24:22 MarkDuplicates Tracking 51759 as yet unmatched pairs. 334 records in RAM. INFO 2026-06-08 08:24:24 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 1s. Last read position: chr1:154,173,102 INFO 2026-06-08 08:24:24 MarkDuplicates Tracking 54680 as yet unmatched pairs. 1107 records in RAM. INFO 2026-06-08 08:24:26 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 2s. Last read position: chr1:154,968,800 INFO 2026-06-08 08:24:26 MarkDuplicates Tracking 55915 as yet unmatched pairs. 91 records in RAM. INFO 2026-06-08 08:24:28 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 1s. Last read position: chr1:155,189,999 INFO 2026-06-08 08:24:28 MarkDuplicates Tracking 58138 as yet unmatched pairs. 190 records in RAM. INFO 2026-06-08 08:24:29 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 1s. Last read position: chr1:155,480,765 INFO 2026-06-08 08:24:29 MarkDuplicates Tracking 59908 as yet unmatched pairs. 153 records in RAM. INFO 2026-06-08 08:24:31 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 1s. Last read position: chr1:156,136,965 INFO 2026-06-08 08:24:31 MarkDuplicates Tracking 62613 as yet unmatched pairs. 516 records in RAM. INFO 2026-06-08 08:24:33 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 1s. Last read position: chr1:156,912,863 INFO 2026-06-08 08:24:33 MarkDuplicates Tracking 64509 as yet unmatched pairs. 52 records in RAM. INFO 2026-06-08 08:24:34 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 1s. Last read position: chr1:161,037,751 INFO 2026-06-08 08:24:34 MarkDuplicates Tracking 66674 as yet unmatched pairs. 143 records in RAM. INFO 2026-06-08 08:24:36 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 1s. Last read position: chr1:161,548,671 INFO 2026-06-08 08:24:36 MarkDuplicates Tracking 68885 as yet unmatched pairs. 213 records in RAM. INFO 2026-06-08 08:24:37 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 1s. Last read position: chr1:167,974,846 INFO 2026-06-08 08:24:37 MarkDuplicates Tracking 70851 as yet unmatched pairs. 185 records in RAM. INFO 2026-06-08 08:24:39 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 1s. Last read position: chr1:171,579,426 INFO 2026-06-08 08:24:39 MarkDuplicates Tracking 73197 as yet unmatched pairs. 314 records in RAM. INFO 2026-06-08 08:24:41 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 1s. Last read position: chr1:180,092,940 INFO 2026-06-08 08:24:41 MarkDuplicates Tracking 75151 as yet unmatched pairs. 161 records in RAM. INFO 2026-06-08 08:24:43 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 1s. Last read position: chr1:184,477,452 INFO 2026-06-08 08:24:43 MarkDuplicates Tracking 77308 as yet unmatched pairs. 107 records in RAM. INFO 2026-06-08 08:24:44 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 1s. Last read position: chr1:193,076,953 INFO 2026-06-08 08:24:44 MarkDuplicates Tracking 79244 as yet unmatched pairs. 68 records in RAM. INFO 2026-06-08 08:24:46 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 1s. Last read position: chr1:202,755,270 INFO 2026-06-08 08:24:46 MarkDuplicates Tracking 81647 as yet unmatched pairs. 151 records in RAM. INFO 2026-06-08 08:24:48 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 1s. Last read position: chr1:204,957,755 INFO 2026-06-08 08:24:48 MarkDuplicates Tracking 83661 as yet unmatched pairs. 44 records in RAM. INFO 2026-06-08 08:24:50 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 1s. Last read position: chr1:211,289,326 INFO 2026-06-08 08:24:50 MarkDuplicates Tracking 85766 as yet unmatched pairs. 168 records in RAM. INFO 2026-06-08 08:24:51 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 1s. Last read position: chr1:219,983,354 INFO 2026-06-08 08:24:51 MarkDuplicates Tracking 87706 as yet unmatched pairs. 20 records in RAM. INFO 2026-06-08 08:24:53 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 1s. Last read position: chr1:224,379,040 INFO 2026-06-08 08:24:53 MarkDuplicates Tracking 89936 as yet unmatched pairs. 33 records in RAM. INFO 2026-06-08 08:24:55 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 1s. Last read position: chr1:227,074,297 INFO 2026-06-08 08:24:55 MarkDuplicates Tracking 91940 as yet unmatched pairs. 52 records in RAM. INFO 2026-06-08 08:24:57 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 2s. Last read position: chr1:229,594,284 INFO 2026-06-08 08:24:57 MarkDuplicates Tracking 94302 as yet unmatched pairs. 53 records in RAM. INFO 2026-06-08 08:24:59 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 1s. Last read position: chr1:235,979,056 INFO 2026-06-08 08:24:59 MarkDuplicates Tracking 96613 as yet unmatched pairs. 63 records in RAM. INFO 2026-06-08 08:25:01 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 1s. Last read position: chr1:246,641,759 INFO 2026-06-08 08:25:01 MarkDuplicates Tracking 98692 as yet unmatched pairs. 1 records in RAM. INFO 2026-06-08 08:25:04 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 3s. Last read position: chr2:11,287,708 INFO 2026-06-08 08:25:04 MarkDuplicates Tracking 100951 as yet unmatched pairs. 100781 records in RAM. INFO 2026-06-08 08:25:06 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 1s. Last read position: chr2:26,109,838 INFO 2026-06-08 08:25:06 MarkDuplicates Tracking 103303 as yet unmatched pairs. 103129 records in RAM. INFO 2026-06-08 08:25:07 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 1s. Last read position: chr2:32,401,526 INFO 2026-06-08 08:25:07 MarkDuplicates Tracking 105497 as yet unmatched pairs. 105322 records in RAM. INFO 2026-06-08 08:25:09 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 08:25:09 MarkDuplicates Tracking 402331 as yet unmatched pairs. 97604 records in RAM. INFO 2026-06-08 08:25:11 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,406 INFO 2026-06-08 08:25:11 MarkDuplicates Tracking 865574 as yet unmatched pairs. 85571 records in RAM. INFO 2026-06-08 08:25:13 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,454 INFO 2026-06-08 08:25:13 MarkDuplicates Tracking 918879 as yet unmatched pairs. 84252 records in RAM. INFO 2026-06-08 08:25:14 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 1s. Last read position: chr2:43,899,322 INFO 2026-06-08 08:25:14 MarkDuplicates Tracking 917902 as yet unmatched pairs. 81810 records in RAM. INFO 2026-06-08 08:25:16 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 1s. Last read position: chr2:55,309,241 INFO 2026-06-08 08:25:16 MarkDuplicates Tracking 916074 as yet unmatched pairs. 79980 records in RAM. INFO 2026-06-08 08:25:18 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 1s. Last read position: chr2:68,826,010 INFO 2026-06-08 08:25:18 MarkDuplicates Tracking 913714 as yet unmatched pairs. 77620 records in RAM. INFO 2026-06-08 08:25:19 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 1s. Last read position: chr2:74,462,487 INFO 2026-06-08 08:25:19 MarkDuplicates Tracking 911645 as yet unmatched pairs. 75549 records in RAM. INFO 2026-06-08 08:25:21 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 1s. Last read position: chr2:87,782,442 INFO 2026-06-08 08:25:21 MarkDuplicates Tracking 909670 as yet unmatched pairs. 73574 records in RAM. INFO 2026-06-08 08:25:22 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 1s. Last read position: chr2:97,211,697 INFO 2026-06-08 08:25:22 MarkDuplicates Tracking 907656 as yet unmatched pairs. 71559 records in RAM. INFO 2026-06-08 08:25:24 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 1s. Last read position: chr2:105,339,645 INFO 2026-06-08 08:25:24 MarkDuplicates Tracking 905650 as yet unmatched pairs. 69546 records in RAM. INFO 2026-06-08 08:25:26 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 1s. Last read position: chr2:109,921,646 INFO 2026-06-08 08:25:26 MarkDuplicates Tracking 904164 as yet unmatched pairs. 68059 records in RAM. INFO 2026-06-08 08:25:27 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 1s. Last read position: chr2:117,819,685 INFO 2026-06-08 08:25:27 MarkDuplicates Tracking 902766 as yet unmatched pairs. 66657 records in RAM. INFO 2026-06-08 08:25:29 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 1s. Last read position: chr2:131,265,738 INFO 2026-06-08 08:25:29 MarkDuplicates Tracking 900573 as yet unmatched pairs. 64462 records in RAM. INFO 2026-06-08 08:25:31 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 1s. Last read position: chr2:151,437,206 INFO 2026-06-08 08:25:31 MarkDuplicates Tracking 898580 as yet unmatched pairs. 62467 records in RAM. INFO 2026-06-08 08:25:32 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 1s. Last read position: chr2:151,646,162 INFO 2026-06-08 08:25:32 MarkDuplicates Tracking 897121 as yet unmatched pairs. 61008 records in RAM. INFO 2026-06-08 08:25:34 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 1s. Last read position: chr2:164,695,358 INFO 2026-06-08 08:25:34 MarkDuplicates Tracking 894932 as yet unmatched pairs. 58814 records in RAM. INFO 2026-06-08 08:25:35 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 1s. Last read position: chr2:174,749,976 INFO 2026-06-08 08:25:35 MarkDuplicates Tracking 892999 as yet unmatched pairs. 56880 records in RAM. INFO 2026-06-08 08:25:38 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 2s. Last read position: chr2:178,542,799 INFO 2026-06-08 08:25:38 MarkDuplicates Tracking 891269 as yet unmatched pairs. 55150 records in RAM. INFO 2026-06-08 08:25:40 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 1s. Last read position: chr2:178,565,922 INFO 2026-06-08 08:25:40 MarkDuplicates Tracking 889384 as yet unmatched pairs. 53265 records in RAM. INFO 2026-06-08 08:25:42 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 2s. Last read position: chr2:178,588,104 INFO 2026-06-08 08:25:42 MarkDuplicates Tracking 887212 as yet unmatched pairs. 51093 records in RAM. INFO 2026-06-08 08:25:44 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 1s. Last read position: chr2:178,615,380 INFO 2026-06-08 08:25:44 MarkDuplicates Tracking 885114 as yet unmatched pairs. 48995 records in RAM. INFO 2026-06-08 08:25:46 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 2s. Last read position: chr2:178,678,484 INFO 2026-06-08 08:25:46 MarkDuplicates Tracking 883365 as yet unmatched pairs. 47246 records in RAM. INFO 2026-06-08 08:25:48 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 1s. Last read position: chr2:178,730,959 INFO 2026-06-08 08:25:48 MarkDuplicates Tracking 881429 as yet unmatched pairs. 45309 records in RAM. INFO 2026-06-08 08:25:50 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 1s. Last read position: chr2:178,804,550 INFO 2026-06-08 08:25:50 MarkDuplicates Tracking 879422 as yet unmatched pairs. 43302 records in RAM. INFO 2026-06-08 08:25:51 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 1s. Last read position: chr2:188,992,190 INFO 2026-06-08 08:25:51 MarkDuplicates Tracking 877592 as yet unmatched pairs. 41469 records in RAM. INFO 2026-06-08 08:25:53 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 2s. Last read position: chr2:189,005,365 INFO 2026-06-08 08:25:53 MarkDuplicates Tracking 875901 as yet unmatched pairs. 39776 records in RAM. INFO 2026-06-08 08:25:55 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr2:189,086,725 INFO 2026-06-08 08:25:55 MarkDuplicates Tracking 871884 as yet unmatched pairs. 35758 records in RAM. INFO 2026-06-08 08:25:57 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 1s. Last read position: chr2:201,160,573 INFO 2026-06-08 08:25:57 MarkDuplicates Tracking 869680 as yet unmatched pairs. 33551 records in RAM. INFO 2026-06-08 08:25:58 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 1s. Last read position: chr2:214,797,105 INFO 2026-06-08 08:25:58 MarkDuplicates Tracking 867486 as yet unmatched pairs. 31356 records in RAM. INFO 2026-06-08 08:26:00 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 1s. Last read position: chr2:215,367,925 INFO 2026-06-08 08:26:00 MarkDuplicates Tracking 867445 as yet unmatched pairs. 31315 records in RAM. INFO 2026-06-08 08:26:02 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 1s. Last read position: chr2:215,372,294 INFO 2026-06-08 08:26:02 MarkDuplicates Tracking 868597 as yet unmatched pairs. 32467 records in RAM. INFO 2026-06-08 08:26:04 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 1s. Last read position: chr2:215,376,633 INFO 2026-06-08 08:26:04 MarkDuplicates Tracking 868682 as yet unmatched pairs. 32552 records in RAM. INFO 2026-06-08 08:26:05 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 1s. Last read position: chr2:215,384,045 INFO 2026-06-08 08:26:05 MarkDuplicates Tracking 860801 as yet unmatched pairs. 24671 records in RAM. INFO 2026-06-08 08:26:07 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 1s. Last read position: chr2:215,393,134 INFO 2026-06-08 08:26:07 MarkDuplicates Tracking 860650 as yet unmatched pairs. 24520 records in RAM. INFO 2026-06-08 08:26:09 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 1s. Last read position: chr2:215,406,215 INFO 2026-06-08 08:26:09 MarkDuplicates Tracking 857196 as yet unmatched pairs. 21066 records in RAM. INFO 2026-06-08 08:26:10 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 1s. Last read position: chr2:215,409,686 INFO 2026-06-08 08:26:10 MarkDuplicates Tracking 854074 as yet unmatched pairs. 17935 records in RAM. INFO 2026-06-08 08:26:12 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 1s. Last read position: chr2:215,423,352 INFO 2026-06-08 08:26:12 MarkDuplicates Tracking 852849 as yet unmatched pairs. 16710 records in RAM. INFO 2026-06-08 08:26:14 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 1s. Last read position: chr2:215,431,858 INFO 2026-06-08 08:26:14 MarkDuplicates Tracking 854031 as yet unmatched pairs. 17891 records in RAM. INFO 2026-06-08 08:26:15 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 1s. Last read position: chr2:218,262,923 INFO 2026-06-08 08:26:15 MarkDuplicates Tracking 846414 as yet unmatched pairs. 10272 records in RAM. INFO 2026-06-08 08:26:17 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 1s. Last read position: chr2:223,901,284 INFO 2026-06-08 08:26:17 MarkDuplicates Tracking 843912 as yet unmatched pairs. 7749 records in RAM. INFO 2026-06-08 08:26:19 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 2s. Last read position: chr2:232,672,361 INFO 2026-06-08 08:26:19 MarkDuplicates Tracking 841930 as yet unmatched pairs. 5765 records in RAM. INFO 2026-06-08 08:26:21 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 1s. Last read position: chr2:237,371,925 INFO 2026-06-08 08:26:21 MarkDuplicates Tracking 840413 as yet unmatched pairs. 4246 records in RAM. INFO 2026-06-08 08:26:22 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 1s. Last read position: chr2:241,052,438 INFO 2026-06-08 08:26:22 MarkDuplicates Tracking 837459 as yet unmatched pairs. 1286 records in RAM. INFO 2026-06-08 08:26:24 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 2s. Last read position: chr3:9,662,292 INFO 2026-06-08 08:26:24 MarkDuplicates Tracking 835320 as yet unmatched pairs. 47135 records in RAM. INFO 2026-06-08 08:26:26 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 1s. Last read position: chr3:13,571,016 INFO 2026-06-08 08:26:26 MarkDuplicates Tracking 833108 as yet unmatched pairs. 44920 records in RAM. INFO 2026-06-08 08:26:28 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 1s. Last read position: chr3:33,092,897 INFO 2026-06-08 08:26:28 MarkDuplicates Tracking 830889 as yet unmatched pairs. 42695 records in RAM. INFO 2026-06-08 08:26:29 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 1s. Last read position: chr3:40,477,954 INFO 2026-06-08 08:26:29 MarkDuplicates Tracking 828964 as yet unmatched pairs. 40768 records in RAM. INFO 2026-06-08 08:26:31 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 1s. Last read position: chr3:46,995,534 INFO 2026-06-08 08:26:31 MarkDuplicates Tracking 826599 as yet unmatched pairs. 38402 records in RAM. INFO 2026-06-08 08:26:33 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 1s. Last read position: chr3:48,501,175 INFO 2026-06-08 08:26:33 MarkDuplicates Tracking 824522 as yet unmatched pairs. 36325 records in RAM. INFO 2026-06-08 08:26:35 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 1s. Last read position: chr3:49,357,420 INFO 2026-06-08 08:26:35 MarkDuplicates Tracking 822370 as yet unmatched pairs. 34173 records in RAM. INFO 2026-06-08 08:26:37 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 1s. Last read position: chr3:50,331,716 INFO 2026-06-08 08:26:37 MarkDuplicates Tracking 819584 as yet unmatched pairs. 31387 records in RAM. INFO 2026-06-08 08:26:38 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 1s. Last read position: chr3:52,523,327 INFO 2026-06-08 08:26:38 MarkDuplicates Tracking 817298 as yet unmatched pairs. 29098 records in RAM. INFO 2026-06-08 08:26:41 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 2s. Last read position: chr3:58,138,505 INFO 2026-06-08 08:26:41 MarkDuplicates Tracking 815394 as yet unmatched pairs. 27191 records in RAM. INFO 2026-06-08 08:26:43 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 1s. Last read position: chr3:82,807,164 INFO 2026-06-08 08:26:43 MarkDuplicates Tracking 813052 as yet unmatched pairs. 24848 records in RAM. INFO 2026-06-08 08:26:45 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 1s. Last read position: chr3:105,550,130 INFO 2026-06-08 08:26:45 MarkDuplicates Tracking 811473 as yet unmatched pairs. 23266 records in RAM. INFO 2026-06-08 08:26:46 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 1s. Last read position: chr3:120,770,862 INFO 2026-06-08 08:26:46 MarkDuplicates Tracking 809071 as yet unmatched pairs. 20860 records in RAM. INFO 2026-06-08 08:26:48 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 1s. Last read position: chr3:125,083,938 INFO 2026-06-08 08:26:48 MarkDuplicates Tracking 807022 as yet unmatched pairs. 18811 records in RAM. INFO 2026-06-08 08:26:50 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 1s. Last read position: chr3:129,415,333 INFO 2026-06-08 08:26:50 MarkDuplicates Tracking 804806 as yet unmatched pairs. 16595 records in RAM. INFO 2026-06-08 08:26:51 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 1s. Last read position: chr3:136,001,537 INFO 2026-06-08 08:26:51 MarkDuplicates Tracking 802583 as yet unmatched pairs. 14371 records in RAM. INFO 2026-06-08 08:26:53 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 1s. Last read position: chr3:149,055,339 INFO 2026-06-08 08:26:53 MarkDuplicates Tracking 800494 as yet unmatched pairs. 12280 records in RAM. INFO 2026-06-08 08:26:55 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: chr3:160,514,140 INFO 2026-06-08 08:26:55 MarkDuplicates Tracking 798491 as yet unmatched pairs. 10246 records in RAM. INFO 2026-06-08 08:26:56 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 1s. Last read position: chr3:179,586,589 INFO 2026-06-08 08:26:56 MarkDuplicates Tracking 796506 as yet unmatched pairs. 8257 records in RAM. INFO 2026-06-08 08:26:58 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 1s. Last read position: chr3:184,317,346 INFO 2026-06-08 08:26:58 MarkDuplicates Tracking 794537 as yet unmatched pairs. 6285 records in RAM. INFO 2026-06-08 08:27:00 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 1s. Last read position: chr3:187,728,405 INFO 2026-06-08 08:27:00 MarkDuplicates Tracking 791745 as yet unmatched pairs. 3491 records in RAM. INFO 2026-06-08 08:27:01 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 1s. Last read position: chr3:196,391,882 INFO 2026-06-08 08:27:01 MarkDuplicates Tracking 789568 as yet unmatched pairs. 1314 records in RAM. INFO 2026-06-08 08:27:03 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 1s. Last read position: chr4:1,225,395 INFO 2026-06-08 08:27:03 MarkDuplicates Tracking 787083 as yet unmatched pairs. 23098 records in RAM. INFO 2026-06-08 08:27:05 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 1s. Last read position: chr4:3,187,690 INFO 2026-06-08 08:27:05 MarkDuplicates Tracking 784908 as yet unmatched pairs. 20914 records in RAM. INFO 2026-06-08 08:27:06 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 1s. Last read position: chr4:15,003,569 INFO 2026-06-08 08:27:06 MarkDuplicates Tracking 782421 as yet unmatched pairs. 18424 records in RAM. INFO 2026-06-08 08:27:08 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 1s. Last read position: chr4:40,102,977 INFO 2026-06-08 08:27:08 MarkDuplicates Tracking 780406 as yet unmatched pairs. 16400 records in RAM. INFO 2026-06-08 08:27:10 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 2s. Last read position: chr4:67,682,151 INFO 2026-06-08 08:27:10 MarkDuplicates Tracking 778563 as yet unmatched pairs. 14554 records in RAM. INFO 2026-06-08 08:27:12 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 1s. Last read position: chr4:78,911,994 INFO 2026-06-08 08:27:12 MarkDuplicates Tracking 776565 as yet unmatched pairs. 12555 records in RAM. INFO 2026-06-08 08:27:13 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 1s. Last read position: chr4:94,455,255 INFO 2026-06-08 08:27:13 MarkDuplicates Tracking 774708 as yet unmatched pairs. 10695 records in RAM. INFO 2026-06-08 08:27:15 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 1s. Last read position: chr4:119,271,554 INFO 2026-06-08 08:27:15 MarkDuplicates Tracking 772367 as yet unmatched pairs. 8350 records in RAM. INFO 2026-06-08 08:27:17 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 2s. Last read position: chr4:140,659,589 INFO 2026-06-08 08:27:17 MarkDuplicates Tracking 770435 as yet unmatched pairs. 6417 records in RAM. INFO 2026-06-08 08:27:19 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 1s. Last read position: chr4:152,888,291 INFO 2026-06-08 08:27:19 MarkDuplicates Tracking 768387 as yet unmatched pairs. 4367 records in RAM. INFO 2026-06-08 08:27:21 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 2s. Last read position: chr4:168,308,005 INFO 2026-06-08 08:27:21 MarkDuplicates Tracking 766003 as yet unmatched pairs. 1970 records in RAM. INFO 2026-06-08 08:27:24 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 2s. Last read position: chr5:876,158 INFO 2026-06-08 08:27:24 MarkDuplicates Tracking 763580 as yet unmatched pairs. 50626 records in RAM. INFO 2026-06-08 08:27:25 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 1s. Last read position: chr5:14,351,275 INFO 2026-06-08 08:27:25 MarkDuplicates Tracking 761400 as yet unmatched pairs. 48445 records in RAM. INFO 2026-06-08 08:27:27 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 1s. Last read position: chr5:32,135,630 INFO 2026-06-08 08:27:27 MarkDuplicates Tracking 759124 as yet unmatched pairs. 46168 records in RAM. INFO 2026-06-08 08:27:29 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 1s. Last read position: chr5:39,721,198 INFO 2026-06-08 08:27:29 MarkDuplicates Tracking 756903 as yet unmatched pairs. 43946 records in RAM. INFO 2026-06-08 08:27:31 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 1s. Last read position: chr5:56,925,335 INFO 2026-06-08 08:27:31 MarkDuplicates Tracking 754914 as yet unmatched pairs. 41945 records in RAM. INFO 2026-06-08 08:27:32 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 1s. Last read position: chr5:69,566,590 INFO 2026-06-08 08:27:32 MarkDuplicates Tracking 753098 as yet unmatched pairs. 40106 records in RAM. INFO 2026-06-08 08:27:34 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 1s. Last read position: chr5:71,045,423 INFO 2026-06-08 08:27:34 MarkDuplicates Tracking 752290 as yet unmatched pairs. 39298 records in RAM. INFO 2026-06-08 08:27:35 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 1s. Last read position: chr5:77,463,195 INFO 2026-06-08 08:27:35 MarkDuplicates Tracking 750438 as yet unmatched pairs. 37446 records in RAM. INFO 2026-06-08 08:27:37 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 1s. Last read position: chr5:83,580,341 INFO 2026-06-08 08:27:37 MarkDuplicates Tracking 748557 as yet unmatched pairs. 35562 records in RAM. INFO 2026-06-08 08:27:39 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 1s. Last read position: chr5:102,959,883 INFO 2026-06-08 08:27:39 MarkDuplicates Tracking 746613 as yet unmatched pairs. 33614 records in RAM. INFO 2026-06-08 08:27:40 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 1s. Last read position: chr5:126,561,092 INFO 2026-06-08 08:27:40 MarkDuplicates Tracking 744725 as yet unmatched pairs. 31726 records in RAM. INFO 2026-06-08 08:27:42 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 1s. Last read position: chr5:134,562,286 INFO 2026-06-08 08:27:42 MarkDuplicates Tracking 742571 as yet unmatched pairs. 29571 records in RAM. INFO 2026-06-08 08:27:44 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 1s. Last read position: chr5:135,571,243 INFO 2026-06-08 08:27:44 MarkDuplicates Tracking 748065 as yet unmatched pairs. 35061 records in RAM. INFO 2026-06-08 08:27:45 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 1s. Last read position: chr5:136,033,772 INFO 2026-06-08 08:27:45 MarkDuplicates Tracking 737997 as yet unmatched pairs. 24992 records in RAM. INFO 2026-06-08 08:27:47 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 1s. Last read position: chr5:139,623,416 INFO 2026-06-08 08:27:47 MarkDuplicates Tracking 736003 as yet unmatched pairs. 22997 records in RAM. INFO 2026-06-08 08:27:48 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 1s. Last read position: chr5:141,476,325 INFO 2026-06-08 08:27:48 MarkDuplicates Tracking 733588 as yet unmatched pairs. 20535 records in RAM. INFO 2026-06-08 08:27:50 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 1s. Last read position: chr5:149,550,080 INFO 2026-06-08 08:27:50 MarkDuplicates Tracking 732175 as yet unmatched pairs. 19120 records in RAM. INFO 2026-06-08 08:27:52 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 1s. Last read position: chr5:150,402,211 INFO 2026-06-08 08:27:52 MarkDuplicates Tracking 740681 as yet unmatched pairs. 27623 records in RAM. INFO 2026-06-08 08:27:54 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 1s. Last read position: chr5:150,405,123 INFO 2026-06-08 08:27:54 MarkDuplicates Tracking 733919 as yet unmatched pairs. 20861 records in RAM. INFO 2026-06-08 08:27:55 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 1s. Last read position: chr5:150,650,056 INFO 2026-06-08 08:27:55 MarkDuplicates Tracking 724570 as yet unmatched pairs. 11511 records in RAM. INFO 2026-06-08 08:27:57 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 1s. Last read position: chr5:157,285,338 INFO 2026-06-08 08:27:57 MarkDuplicates Tracking 722408 as yet unmatched pairs. 9348 records in RAM. INFO 2026-06-08 08:27:59 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr5:172,211,866 INFO 2026-06-08 08:27:59 MarkDuplicates Tracking 720525 as yet unmatched pairs. 7462 records in RAM. INFO 2026-06-08 08:28:00 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr5:177,436,423 INFO 2026-06-08 08:28:00 MarkDuplicates Tracking 718224 as yet unmatched pairs. 5159 records in RAM. INFO 2026-06-08 08:28:02 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 1s. Last read position: chr5:179,774,765 INFO 2026-06-08 08:28:02 MarkDuplicates Tracking 716576 as yet unmatched pairs. 3511 records in RAM. INFO 2026-06-08 08:28:04 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 1s. Last read position: chr5:181,238,099 INFO 2026-06-08 08:28:04 MarkDuplicates Tracking 713728 as yet unmatched pairs. 663 records in RAM. INFO 2026-06-08 08:28:06 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 2s. Last read position: chr6:7,583,034 INFO 2026-06-08 08:28:06 MarkDuplicates Tracking 711318 as yet unmatched pairs. 42413 records in RAM. INFO 2026-06-08 08:28:08 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 2s. Last read position: chr6:18,257,954 INFO 2026-06-08 08:28:08 MarkDuplicates Tracking 709282 as yet unmatched pairs. 40372 records in RAM. INFO 2026-06-08 08:28:10 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 1s. Last read position: chr6:28,276,831 INFO 2026-06-08 08:28:10 MarkDuplicates Tracking 706969 as yet unmatched pairs. 38057 records in RAM. INFO 2026-06-08 08:28:12 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 1s. Last read position: chr6:30,892,469 INFO 2026-06-08 08:28:12 MarkDuplicates Tracking 705240 as yet unmatched pairs. 36328 records in RAM. INFO 2026-06-08 08:28:13 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 1s. Last read position: chr6:31,632,642 INFO 2026-06-08 08:28:13 MarkDuplicates Tracking 702857 as yet unmatched pairs. 33944 records in RAM. INFO 2026-06-08 08:28:15 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 1s. Last read position: chr6:31,817,014 INFO 2026-06-08 08:28:15 MarkDuplicates Tracking 701098 as yet unmatched pairs. 32185 records in RAM. INFO 2026-06-08 08:28:16 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 1s. Last read position: chr6:31,954,372 INFO 2026-06-08 08:28:16 MarkDuplicates Tracking 698930 as yet unmatched pairs. 30015 records in RAM. INFO 2026-06-08 08:28:18 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 1s. Last read position: chr6:32,029,657 INFO 2026-06-08 08:28:18 MarkDuplicates Tracking 698364 as yet unmatched pairs. 29449 records in RAM. INFO 2026-06-08 08:28:20 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 1s. Last read position: chr6:32,847,944 INFO 2026-06-08 08:28:20 MarkDuplicates Tracking 695575 as yet unmatched pairs. 26659 records in RAM. INFO 2026-06-08 08:28:21 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 1s. Last read position: chr6:33,313,719 INFO 2026-06-08 08:28:21 MarkDuplicates Tracking 693407 as yet unmatched pairs. 24491 records in RAM. INFO 2026-06-08 08:28:23 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 1s. Last read position: chr6:36,130,537 INFO 2026-06-08 08:28:23 MarkDuplicates Tracking 690804 as yet unmatched pairs. 21884 records in RAM. INFO 2026-06-08 08:28:25 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 1s. Last read position: chr6:43,073,928 INFO 2026-06-08 08:28:25 MarkDuplicates Tracking 688546 as yet unmatched pairs. 19625 records in RAM. INFO 2026-06-08 08:28:26 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 1s. Last read position: chr6:52,279,408 INFO 2026-06-08 08:28:26 MarkDuplicates Tracking 686328 as yet unmatched pairs. 17405 records in RAM. INFO 2026-06-08 08:28:28 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 1s. Last read position: chr6:73,466,536 INFO 2026-06-08 08:28:28 MarkDuplicates Tracking 684134 as yet unmatched pairs. 15209 records in RAM. INFO 2026-06-08 08:28:30 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 1s. Last read position: chr6:82,364,999 INFO 2026-06-08 08:28:30 MarkDuplicates Tracking 682230 as yet unmatched pairs. 13299 records in RAM. INFO 2026-06-08 08:28:32 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 1s. Last read position: chr6:108,664,381 INFO 2026-06-08 08:28:32 MarkDuplicates Tracking 680157 as yet unmatched pairs. 11223 records in RAM. INFO 2026-06-08 08:28:33 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 1s. Last read position: chr6:129,401,303 INFO 2026-06-08 08:28:33 MarkDuplicates Tracking 677880 as yet unmatched pairs. 8924 records in RAM. INFO 2026-06-08 08:28:35 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 1s. Last read position: chr6:144,533,251 INFO 2026-06-08 08:28:35 MarkDuplicates Tracking 675808 as yet unmatched pairs. 6851 records in RAM. INFO 2026-06-08 08:28:36 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 1s. Last read position: chr6:151,944,506 INFO 2026-06-08 08:28:36 MarkDuplicates Tracking 674280 as yet unmatched pairs. 5323 records in RAM. INFO 2026-06-08 08:28:38 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 1s. Last read position: chr6:158,999,442 INFO 2026-06-08 08:28:38 MarkDuplicates Tracking 671325 as yet unmatched pairs. 2363 records in RAM. INFO 2026-06-08 08:28:40 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 1s. Last read position: chr6:170,564,600 INFO 2026-06-08 08:28:40 MarkDuplicates Tracking 669027 as yet unmatched pairs. 64 records in RAM. INFO 2026-06-08 08:28:43 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 2s. Last read position: chr7:5,351,865 INFO 2026-06-08 08:28:43 MarkDuplicates Tracking 666422 as yet unmatched pairs. 42818 records in RAM. INFO 2026-06-08 08:28:44 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 1s. Last read position: chr7:5,528,627 INFO 2026-06-08 08:28:44 MarkDuplicates Tracking 664183 as yet unmatched pairs. 40578 records in RAM. INFO 2026-06-08 08:28:46 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 1s. Last read position: chr7:16,776,253 INFO 2026-06-08 08:28:46 MarkDuplicates Tracking 661803 as yet unmatched pairs. 38196 records in RAM. INFO 2026-06-08 08:28:48 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 1s. Last read position: chr7:30,609,597 INFO 2026-06-08 08:28:48 MarkDuplicates Tracking 659587 as yet unmatched pairs. 35980 records in RAM. INFO 2026-06-08 08:28:49 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 1s. Last read position: chr7:44,108,915 INFO 2026-06-08 08:28:49 MarkDuplicates Tracking 657549 as yet unmatched pairs. 33938 records in RAM. INFO 2026-06-08 08:28:51 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 1s. Last read position: chr7:55,953,191 INFO 2026-06-08 08:28:51 MarkDuplicates Tracking 655249 as yet unmatched pairs. 31635 records in RAM. INFO 2026-06-08 08:28:52 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 1s. Last read position: chr7:73,195,953 INFO 2026-06-08 08:28:52 MarkDuplicates Tracking 653740 as yet unmatched pairs. 30125 records in RAM. INFO 2026-06-08 08:28:54 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 1s. Last read position: chr7:75,418,772 INFO 2026-06-08 08:28:54 MarkDuplicates Tracking 652083 as yet unmatched pairs. 28468 records in RAM. INFO 2026-06-08 08:28:55 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 1s. Last read position: chr7:76,618,102 INFO 2026-06-08 08:28:55 MarkDuplicates Tracking 649985 as yet unmatched pairs. 26366 records in RAM. INFO 2026-06-08 08:28:57 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 1s. Last read position: chr7:92,065,258 INFO 2026-06-08 08:28:57 MarkDuplicates Tracking 648502 as yet unmatched pairs. 24882 records in RAM. INFO 2026-06-08 08:28:59 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 1s. Last read position: chr7:94,405,217 INFO 2026-06-08 08:28:59 MarkDuplicates Tracking 647137 as yet unmatched pairs. 23517 records in RAM. INFO 2026-06-08 08:29:01 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 1s. Last read position: chr7:94,421,033 INFO 2026-06-08 08:29:01 MarkDuplicates Tracking 644323 as yet unmatched pairs. 20701 records in RAM. INFO 2026-06-08 08:29:02 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 1s. Last read position: chr7:98,897,838 INFO 2026-06-08 08:29:02 MarkDuplicates Tracking 641145 as yet unmatched pairs. 17522 records in RAM. INFO 2026-06-08 08:29:04 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 1s. Last read position: chr7:100,353,835 INFO 2026-06-08 08:29:04 MarkDuplicates Tracking 638924 as yet unmatched pairs. 15300 records in RAM. INFO 2026-06-08 08:29:05 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 1s. Last read position: chr7:102,355,764 INFO 2026-06-08 08:29:05 MarkDuplicates Tracking 636629 as yet unmatched pairs. 13003 records in RAM. INFO 2026-06-08 08:29:07 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 1s. Last read position: chr7:103,234,671 INFO 2026-06-08 08:29:07 MarkDuplicates Tracking 635773 as yet unmatched pairs. 12146 records in RAM. INFO 2026-06-08 08:29:08 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 1s. Last read position: chr7:117,138,488 INFO 2026-06-08 08:29:08 MarkDuplicates Tracking 633826 as yet unmatched pairs. 10195 records in RAM. INFO 2026-06-08 08:29:10 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 1s. Last read position: chr7:129,458,288 INFO 2026-06-08 08:29:10 MarkDuplicates Tracking 631773 as yet unmatched pairs. 8142 records in RAM. INFO 2026-06-08 08:29:12 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 1s. Last read position: chr7:139,572,920 INFO 2026-06-08 08:29:12 MarkDuplicates Tracking 629702 as yet unmatched pairs. 6069 records in RAM. INFO 2026-06-08 08:29:14 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 1s. Last read position: chr7:144,269,111 INFO 2026-06-08 08:29:14 MarkDuplicates Tracking 627832 as yet unmatched pairs. 4198 records in RAM. INFO 2026-06-08 08:29:15 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:05:43s. Time for last 1,000,000: 1s. Last read position: chr7:151,086,856 INFO 2026-06-08 08:29:15 MarkDuplicates Tracking 625601 as yet unmatched pairs. 1967 records in RAM. INFO 2026-06-08 08:29:18 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 2s. Last read position: chr8:6,730,733 INFO 2026-06-08 08:29:18 MarkDuplicates Tracking 623415 as yet unmatched pairs. 35261 records in RAM. INFO 2026-06-08 08:29:20 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 1s. Last read position: chr8:20,204,524 INFO 2026-06-08 08:29:20 MarkDuplicates Tracking 621608 as yet unmatched pairs. 33452 records in RAM. INFO 2026-06-08 08:29:21 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 1s. Last read position: chr8:30,544,560 INFO 2026-06-08 08:29:21 MarkDuplicates Tracking 619220 as yet unmatched pairs. 31063 records in RAM. INFO 2026-06-08 08:29:23 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 1s. Last read position: chr8:38,820,416 INFO 2026-06-08 08:29:23 MarkDuplicates Tracking 616856 as yet unmatched pairs. 28698 records in RAM. INFO 2026-06-08 08:29:25 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 1s. Last read position: chr8:47,836,487 INFO 2026-06-08 08:29:25 MarkDuplicates Tracking 614606 as yet unmatched pairs. 26446 records in RAM. INFO 2026-06-08 08:29:26 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 1s. Last read position: chr8:66,371,306 INFO 2026-06-08 08:29:26 MarkDuplicates Tracking 612439 as yet unmatched pairs. 24278 records in RAM. INFO 2026-06-08 08:29:28 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 1s. Last read position: chr8:76,854,602 INFO 2026-06-08 08:29:28 MarkDuplicates Tracking 610440 as yet unmatched pairs. 22277 records in RAM. INFO 2026-06-08 08:29:29 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 1s. Last read position: chr8:96,231,923 INFO 2026-06-08 08:29:29 MarkDuplicates Tracking 608645 as yet unmatched pairs. 20481 records in RAM. INFO 2026-06-08 08:29:31 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 1s. Last read position: chr8:101,200,008 INFO 2026-06-08 08:29:31 MarkDuplicates Tracking 606534 as yet unmatched pairs. 18369 records in RAM. INFO 2026-06-08 08:29:33 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 1s. Last read position: chr8:115,587,278 INFO 2026-06-08 08:29:33 MarkDuplicates Tracking 605110 as yet unmatched pairs. 16944 records in RAM. INFO 2026-06-08 08:29:35 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 1s. Last read position: chr8:123,805,266 INFO 2026-06-08 08:29:35 MarkDuplicates Tracking 602264 as yet unmatched pairs. 14096 records in RAM. INFO 2026-06-08 08:29:36 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 1s. Last read position: chr8:140,846,632 INFO 2026-06-08 08:29:36 MarkDuplicates Tracking 600151 as yet unmatched pairs. 11976 records in RAM. INFO 2026-06-08 08:29:38 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 1s. Last read position: chr8:143,816,640 INFO 2026-06-08 08:29:38 MarkDuplicates Tracking 597256 as yet unmatched pairs. 9079 records in RAM. INFO 2026-06-08 08:29:39 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 1s. Last read position: chr8:143,861,447 INFO 2026-06-08 08:29:39 MarkDuplicates Tracking 596191 as yet unmatched pairs. 8014 records in RAM. INFO 2026-06-08 08:29:40 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 1s. Last read position: chr8:143,865,020 INFO 2026-06-08 08:29:40 MarkDuplicates Tracking 594931 as yet unmatched pairs. 6754 records in RAM. INFO 2026-06-08 08:29:42 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:06:09s. Time for last 1,000,000: 1s. Last read position: chr8:143,921,313 INFO 2026-06-08 08:29:42 MarkDuplicates Tracking 593794 as yet unmatched pairs. 5617 records in RAM. INFO 2026-06-08 08:29:43 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 1s. Last read position: chr8:144,260,249 INFO 2026-06-08 08:29:43 MarkDuplicates Tracking 590466 as yet unmatched pairs. 2288 records in RAM. INFO 2026-06-08 08:29:47 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 3s. Last read position: chr9:734,819 INFO 2026-06-08 08:29:47 MarkDuplicates Tracking 587891 as yet unmatched pairs. 31395 records in RAM. INFO 2026-06-08 08:29:50 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 2s. Last read position: chr9:21,854,699 INFO 2026-06-08 08:29:50 MarkDuplicates Tracking 585851 as yet unmatched pairs. 29349 records in RAM. INFO 2026-06-08 08:29:51 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 1s. Last read position: chr9:35,399,429 INFO 2026-06-08 08:29:51 MarkDuplicates Tracking 583601 as yet unmatched pairs. 27093 records in RAM. INFO 2026-06-08 08:29:53 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 1s. Last read position: chr9:65,733,085 INFO 2026-06-08 08:29:53 MarkDuplicates Tracking 581740 as yet unmatched pairs. 25220 records in RAM. INFO 2026-06-08 08:29:55 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 1s. Last read position: chr9:87,706,361 INFO 2026-06-08 08:29:55 MarkDuplicates Tracking 579672 as yet unmatched pairs. 23143 records in RAM. INFO 2026-06-08 08:29:56 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 1s. Last read position: chr9:95,972,788 INFO 2026-06-08 08:29:56 MarkDuplicates Tracking 577341 as yet unmatched pairs. 20811 records in RAM. INFO 2026-06-08 08:29:58 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 1s. Last read position: chr9:110,251,391 INFO 2026-06-08 08:29:58 MarkDuplicates Tracking 575317 as yet unmatched pairs. 18786 records in RAM. INFO 2026-06-08 08:29:59 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 1s. Last read position: chr9:117,712,943 INFO 2026-06-08 08:29:59 MarkDuplicates Tracking 573059 as yet unmatched pairs. 16528 records in RAM. INFO 2026-06-08 08:30:01 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 1s. Last read position: chr9:125,149,637 INFO 2026-06-08 08:30:01 MarkDuplicates Tracking 570811 as yet unmatched pairs. 14279 records in RAM. INFO 2026-06-08 08:30:03 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:06:30s. Time for last 1,000,000: 1s. Last read position: chr9:128,268,138 INFO 2026-06-08 08:30:03 MarkDuplicates Tracking 568465 as yet unmatched pairs. 11931 records in RAM. INFO 2026-06-08 08:30:04 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 1s. Last read position: chr9:130,433,597 INFO 2026-06-08 08:30:04 MarkDuplicates Tracking 565893 as yet unmatched pairs. 9349 records in RAM. INFO 2026-06-08 08:30:06 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:06:33s. Time for last 1,000,000: 1s. Last read position: chr9:133,341,631 INFO 2026-06-08 08:30:06 MarkDuplicates Tracking 563616 as yet unmatched pairs. 7069 records in RAM. INFO 2026-06-08 08:30:09 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 3s. Last read position: chr9:136,219,115 INFO 2026-06-08 08:30:09 MarkDuplicates Tracking 561164 as yet unmatched pairs. 4617 records in RAM. INFO 2026-06-08 08:30:11 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 1s. Last read position: chr9:137,108,525 INFO 2026-06-08 08:30:11 MarkDuplicates Tracking 558728 as yet unmatched pairs. 2181 records in RAM. INFO 2026-06-08 08:30:13 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 1s. Last read position: chr10:3,165,280 INFO 2026-06-08 08:30:13 MarkDuplicates Tracking 556093 as yet unmatched pairs. 29099 records in RAM. INFO 2026-06-08 08:30:14 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 1s. Last read position: chr10:13,440,619 INFO 2026-06-08 08:30:14 MarkDuplicates Tracking 554044 as yet unmatched pairs. 27049 records in RAM. INFO 2026-06-08 08:30:16 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 1s. Last read position: chr10:27,155,510 INFO 2026-06-08 08:30:16 MarkDuplicates Tracking 551928 as yet unmatched pairs. 24930 records in RAM. INFO 2026-06-08 08:30:17 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 1s. Last read position: chr10:32,922,282 INFO 2026-06-08 08:30:17 MarkDuplicates Tracking 550220 as yet unmatched pairs. 23221 records in RAM. INFO 2026-06-08 08:30:19 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:06:46s. Time for last 1,000,000: 1s. Last read position: chr10:43,116,606 INFO 2026-06-08 08:30:19 MarkDuplicates Tracking 547559 as yet unmatched pairs. 20558 records in RAM. INFO 2026-06-08 08:30:21 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 1s. Last read position: chr10:46,358,176 INFO 2026-06-08 08:30:21 MarkDuplicates Tracking 545081 as yet unmatched pairs. 18080 records in RAM. INFO 2026-06-08 08:30:22 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 1s. Last read position: chr10:68,364,003 INFO 2026-06-08 08:30:22 MarkDuplicates Tracking 543222 as yet unmatched pairs. 16209 records in RAM. INFO 2026-06-08 08:30:24 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:06:51s. Time for last 1,000,000: 1s. Last read position: chr10:73,793,659 INFO 2026-06-08 08:30:24 MarkDuplicates Tracking 541122 as yet unmatched pairs. 14109 records in RAM. INFO 2026-06-08 08:30:25 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 1s. Last read position: chr10:80,163,608 INFO 2026-06-08 08:30:25 MarkDuplicates Tracking 539048 as yet unmatched pairs. 12033 records in RAM. INFO 2026-06-08 08:30:27 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 1s. Last read position: chr10:92,081,391 INFO 2026-06-08 08:30:27 MarkDuplicates Tracking 537096 as yet unmatched pairs. 10081 records in RAM. INFO 2026-06-08 08:30:29 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 1s. Last read position: chr10:98,417,150 INFO 2026-06-08 08:30:29 MarkDuplicates Tracking 534810 as yet unmatched pairs. 7795 records in RAM. INFO 2026-06-08 08:30:31 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 2s. Last read position: chr10:103,387,600 INFO 2026-06-08 08:30:31 MarkDuplicates Tracking 532636 as yet unmatched pairs. 5620 records in RAM. INFO 2026-06-08 08:30:33 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:07:00s. Time for last 1,000,000: 1s. Last read position: chr10:117,285,079 INFO 2026-06-08 08:30:33 MarkDuplicates Tracking 530650 as yet unmatched pairs. 3630 records in RAM. INFO 2026-06-08 08:30:35 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 2s. Last read position: chr10:124,994,651 INFO 2026-06-08 08:30:35 MarkDuplicates Tracking 528601 as yet unmatched pairs. 1577 records in RAM. INFO 2026-06-08 08:30:37 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:07:04s. Time for last 1,000,000: 2s. Last read position: chr11:293,610 INFO 2026-06-08 08:30:37 MarkDuplicates Tracking 527198 as yet unmatched pairs. 59690 records in RAM. INFO 2026-06-08 08:30:38 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 1s. Last read position: chr11:554,935 INFO 2026-06-08 08:30:38 MarkDuplicates Tracking 523929 as yet unmatched pairs. 56421 records in RAM. INFO 2026-06-08 08:30:40 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:07:07s. Time for last 1,000,000: 1s. Last read position: chr11:1,761,384 INFO 2026-06-08 08:30:40 MarkDuplicates Tracking 521855 as yet unmatched pairs. 54345 records in RAM. INFO 2026-06-08 08:30:42 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:07:09s. Time for last 1,000,000: 1s. Last read position: chr11:6,609,511 INFO 2026-06-08 08:30:42 MarkDuplicates Tracking 519177 as yet unmatched pairs. 51667 records in RAM. INFO 2026-06-08 08:30:43 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 1s. Last read position: chr11:10,803,210 INFO 2026-06-08 08:30:43 MarkDuplicates Tracking 517159 as yet unmatched pairs. 49649 records in RAM. INFO 2026-06-08 08:30:45 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:07:12s. Time for last 1,000,000: 1s. Last read position: chr11:20,367,237 INFO 2026-06-08 08:30:45 MarkDuplicates Tracking 514932 as yet unmatched pairs. 47422 records in RAM. INFO 2026-06-08 08:30:46 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:07:14s. Time for last 1,000,000: 1s. Last read position: chr11:44,109,205 INFO 2026-06-08 08:30:46 MarkDuplicates Tracking 512896 as yet unmatched pairs. 45386 records in RAM. INFO 2026-06-08 08:30:48 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:07:15s. Time for last 1,000,000: 1s. Last read position: chr11:47,473,101 INFO 2026-06-08 08:30:48 MarkDuplicates Tracking 510669 as yet unmatched pairs. 43158 records in RAM. INFO 2026-06-08 08:30:50 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:07:17s. Time for last 1,000,000: 1s. Last read position: chr11:59,125,230 INFO 2026-06-08 08:30:50 MarkDuplicates Tracking 508464 as yet unmatched pairs. 40953 records in RAM. INFO 2026-06-08 08:30:52 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:07:19s. Time for last 1,000,000: 1s. Last read position: chr11:61,967,330 INFO 2026-06-08 08:30:52 MarkDuplicates Tracking 506562 as yet unmatched pairs. 39047 records in RAM. INFO 2026-06-08 08:30:53 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:07:20s. Time for last 1,000,000: 1s. Last read position: chr11:62,520,102 INFO 2026-06-08 08:30:53 MarkDuplicates Tracking 504896 as yet unmatched pairs. 37381 records in RAM. INFO 2026-06-08 08:30:55 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:07:22s. Time for last 1,000,000: 1s. Last read position: chr11:62,527,941 INFO 2026-06-08 08:30:55 MarkDuplicates Tracking 503556 as yet unmatched pairs. 36041 records in RAM. INFO 2026-06-08 08:30:56 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:07:24s. Time for last 1,000,000: 1s. Last read position: chr11:62,572,644 INFO 2026-06-08 08:30:56 MarkDuplicates Tracking 500542 as yet unmatched pairs. 33026 records in RAM. INFO 2026-06-08 08:30:58 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:07:25s. Time for last 1,000,000: 1s. Last read position: chr11:64,234,838 INFO 2026-06-08 08:30:58 MarkDuplicates Tracking 498294 as yet unmatched pairs. 30778 records in RAM. INFO 2026-06-08 08:31:59 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:08:26s. Time for last 1,000,000: 60s. Last read position: chr11:65,381,975 INFO 2026-06-08 08:31:59 MarkDuplicates Tracking 495514 as yet unmatched pairs. 27997 records in RAM. INFO 2026-06-08 08:32:01 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 2s. Last read position: chr11:65,921,328 INFO 2026-06-08 08:32:01 MarkDuplicates Tracking 492966 as yet unmatched pairs. 25447 records in RAM. INFO 2026-06-08 08:32:03 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:08:30s. Time for last 1,000,000: 1s. Last read position: chr11:67,441,991 INFO 2026-06-08 08:32:03 MarkDuplicates Tracking 490387 as yet unmatched pairs. 22865 records in RAM. INFO 2026-06-08 08:32:05 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 1s. Last read position: chr11:70,421,538 INFO 2026-06-08 08:32:05 MarkDuplicates Tracking 487977 as yet unmatched pairs. 20454 records in RAM. INFO 2026-06-08 08:32:06 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 1s. Last read position: chr11:72,688,492 INFO 2026-06-08 08:32:06 MarkDuplicates Tracking 485714 as yet unmatched pairs. 18191 records in RAM. INFO 2026-06-08 08:32:08 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 1s. Last read position: chr11:75,151,277 INFO 2026-06-08 08:32:08 MarkDuplicates Tracking 483364 as yet unmatched pairs. 15840 records in RAM. INFO 2026-06-08 08:32:09 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 1s. Last read position: chr11:76,472,648 INFO 2026-06-08 08:32:09 MarkDuplicates Tracking 481072 as yet unmatched pairs. 13547 records in RAM. INFO 2026-06-08 08:32:11 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:08:38s. Time for last 1,000,000: 1s. Last read position: chr11:77,921,347 INFO 2026-06-08 08:32:11 MarkDuplicates Tracking 478998 as yet unmatched pairs. 11470 records in RAM. INFO 2026-06-08 08:32:13 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 1s. Last read position: chr11:85,696,331 INFO 2026-06-08 08:32:13 MarkDuplicates Tracking 476544 as yet unmatched pairs. 9016 records in RAM. INFO 2026-06-08 08:32:14 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:08:42s. Time for last 1,000,000: 1s. Last read position: chr11:103,199,262 INFO 2026-06-08 08:32:14 MarkDuplicates Tracking 474366 as yet unmatched pairs. 6838 records in RAM. INFO 2026-06-08 08:32:16 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:08:43s. Time for last 1,000,000: 1s. Last read position: chr11:118,499,303 INFO 2026-06-08 08:32:16 MarkDuplicates Tracking 472297 as yet unmatched pairs. 4765 records in RAM. INFO 2026-06-08 08:32:18 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:08:45s. Time for last 1,000,000: 1s. Last read position: chr11:122,730,192 INFO 2026-06-08 08:32:18 MarkDuplicates Tracking 470104 as yet unmatched pairs. 2570 records in RAM. INFO 2026-06-08 08:32:19 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:08:46s. Time for last 1,000,000: 1s. Last read position: chr11:130,194,168 INFO 2026-06-08 08:32:19 MarkDuplicates Tracking 468019 as yet unmatched pairs. 484 records in RAM. INFO 2026-06-08 08:32:21 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 2s. Last read position: chr12:2,799,881 INFO 2026-06-08 08:32:21 MarkDuplicates Tracking 465964 as yet unmatched pairs. 63170 records in RAM. INFO 2026-06-08 08:32:23 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:08:50s. Time for last 1,000,000: 1s. Last read position: chr12:6,563,336 INFO 2026-06-08 08:32:23 MarkDuplicates Tracking 463493 as yet unmatched pairs. 60694 records in RAM. INFO 2026-06-08 08:32:25 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:08:52s. Time for last 1,000,000: 1s. Last read position: chr12:7,149,056 INFO 2026-06-08 08:32:25 MarkDuplicates Tracking 461147 as yet unmatched pairs. 58347 records in RAM. INFO 2026-06-08 08:32:26 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 1s. Last read position: chr12:12,908,444 INFO 2026-06-08 08:32:26 MarkDuplicates Tracking 459684 as yet unmatched pairs. 56882 records in RAM. INFO 2026-06-08 08:32:28 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:08:55s. Time for last 1,000,000: 1s. Last read position: chr12:26,486,211 INFO 2026-06-08 08:32:28 MarkDuplicates Tracking 457287 as yet unmatched pairs. 54484 records in RAM. INFO 2026-06-08 08:32:29 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:08:57s. Time for last 1,000,000: 1s. Last read position: chr12:40,426,447 INFO 2026-06-08 08:32:29 MarkDuplicates Tracking 455659 as yet unmatched pairs. 52855 records in RAM. INFO 2026-06-08 08:32:31 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:08:58s. Time for last 1,000,000: 1s. Last read position: chr12:40,483,305 INFO 2026-06-08 08:32:31 MarkDuplicates Tracking 453065 as yet unmatched pairs. 50260 records in RAM. INFO 2026-06-08 08:32:33 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:09:00s. Time for last 1,000,000: 1s. Last read position: chr12:40,487,309 INFO 2026-06-08 08:32:33 MarkDuplicates Tracking 452366 as yet unmatched pairs. 49555 records in RAM. INFO 2026-06-08 08:32:34 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:09:02s. Time for last 1,000,000: 1s. Last read position: chr12:40,489,708 INFO 2026-06-08 08:32:34 MarkDuplicates Tracking 449567 as yet unmatched pairs. 46756 records in RAM. INFO 2026-06-08 08:32:37 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:09:04s. Time for last 1,000,000: 2s. Last read position: chr12:40,531,067 INFO 2026-06-08 08:32:37 MarkDuplicates Tracking 447199 as yet unmatched pairs. 44388 records in RAM. INFO 2026-06-08 08:32:39 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:09:06s. Time for last 1,000,000: 2s. Last read position: chr12:45,421,232 INFO 2026-06-08 08:32:39 MarkDuplicates Tracking 444705 as yet unmatched pairs. 41894 records in RAM. INFO 2026-06-08 08:32:41 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 1s. Last read position: chr12:49,002,915 INFO 2026-06-08 08:32:41 MarkDuplicates Tracking 442544 as yet unmatched pairs. 39733 records in RAM. INFO 2026-06-08 08:32:42 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:09:10s. Time for last 1,000,000: 1s. Last read position: chr12:49,272,601 INFO 2026-06-08 08:32:42 MarkDuplicates Tracking 440733 as yet unmatched pairs. 37922 records in RAM. INFO 2026-06-08 08:32:44 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:09:11s. Time for last 1,000,000: 1s. Last read position: chr12:52,079,894 INFO 2026-06-08 08:32:44 MarkDuplicates Tracking 438559 as yet unmatched pairs. 35747 records in RAM. INFO 2026-06-08 08:32:46 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:09:13s. Time for last 1,000,000: 1s. Last read position: chr12:53,459,381 INFO 2026-06-08 08:32:46 MarkDuplicates Tracking 436678 as yet unmatched pairs. 33866 records in RAM. INFO 2026-06-08 08:32:47 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 1s. Last read position: chr12:55,827,497 INFO 2026-06-08 08:32:47 MarkDuplicates Tracking 434168 as yet unmatched pairs. 31354 records in RAM. INFO 2026-06-08 08:32:49 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 1s. Last read position: chr12:56,181,537 INFO 2026-06-08 08:32:49 MarkDuplicates Tracking 431919 as yet unmatched pairs. 29104 records in RAM. INFO 2026-06-08 08:32:51 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:09:18s. Time for last 1,000,000: 1s. Last read position: chr12:56,721,177 INFO 2026-06-08 08:32:51 MarkDuplicates Tracking 429895 as yet unmatched pairs. 27080 records in RAM. INFO 2026-06-08 08:32:52 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 1s. Last read position: chr12:57,196,164 INFO 2026-06-08 08:32:52 MarkDuplicates Tracking 427387 as yet unmatched pairs. 24572 records in RAM. INFO 2026-06-08 08:32:54 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:09:21s. Time for last 1,000,000: 1s. Last read position: chr12:62,537,686 INFO 2026-06-08 08:32:54 MarkDuplicates Tracking 425079 as yet unmatched pairs. 22264 records in RAM. INFO 2026-06-08 08:32:56 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:09:23s. Time for last 1,000,000: 1s. Last read position: chr12:71,632,934 INFO 2026-06-08 08:32:56 MarkDuplicates Tracking 422829 as yet unmatched pairs. 20014 records in RAM. INFO 2026-06-08 08:32:57 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:09:24s. Time for last 1,000,000: 1s. Last read position: chr12:93,488,351 INFO 2026-06-08 08:32:57 MarkDuplicates Tracking 420842 as yet unmatched pairs. 18025 records in RAM. INFO 2026-06-08 08:32:59 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:09:26s. Time for last 1,000,000: 2s. Last read position: chr12:101,720,093 INFO 2026-06-08 08:32:59 MarkDuplicates Tracking 419629 as yet unmatched pairs. 16811 records in RAM. INFO 2026-06-08 08:33:01 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:09:28s. Time for last 1,000,000: 1s. Last read position: chr12:108,623,554 INFO 2026-06-08 08:33:01 MarkDuplicates Tracking 416712 as yet unmatched pairs. 13892 records in RAM. INFO 2026-06-08 08:33:02 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:09:29s. Time for last 1,000,000: 1s. Last read position: chr12:112,043,726 INFO 2026-06-08 08:33:02 MarkDuplicates Tracking 414398 as yet unmatched pairs. 11578 records in RAM. INFO 2026-06-08 08:33:04 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:09:31s. Time for last 1,000,000: 1s. Last read position: chr12:115,961,190 INFO 2026-06-08 08:33:04 MarkDuplicates Tracking 412777 as yet unmatched pairs. 9957 records in RAM. INFO 2026-06-08 08:33:05 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:09:33s. Time for last 1,000,000: 1s. Last read position: chr12:120,438,210 INFO 2026-06-08 08:33:05 MarkDuplicates Tracking 410791 as yet unmatched pairs. 7962 records in RAM. INFO 2026-06-08 08:33:07 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:09:34s. Time for last 1,000,000: 1s. Last read position: chr12:122,752,885 INFO 2026-06-08 08:33:07 MarkDuplicates Tracking 407764 as yet unmatched pairs. 4934 records in RAM. INFO 2026-06-08 08:33:08 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:09:36s. Time for last 1,000,000: 1s. Last read position: chr12:124,911,981 INFO 2026-06-08 08:33:08 MarkDuplicates Tracking 405535 as yet unmatched pairs. 2704 records in RAM. INFO 2026-06-08 08:33:10 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 1s. Last read position: chr12:132,813,340 INFO 2026-06-08 08:33:10 MarkDuplicates Tracking 403452 as yet unmatched pairs. 621 records in RAM. INFO 2026-06-08 08:33:12 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:09:39s. Time for last 1,000,000: 1s. Last read position: chr13:30,461,334 INFO 2026-06-08 08:33:12 MarkDuplicates Tracking 401040 as yet unmatched pairs. 8865 records in RAM. INFO 2026-06-08 08:33:14 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:09:41s. Time for last 1,000,000: 1s. Last read position: chr13:42,300,927 INFO 2026-06-08 08:33:14 MarkDuplicates Tracking 399033 as yet unmatched pairs. 6857 records in RAM. INFO 2026-06-08 08:33:15 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:09:43s. Time for last 1,000,000: 1s. Last read position: chr13:67,226,827 INFO 2026-06-08 08:33:15 MarkDuplicates Tracking 396914 as yet unmatched pairs. 4734 records in RAM. INFO 2026-06-08 08:33:17 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 1s. Last read position: chr13:101,104,333 INFO 2026-06-08 08:33:17 MarkDuplicates Tracking 394731 as yet unmatched pairs. 2550 records in RAM. INFO 2026-06-08 08:33:19 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:09:46s. Time for last 1,000,000: 1s. Last read position: chr13:113,820,604 INFO 2026-06-08 08:33:19 MarkDuplicates Tracking 392429 as yet unmatched pairs. 244 records in RAM. INFO 2026-06-08 08:33:21 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:09:48s. Time for last 1,000,000: 1s. Last read position: chr14:22,778,875 INFO 2026-06-08 08:33:21 MarkDuplicates Tracking 390235 as yet unmatched pairs. 29140 records in RAM. INFO 2026-06-08 08:33:23 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:09:50s. Time for last 1,000,000: 1s. Last read position: chr14:24,117,692 INFO 2026-06-08 08:33:23 MarkDuplicates Tracking 388057 as yet unmatched pairs. 26962 records in RAM. INFO 2026-06-08 08:33:25 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:09:52s. Time for last 1,000,000: 1s. Last read position: chr14:31,128,987 INFO 2026-06-08 08:33:25 MarkDuplicates Tracking 385715 as yet unmatched pairs. 24619 records in RAM. INFO 2026-06-08 08:33:26 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:09:54s. Time for last 1,000,000: 1s. Last read position: chr14:44,945,767 INFO 2026-06-08 08:33:26 MarkDuplicates Tracking 383602 as yet unmatched pairs. 22503 records in RAM. INFO 2026-06-08 08:33:28 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:09:55s. Time for last 1,000,000: 1s. Last read position: chr14:53,152,486 INFO 2026-06-08 08:33:28 MarkDuplicates Tracking 381477 as yet unmatched pairs. 20377 records in RAM. INFO 2026-06-08 08:33:30 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:09:57s. Time for last 1,000,000: 1s. Last read position: chr14:63,698,578 INFO 2026-06-08 08:33:30 MarkDuplicates Tracking 379616 as yet unmatched pairs. 18515 records in RAM. INFO 2026-06-08 08:33:31 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:09:58s. Time for last 1,000,000: 1s. Last read position: chr14:68,790,477 INFO 2026-06-08 08:33:31 MarkDuplicates Tracking 377624 as yet unmatched pairs. 16521 records in RAM. INFO 2026-06-08 08:33:33 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:10:00s. Time for last 1,000,000: 1s. Last read position: chr14:73,903,989 INFO 2026-06-08 08:33:33 MarkDuplicates Tracking 375108 as yet unmatched pairs. 14001 records in RAM. INFO 2026-06-08 08:33:35 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:10:02s. Time for last 1,000,000: 1s. Last read position: chr14:77,458,129 INFO 2026-06-08 08:33:35 MarkDuplicates Tracking 372815 as yet unmatched pairs. 11708 records in RAM. INFO 2026-06-08 08:33:36 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:10:03s. Time for last 1,000,000: 1s. Last read position: chr14:93,115,082 INFO 2026-06-08 08:33:36 MarkDuplicates Tracking 370700 as yet unmatched pairs. 9591 records in RAM. INFO 2026-06-08 08:33:38 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:10:05s. Time for last 1,000,000: 1s. Last read position: chr14:99,465,753 INFO 2026-06-08 08:33:38 MarkDuplicates Tracking 368547 as yet unmatched pairs. 7422 records in RAM. INFO 2026-06-08 08:33:39 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:10:07s. Time for last 1,000,000: 1s. Last read position: chr14:102,040,400 INFO 2026-06-08 08:33:39 MarkDuplicates Tracking 366261 as yet unmatched pairs. 5136 records in RAM. INFO 2026-06-08 08:33:41 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:10:08s. Time for last 1,000,000: 1s. Last read position: chr14:104,772,925 INFO 2026-06-08 08:33:41 MarkDuplicates Tracking 364065 as yet unmatched pairs. 2939 records in RAM. INFO 2026-06-08 08:33:43 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:10:10s. Time for last 1,000,000: 1s. Last read position: chr14:105,741,494 INFO 2026-06-08 08:33:43 MarkDuplicates Tracking 362034 as yet unmatched pairs. 908 records in RAM. INFO 2026-06-08 08:33:44 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 1s. Last read position: chr15:28,233,718 INFO 2026-06-08 08:33:44 MarkDuplicates Tracking 359921 as yet unmatched pairs. 21606 records in RAM. INFO 2026-06-08 08:33:46 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:10:13s. Time for last 1,000,000: 1s. Last read position: chr15:39,582,494 INFO 2026-06-08 08:33:46 MarkDuplicates Tracking 358491 as yet unmatched pairs. 20172 records in RAM. INFO 2026-06-08 08:33:47 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:10:15s. Time for last 1,000,000: 1s. Last read position: chr15:41,736,278 INFO 2026-06-08 08:33:47 MarkDuplicates Tracking 356070 as yet unmatched pairs. 17725 records in RAM. INFO 2026-06-08 08:33:50 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:10:17s. Time for last 1,000,000: 2s. Last read position: chr15:43,792,353 INFO 2026-06-08 08:33:50 MarkDuplicates Tracking 354173 as yet unmatched pairs. 15824 records in RAM. INFO 2026-06-08 08:33:52 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:10:20s. Time for last 1,000,000: 2s. Last read position: chr15:49,145,018 INFO 2026-06-08 08:33:52 MarkDuplicates Tracking 351534 as yet unmatched pairs. 13185 records in RAM. INFO 2026-06-08 08:33:54 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:10:22s. Time for last 1,000,000: 2s. Last read position: chr15:59,058,439 INFO 2026-06-08 08:33:54 MarkDuplicates Tracking 349508 as yet unmatched pairs. 11156 records in RAM. INFO 2026-06-08 08:33:56 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:10:23s. Time for last 1,000,000: 1s. Last read position: chr15:65,157,753 INFO 2026-06-08 08:33:56 MarkDuplicates Tracking 347385 as yet unmatched pairs. 9031 records in RAM. INFO 2026-06-08 08:33:58 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:10:25s. Time for last 1,000,000: 1s. Last read position: chr15:72,250,908 INFO 2026-06-08 08:33:58 MarkDuplicates Tracking 345237 as yet unmatched pairs. 6882 records in RAM. INFO 2026-06-08 08:33:59 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 1s. Last read position: chr15:76,766,971 INFO 2026-06-08 08:33:59 MarkDuplicates Tracking 342847 as yet unmatched pairs. 4491 records in RAM. INFO 2026-06-08 08:34:01 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:10:28s. Time for last 1,000,000: 1s. Last read position: chr15:85,741,306 INFO 2026-06-08 08:34:01 MarkDuplicates Tracking 340958 as yet unmatched pairs. 2592 records in RAM. INFO 2026-06-08 08:34:02 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:10:29s. Time for last 1,000,000: 1s. Last read position: chr15:100,900,621 INFO 2026-06-08 08:34:02 MarkDuplicates Tracking 338756 as yet unmatched pairs. 387 records in RAM. INFO 2026-06-08 08:34:04 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:10:31s. Time for last 1,000,000: 1s. Last read position: chr16:651,954 INFO 2026-06-08 08:34:04 MarkDuplicates Tracking 336369 as yet unmatched pairs. 50881 records in RAM. INFO 2026-06-08 08:34:06 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:10:33s. Time for last 1,000,000: 1s. Last read position: chr16:1,348,272 INFO 2026-06-08 08:34:06 MarkDuplicates Tracking 333582 as yet unmatched pairs. 48090 records in RAM. INFO 2026-06-08 08:34:07 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:10:35s. Time for last 1,000,000: 1s. Last read position: chr16:2,037,828 INFO 2026-06-08 08:34:07 MarkDuplicates Tracking 330846 as yet unmatched pairs. 45354 records in RAM. INFO 2026-06-08 08:34:09 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:10:36s. Time for last 1,000,000: 1s. Last read position: chr16:2,289,567 INFO 2026-06-08 08:34:09 MarkDuplicates Tracking 328384 as yet unmatched pairs. 42891 records in RAM. INFO 2026-06-08 08:34:10 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:10:38s. Time for last 1,000,000: 1s. Last read position: chr16:2,775,455 INFO 2026-06-08 08:34:10 MarkDuplicates Tracking 326755 as yet unmatched pairs. 41259 records in RAM. INFO 2026-06-08 08:34:12 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:10:39s. Time for last 1,000,000: 1s. Last read position: chr16:4,114,933 INFO 2026-06-08 08:34:12 MarkDuplicates Tracking 323995 as yet unmatched pairs. 38495 records in RAM. INFO 2026-06-08 08:34:14 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:10:42s. Time for last 1,000,000: 2s. Last read position: chr16:10,480,871 INFO 2026-06-08 08:34:14 MarkDuplicates Tracking 321631 as yet unmatched pairs. 36131 records in RAM. INFO 2026-06-08 08:34:17 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:10:44s. Time for last 1,000,000: 2s. Last read position: chr16:14,725,892 INFO 2026-06-08 08:34:17 MarkDuplicates Tracking 319501 as yet unmatched pairs. 34001 records in RAM. INFO 2026-06-08 08:34:18 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 1s. Last read position: chr16:15,017,359 INFO 2026-06-08 08:34:18 MarkDuplicates Tracking 318680 as yet unmatched pairs. 33180 records in RAM. INFO 2026-06-08 08:34:20 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:10:47s. Time for last 1,000,000: 1s. Last read position: chr16:16,317,275 INFO 2026-06-08 08:34:20 MarkDuplicates Tracking 317210 as yet unmatched pairs. 31710 records in RAM. INFO 2026-06-08 08:34:21 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:10:48s. Time for last 1,000,000: 1s. Last read position: chr16:16,366,113 INFO 2026-06-08 08:34:21 MarkDuplicates Tracking 316960 as yet unmatched pairs. 31460 records in RAM. INFO 2026-06-08 08:34:22 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:10:49s. Time for last 1,000,000: 1s. Last read position: chr16:18,358,322 INFO 2026-06-08 08:34:22 MarkDuplicates Tracking 316126 as yet unmatched pairs. 30626 records in RAM. INFO 2026-06-08 08:34:23 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:10:51s. Time for last 1,000,000: 1s. Last read position: chr16:18,793,352 INFO 2026-06-08 08:34:23 MarkDuplicates Tracking 314999 as yet unmatched pairs. 29498 records in RAM. INFO 2026-06-08 08:34:25 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:10:52s. Time for last 1,000,000: 1s. Last read position: chr16:21,404,077 INFO 2026-06-08 08:34:25 MarkDuplicates Tracking 313116 as yet unmatched pairs. 27613 records in RAM. INFO 2026-06-08 08:34:26 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:10:54s. Time for last 1,000,000: 1s. Last read position: chr16:21,851,795 INFO 2026-06-08 08:34:26 MarkDuplicates Tracking 312227 as yet unmatched pairs. 26724 records in RAM. INFO 2026-06-08 08:34:28 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:10:55s. Time for last 1,000,000: 1s. Last read position: chr16:22,534,676 INFO 2026-06-08 08:34:28 MarkDuplicates Tracking 311670 as yet unmatched pairs. 26167 records in RAM. INFO 2026-06-08 08:34:30 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:10:57s. Time for last 1,000,000: 2s. Last read position: chr16:28,176,067 INFO 2026-06-08 08:34:30 MarkDuplicates Tracking 309818 as yet unmatched pairs. 24315 records in RAM. INFO 2026-06-08 08:34:32 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:10:59s. Time for last 1,000,000: 2s. Last read position: chr16:29,050,682 INFO 2026-06-08 08:34:32 MarkDuplicates Tracking 307845 as yet unmatched pairs. 22341 records in RAM. INFO 2026-06-08 08:34:33 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:11:00s. Time for last 1,000,000: 1s. Last read position: chr16:29,799,414 INFO 2026-06-08 08:34:33 MarkDuplicates Tracking 307293 as yet unmatched pairs. 21789 records in RAM. INFO 2026-06-08 08:34:35 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:11:02s. Time for last 1,000,000: 1s. Last read position: chr16:30,192,960 INFO 2026-06-08 08:34:35 MarkDuplicates Tracking 304809 as yet unmatched pairs. 19305 records in RAM. INFO 2026-06-08 08:34:36 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:11:03s. Time for last 1,000,000: 1s. Last read position: chr16:30,662,662 INFO 2026-06-08 08:34:36 MarkDuplicates Tracking 303370 as yet unmatched pairs. 17866 records in RAM. INFO 2026-06-08 08:34:38 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:11:05s. Time for last 1,000,000: 1s. Last read position: chr16:31,182,397 INFO 2026-06-08 08:34:38 MarkDuplicates Tracking 301489 as yet unmatched pairs. 15982 records in RAM. INFO 2026-06-08 08:34:39 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:11:06s. Time for last 1,000,000: 1s. Last read position: chr16:50,305,836 INFO 2026-06-08 08:34:39 MarkDuplicates Tracking 298996 as yet unmatched pairs. 13489 records in RAM. INFO 2026-06-08 08:34:41 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:11:08s. Time for last 1,000,000: 1s. Last read position: chr16:57,641,630 INFO 2026-06-08 08:34:41 MarkDuplicates Tracking 296748 as yet unmatched pairs. 11239 records in RAM. INFO 2026-06-08 08:34:42 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:11:10s. Time for last 1,000,000: 1s. Last read position: chr16:67,877,216 INFO 2026-06-08 08:34:42 MarkDuplicates Tracking 294217 as yet unmatched pairs. 8706 records in RAM. INFO 2026-06-08 08:34:44 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:11:11s. Time for last 1,000,000: 1s. Last read position: chr16:70,541,705 INFO 2026-06-08 08:34:44 MarkDuplicates Tracking 292074 as yet unmatched pairs. 6560 records in RAM. INFO 2026-06-08 08:34:45 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:11:13s. Time for last 1,000,000: 1s. Last read position: chr16:83,899,633 INFO 2026-06-08 08:34:45 MarkDuplicates Tracking 289868 as yet unmatched pairs. 4351 records in RAM. INFO 2026-06-08 08:34:47 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:11:14s. Time for last 1,000,000: 1s. Last read position: chr16:88,726,334 INFO 2026-06-08 08:34:47 MarkDuplicates Tracking 287425 as yet unmatched pairs. 1907 records in RAM. INFO 2026-06-08 08:34:50 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:11:17s. Time for last 1,000,000: 2s. Last read position: chr17:1,365,002 INFO 2026-06-08 08:34:50 MarkDuplicates Tracking 285393 as yet unmatched pairs. 116457 records in RAM. INFO 2026-06-08 08:34:52 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:11:19s. Time for last 1,000,000: 2s. Last read position: chr17:4,242,273 INFO 2026-06-08 08:34:52 MarkDuplicates Tracking 282671 as yet unmatched pairs. 113735 records in RAM. INFO 2026-06-08 08:34:54 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:11:21s. Time for last 1,000,000: 2s. Last read position: chr17:7,240,850 INFO 2026-06-08 08:34:54 MarkDuplicates Tracking 280670 as yet unmatched pairs. 111734 records in RAM. INFO 2026-06-08 08:34:56 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:11:23s. Time for last 1,000,000: 1s. Last read position: chr17:7,856,698 INFO 2026-06-08 08:34:56 MarkDuplicates Tracking 278392 as yet unmatched pairs. 109455 records in RAM. INFO 2026-06-08 08:34:58 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:11:25s. Time for last 1,000,000: 1s. Last read position: chr17:15,259,131 INFO 2026-06-08 08:34:58 MarkDuplicates Tracking 276528 as yet unmatched pairs. 107591 records in RAM. INFO 2026-06-08 08:34:59 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:11:26s. Time for last 1,000,000: 1s. Last read position: chr17:18,672,920 INFO 2026-06-08 08:34:59 MarkDuplicates Tracking 273920 as yet unmatched pairs. 104982 records in RAM. INFO 2026-06-08 08:35:01 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:11:28s. Time for last 1,000,000: 1s. Last read position: chr17:28,749,058 INFO 2026-06-08 08:35:01 MarkDuplicates Tracking 272003 as yet unmatched pairs. 103064 records in RAM. INFO 2026-06-08 08:35:02 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:11:30s. Time for last 1,000,000: 1s. Last read position: chr17:31,318,347 INFO 2026-06-08 08:35:02 MarkDuplicates Tracking 270040 as yet unmatched pairs. 101101 records in RAM. INFO 2026-06-08 08:35:04 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:11:31s. Time for last 1,000,000: 1s. Last read position: chr17:35,844,733 INFO 2026-06-08 08:35:04 MarkDuplicates Tracking 267830 as yet unmatched pairs. 98890 records in RAM. INFO 2026-06-08 08:35:05 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:11:33s. Time for last 1,000,000: 1s. Last read position: chr17:38,257,022 INFO 2026-06-08 08:35:05 MarkDuplicates Tracking 266504 as yet unmatched pairs. 97564 records in RAM. INFO 2026-06-08 08:35:07 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:11:34s. Time for last 1,000,000: 1s. Last read position: chr17:39,419,907 INFO 2026-06-08 08:35:07 MarkDuplicates Tracking 264278 as yet unmatched pairs. 95338 records in RAM. INFO 2026-06-08 08:35:09 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:11:36s. Time for last 1,000,000: 1s. Last read position: chr17:39,712,331 INFO 2026-06-08 08:35:09 MarkDuplicates Tracking 263209 as yet unmatched pairs. 94265 records in RAM. INFO 2026-06-08 08:35:10 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:11:38s. Time for last 1,000,000: 1s. Last read position: chr17:39,724,742 INFO 2026-06-08 08:35:10 MarkDuplicates Tracking 260995 as yet unmatched pairs. 92051 records in RAM. INFO 2026-06-08 08:35:12 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:11:39s. Time for last 1,000,000: 1s. Last read position: chr17:40,123,102 INFO 2026-06-08 08:35:12 MarkDuplicates Tracking 257336 as yet unmatched pairs. 88392 records in RAM. INFO 2026-06-08 08:35:14 MarkDuplicates Read 368,000,000 records. Elapsed time: 00:11:41s. Time for last 1,000,000: 2s. Last read position: chr17:41,524,848 INFO 2026-06-08 08:35:14 MarkDuplicates Tracking 256043 as yet unmatched pairs. 87099 records in RAM. INFO 2026-06-08 08:35:17 MarkDuplicates Read 369,000,000 records. Elapsed time: 00:11:44s. Time for last 1,000,000: 2s. Last read position: chr17:42,115,821 INFO 2026-06-08 08:35:17 MarkDuplicates Tracking 252392 as yet unmatched pairs. 83448 records in RAM. INFO 2026-06-08 08:35:19 MarkDuplicates Read 370,000,000 records. Elapsed time: 00:11:46s. Time for last 1,000,000: 1s. Last read position: chr17:42,854,591 INFO 2026-06-08 08:35:19 MarkDuplicates Tracking 249899 as yet unmatched pairs. 80954 records in RAM. INFO 2026-06-08 08:35:20 MarkDuplicates Read 371,000,000 records. Elapsed time: 00:11:48s. Time for last 1,000,000: 1s. Last read position: chr17:44,351,586 INFO 2026-06-08 08:35:20 MarkDuplicates Tracking 247945 as yet unmatched pairs. 79000 records in RAM. INFO 2026-06-08 08:35:22 MarkDuplicates Read 372,000,000 records. Elapsed time: 00:11:49s. Time for last 1,000,000: 1s. Last read position: chr17:46,548,302 INFO 2026-06-08 08:35:22 MarkDuplicates Tracking 245610 as yet unmatched pairs. 76665 records in RAM. INFO 2026-06-08 08:35:23 MarkDuplicates Read 373,000,000 records. Elapsed time: 00:11:51s. Time for last 1,000,000: 1s. Last read position: chr17:48,862,941 INFO 2026-06-08 08:35:23 MarkDuplicates Tracking 243675 as yet unmatched pairs. 74729 records in RAM. INFO 2026-06-08 08:35:25 MarkDuplicates Read 374,000,000 records. Elapsed time: 00:11:52s. Time for last 1,000,000: 1s. Last read position: chr17:50,185,813 INFO 2026-06-08 08:35:25 MarkDuplicates Tracking 243109 as yet unmatched pairs. 74163 records in RAM. INFO 2026-06-08 08:35:27 MarkDuplicates Read 375,000,000 records. Elapsed time: 00:11:54s. Time for last 1,000,000: 1s. Last read position: chr17:50,186,829 INFO 2026-06-08 08:35:27 MarkDuplicates Tracking 242471 as yet unmatched pairs. 73525 records in RAM. INFO 2026-06-08 08:35:28 MarkDuplicates Read 376,000,000 records. Elapsed time: 00:11:56s. Time for last 1,000,000: 1s. Last read position: chr17:50,187,491 INFO 2026-06-08 08:35:28 MarkDuplicates Tracking 247573 as yet unmatched pairs. 78626 records in RAM. INFO 2026-06-08 08:35:30 MarkDuplicates Read 377,000,000 records. Elapsed time: 00:11:57s. Time for last 1,000,000: 1s. Last read position: chr17:50,188,132 INFO 2026-06-08 08:35:30 MarkDuplicates Tracking 242720 as yet unmatched pairs. 73773 records in RAM. INFO 2026-06-08 08:35:32 MarkDuplicates Read 378,000,000 records. Elapsed time: 00:11:59s. Time for last 1,000,000: 1s. Last read position: chr17:50,188,913 INFO 2026-06-08 08:35:32 MarkDuplicates Tracking 244727 as yet unmatched pairs. 75780 records in RAM. INFO 2026-06-08 08:35:34 MarkDuplicates Read 379,000,000 records. Elapsed time: 00:12:01s. Time for last 1,000,000: 1s. Last read position: chr17:50,189,445 INFO 2026-06-08 08:35:34 MarkDuplicates Tracking 237980 as yet unmatched pairs. 69033 records in RAM. INFO 2026-06-08 08:35:35 MarkDuplicates Read 380,000,000 records. Elapsed time: 00:12:03s. Time for last 1,000,000: 1s. Last read position: chr17:50,190,007 INFO 2026-06-08 08:35:35 MarkDuplicates Tracking 233653 as yet unmatched pairs. 64706 records in RAM. INFO 2026-06-08 08:35:38 MarkDuplicates Read 381,000,000 records. Elapsed time: 00:12:06s. Time for last 1,000,000: 2s. Last read position: chr17:50,190,817 INFO 2026-06-08 08:35:38 MarkDuplicates Tracking 228142 as yet unmatched pairs. 59195 records in RAM. INFO 2026-06-08 08:35:40 MarkDuplicates Read 382,000,000 records. Elapsed time: 00:12:08s. Time for last 1,000,000: 1s. Last read position: chr17:50,191,842 INFO 2026-06-08 08:35:40 MarkDuplicates Tracking 230680 as yet unmatched pairs. 61733 records in RAM. INFO 2026-06-08 08:35:42 MarkDuplicates Read 383,000,000 records. Elapsed time: 00:12:09s. Time for last 1,000,000: 1s. Last read position: chr17:50,192,796 INFO 2026-06-08 08:35:42 MarkDuplicates Tracking 228609 as yet unmatched pairs. 59661 records in RAM. INFO 2026-06-08 08:35:44 MarkDuplicates Read 384,000,000 records. Elapsed time: 00:12:11s. Time for last 1,000,000: 1s. Last read position: chr17:50,194,004 INFO 2026-06-08 08:35:44 MarkDuplicates Tracking 226439 as yet unmatched pairs. 57491 records in RAM. INFO 2026-06-08 08:35:45 MarkDuplicates Read 385,000,000 records. Elapsed time: 00:12:13s. Time for last 1,000,000: 1s. Last read position: chr17:50,194,421 INFO 2026-06-08 08:35:45 MarkDuplicates Tracking 224604 as yet unmatched pairs. 55656 records in RAM. INFO 2026-06-08 08:35:47 MarkDuplicates Read 386,000,000 records. Elapsed time: 00:12:14s. Time for last 1,000,000: 1s. Last read position: chr17:50,195,051 INFO 2026-06-08 08:35:47 MarkDuplicates Tracking 222873 as yet unmatched pairs. 53925 records in RAM. INFO 2026-06-08 08:35:49 MarkDuplicates Read 387,000,000 records. Elapsed time: 00:12:16s. Time for last 1,000,000: 1s. Last read position: chr17:50,195,597 INFO 2026-06-08 08:35:49 MarkDuplicates Tracking 223158 as yet unmatched pairs. 54210 records in RAM. INFO 2026-06-08 08:35:50 MarkDuplicates Read 388,000,000 records. Elapsed time: 00:12:18s. Time for last 1,000,000: 1s. Last read position: chr17:50,196,185 INFO 2026-06-08 08:35:50 MarkDuplicates Tracking 224871 as yet unmatched pairs. 55923 records in RAM. INFO 2026-06-08 08:35:52 MarkDuplicates Read 389,000,000 records. Elapsed time: 00:12:20s. Time for last 1,000,000: 1s. Last read position: chr17:50,196,642 INFO 2026-06-08 08:35:52 MarkDuplicates Tracking 215386 as yet unmatched pairs. 46438 records in RAM. INFO 2026-06-08 08:35:54 MarkDuplicates Read 390,000,000 records. Elapsed time: 00:12:21s. Time for last 1,000,000: 1s. Last read position: chr17:50,197,739 INFO 2026-06-08 08:35:54 MarkDuplicates Tracking 220382 as yet unmatched pairs. 51434 records in RAM. INFO 2026-06-08 08:35:56 MarkDuplicates Read 391,000,000 records. Elapsed time: 00:12:23s. Time for last 1,000,000: 1s. Last read position: chr17:50,199,226 INFO 2026-06-08 08:35:56 MarkDuplicates Tracking 203960 as yet unmatched pairs. 35012 records in RAM. INFO 2026-06-08 08:35:57 MarkDuplicates Read 392,000,000 records. Elapsed time: 00:12:25s. Time for last 1,000,000: 1s. Last read position: chr17:50,199,768 INFO 2026-06-08 08:35:57 MarkDuplicates Tracking 202371 as yet unmatched pairs. 33423 records in RAM. INFO 2026-06-08 08:35:59 MarkDuplicates Read 393,000,000 records. Elapsed time: 00:12:26s. Time for last 1,000,000: 1s. Last read position: chr17:50,863,454 INFO 2026-06-08 08:35:59 MarkDuplicates Tracking 194947 as yet unmatched pairs. 25999 records in RAM. INFO 2026-06-08 08:36:01 MarkDuplicates Read 394,000,000 records. Elapsed time: 00:12:28s. Time for last 1,000,000: 1s. Last read position: chr17:59,668,803 INFO 2026-06-08 08:36:01 MarkDuplicates Tracking 193110 as yet unmatched pairs. 24159 records in RAM. INFO 2026-06-08 08:36:03 MarkDuplicates Read 395,000,000 records. Elapsed time: 00:12:30s. Time for last 1,000,000: 1s. Last read position: chr17:62,424,289 INFO 2026-06-08 08:36:03 MarkDuplicates Tracking 190803 as yet unmatched pairs. 21852 records in RAM. INFO 2026-06-08 08:36:05 MarkDuplicates Read 396,000,000 records. Elapsed time: 00:12:33s. Time for last 1,000,000: 2s. Last read position: chr17:64,500,023 INFO 2026-06-08 08:36:05 MarkDuplicates Tracking 188823 as yet unmatched pairs. 19871 records in RAM. INFO 2026-06-08 08:36:07 MarkDuplicates Read 397,000,000 records. Elapsed time: 00:12:34s. Time for last 1,000,000: 1s. Last read position: chr17:68,123,605 INFO 2026-06-08 08:36:07 MarkDuplicates Tracking 186449 as yet unmatched pairs. 17497 records in RAM. INFO 2026-06-08 08:36:09 MarkDuplicates Read 398,000,000 records. Elapsed time: 00:12:36s. Time for last 1,000,000: 1s. Last read position: chr17:74,209,238 INFO 2026-06-08 08:36:09 MarkDuplicates Tracking 184246 as yet unmatched pairs. 15294 records in RAM. INFO 2026-06-08 08:36:10 MarkDuplicates Read 399,000,000 records. Elapsed time: 00:12:37s. Time for last 1,000,000: 1s. Last read position: chr17:75,647,508 INFO 2026-06-08 08:36:10 MarkDuplicates Tracking 181804 as yet unmatched pairs. 12848 records in RAM. INFO 2026-06-08 08:36:12 MarkDuplicates Read 400,000,000 records. Elapsed time: 00:12:39s. Time for last 1,000,000: 1s. Last read position: chr17:78,126,543 INFO 2026-06-08 08:36:12 MarkDuplicates Tracking 179574 as yet unmatched pairs. 10618 records in RAM. INFO 2026-06-08 08:36:13 MarkDuplicates Read 401,000,000 records. Elapsed time: 00:12:41s. Time for last 1,000,000: 1s. Last read position: chr17:80,287,938 INFO 2026-06-08 08:36:13 MarkDuplicates Tracking 177324 as yet unmatched pairs. 8368 records in RAM. INFO 2026-06-08 08:36:15 MarkDuplicates Read 402,000,000 records. Elapsed time: 00:12:42s. Time for last 1,000,000: 1s. Last read position: chr17:81,119,423 INFO 2026-06-08 08:36:15 MarkDuplicates Tracking 174889 as yet unmatched pairs. 5933 records in RAM. INFO 2026-06-08 08:36:17 MarkDuplicates Read 403,000,000 records. Elapsed time: 00:12:44s. Time for last 1,000,000: 1s. Last read position: chr17:81,917,833 INFO 2026-06-08 08:36:17 MarkDuplicates Tracking 172307 as yet unmatched pairs. 3351 records in RAM. INFO 2026-06-08 08:36:18 MarkDuplicates Read 404,000,000 records. Elapsed time: 00:12:45s. Time for last 1,000,000: 1s. Last read position: chr17:82,443,840 INFO 2026-06-08 08:36:18 MarkDuplicates Tracking 169715 as yet unmatched pairs. 758 records in RAM. INFO 2026-06-08 08:36:20 MarkDuplicates Read 405,000,000 records. Elapsed time: 00:12:47s. Time for last 1,000,000: 1s. Last read position: chr18:10,471,835 INFO 2026-06-08 08:36:20 MarkDuplicates Tracking 167446 as yet unmatched pairs. 7225 records in RAM. INFO 2026-06-08 08:36:22 MarkDuplicates Read 406,000,000 records. Elapsed time: 00:12:49s. Time for last 1,000,000: 1s. Last read position: chr18:31,874,606 INFO 2026-06-08 08:36:22 MarkDuplicates Tracking 165444 as yet unmatched pairs. 5221 records in RAM. INFO 2026-06-08 08:36:23 MarkDuplicates Read 407,000,000 records. Elapsed time: 00:12:50s. Time for last 1,000,000: 1s. Last read position: chr18:51,176,642 INFO 2026-06-08 08:36:23 MarkDuplicates Tracking 163390 as yet unmatched pairs. 3166 records in RAM. INFO 2026-06-08 08:36:26 MarkDuplicates Read 408,000,000 records. Elapsed time: 00:12:53s. Time for last 1,000,000: 2s. Last read position: chr18:72,542,029 INFO 2026-06-08 08:36:26 MarkDuplicates Tracking 161150 as yet unmatched pairs. 926 records in RAM. INFO 2026-06-08 08:36:28 MarkDuplicates Read 409,000,000 records. Elapsed time: 00:12:56s. Time for last 1,000,000: 2s. Last read position: chr19:1,145,391 INFO 2026-06-08 08:36:28 MarkDuplicates Tracking 158401 as yet unmatched pairs. 62581 records in RAM. INFO 2026-06-08 08:36:30 MarkDuplicates Read 410,000,000 records. Elapsed time: 00:12:57s. Time for last 1,000,000: 1s. Last read position: chr19:2,732,889 INFO 2026-06-08 08:36:30 MarkDuplicates Tracking 155633 as yet unmatched pairs. 59813 records in RAM. INFO 2026-06-08 08:36:32 MarkDuplicates Read 411,000,000 records. Elapsed time: 00:12:59s. Time for last 1,000,000: 1s. Last read position: chr19:5,211,612 INFO 2026-06-08 08:36:32 MarkDuplicates Tracking 153026 as yet unmatched pairs. 57205 records in RAM. INFO 2026-06-08 08:36:33 MarkDuplicates Read 412,000,000 records. Elapsed time: 00:13:01s. Time for last 1,000,000: 1s. Last read position: chr19:7,645,210 INFO 2026-06-08 08:36:33 MarkDuplicates Tracking 150759 as yet unmatched pairs. 54938 records in RAM. INFO 2026-06-08 08:36:35 MarkDuplicates Read 413,000,000 records. Elapsed time: 00:13:02s. Time for last 1,000,000: 1s. Last read position: chr19:10,180,800 INFO 2026-06-08 08:36:35 MarkDuplicates Tracking 148274 as yet unmatched pairs. 52452 records in RAM. INFO 2026-06-08 08:36:37 MarkDuplicates Read 414,000,000 records. Elapsed time: 00:13:04s. Time for last 1,000,000: 1s. Last read position: chr19:11,438,066 INFO 2026-06-08 08:36:37 MarkDuplicates Tracking 145626 as yet unmatched pairs. 49804 records in RAM. INFO 2026-06-08 08:36:38 MarkDuplicates Read 415,000,000 records. Elapsed time: 00:13:06s. Time for last 1,000,000: 1s. Last read position: chr19:13,153,343 INFO 2026-06-08 08:36:38 MarkDuplicates Tracking 143360 as yet unmatched pairs. 47538 records in RAM. INFO 2026-06-08 08:36:40 MarkDuplicates Read 416,000,000 records. Elapsed time: 00:13:07s. Time for last 1,000,000: 1s. Last read position: chr19:15,185,374 INFO 2026-06-08 08:36:40 MarkDuplicates Tracking 140729 as yet unmatched pairs. 44907 records in RAM. INFO 2026-06-08 08:36:42 MarkDuplicates Read 417,000,000 records. Elapsed time: 00:13:09s. Time for last 1,000,000: 2s. Last read position: chr19:17,101,997 INFO 2026-06-08 08:36:42 MarkDuplicates Tracking 138384 as yet unmatched pairs. 42562 records in RAM. INFO 2026-06-08 08:36:44 MarkDuplicates Read 418,000,000 records. Elapsed time: 00:13:12s. Time for last 1,000,000: 2s. Last read position: chr19:18,396,349 INFO 2026-06-08 08:36:44 MarkDuplicates Tracking 135872 as yet unmatched pairs. 40047 records in RAM. INFO 2026-06-08 08:36:46 MarkDuplicates Read 419,000,000 records. Elapsed time: 00:13:13s. Time for last 1,000,000: 1s. Last read position: chr19:23,359,765 INFO 2026-06-08 08:36:46 MarkDuplicates Tracking 133525 as yet unmatched pairs. 37700 records in RAM. INFO 2026-06-08 08:36:47 MarkDuplicates Read 420,000,000 records. Elapsed time: 00:13:15s. Time for last 1,000,000: 1s. Last read position: chr19:35,270,511 INFO 2026-06-08 08:36:47 MarkDuplicates Tracking 131232 as yet unmatched pairs. 35406 records in RAM. INFO 2026-06-08 08:36:49 MarkDuplicates Read 421,000,000 records. Elapsed time: 00:13:16s. Time for last 1,000,000: 1s. Last read position: chr19:38,291,921 INFO 2026-06-08 08:36:49 MarkDuplicates Tracking 128756 as yet unmatched pairs. 32929 records in RAM. INFO 2026-06-08 08:36:51 MarkDuplicates Read 422,000,000 records. Elapsed time: 00:13:18s. Time for last 1,000,000: 1s. Last read position: chr19:39,474,270 INFO 2026-06-08 08:36:51 MarkDuplicates Tracking 126160 as yet unmatched pairs. 30333 records in RAM. INFO 2026-06-08 08:36:52 MarkDuplicates Read 423,000,000 records. Elapsed time: 00:13:19s. Time for last 1,000,000: 1s. Last read position: chr19:40,213,738 INFO 2026-06-08 08:36:52 MarkDuplicates Tracking 124243 as yet unmatched pairs. 28416 records in RAM. INFO 2026-06-08 08:36:54 MarkDuplicates Read 424,000,000 records. Elapsed time: 00:13:21s. Time for last 1,000,000: 1s. Last read position: chr19:41,709,714 INFO 2026-06-08 08:36:54 MarkDuplicates Tracking 122046 as yet unmatched pairs. 26219 records in RAM. INFO 2026-06-08 08:36:56 MarkDuplicates Read 425,000,000 records. Elapsed time: 00:13:23s. Time for last 1,000,000: 1s. Last read position: chr19:42,292,847 INFO 2026-06-08 08:36:56 MarkDuplicates Tracking 120127 as yet unmatched pairs. 24300 records in RAM. INFO 2026-06-08 08:36:58 MarkDuplicates Read 426,000,000 records. Elapsed time: 00:13:26s. Time for last 1,000,000: 2s. Last read position: chr19:44,909,012 INFO 2026-06-08 08:36:58 MarkDuplicates Tracking 117215 as yet unmatched pairs. 21382 records in RAM. INFO 2026-06-08 08:37:00 MarkDuplicates Read 427,000,000 records. Elapsed time: 00:13:27s. Time for last 1,000,000: 1s. Last read position: chr19:45,785,705 INFO 2026-06-08 08:37:00 MarkDuplicates Tracking 114596 as yet unmatched pairs. 18763 records in RAM. INFO 2026-06-08 08:37:01 MarkDuplicates Read 428,000,000 records. Elapsed time: 00:13:29s. Time for last 1,000,000: 1s. Last read position: chr19:47,694,094 INFO 2026-06-08 08:37:01 MarkDuplicates Tracking 112018 as yet unmatched pairs. 16184 records in RAM. INFO 2026-06-08 08:37:03 MarkDuplicates Read 429,000,000 records. Elapsed time: 00:13:30s. Time for last 1,000,000: 1s. Last read position: chr19:49,148,222 INFO 2026-06-08 08:37:03 MarkDuplicates Tracking 109559 as yet unmatched pairs. 13725 records in RAM. INFO 2026-06-08 08:37:05 MarkDuplicates Read 430,000,000 records. Elapsed time: 00:13:32s. Time for last 1,000,000: 1s. Last read position: chr19:49,781,949 INFO 2026-06-08 08:37:05 MarkDuplicates Tracking 107121 as yet unmatched pairs. 11287 records in RAM. INFO 2026-06-08 08:37:06 MarkDuplicates Read 431,000,000 records. Elapsed time: 00:13:34s. Time for last 1,000,000: 1s. Last read position: chr19:52,705,542 INFO 2026-06-08 08:37:06 MarkDuplicates Tracking 104643 as yet unmatched pairs. 8808 records in RAM. INFO 2026-06-08 08:37:08 MarkDuplicates Read 432,000,000 records. Elapsed time: 00:13:35s. Time for last 1,000,000: 1s. Last read position: chr19:54,633,213 INFO 2026-06-08 08:37:08 MarkDuplicates Tracking 102376 as yet unmatched pairs. 6541 records in RAM. INFO 2026-06-08 08:37:09 MarkDuplicates Read 433,000,000 records. Elapsed time: 00:13:37s. Time for last 1,000,000: 1s. Last read position: chr19:55,659,304 INFO 2026-06-08 08:37:09 MarkDuplicates Tracking 99905 as yet unmatched pairs. 4069 records in RAM. INFO 2026-06-08 08:37:11 MarkDuplicates Read 434,000,000 records. Elapsed time: 00:13:38s. Time for last 1,000,000: 1s. Last read position: chr19:57,849,997 INFO 2026-06-08 08:37:11 MarkDuplicates Tracking 97957 as yet unmatched pairs. 2118 records in RAM. INFO 2026-06-08 08:37:13 MarkDuplicates Read 435,000,000 records. Elapsed time: 00:13:40s. Time for last 1,000,000: 1s. Last read position: chr20:484,003 INFO 2026-06-08 08:37:13 MarkDuplicates Tracking 95584 as yet unmatched pairs. 24209 records in RAM. INFO 2026-06-08 08:37:14 MarkDuplicates Read 436,000,000 records. Elapsed time: 00:13:42s. Time for last 1,000,000: 1s. Last read position: chr20:3,802,057 INFO 2026-06-08 08:37:14 MarkDuplicates Tracking 93131 as yet unmatched pairs. 21755 records in RAM. INFO 2026-06-08 08:37:16 MarkDuplicates Read 437,000,000 records. Elapsed time: 00:13:43s. Time for last 1,000,000: 1s. Last read position: chr20:18,162,665 INFO 2026-06-08 08:37:16 MarkDuplicates Tracking 90966 as yet unmatched pairs. 19590 records in RAM. INFO 2026-06-08 08:37:18 MarkDuplicates Read 438,000,000 records. Elapsed time: 00:13:45s. Time for last 1,000,000: 2s. Last read position: chr20:32,158,450 INFO 2026-06-08 08:37:18 MarkDuplicates Tracking 88835 as yet unmatched pairs. 17457 records in RAM. INFO 2026-06-08 08:37:21 MarkDuplicates Read 439,000,000 records. Elapsed time: 00:13:48s. Time for last 1,000,000: 2s. Last read position: chr20:35,548,815 INFO 2026-06-08 08:37:21 MarkDuplicates Tracking 86789 as yet unmatched pairs. 15410 records in RAM. INFO 2026-06-08 08:37:22 MarkDuplicates Read 440,000,000 records. Elapsed time: 00:13:50s. Time for last 1,000,000: 1s. Last read position: chr20:38,972,612 INFO 2026-06-08 08:37:22 MarkDuplicates Tracking 84226 as yet unmatched pairs. 12846 records in RAM. INFO 2026-06-08 08:37:24 MarkDuplicates Read 441,000,000 records. Elapsed time: 00:13:51s. Time for last 1,000,000: 1s. Last read position: chr20:45,418,897 INFO 2026-06-08 08:37:24 MarkDuplicates Tracking 81986 as yet unmatched pairs. 10605 records in RAM. INFO 2026-06-08 08:37:26 MarkDuplicates Read 442,000,000 records. Elapsed time: 00:13:53s. Time for last 1,000,000: 1s. Last read position: chr20:49,253,718 INFO 2026-06-08 08:37:26 MarkDuplicates Tracking 79602 as yet unmatched pairs. 8221 records in RAM. INFO 2026-06-08 08:37:28 MarkDuplicates Read 443,000,000 records. Elapsed time: 00:13:55s. Time for last 1,000,000: 1s. Last read position: chr20:58,891,846 INFO 2026-06-08 08:37:28 MarkDuplicates Tracking 77687 as yet unmatched pairs. 6305 records in RAM. INFO 2026-06-08 08:37:29 MarkDuplicates Read 444,000,000 records. Elapsed time: 00:13:57s. Time for last 1,000,000: 1s. Last read position: chr20:62,812,734 INFO 2026-06-08 08:37:29 MarkDuplicates Tracking 74576 as yet unmatched pairs. 3194 records in RAM. INFO 2026-06-08 08:37:31 MarkDuplicates Read 445,000,000 records. Elapsed time: 00:13:58s. Time for last 1,000,000: 1s. Last read position: chr20:63,882,763 INFO 2026-06-08 08:37:31 MarkDuplicates Tracking 72006 as yet unmatched pairs. 624 records in RAM. INFO 2026-06-08 08:37:33 MarkDuplicates Read 446,000,000 records. Elapsed time: 00:14:00s. Time for last 1,000,000: 1s. Last read position: chr21:8,257,090 INFO 2026-06-08 08:37:33 MarkDuplicates Tracking 70335 as yet unmatched pairs. 12492 records in RAM. INFO 2026-06-08 08:37:34 MarkDuplicates Read 447,000,000 records. Elapsed time: 00:14:01s. Time for last 1,000,000: 1s. Last read position: chr21:8,442,006 INFO 2026-06-08 08:37:34 MarkDuplicates Tracking 69539 as yet unmatched pairs. 11691 records in RAM. INFO 2026-06-08 08:37:35 MarkDuplicates Read 448,000,000 records. Elapsed time: 00:14:03s. Time for last 1,000,000: 1s. Last read position: chr21:29,776,744 INFO 2026-06-08 08:37:35 MarkDuplicates Tracking 67459 as yet unmatched pairs. 9611 records in RAM. INFO 2026-06-08 08:37:38 MarkDuplicates Read 449,000,000 records. Elapsed time: 00:14:05s. Time for last 1,000,000: 2s. Last read position: chr21:37,069,606 INFO 2026-06-08 08:37:38 MarkDuplicates Tracking 65229 as yet unmatched pairs. 7381 records in RAM. INFO 2026-06-08 08:37:39 MarkDuplicates Read 450,000,000 records. Elapsed time: 00:14:07s. Time for last 1,000,000: 1s. Last read position: chr21:42,315,278 INFO 2026-06-08 08:37:39 MarkDuplicates Tracking 62971 as yet unmatched pairs. 5123 records in RAM. INFO 2026-06-08 08:37:41 MarkDuplicates Read 451,000,000 records. Elapsed time: 00:14:08s. Time for last 1,000,000: 1s. Last read position: chr21:45,981,822 INFO 2026-06-08 08:37:41 MarkDuplicates Tracking 61127 as yet unmatched pairs. 3279 records in RAM. INFO 2026-06-08 08:37:42 MarkDuplicates Read 452,000,000 records. Elapsed time: 00:14:10s. Time for last 1,000,000: 1s. Last read position: chr21:46,411,624 INFO 2026-06-08 08:37:42 MarkDuplicates Tracking 58181 as yet unmatched pairs. 333 records in RAM. INFO 2026-06-08 08:37:44 MarkDuplicates Read 453,000,000 records. Elapsed time: 00:14:12s. Time for last 1,000,000: 1s. Last read position: chr22:20,427,398 INFO 2026-06-08 08:37:44 MarkDuplicates Tracking 55786 as yet unmatched pairs. 25068 records in RAM. INFO 2026-06-08 08:37:46 MarkDuplicates Read 454,000,000 records. Elapsed time: 00:14:13s. Time for last 1,000,000: 1s. Last read position: chr22:23,779,247 INFO 2026-06-08 08:37:46 MarkDuplicates Tracking 53229 as yet unmatched pairs. 22511 records in RAM. INFO 2026-06-08 08:37:47 MarkDuplicates Read 455,000,000 records. Elapsed time: 00:14:15s. Time for last 1,000,000: 1s. Last read position: chr22:28,795,298 INFO 2026-06-08 08:37:47 MarkDuplicates Tracking 52502 as yet unmatched pairs. 21784 records in RAM. INFO 2026-06-08 08:37:49 MarkDuplicates Read 456,000,000 records. Elapsed time: 00:14:16s. Time for last 1,000,000: 1s. Last read position: chr22:29,356,501 INFO 2026-06-08 08:37:49 MarkDuplicates Tracking 48451 as yet unmatched pairs. 17733 records in RAM. INFO 2026-06-08 08:37:51 MarkDuplicates Read 457,000,000 records. Elapsed time: 00:14:18s. Time for last 1,000,000: 1s. Last read position: chr22:35,288,236 INFO 2026-06-08 08:37:51 MarkDuplicates Tracking 46104 as yet unmatched pairs. 15386 records in RAM. INFO 2026-06-08 08:37:52 MarkDuplicates Read 458,000,000 records. Elapsed time: 00:14:20s. Time for last 1,000,000: 1s. Last read position: chr22:36,349,031 INFO 2026-06-08 08:37:52 MarkDuplicates Tracking 43714 as yet unmatched pairs. 12996 records in RAM. INFO 2026-06-08 08:37:54 MarkDuplicates Read 459,000,000 records. Elapsed time: 00:14:21s. Time for last 1,000,000: 1s. Last read position: chr22:38,297,074 INFO 2026-06-08 08:37:54 MarkDuplicates Tracking 41052 as yet unmatched pairs. 10334 records in RAM. INFO 2026-06-08 08:37:55 MarkDuplicates Read 460,000,000 records. Elapsed time: 00:14:23s. Time for last 1,000,000: 1s. Last read position: chr22:40,019,943 INFO 2026-06-08 08:37:55 MarkDuplicates Tracking 38668 as yet unmatched pairs. 7950 records in RAM. INFO 2026-06-08 08:37:57 MarkDuplicates Read 461,000,000 records. Elapsed time: 00:14:24s. Time for last 1,000,000: 1s. Last read position: chr22:42,619,738 INFO 2026-06-08 08:37:57 MarkDuplicates Tracking 36524 as yet unmatched pairs. 5806 records in RAM. INFO 2026-06-08 08:37:58 MarkDuplicates Read 462,000,000 records. Elapsed time: 00:14:26s. Time for last 1,000,000: 1s. Last read position: chr22:46,793,501 INFO 2026-06-08 08:37:58 MarkDuplicates Tracking 33935 as yet unmatched pairs. 3217 records in RAM. INFO 2026-06-08 08:38:00 MarkDuplicates Read 463,000,000 records. Elapsed time: 00:14:27s. Time for last 1,000,000: 1s. Last read position: chr22:50,678,765 INFO 2026-06-08 08:38:00 MarkDuplicates Tracking 30925 as yet unmatched pairs. 207 records in RAM. INFO 2026-06-08 08:38:02 MarkDuplicates Read 464,000,000 records. Elapsed time: 00:14:29s. Time for last 1,000,000: 1s. Last read position: chrX:12,885,511 INFO 2026-06-08 08:38:02 MarkDuplicates Tracking 28698 as yet unmatched pairs. 23113 records in RAM. INFO 2026-06-08 08:38:03 MarkDuplicates Read 465,000,000 records. Elapsed time: 00:14:31s. Time for last 1,000,000: 1s. Last read position: chrX:24,429,527 INFO 2026-06-08 08:38:03 MarkDuplicates Tracking 26596 as yet unmatched pairs. 21002 records in RAM. INFO 2026-06-08 08:38:05 MarkDuplicates Read 466,000,000 records. Elapsed time: 00:14:32s. Time for last 1,000,000: 1s. Last read position: chrX:41,853,190 INFO 2026-06-08 08:38:05 MarkDuplicates Tracking 24594 as yet unmatched pairs. 19000 records in RAM. INFO 2026-06-08 08:38:07 MarkDuplicates Read 467,000,000 records. Elapsed time: 00:14:34s. Time for last 1,000,000: 1s. Last read position: chrX:49,039,320 INFO 2026-06-08 08:38:07 MarkDuplicates Tracking 22459 as yet unmatched pairs. 16863 records in RAM. INFO 2026-06-08 08:38:08 MarkDuplicates Read 468,000,000 records. Elapsed time: 00:14:36s. Time for last 1,000,000: 1s. Last read position: chrX:53,647,472 INFO 2026-06-08 08:38:08 MarkDuplicates Tracking 20121 as yet unmatched pairs. 14525 records in RAM. INFO 2026-06-08 08:38:10 MarkDuplicates Read 469,000,000 records. Elapsed time: 00:14:37s. Time for last 1,000,000: 1s. Last read position: chrX:71,252,760 INFO 2026-06-08 08:38:10 MarkDuplicates Tracking 17729 as yet unmatched pairs. 12133 records in RAM. INFO 2026-06-08 08:38:12 MarkDuplicates Read 470,000,000 records. Elapsed time: 00:14:39s. Time for last 1,000,000: 1s. Last read position: chrX:77,688,763 INFO 2026-06-08 08:38:12 MarkDuplicates Tracking 16102 as yet unmatched pairs. 10506 records in RAM. INFO 2026-06-08 08:38:14 MarkDuplicates Read 471,000,000 records. Elapsed time: 00:14:41s. Time for last 1,000,000: 2s. Last read position: chrX:103,676,949 INFO 2026-06-08 08:38:14 MarkDuplicates Tracking 13827 as yet unmatched pairs. 8231 records in RAM. INFO 2026-06-08 08:38:16 MarkDuplicates Read 472,000,000 records. Elapsed time: 00:14:44s. Time for last 1,000,000: 2s. Last read position: chrX:123,665,700 INFO 2026-06-08 08:38:16 MarkDuplicates Tracking 11479 as yet unmatched pairs. 5883 records in RAM. INFO 2026-06-08 08:38:18 MarkDuplicates Read 473,000,000 records. Elapsed time: 00:14:45s. Time for last 1,000,000: 1s. Last read position: chrX:152,915,183 INFO 2026-06-08 08:38:18 MarkDuplicates Tracking 9393 as yet unmatched pairs. 3797 records in RAM. INFO 2026-06-08 08:38:20 MarkDuplicates Read 474,000,000 records. Elapsed time: 00:14:47s. Time for last 1,000,000: 1s. Last read position: chrX:154,367,698 INFO 2026-06-08 08:38:20 MarkDuplicates Tracking 7202 as yet unmatched pairs. 1606 records in RAM. INFO 2026-06-08 08:38:21 MarkDuplicates Read 475,000,000 records. Elapsed time: 00:14:48s. Time for last 1,000,000: 1s. Last read position: GL000220.1:114,199 INFO 2026-06-08 08:38:21 MarkDuplicates Tracking 5419 as yet unmatched pairs. 1446 records in RAM. INFO 2026-06-08 08:38:22 MarkDuplicates Read 476,000,000 records. Elapsed time: 00:14:49s. Time for last 1,000,000: 1s. Last read position: GL000221.1:79,782 INFO 2026-06-08 08:38:22 MarkDuplicates Tracking 3973 as yet unmatched pairs. 0 records in RAM. INFO 2026-06-08 08:38:23 MarkDuplicates Read 477,000,000 records. Elapsed time: 00:14:51s. Time for last 1,000,000: 1s. Last read position: KI270733.1:177,397 INFO 2026-06-08 08:38:23 MarkDuplicates Tracking 142 as yet unmatched pairs. 72 records in RAM. INFO 2026-06-08 08:38:24 MarkDuplicates Read 477445782 records. 0 pairs never matched. INFO 2026-06-08 08:39:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 40988302344; totalMemory: 58518929408; maxMemory: 63585648640 INFO 2026-06-08 08:39:25 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk. INFO 2026-06-08 08:39:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2026-06-08 08:40:05 OpticalDuplicateFinder Large duplicate set. size = 2220 INFO 2026-06-08 08:40:05 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,537 INFO 2026-06-08 08:40:05 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:17,496 INFO 2026-06-08 08:40:05 OpticalDuplicateFinder Large duplicate set. size = 1119 INFO 2026-06-08 08:40:05 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,941 INFO 2026-06-08 08:40:05 OpticalDuplicateFinder Large duplicate set. size = 1122 INFO 2026-06-08 08:40:05 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,619 INFO 2026-06-08 08:40:13 OpticalDuplicateFinder Large duplicate set. size = 1130 INFO 2026-06-08 08:40:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:15,716 INFO 2026-06-08 08:40:13 OpticalDuplicateFinder Large duplicate set. size = 1003 INFO 2026-06-08 08:40:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:26,370 INFO 2026-06-08 08:40:13 OpticalDuplicateFinder Large duplicate set. size = 1704 INFO 2026-06-08 08:40:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,557 INFO 2026-06-08 08:40:18 OpticalDuplicateFinder Large duplicate set. size = 1017 INFO 2026-06-08 08:40:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,752 INFO 2026-06-08 08:40:39 OpticalDuplicateFinder Large duplicate set. size = 1593 INFO 2026-06-08 08:40:39 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,472 INFO 2026-06-08 08:40:39 OpticalDuplicateFinder Large duplicate set. size = 1307 INFO 2026-06-08 08:40:39 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:31,362 INFO 2026-06-08 08:40:39 OpticalDuplicateFinder Large duplicate set. size = 1237 INFO 2026-06-08 08:40:39 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:1,405 INFO 2026-06-08 08:40:39 OpticalDuplicateFinder Large duplicate set. size = 1281 INFO 2026-06-08 08:40:39 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:4,907 INFO 2026-06-08 08:40:39 OpticalDuplicateFinder Large duplicate set. size = 1004 INFO 2026-06-08 08:40:39 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:4,438 INFO 2026-06-08 08:40:39 OpticalDuplicateFinder Large duplicate set. size = 1408 INFO 2026-06-08 08:40:39 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 08:40:39 OpticalDuplicateFinder Large duplicate set. size = 1262 INFO 2026-06-08 08:40:39 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,519 INFO 2026-06-08 08:40:40 OpticalDuplicateFinder Large duplicate set. size = 1137 INFO 2026-06-08 08:40:40 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,246 INFO 2026-06-08 08:40:40 OpticalDuplicateFinder Large duplicate set. size = 1111 INFO 2026-06-08 08:40:40 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,678 INFO 2026-06-08 08:40:40 OpticalDuplicateFinder Large duplicate set. size = 1231 INFO 2026-06-08 08:40:40 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,145 INFO 2026-06-08 08:40:40 OpticalDuplicateFinder Large duplicate set. size = 1739 INFO 2026-06-08 08:40:40 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:25,197 INFO 2026-06-08 08:40:40 OpticalDuplicateFinder Large duplicate set. size = 1044 INFO 2026-06-08 08:40:40 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,480 INFO 2026-06-08 08:40:40 OpticalDuplicateFinder Large duplicate set. size = 1161 INFO 2026-06-08 08:40:40 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,577 INFO 2026-06-08 08:40:40 OpticalDuplicateFinder Large duplicate set. size = 1089 INFO 2026-06-08 08:40:40 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:1,534 INFO 2026-06-08 08:40:40 OpticalDuplicateFinder Large duplicate set. size = 1490 INFO 2026-06-08 08:40:40 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-25,558 INFO 2026-06-08 08:40:40 OpticalDuplicateFinder Large duplicate set. size = 1127 INFO 2026-06-08 08:40:40 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,988 INFO 2026-06-08 08:40:40 OpticalDuplicateFinder Large duplicate set. size = 1092 INFO 2026-06-08 08:40:40 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:26,848 INFO 2026-06-08 08:40:40 OpticalDuplicateFinder Large duplicate set. size = 1059 INFO 2026-06-08 08:40:40 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:8,095 INFO 2026-06-08 08:40:40 OpticalDuplicateFinder Large duplicate set. size = 1154 INFO 2026-06-08 08:40:40 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-14,427 INFO 2026-06-08 08:40:40 OpticalDuplicateFinder Large duplicate set. size = 1151 INFO 2026-06-08 08:40:40 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,684 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder Large duplicate set. size = 1234 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,361 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder Large duplicate set. size = 1035 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:2,780 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder Large duplicate set. size = 1009 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:5,490 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder Large duplicate set. size = 1023 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:31,702 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder Large duplicate set. size = 1644 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-13,504 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder Large duplicate set. size = 1149 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:31,718 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder Large duplicate set. size = 1011 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,041 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder Large duplicate set. size = 1103 INFO 2026-06-08 08:40:41 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 08:40:41 OpticalDuplicateFinder Large duplicate set. size = 1103 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:1,712 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder Large duplicate set. size = 1067 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,987 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder Large duplicate set. size = 1244 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:23,013 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder Large duplicate set. size = 1032 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,733 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder Large duplicate set. size = 1098 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,737 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder Large duplicate set. size = 1208 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,223 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder Large duplicate set. size = 1533 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,553 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder Large duplicate set. size = 1113 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,983 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder Large duplicate set. size = 1751 INFO 2026-06-08 08:40:41 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,884 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder Large duplicate set. size = 1458 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,354 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder Large duplicate set. size = 1054 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,870 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder Large duplicate set. size = 1030 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,170 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder Large duplicate set. size = 1250 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,084 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder Large duplicate set. size = 1472 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-18,334 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder Large duplicate set. size = 1394 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,447 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder Large duplicate set. size = 1004 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,269 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder Large duplicate set. size = 1492 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:15,449 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder Large duplicate set. size = 1017 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,559 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder Large duplicate set. size = 1070 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:5,919 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder Large duplicate set. size = 1511 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:7,068 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder Large duplicate set. size = 2866 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,757 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,447 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder Large duplicate set. size = 1014 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:25,941 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder Large duplicate set. size = 1728 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,791 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder Large duplicate set. size = 2026 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,127 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,627 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder Large duplicate set. size = 2325 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:14,332 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,661 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder Large duplicate set. size = 1709 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,028 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder Large duplicate set. size = 1145 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,824 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder Large duplicate set. size = 1002 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,370 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder Large duplicate set. size = 1738 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,076 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder Large duplicate set. size = 1020 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:6,339 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder Large duplicate set. size = 1158 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-22,436 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder Large duplicate set. size = 1310 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:23,531 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder Large duplicate set. size = 1075 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:26,443 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder Large duplicate set. size = 1780 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,618 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder Large duplicate set. size = 1009 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,073 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder Large duplicate set. size = 1551 INFO 2026-06-08 08:40:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:2,391 INFO 2026-06-08 08:40:43 OpticalDuplicateFinder Large duplicate set. size = 1538 INFO 2026-06-08 08:40:43 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,201 INFO 2026-06-08 08:41:06 MarkDuplicates Traversing fragment information and detecting duplicates. WARNING 2026-06-08 08:41:06 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered. INFO 2026-06-08 08:41:57 MarkDuplicates Sorting list of duplicate records. INFO 2026-06-08 08:42:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 204595304; totalMemory: 234881024; maxMemory: 63585648640 INFO 2026-06-08 08:42:00 MarkDuplicates Marking 323456479 records as duplicates. INFO 2026-06-08 08:42:00 MarkDuplicates Found 8207043 optical duplicate clusters. INFO 2026-06-08 08:42:00 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2026-06-08 08:42:17 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:16s. Time for last 10,000,000: 16s. Last read position: chr1:42,459,600 INFO 2026-06-08 08:42:32 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:31s. Time for last 10,000,000: 15s. Last read position: chr1:146,142,657 INFO 2026-06-08 08:42:48 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:47s. Time for last 10,000,000: 15s. Last read position: chr1:156,136,965 INFO 2026-06-08 08:43:03 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:02s. Time for last 10,000,000: 15s. Last read position: chr1:204,957,755 INFO 2026-06-08 08:43:18 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:17s. Time for last 10,000,000: 15s. Last read position: chr2:32,401,526 INFO 2026-06-08 08:43:33 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:32s. Time for last 10,000,000: 15s. Last read position: chr2:105,339,645 INFO 2026-06-08 08:43:49 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:01:48s. Time for last 10,000,000: 15s. Last read position: chr2:178,588,104 INFO 2026-06-08 08:44:04 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:03s. Time for last 10,000,000: 15s. Last read position: chr2:215,367,925 INFO 2026-06-08 08:44:19 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:18s. Time for last 10,000,000: 14s. Last read position: chr2:223,901,284 INFO 2026-06-08 08:44:34 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:33s. Time for last 10,000,000: 14s. Last read position: chr3:49,357,420 INFO 2026-06-08 08:44:49 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:02:48s. Time for last 10,000,000: 15s. Last read position: chr3:149,055,339 INFO 2026-06-08 08:45:04 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:03s. Time for last 10,000,000: 15s. Last read position: chr4:67,682,151 INFO 2026-06-08 08:45:19 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:18s. Time for last 10,000,000: 15s. Last read position: chr5:39,721,198 INFO 2026-06-08 08:45:35 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:03:34s. Time for last 10,000,000: 15s. Last read position: chr5:136,033,772 INFO 2026-06-08 08:45:49 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:03:49s. Time for last 10,000,000: 14s. Last read position: chr5:179,774,765 INFO 2026-06-08 08:46:04 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:03s. Time for last 10,000,000: 14s. Last read position: chr6:32,847,944 INFO 2026-06-08 08:46:19 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:04:19s. Time for last 10,000,000: 15s. Last read position: chr6:151,944,506 INFO 2026-06-08 08:46:35 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:04:34s. Time for last 10,000,000: 15s. Last read position: chr7:75,418,772 INFO 2026-06-08 08:46:50 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:04:49s. Time for last 10,000,000: 15s. Last read position: chr7:129,458,288 INFO 2026-06-08 08:47:05 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:05:04s. Time for last 10,000,000: 15s. Last read position: chr8:76,854,602 INFO 2026-06-08 08:47:20 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:05:19s. Time for last 10,000,000: 15s. Last read position: chr8:144,260,249 INFO 2026-06-08 08:47:35 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:05:34s. Time for last 10,000,000: 15s. Last read position: chr9:128,268,138 INFO 2026-06-08 08:47:50 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:05:49s. Time for last 10,000,000: 14s. Last read position: chr10:46,358,176 INFO 2026-06-08 08:48:05 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:06:04s. Time for last 10,000,000: 15s. Last read position: chr11:554,935 INFO 2026-06-08 08:48:20 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:06:19s. Time for last 10,000,000: 14s. Last read position: chr11:62,527,941 INFO 2026-06-08 08:48:35 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:06:35s. Time for last 10,000,000: 15s. Last read position: chr11:77,921,347 INFO 2026-06-08 08:48:51 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:06:50s. Time for last 10,000,000: 15s. Last read position: chr12:26,486,211 INFO 2026-06-08 08:49:06 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:07:05s. Time for last 10,000,000: 14s. Last read position: chr12:53,459,381 INFO 2026-06-08 08:49:20 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:07:20s. Time for last 10,000,000: 14s. Last read position: chr12:112,043,726 INFO 2026-06-08 08:49:36 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:07:35s. Time for last 10,000,000: 15s. Last read position: chr13:113,820,604 INFO 2026-06-08 08:49:51 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:07:50s. Time for last 10,000,000: 15s. Last read position: chr14:93,115,082 INFO 2026-06-08 08:50:06 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:08:05s. Time for last 10,000,000: 14s. Last read position: chr15:59,058,439 INFO 2026-06-08 08:50:21 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:08:20s. Time for last 10,000,000: 14s. Last read position: chr16:2,775,455 INFO 2026-06-08 08:50:36 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:08:35s. Time for last 10,000,000: 14s. Last read position: chr16:21,851,795 INFO 2026-06-08 08:50:51 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:08:50s. Time for last 10,000,000: 14s. Last read position: chr16:67,877,216 INFO 2026-06-08 08:51:05 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:09:04s. Time for last 10,000,000: 14s. Last read position: chr17:28,749,058 INFO 2026-06-08 08:51:20 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:09:19s. Time for last 10,000,000: 14s. Last read position: chr17:42,854,591 INFO 2026-06-08 08:51:35 MarkDuplicates Written 380,000,000 records. Elapsed time: 00:09:34s. Time for last 10,000,000: 14s. Last read position: chr17:50,190,007 INFO 2026-06-08 08:51:49 MarkDuplicates Written 390,000,000 records. Elapsed time: 00:09:49s. Time for last 10,000,000: 14s. Last read position: chr17:50,197,739 INFO 2026-06-08 08:52:04 MarkDuplicates Written 400,000,000 records. Elapsed time: 00:10:03s. Time for last 10,000,000: 14s. Last read position: chr17:78,126,543 INFO 2026-06-08 08:52:19 MarkDuplicates Written 410,000,000 records. Elapsed time: 00:10:18s. Time for last 10,000,000: 14s. Last read position: chr19:2,732,889 INFO 2026-06-08 08:52:34 MarkDuplicates Written 420,000,000 records. Elapsed time: 00:10:33s. Time for last 10,000,000: 14s. Last read position: chr19:35,270,511 INFO 2026-06-08 08:52:48 MarkDuplicates Written 430,000,000 records. Elapsed time: 00:10:47s. Time for last 10,000,000: 14s. Last read position: chr19:49,781,949 INFO 2026-06-08 08:53:03 MarkDuplicates Written 440,000,000 records. Elapsed time: 00:11:02s. Time for last 10,000,000: 14s. Last read position: chr20:38,972,612 INFO 2026-06-08 08:53:18 MarkDuplicates Written 450,000,000 records. Elapsed time: 00:11:17s. Time for last 10,000,000: 14s. Last read position: chr21:42,315,278 INFO 2026-06-08 08:53:32 MarkDuplicates Written 460,000,000 records. Elapsed time: 00:11:31s. Time for last 10,000,000: 14s. Last read position: chr22:40,019,943 INFO 2026-06-08 08:53:47 MarkDuplicates Written 470,000,000 records. Elapsed time: 00:11:46s. Time for last 10,000,000: 14s. Last read position: chrX:77,688,763 INFO 2026-06-08 08:54:04 MarkDuplicates Written 480,000,000 records. Elapsed time: 00:12:03s. Time for last 10,000,000: 16s. Last read position: */* INFO 2026-06-08 08:54:05 MarkDuplicates Writing complete. Closing input iterator. INFO 2026-06-08 08:54:05 MarkDuplicates Duplicate Index cleanup. INFO 2026-06-08 08:54:05 MarkDuplicates Getting Memory Stats. INFO 2026-06-08 08:54:05 MarkDuplicates Before output close freeMemory: 204593336; totalMemory: 234881024; maxMemory: 63585648640 INFO 2026-06-08 08:54:05 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2026-06-08 08:54:05 MarkDuplicates After output close freeMemory: 104813656; totalMemory: 134217728; maxMemory: 63585648640 [Mon Jun 08 08:54:05 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 30.57 minutes. Runtime.totalMemory()=134217728 ls: *cram: No such file or directory ls: *.crai: No such file or directory