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_01_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_2.md.bam --METRICS_FILE BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_2.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT 08:34:28.231 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 08:34:28 GMT 2026] MarkDuplicates --INPUT BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_2.md.bam --METRICS_FILE BVT_FFPE_TRNA_bst_01_01_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 08:34:28 GMT 2026] Executing as ?@nf-35043b795802482128169ffafa05b5b6-1135b-dqs2p 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 08:34:28 MarkDuplicates Start of doWork freeMemory: 105828672; totalMemory: 134217728; maxMemory: 63585648640 INFO 2026-06-08 08:34:28 MarkDuplicates Reading input file and constructing read end information. INFO 2026-06-08 08:34:28 MarkDuplicates Will retain up to 230382784 data points before spilling to disk. INFO 2026-06-08 08:34:32 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:2,402,069 INFO 2026-06-08 08:34:32 MarkDuplicates Tracking 2669 as yet unmatched pairs. 119 records in RAM. INFO 2026-06-08 08:34:33 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: chr1:10,639,495 INFO 2026-06-08 08:34:33 MarkDuplicates Tracking 4863 as yet unmatched pairs. 25 records in RAM. INFO 2026-06-08 08:34:36 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: chr1:16,393,412 INFO 2026-06-08 08:34:36 MarkDuplicates Tracking 7337 as yet unmatched pairs. 134 records in RAM. INFO 2026-06-08 08:34:37 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: chr1:21,823,277 INFO 2026-06-08 08:34:37 MarkDuplicates Tracking 9445 as yet unmatched pairs. 98 records in RAM. INFO 2026-06-08 08:34:39 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 2s. Last read position: chr1:23,069,072 INFO 2026-06-08 08:34:39 MarkDuplicates Tracking 11847 as yet unmatched pairs. 99 records in RAM. INFO 2026-06-08 08:34:41 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: chr1:27,334,188 INFO 2026-06-08 08:34:41 MarkDuplicates Tracking 13938 as yet unmatched pairs. 51 records in RAM. INFO 2026-06-08 08:34:43 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: chr1:31,918,974 INFO 2026-06-08 08:34:43 MarkDuplicates Tracking 16716 as yet unmatched pairs. 442 records in RAM. INFO 2026-06-08 08:34:46 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr1:36,287,192 INFO 2026-06-08 08:34:46 MarkDuplicates Tracking 18593 as yet unmatched pairs. 71 records in RAM. INFO 2026-06-08 08:34:48 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: chr1:40,416,184 INFO 2026-06-08 08:34:48 MarkDuplicates Tracking 20643 as yet unmatched pairs. 11 records in RAM. INFO 2026-06-08 08:34:50 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 2s. Last read position: chr1:45,511,379 INFO 2026-06-08 08:34:50 MarkDuplicates Tracking 23020 as yet unmatched pairs. 122 records in RAM. INFO 2026-06-08 08:34:51 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: chr1:54,216,186 INFO 2026-06-08 08:34:51 MarkDuplicates Tracking 25211 as yet unmatched pairs. 27 records in RAM. INFO 2026-06-08 08:34:53 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 1s. Last read position: chr1:77,810,848 INFO 2026-06-08 08:34:53 MarkDuplicates Tracking 27184 as yet unmatched pairs. 18 records in RAM. INFO 2026-06-08 08:34:55 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 2s. Last read position: chr1:99,742,200 INFO 2026-06-08 08:34:55 MarkDuplicates Tracking 29183 as yet unmatched pairs. 28 records in RAM. INFO 2026-06-08 08:34:57 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 1s. Last read position: chr1:109,923,583 INFO 2026-06-08 08:34:57 MarkDuplicates Tracking 31490 as yet unmatched pairs. 210 records in RAM. INFO 2026-06-08 08:34:59 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 2s. Last read position: chr1:114,718,616 INFO 2026-06-08 08:34:59 MarkDuplicates Tracking 33652 as yet unmatched pairs. 177 records in RAM. INFO 2026-06-08 08:35:02 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 2s. Last read position: chr1:119,922,747 INFO 2026-06-08 08:35:02 MarkDuplicates Tracking 35847 as yet unmatched pairs. 202 records in RAM. INFO 2026-06-08 08:35:03 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 1s. Last read position: chr1:120,530,340 INFO 2026-06-08 08:35:03 MarkDuplicates Tracking 37715 as yet unmatched pairs. 58 records in RAM. INFO 2026-06-08 08:35:05 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 1s. Last read position: chr1:146,073,499 INFO 2026-06-08 08:35:05 MarkDuplicates Tracking 38970 as yet unmatched pairs. 63 records in RAM. INFO 2026-06-08 08:35:07 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 1s. Last read position: chr1:148,535,462 INFO 2026-06-08 08:35:07 MarkDuplicates Tracking 40112 as yet unmatched pairs. 293 records in RAM. INFO 2026-06-08 08:35:08 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 1s. Last read position: chr1:149,463,915 INFO 2026-06-08 08:35:08 MarkDuplicates Tracking 40630 as yet unmatched pairs. 25 records in RAM. INFO 2026-06-08 08:35:10 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 2s. Last read position: chr1:150,325,068 INFO 2026-06-08 08:35:10 MarkDuplicates Tracking 42142 as yet unmatched pairs. 20 records in RAM. INFO 2026-06-08 08:35:12 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 1s. Last read position: chr1:151,239,920 INFO 2026-06-08 08:35:12 MarkDuplicates Tracking 44550 as yet unmatched pairs. 171 records in RAM. INFO 2026-06-08 08:35:14 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 1s. Last read position: chr1:153,664,042 INFO 2026-06-08 08:35:14 MarkDuplicates Tracking 46860 as yet unmatched pairs. 185 records in RAM. INFO 2026-06-08 08:35:16 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 1s. Last read position: chr1:154,241,545 INFO 2026-06-08 08:35:16 MarkDuplicates Tracking 48602 as yet unmatched pairs. 101 records in RAM. INFO 2026-06-08 08:35:17 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 1s. Last read position: chr1:155,063,808 INFO 2026-06-08 08:35:17 MarkDuplicates Tracking 50741 as yet unmatched pairs. 63 records in RAM. INFO 2026-06-08 08:35:19 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 1s. Last read position: chr1:155,201,474 INFO 2026-06-08 08:35:19 MarkDuplicates Tracking 52610 as yet unmatched pairs. 101 records in RAM. INFO 2026-06-08 08:35:20 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 1s. Last read position: chr1:155,925,744 INFO 2026-06-08 08:35:20 MarkDuplicates Tracking 54617 as yet unmatched pairs. 110 records in RAM. INFO 2026-06-08 08:35:22 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 2s. Last read position: chr1:156,592,100 INFO 2026-06-08 08:35:22 MarkDuplicates Tracking 56817 as yet unmatched pairs. 49 records in RAM. INFO 2026-06-08 08:35:24 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 1s. Last read position: chr1:160,305,677 INFO 2026-06-08 08:35:24 MarkDuplicates Tracking 59159 as yet unmatched pairs. 125 records in RAM. INFO 2026-06-08 08:35:25 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 1s. Last read position: chr1:161,542,655 INFO 2026-06-08 08:35:25 MarkDuplicates Tracking 63139 as yet unmatched pairs. 1946 records in RAM. INFO 2026-06-08 08:35:28 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 2s. Last read position: chr1:166,841,045 INFO 2026-06-08 08:35:28 MarkDuplicates Tracking 63482 as yet unmatched pairs. 90 records in RAM. INFO 2026-06-08 08:35:30 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 2s. Last read position: chr1:171,541,958 INFO 2026-06-08 08:35:30 MarkDuplicates Tracking 65760 as yet unmatched pairs. 133 records in RAM. INFO 2026-06-08 08:35:32 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 1s. Last read position: chr1:180,020,127 INFO 2026-06-08 08:35:32 MarkDuplicates Tracking 67652 as yet unmatched pairs. 51 records in RAM. INFO 2026-06-08 08:35:34 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 1s. Last read position: chr1:184,054,835 INFO 2026-06-08 08:35:34 MarkDuplicates Tracking 70150 as yet unmatched pairs. 355 records in RAM. INFO 2026-06-08 08:35:36 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 2s. Last read position: chr1:193,138,095 INFO 2026-06-08 08:35:36 MarkDuplicates Tracking 71718 as yet unmatched pairs. 97 records in RAM. INFO 2026-06-08 08:35:37 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 1s. Last read position: chr1:202,943,781 INFO 2026-06-08 08:35:37 MarkDuplicates Tracking 74214 as yet unmatched pairs. 351 records in RAM. INFO 2026-06-08 08:35:39 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 1s. Last read position: chr1:205,620,429 INFO 2026-06-08 08:35:39 MarkDuplicates Tracking 76148 as yet unmatched pairs. 223 records in RAM. INFO 2026-06-08 08:35:40 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 1s. Last read position: chr1:212,444,349 INFO 2026-06-08 08:35:40 MarkDuplicates Tracking 78281 as yet unmatched pairs. 281 records in RAM. INFO 2026-06-08 08:35:42 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 1s. Last read position: chr1:221,739,408 INFO 2026-06-08 08:35:42 MarkDuplicates Tracking 80108 as yet unmatched pairs. 66 records in RAM. INFO 2026-06-08 08:35:44 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 1s. Last read position: chr1:225,652,694 INFO 2026-06-08 08:35:44 MarkDuplicates Tracking 82334 as yet unmatched pairs. 120 records in RAM. INFO 2026-06-08 08:35:45 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 1s. Last read position: chr1:228,294,251 INFO 2026-06-08 08:35:45 MarkDuplicates Tracking 84465 as yet unmatched pairs. 67 records in RAM. INFO 2026-06-08 08:35:47 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 1s. Last read position: chr1:234,607,760 INFO 2026-06-08 08:35:47 MarkDuplicates Tracking 86969 as yet unmatched pairs. 189 records in RAM. INFO 2026-06-08 08:35:49 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 1s. Last read position: chr1:244,855,426 INFO 2026-06-08 08:35:49 MarkDuplicates Tracking 89157 as yet unmatched pairs. 398 records in RAM. INFO 2026-06-08 08:35:51 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 2s. Last read position: chr2:9,327,837 INFO 2026-06-08 08:35:51 MarkDuplicates Tracking 91166 as yet unmatched pairs. 91056 records in RAM. INFO 2026-06-08 08:35:53 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 1s. Last read position: chr2:24,741,877 INFO 2026-06-08 08:35:53 MarkDuplicates Tracking 93380 as yet unmatched pairs. 93267 records in RAM. INFO 2026-06-08 08:35:54 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 1s. Last read position: chr2:30,475,007 INFO 2026-06-08 08:35:54 MarkDuplicates Tracking 95642 as yet unmatched pairs. 95527 records in RAM. INFO 2026-06-08 08:35:56 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,264 INFO 2026-06-08 08:35:56 MarkDuplicates Tracking 358647 as yet unmatched pairs. 89496 records in RAM. INFO 2026-06-08 08:35:58 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,406 INFO 2026-06-08 08:35:58 MarkDuplicates Tracking 797346 as yet unmatched pairs. 78797 records in RAM. INFO 2026-06-08 08:35:59 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 1s. Last read position: chr2:36,966,363 INFO 2026-06-08 08:35:59 MarkDuplicates Tracking 846713 as yet unmatched pairs. 77236 records in RAM. INFO 2026-06-08 08:36:01 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 1s. Last read position: chr2:47,162,287 INFO 2026-06-08 08:36:01 MarkDuplicates Tracking 845251 as yet unmatched pairs. 75771 records in RAM. INFO 2026-06-08 08:36:03 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 1s. Last read position: chr2:58,802,753 INFO 2026-06-08 08:36:03 MarkDuplicates Tracking 842437 as yet unmatched pairs. 72948 records in RAM. INFO 2026-06-08 08:36:04 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 1s. Last read position: chr2:70,277,257 INFO 2026-06-08 08:36:04 MarkDuplicates Tracking 840163 as yet unmatched pairs. 70673 records in RAM. INFO 2026-06-08 08:36:06 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 1s. Last read position: chr2:85,394,876 INFO 2026-06-08 08:36:06 MarkDuplicates Tracking 838175 as yet unmatched pairs. 68683 records in RAM. INFO 2026-06-08 08:36:08 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 1s. Last read position: chr2:96,253,820 INFO 2026-06-08 08:36:08 MarkDuplicates Tracking 836414 as yet unmatched pairs. 66920 records in RAM. INFO 2026-06-08 08:36:09 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 1s. Last read position: chr2:99,727,091 INFO 2026-06-08 08:36:09 MarkDuplicates Tracking 834173 as yet unmatched pairs. 64677 records in RAM. INFO 2026-06-08 08:36:12 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 3s. Last read position: chr2:108,766,728 INFO 2026-06-08 08:36:12 MarkDuplicates Tracking 832078 as yet unmatched pairs. 62581 records in RAM. INFO 2026-06-08 08:36:15 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 2s. Last read position: chr2:112,662,864 INFO 2026-06-08 08:36:15 MarkDuplicates Tracking 830974 as yet unmatched pairs. 61476 records in RAM. INFO 2026-06-08 08:36:16 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 1s. Last read position: chr2:130,339,143 INFO 2026-06-08 08:36:16 MarkDuplicates Tracking 828956 as yet unmatched pairs. 59455 records in RAM. INFO 2026-06-08 08:36:18 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 1s. Last read position: chr2:145,341,894 INFO 2026-06-08 08:36:18 MarkDuplicates Tracking 827084 as yet unmatched pairs. 57581 records in RAM. INFO 2026-06-08 08:36:19 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 1s. Last read position: chr2:151,655,920 INFO 2026-06-08 08:36:19 MarkDuplicates Tracking 825628 as yet unmatched pairs. 56125 records in RAM. INFO 2026-06-08 08:36:21 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 1s. Last read position: chr2:167,248,192 INFO 2026-06-08 08:36:21 MarkDuplicates Tracking 823608 as yet unmatched pairs. 54104 records in RAM. INFO 2026-06-08 08:36:23 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 1s. Last read position: chr2:177,219,082 INFO 2026-06-08 08:36:23 MarkDuplicates Tracking 821790 as yet unmatched pairs. 52284 records in RAM. INFO 2026-06-08 08:36:24 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 1s. Last read position: chr2:178,549,774 INFO 2026-06-08 08:36:24 MarkDuplicates Tracking 819819 as yet unmatched pairs. 50312 records in RAM. INFO 2026-06-08 08:36:26 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 1s. Last read position: chr2:178,576,277 INFO 2026-06-08 08:36:26 MarkDuplicates Tracking 817635 as yet unmatched pairs. 48128 records in RAM. INFO 2026-06-08 08:36:27 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 1s. Last read position: chr2:178,609,542 INFO 2026-06-08 08:36:27 MarkDuplicates Tracking 815672 as yet unmatched pairs. 46163 records in RAM. INFO 2026-06-08 08:36:29 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 1s. Last read position: chr2:178,672,101 INFO 2026-06-08 08:36:29 MarkDuplicates Tracking 814105 as yet unmatched pairs. 44596 records in RAM. INFO 2026-06-08 08:36:31 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 1s. Last read position: chr2:178,733,098 INFO 2026-06-08 08:36:31 MarkDuplicates Tracking 812141 as yet unmatched pairs. 42632 records in RAM. INFO 2026-06-08 08:36:32 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 1s. Last read position: chr2:182,930,751 INFO 2026-06-08 08:36:32 MarkDuplicates Tracking 810085 as yet unmatched pairs. 40576 records in RAM. INFO 2026-06-08 08:36:34 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 1s. Last read position: chr2:188,997,202 INFO 2026-06-08 08:36:34 MarkDuplicates Tracking 808403 as yet unmatched pairs. 38894 records in RAM. INFO 2026-06-08 08:36:36 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 1s. Last read position: chr2:189,034,122 INFO 2026-06-08 08:36:36 MarkDuplicates Tracking 805199 as yet unmatched pairs. 35688 records in RAM. INFO 2026-06-08 08:36:37 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 1s. Last read position: chr2:197,423,807 INFO 2026-06-08 08:36:37 MarkDuplicates Tracking 802709 as yet unmatched pairs. 33198 records in RAM. INFO 2026-06-08 08:36:39 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 1s. Last read position: chr2:207,555,649 INFO 2026-06-08 08:36:39 MarkDuplicates Tracking 800745 as yet unmatched pairs. 31232 records in RAM. INFO 2026-06-08 08:36:41 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 1s. Last read position: chr2:215,365,507 INFO 2026-06-08 08:36:41 MarkDuplicates Tracking 802115 as yet unmatched pairs. 32601 records in RAM. INFO 2026-06-08 08:36:42 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 1s. Last read position: chr2:215,372,166 INFO 2026-06-08 08:36:42 MarkDuplicates Tracking 806758 as yet unmatched pairs. 37243 records in RAM. INFO 2026-06-08 08:36:44 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 1s. Last read position: chr2:215,376,496 INFO 2026-06-08 08:36:44 MarkDuplicates Tracking 798652 as yet unmatched pairs. 29137 records in RAM. INFO 2026-06-08 08:36:46 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 1s. Last read position: chr2:215,382,213 INFO 2026-06-08 08:36:46 MarkDuplicates Tracking 797366 as yet unmatched pairs. 27851 records in RAM. INFO 2026-06-08 08:36:47 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 1s. Last read position: chr2:215,388,244 INFO 2026-06-08 08:36:47 MarkDuplicates Tracking 798354 as yet unmatched pairs. 28839 records in RAM. INFO 2026-06-08 08:36:49 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 1s. Last read position: chr2:215,399,293 INFO 2026-06-08 08:36:49 MarkDuplicates Tracking 791124 as yet unmatched pairs. 21607 records in RAM. INFO 2026-06-08 08:36:50 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 1s. Last read position: chr2:215,408,173 INFO 2026-06-08 08:36:50 MarkDuplicates Tracking 790712 as yet unmatched pairs. 21195 records in RAM. INFO 2026-06-08 08:36:53 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 2s. Last read position: chr2:215,419,320 INFO 2026-06-08 08:36:53 MarkDuplicates Tracking 785529 as yet unmatched pairs. 16012 records in RAM. INFO 2026-06-08 08:36:54 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 1s. Last read position: chr2:215,428,286 INFO 2026-06-08 08:36:54 MarkDuplicates Tracking 785514 as yet unmatched pairs. 15997 records in RAM. INFO 2026-06-08 08:36:56 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 1s. Last read position: chr2:216,501,342 INFO 2026-06-08 08:36:56 MarkDuplicates Tracking 780147 as yet unmatched pairs. 10629 records in RAM. INFO 2026-06-08 08:36:58 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 2s. Last read position: chr2:219,559,355 INFO 2026-06-08 08:36:58 MarkDuplicates Tracking 777716 as yet unmatched pairs. 8195 records in RAM. INFO 2026-06-08 08:37:00 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 1s. Last read position: chr2:231,794,276 INFO 2026-06-08 08:37:00 MarkDuplicates Tracking 775565 as yet unmatched pairs. 6039 records in RAM. INFO 2026-06-08 08:37:02 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 1s. Last read position: chr2:237,371,790 INFO 2026-06-08 08:37:02 MarkDuplicates Tracking 773791 as yet unmatched pairs. 4262 records in RAM. INFO 2026-06-08 08:37:03 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 1s. Last read position: chr2:241,142,881 INFO 2026-06-08 08:37:03 MarkDuplicates Tracking 770676 as yet unmatched pairs. 1144 records in RAM. INFO 2026-06-08 08:37:05 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 2s. Last read position: chr3:9,825,924 INFO 2026-06-08 08:37:05 MarkDuplicates Tracking 768533 as yet unmatched pairs. 42938 records in RAM. INFO 2026-06-08 08:37:07 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 1s. Last read position: chr3:15,078,081 INFO 2026-06-08 08:37:07 MarkDuplicates Tracking 766253 as yet unmatched pairs. 40656 records in RAM. INFO 2026-06-08 08:37:09 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 1s. Last read position: chr3:36,892,300 INFO 2026-06-08 08:37:09 MarkDuplicates Tracking 764299 as yet unmatched pairs. 38696 records in RAM. INFO 2026-06-08 08:37:10 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 1s. Last read position: chr3:42,620,037 INFO 2026-06-08 08:37:10 MarkDuplicates Tracking 762211 as yet unmatched pairs. 36607 records in RAM. INFO 2026-06-08 08:37:12 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 1s. Last read position: chr3:47,827,388 INFO 2026-06-08 08:37:12 MarkDuplicates Tracking 759702 as yet unmatched pairs. 34097 records in RAM. INFO 2026-06-08 08:37:13 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 1s. Last read position: chr3:49,101,420 INFO 2026-06-08 08:37:13 MarkDuplicates Tracking 757404 as yet unmatched pairs. 31799 records in RAM. INFO 2026-06-08 08:37:15 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 1s. Last read position: chr3:50,057,973 INFO 2026-06-08 08:37:15 MarkDuplicates Tracking 754968 as yet unmatched pairs. 29350 records in RAM. INFO 2026-06-08 08:37:16 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 1s. Last read position: chr3:52,509,964 INFO 2026-06-08 08:37:16 MarkDuplicates Tracking 752765 as yet unmatched pairs. 27140 records in RAM. INFO 2026-06-08 08:37:18 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 1s. Last read position: chr3:58,106,772 INFO 2026-06-08 08:37:18 MarkDuplicates Tracking 750584 as yet unmatched pairs. 24955 records in RAM. INFO 2026-06-08 08:37:20 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 1s. Last read position: chr3:73,404,185 INFO 2026-06-08 08:37:20 MarkDuplicates Tracking 748336 as yet unmatched pairs. 22705 records in RAM. INFO 2026-06-08 08:37:21 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 1s. Last read position: chr3:105,524,289 INFO 2026-06-08 08:37:21 MarkDuplicates Tracking 746420 as yet unmatched pairs. 20781 records in RAM. INFO 2026-06-08 08:37:23 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 1s. Last read position: chr3:121,483,449 INFO 2026-06-08 08:37:23 MarkDuplicates Tracking 744427 as yet unmatched pairs. 18784 records in RAM. INFO 2026-06-08 08:37:24 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 1s. Last read position: chr3:125,323,386 INFO 2026-06-08 08:37:24 MarkDuplicates Tracking 742373 as yet unmatched pairs. 16730 records in RAM. INFO 2026-06-08 08:37:26 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 1s. Last read position: chr3:129,561,670 INFO 2026-06-08 08:37:26 MarkDuplicates Tracking 740275 as yet unmatched pairs. 14624 records in RAM. INFO 2026-06-08 08:37:28 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 1s. Last read position: chr3:138,264,179 INFO 2026-06-08 08:37:28 MarkDuplicates Tracking 737970 as yet unmatched pairs. 12312 records in RAM. INFO 2026-06-08 08:37:30 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 1s. Last read position: chr3:150,546,059 INFO 2026-06-08 08:37:30 MarkDuplicates Tracking 736077 as yet unmatched pairs. 10400 records in RAM. INFO 2026-06-08 08:37:32 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 2s. Last read position: chr3:170,129,474 INFO 2026-06-08 08:37:32 MarkDuplicates Tracking 734211 as yet unmatched pairs. 8533 records in RAM. INFO 2026-06-08 08:37:34 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 2s. Last read position: chr3:183,927,411 INFO 2026-06-08 08:37:34 MarkDuplicates Tracking 732258 as yet unmatched pairs. 6572 records in RAM. INFO 2026-06-08 08:37:36 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 1s. Last read position: chr3:184,386,559 INFO 2026-06-08 08:37:36 MarkDuplicates Tracking 730044 as yet unmatched pairs. 4357 records in RAM. INFO 2026-06-08 08:37:37 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 1s. Last read position: chr3:195,324,659 INFO 2026-06-08 08:37:37 MarkDuplicates Tracking 727540 as yet unmatched pairs. 1853 records in RAM. INFO 2026-06-08 08:37:39 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 1s. Last read position: chr4:850,954 INFO 2026-06-08 08:37:39 MarkDuplicates Tracking 725486 as yet unmatched pairs. 22331 records in RAM. INFO 2026-06-08 08:37:41 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 1s. Last read position: chr4:2,928,197 INFO 2026-06-08 08:37:41 MarkDuplicates Tracking 723301 as yet unmatched pairs. 20144 records in RAM. INFO 2026-06-08 08:37:42 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 1s. Last read position: chr4:11,372,306 INFO 2026-06-08 08:37:42 MarkDuplicates Tracking 720838 as yet unmatched pairs. 17681 records in RAM. INFO 2026-06-08 08:37:44 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 1s. Last read position: chr4:39,898,389 INFO 2026-06-08 08:37:44 MarkDuplicates Tracking 718894 as yet unmatched pairs. 15734 records in RAM. INFO 2026-06-08 08:37:45 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 1s. Last read position: chr4:68,316,327 INFO 2026-06-08 08:37:45 MarkDuplicates Tracking 716611 as yet unmatched pairs. 13448 records in RAM. INFO 2026-06-08 08:37:47 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 1s. Last read position: chr4:82,428,054 INFO 2026-06-08 08:37:47 MarkDuplicates Tracking 714471 as yet unmatched pairs. 11307 records in RAM. INFO 2026-06-08 08:37:48 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 1s. Last read position: chr4:98,261,502 INFO 2026-06-08 08:37:48 MarkDuplicates Tracking 712645 as yet unmatched pairs. 9477 records in RAM. INFO 2026-06-08 08:37:50 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 1s. Last read position: chr4:121,810,012 INFO 2026-06-08 08:37:50 MarkDuplicates Tracking 710409 as yet unmatched pairs. 7230 records in RAM. INFO 2026-06-08 08:37:52 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: chr4:142,208,518 INFO 2026-06-08 08:37:52 MarkDuplicates Tracking 708309 as yet unmatched pairs. 5130 records in RAM. INFO 2026-06-08 08:37:54 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 1s. Last read position: chr4:156,837,627 INFO 2026-06-08 08:37:54 MarkDuplicates Tracking 706384 as yet unmatched pairs. 3202 records in RAM. INFO 2026-06-08 08:37:55 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 1s. Last read position: chr4:173,248,315 INFO 2026-06-08 08:37:55 MarkDuplicates Tracking 704267 as yet unmatched pairs. 1084 records in RAM. INFO 2026-06-08 08:37:57 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 1s. Last read position: chr5:6,749,604 INFO 2026-06-08 08:37:57 MarkDuplicates Tracking 702117 as yet unmatched pairs. 47844 records in RAM. INFO 2026-06-08 08:37:59 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 1s. Last read position: chr5:14,485,155 INFO 2026-06-08 08:37:59 MarkDuplicates Tracking 699833 as yet unmatched pairs. 45560 records in RAM. INFO 2026-06-08 08:38:00 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 1s. Last read position: chr5:36,984,671 INFO 2026-06-08 08:38:00 MarkDuplicates Tracking 697651 as yet unmatched pairs. 43371 records in RAM. INFO 2026-06-08 08:38:02 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 1s. Last read position: chr5:54,519,434 INFO 2026-06-08 08:38:02 MarkDuplicates Tracking 695645 as yet unmatched pairs. 41360 records in RAM. INFO 2026-06-08 08:38:03 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 1s. Last read position: chr5:67,163,253 INFO 2026-06-08 08:38:03 MarkDuplicates Tracking 693774 as yet unmatched pairs. 39489 records in RAM. INFO 2026-06-08 08:38:05 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 1s. Last read position: chr5:70,795,788 INFO 2026-06-08 08:38:05 MarkDuplicates Tracking 692622 as yet unmatched pairs. 38337 records in RAM. INFO 2026-06-08 08:38:06 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 1s. Last read position: chr5:74,840,148 INFO 2026-06-08 08:38:06 MarkDuplicates Tracking 691236 as yet unmatched pairs. 36950 records in RAM. INFO 2026-06-08 08:38:08 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 1s. Last read position: chr5:83,538,783 INFO 2026-06-08 08:38:08 MarkDuplicates Tracking 689344 as yet unmatched pairs. 35055 records in RAM. INFO 2026-06-08 08:38:11 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 2s. Last read position: chr5:98,896,344 INFO 2026-06-08 08:38:11 MarkDuplicates Tracking 687336 as yet unmatched pairs. 33046 records in RAM. INFO 2026-06-08 08:38:13 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 2s. Last read position: chr5:123,575,947 INFO 2026-06-08 08:38:13 MarkDuplicates Tracking 685013 as yet unmatched pairs. 30722 records in RAM. INFO 2026-06-08 08:38:15 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 1s. Last read position: chr5:134,380,768 INFO 2026-06-08 08:38:15 MarkDuplicates Tracking 683169 as yet unmatched pairs. 28866 records in RAM. INFO 2026-06-08 08:38:16 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 1s. Last read position: chr5:135,571,286 INFO 2026-06-08 08:38:16 MarkDuplicates Tracking 685630 as yet unmatched pairs. 31321 records in RAM. INFO 2026-06-08 08:38:18 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 1s. Last read position: chr5:138,164,889 INFO 2026-06-08 08:38:18 MarkDuplicates Tracking 678148 as yet unmatched pairs. 23838 records in RAM. INFO 2026-06-08 08:38:20 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 1s. Last read position: chr5:140,557,151 INFO 2026-06-08 08:38:20 MarkDuplicates Tracking 675922 as yet unmatched pairs. 21587 records in RAM. INFO 2026-06-08 08:38:21 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 1s. Last read position: chr5:141,923,962 INFO 2026-06-08 08:38:21 MarkDuplicates Tracking 673694 as yet unmatched pairs. 19356 records in RAM. INFO 2026-06-08 08:38:23 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 1s. Last read position: chr5:150,129,915 INFO 2026-06-08 08:38:23 MarkDuplicates Tracking 671917 as yet unmatched pairs. 17578 records in RAM. INFO 2026-06-08 08:38:24 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 1s. Last read position: chr5:150,403,154 INFO 2026-06-08 08:38:24 MarkDuplicates Tracking 673954 as yet unmatched pairs. 19615 records in RAM. INFO 2026-06-08 08:38:26 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 1s. Last read position: chr5:150,406,307 INFO 2026-06-08 08:38:26 MarkDuplicates Tracking 676288 as yet unmatched pairs. 21948 records in RAM. INFO 2026-06-08 08:38:28 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 1s. Last read position: chr5:151,666,358 INFO 2026-06-08 08:38:28 MarkDuplicates Tracking 665035 as yet unmatched pairs. 10693 records in RAM. INFO 2026-06-08 08:38:29 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 1s. Last read position: chr5:169,698,418 INFO 2026-06-08 08:38:29 MarkDuplicates Tracking 662181 as yet unmatched pairs. 7837 records in RAM. INFO 2026-06-08 08:38:32 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 2s. Last read position: chr5:176,347,619 INFO 2026-06-08 08:38:32 MarkDuplicates Tracking 660198 as yet unmatched pairs. 5854 records in RAM. INFO 2026-06-08 08:38:33 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 1s. Last read position: chr5:179,614,854 INFO 2026-06-08 08:38:33 MarkDuplicates Tracking 657913 as yet unmatched pairs. 3566 records in RAM. INFO 2026-06-08 08:38:35 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 1s. Last read position: chr5:179,873,119 INFO 2026-06-08 08:38:35 MarkDuplicates Tracking 655406 as yet unmatched pairs. 1059 records in RAM. INFO 2026-06-08 08:38:37 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 1s. Last read position: chr6:7,229,646 INFO 2026-06-08 08:38:37 MarkDuplicates Tracking 653267 as yet unmatched pairs. 39686 records in RAM. INFO 2026-06-08 08:38:38 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 1s. Last read position: chr6:17,626,330 INFO 2026-06-08 08:38:38 MarkDuplicates Tracking 650939 as yet unmatched pairs. 37356 records in RAM. INFO 2026-06-08 08:38:40 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 1s. Last read position: chr6:27,814,541 INFO 2026-06-08 08:38:40 MarkDuplicates Tracking 648854 as yet unmatched pairs. 35271 records in RAM. INFO 2026-06-08 08:38:41 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 1s. Last read position: chr6:30,889,312 INFO 2026-06-08 08:38:41 MarkDuplicates Tracking 647111 as yet unmatched pairs. 33527 records in RAM. INFO 2026-06-08 08:38:43 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 1s. Last read position: chr6:31,633,477 INFO 2026-06-08 08:38:43 MarkDuplicates Tracking 644680 as yet unmatched pairs. 31096 records in RAM. INFO 2026-06-08 08:38:44 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 1s. Last read position: chr6:31,817,220 INFO 2026-06-08 08:38:44 MarkDuplicates Tracking 643083 as yet unmatched pairs. 29499 records in RAM. INFO 2026-06-08 08:38:46 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 1s. Last read position: chr6:31,969,292 INFO 2026-06-08 08:38:46 MarkDuplicates Tracking 640985 as yet unmatched pairs. 27400 records in RAM. INFO 2026-06-08 08:38:47 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 1s. Last read position: chr6:32,034,232 INFO 2026-06-08 08:38:47 MarkDuplicates Tracking 640219 as yet unmatched pairs. 26625 records in RAM. INFO 2026-06-08 08:38:49 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 1s. Last read position: chr6:32,977,841 INFO 2026-06-08 08:38:49 MarkDuplicates Tracking 637582 as yet unmatched pairs. 23988 records in RAM. INFO 2026-06-08 08:38:51 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 2s. Last read position: chr6:33,417,517 INFO 2026-06-08 08:38:51 MarkDuplicates Tracking 635429 as yet unmatched pairs. 21835 records in RAM. INFO 2026-06-08 08:38:53 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 1s. Last read position: chr6:37,931,890 INFO 2026-06-08 08:38:53 MarkDuplicates Tracking 632960 as yet unmatched pairs. 19363 records in RAM. INFO 2026-06-08 08:38:54 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 1s. Last read position: chr6:44,136,382 INFO 2026-06-08 08:38:54 MarkDuplicates Tracking 630677 as yet unmatched pairs. 17079 records in RAM. INFO 2026-06-08 08:38:56 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr6:56,606,315 INFO 2026-06-08 08:38:56 MarkDuplicates Tracking 628660 as yet unmatched pairs. 15061 records in RAM. INFO 2026-06-08 08:38:58 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 2s. Last read position: chr6:75,184,026 INFO 2026-06-08 08:38:58 MarkDuplicates Tracking 626765 as yet unmatched pairs. 13164 records in RAM. INFO 2026-06-08 08:39:00 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 1s. Last read position: chr6:97,282,323 INFO 2026-06-08 08:39:00 MarkDuplicates Tracking 624650 as yet unmatched pairs. 11048 records in RAM. INFO 2026-06-08 08:39:02 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 2s. Last read position: chr6:117,675,753 INFO 2026-06-08 08:39:02 MarkDuplicates Tracking 622594 as yet unmatched pairs. 8984 records in RAM. INFO 2026-06-08 08:39:04 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 1s. Last read position: chr6:138,944,595 INFO 2026-06-08 08:39:04 MarkDuplicates Tracking 620596 as yet unmatched pairs. 6980 records in RAM. INFO 2026-06-08 08:39:06 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 1s. Last read position: chr6:151,842,719 INFO 2026-06-08 08:39:06 MarkDuplicates Tracking 620587 as yet unmatched pairs. 6970 records in RAM. INFO 2026-06-08 08:39:07 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 1s. Last read position: chr6:158,783,551 INFO 2026-06-08 08:39:07 MarkDuplicates Tracking 616858 as yet unmatched pairs. 3241 records in RAM. INFO 2026-06-08 08:39:09 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 1s. Last read position: chr6:169,723,999 INFO 2026-06-08 08:39:09 MarkDuplicates Tracking 613826 as yet unmatched pairs. 206 records in RAM. INFO 2026-06-08 08:39:11 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 2s. Last read position: chr7:5,359,445 INFO 2026-06-08 08:39:11 MarkDuplicates Tracking 611234 as yet unmatched pairs. 40361 records in RAM. INFO 2026-06-08 08:39:13 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 1s. Last read position: chr7:5,529,210 INFO 2026-06-08 08:39:13 MarkDuplicates Tracking 610994 as yet unmatched pairs. 40106 records in RAM. INFO 2026-06-08 08:39:14 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 1s. Last read position: chr7:16,801,694 INFO 2026-06-08 08:39:14 MarkDuplicates Tracking 606671 as yet unmatched pairs. 35776 records in RAM. INFO 2026-06-08 08:39:16 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 1s. Last read position: chr7:33,257,278 INFO 2026-06-08 08:39:16 MarkDuplicates Tracking 604538 as yet unmatched pairs. 33643 records in RAM. INFO 2026-06-08 08:39:18 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 1s. Last read position: chr7:44,114,789 INFO 2026-06-08 08:39:18 MarkDuplicates Tracking 602482 as yet unmatched pairs. 31585 records in RAM. INFO 2026-06-08 08:39:19 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 1s. Last read position: chr7:65,970,333 INFO 2026-06-08 08:39:19 MarkDuplicates Tracking 600143 as yet unmatched pairs. 29246 records in RAM. INFO 2026-06-08 08:39:21 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 1s. Last read position: chr7:74,121,164 INFO 2026-06-08 08:39:21 MarkDuplicates Tracking 598673 as yet unmatched pairs. 27775 records in RAM. INFO 2026-06-08 08:39:22 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 1s. Last read position: chr7:76,302,822 INFO 2026-06-08 08:39:22 MarkDuplicates Tracking 597615 as yet unmatched pairs. 26715 records in RAM. INFO 2026-06-08 08:39:24 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 1s. Last read position: chr7:82,955,724 INFO 2026-06-08 08:39:24 MarkDuplicates Tracking 594828 as yet unmatched pairs. 23926 records in RAM. INFO 2026-06-08 08:39:26 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 1s. Last read position: chr7:93,131,216 INFO 2026-06-08 08:39:26 MarkDuplicates Tracking 592997 as yet unmatched pairs. 22092 records in RAM. INFO 2026-06-08 08:39:27 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 1s. Last read position: chr7:94,415,225 INFO 2026-06-08 08:39:27 MarkDuplicates Tracking 591471 as yet unmatched pairs. 20563 records in RAM. INFO 2026-06-08 08:39:29 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 1s. Last read position: chr7:95,587,034 INFO 2026-06-08 08:39:29 MarkDuplicates Tracking 588288 as yet unmatched pairs. 17380 records in RAM. INFO 2026-06-08 08:39:31 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 1s. Last read position: chr7:100,213,784 INFO 2026-06-08 08:39:31 MarkDuplicates Tracking 586045 as yet unmatched pairs. 15134 records in RAM. INFO 2026-06-08 08:39:33 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 2s. Last read position: chr7:102,355,755 INFO 2026-06-08 08:39:33 MarkDuplicates Tracking 583852 as yet unmatched pairs. 12941 records in RAM. INFO 2026-06-08 08:39:35 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 1s. Last read position: chr7:105,040,892 INFO 2026-06-08 08:39:35 MarkDuplicates Tracking 583288 as yet unmatched pairs. 12377 records in RAM. INFO 2026-06-08 08:39:36 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 1s. Last read position: chr7:123,694,794 INFO 2026-06-08 08:39:36 MarkDuplicates Tracking 580635 as yet unmatched pairs. 9722 records in RAM. INFO 2026-06-08 08:39:38 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 1s. Last read position: chr7:133,035,069 INFO 2026-06-08 08:39:38 MarkDuplicates Tracking 578441 as yet unmatched pairs. 7525 records in RAM. INFO 2026-06-08 08:39:39 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 1s. Last read position: chr7:140,753,227 INFO 2026-06-08 08:39:39 MarkDuplicates Tracking 576296 as yet unmatched pairs. 5379 records in RAM. INFO 2026-06-08 08:39:41 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 1s. Last read position: chr7:149,005,960 INFO 2026-06-08 08:39:41 MarkDuplicates Tracking 574573 as yet unmatched pairs. 3656 records in RAM. INFO 2026-06-08 08:39:42 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 1s. Last read position: chr7:152,230,309 INFO 2026-06-08 08:39:42 MarkDuplicates Tracking 571952 as yet unmatched pairs. 1034 records in RAM. INFO 2026-06-08 08:39:44 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 1s. Last read position: chr8:16,168,466 INFO 2026-06-08 08:39:44 MarkDuplicates Tracking 569790 as yet unmatched pairs. 31208 records in RAM. INFO 2026-06-08 08:39:46 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 1s. Last read position: chr8:24,339,506 INFO 2026-06-08 08:39:46 MarkDuplicates Tracking 567472 as yet unmatched pairs. 28889 records in RAM. INFO 2026-06-08 08:39:48 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 1s. Last read position: chr8:38,321,150 INFO 2026-06-08 08:39:48 MarkDuplicates Tracking 565428 as yet unmatched pairs. 26836 records in RAM. INFO 2026-06-08 08:39:49 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 1s. Last read position: chr8:43,122,151 INFO 2026-06-08 08:39:49 MarkDuplicates Tracking 563156 as yet unmatched pairs. 24562 records in RAM. INFO 2026-06-08 08:39:51 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 1s. Last read position: chr8:58,605,994 INFO 2026-06-08 08:39:51 MarkDuplicates Tracking 560659 as yet unmatched pairs. 22061 records in RAM. INFO 2026-06-08 08:39:52 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 1s. Last read position: chr8:73,030,362 INFO 2026-06-08 08:39:52 MarkDuplicates Tracking 558741 as yet unmatched pairs. 20142 records in RAM. INFO 2026-06-08 08:39:54 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 1s. Last read position: chr8:94,646,267 INFO 2026-06-08 08:39:54 MarkDuplicates Tracking 557183 as yet unmatched pairs. 18582 records in RAM. INFO 2026-06-08 08:39:56 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 2s. Last read position: chr8:100,721,472 INFO 2026-06-08 08:39:56 MarkDuplicates Tracking 554990 as yet unmatched pairs. 16389 records in RAM. INFO 2026-06-08 08:39:58 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 1s. Last read position: chr8:115,415,051 INFO 2026-06-08 08:39:58 MarkDuplicates Tracking 552979 as yet unmatched pairs. 14376 records in RAM. INFO 2026-06-08 08:39:59 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 1s. Last read position: chr8:123,768,731 INFO 2026-06-08 08:39:59 MarkDuplicates Tracking 550714 as yet unmatched pairs. 12086 records in RAM. INFO 2026-06-08 08:40:01 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 1s. Last read position: chr8:140,879,591 INFO 2026-06-08 08:40:01 MarkDuplicates Tracking 548553 as yet unmatched pairs. 9919 records in RAM. INFO 2026-06-08 08:40:04 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 3s. Last read position: chr8:143,858,220 INFO 2026-06-08 08:40:04 MarkDuplicates Tracking 546125 as yet unmatched pairs. 7491 records in RAM. INFO 2026-06-08 08:40:06 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 1s. Last read position: chr8:143,862,506 INFO 2026-06-08 08:40:06 MarkDuplicates Tracking 545700 as yet unmatched pairs. 7066 records in RAM. INFO 2026-06-08 08:40:07 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 1s. Last read position: chr8:143,869,405 INFO 2026-06-08 08:40:07 MarkDuplicates Tracking 544814 as yet unmatched pairs. 6179 records in RAM. INFO 2026-06-08 08:40:08 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 1s. Last read position: chr8:143,985,028 INFO 2026-06-08 08:40:08 MarkDuplicates Tracking 541759 as yet unmatched pairs. 3124 records in RAM. INFO 2026-06-08 08:40:10 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 1s. Last read position: chr8:144,841,371 INFO 2026-06-08 08:40:10 MarkDuplicates Tracking 538956 as yet unmatched pairs. 320 records in RAM. INFO 2026-06-08 08:40:11 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 1s. Last read position: chr9:19,360,410 INFO 2026-06-08 08:40:11 MarkDuplicates Tracking 536826 as yet unmatched pairs. 27174 records in RAM. INFO 2026-06-08 08:40:13 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:05:43s. Time for last 1,000,000: 1s. Last read position: chr9:35,091,614 INFO 2026-06-08 08:40:13 MarkDuplicates Tracking 534546 as yet unmatched pairs. 24892 records in RAM. INFO 2026-06-08 08:40:14 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 1s. Last read position: chr9:66,920,305 INFO 2026-06-08 08:40:14 MarkDuplicates Tracking 532565 as yet unmatched pairs. 22902 records in RAM. INFO 2026-06-08 08:40:16 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 1s. Last read position: chr9:88,475,476 INFO 2026-06-08 08:40:16 MarkDuplicates Tracking 530580 as yet unmatched pairs. 20913 records in RAM. INFO 2026-06-08 08:40:18 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 1s. Last read position: chr9:97,700,607 INFO 2026-06-08 08:40:18 MarkDuplicates Tracking 528542 as yet unmatched pairs. 18874 records in RAM. INFO 2026-06-08 08:40:19 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 1s. Last read position: chr9:112,234,818 INFO 2026-06-08 08:40:19 MarkDuplicates Tracking 526370 as yet unmatched pairs. 16700 records in RAM. INFO 2026-06-08 08:40:21 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 1s. Last read position: chr9:121,301,961 INFO 2026-06-08 08:40:21 MarkDuplicates Tracking 524791 as yet unmatched pairs. 15121 records in RAM. INFO 2026-06-08 08:40:22 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 1s. Last read position: chr9:127,449,658 INFO 2026-06-08 08:40:22 MarkDuplicates Tracking 522484 as yet unmatched pairs. 12814 records in RAM. INFO 2026-06-08 08:40:24 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 1s. Last read position: chr9:128,741,596 INFO 2026-06-08 08:40:24 MarkDuplicates Tracking 519528 as yet unmatched pairs. 9857 records in RAM. INFO 2026-06-08 08:40:25 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 1s. Last read position: chr9:131,584,557 INFO 2026-06-08 08:40:25 MarkDuplicates Tracking 517062 as yet unmatched pairs. 7391 records in RAM. INFO 2026-06-08 08:40:28 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 2s. Last read position: chr9:134,814,825 INFO 2026-06-08 08:40:28 MarkDuplicates Tracking 514698 as yet unmatched pairs. 5025 records in RAM. INFO 2026-06-08 08:40:30 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 2s. Last read position: chr9:137,020,400 INFO 2026-06-08 08:40:30 MarkDuplicates Tracking 511960 as yet unmatched pairs. 2276 records in RAM. INFO 2026-06-08 08:40:32 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 1s. Last read position: chr10:3,158,004 INFO 2026-06-08 08:40:32 MarkDuplicates Tracking 509248 as yet unmatched pairs. 26970 records in RAM. INFO 2026-06-08 08:40:34 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 1s. Last read position: chr10:13,666,086 INFO 2026-06-08 08:40:34 MarkDuplicates Tracking 507022 as yet unmatched pairs. 24744 records in RAM. INFO 2026-06-08 08:40:35 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 1s. Last read position: chr10:27,894,758 INFO 2026-06-08 08:40:35 MarkDuplicates Tracking 504835 as yet unmatched pairs. 22555 records in RAM. INFO 2026-06-08 08:40:37 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 1s. Last read position: chr10:33,213,680 INFO 2026-06-08 08:40:37 MarkDuplicates Tracking 503032 as yet unmatched pairs. 20752 records in RAM. INFO 2026-06-08 08:40:39 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:06:09s. Time for last 1,000,000: 1s. Last read position: chr10:43,123,798 INFO 2026-06-08 08:40:39 MarkDuplicates Tracking 501821 as yet unmatched pairs. 19540 records in RAM. INFO 2026-06-08 08:40:40 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 1s. Last read position: chr10:50,008,754 INFO 2026-06-08 08:40:40 MarkDuplicates Tracking 498762 as yet unmatched pairs. 16479 records in RAM. INFO 2026-06-08 08:40:42 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 1s. Last read position: chr10:70,844,601 INFO 2026-06-08 08:40:42 MarkDuplicates Tracking 496765 as yet unmatched pairs. 14482 records in RAM. INFO 2026-06-08 08:40:43 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 1s. Last read position: chr10:77,830,331 INFO 2026-06-08 08:40:43 MarkDuplicates Tracking 494730 as yet unmatched pairs. 12446 records in RAM. INFO 2026-06-08 08:40:45 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 1s. Last read position: chr10:87,965,320 INFO 2026-06-08 08:40:45 MarkDuplicates Tracking 493464 as yet unmatched pairs. 11171 records in RAM. INFO 2026-06-08 08:40:46 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 1s. Last read position: chr10:96,576,820 INFO 2026-06-08 08:40:46 MarkDuplicates Tracking 490623 as yet unmatched pairs. 8327 records in RAM. INFO 2026-06-08 08:40:48 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 1s. Last read position: chr10:102,369,285 INFO 2026-06-08 08:40:48 MarkDuplicates Tracking 488305 as yet unmatched pairs. 5987 records in RAM. INFO 2026-06-08 08:40:49 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 1s. Last read position: chr10:116,906,669 INFO 2026-06-08 08:40:49 MarkDuplicates Tracking 486353 as yet unmatched pairs. 4013 records in RAM. INFO 2026-06-08 08:40:51 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 1s. Last read position: chr10:124,400,889 INFO 2026-06-08 08:40:51 MarkDuplicates Tracking 483861 as yet unmatched pairs. 1521 records in RAM. INFO 2026-06-08 08:40:53 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 1s. Last read position: chr11:293,662 INFO 2026-06-08 08:40:53 MarkDuplicates Tracking 483024 as yet unmatched pairs. 56976 records in RAM. INFO 2026-06-08 08:40:55 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 2s. Last read position: chr11:607,726 INFO 2026-06-08 08:40:55 MarkDuplicates Tracking 479375 as yet unmatched pairs. 53327 records in RAM. INFO 2026-06-08 08:40:57 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 1s. Last read position: chr11:2,377,556 INFO 2026-06-08 08:40:57 MarkDuplicates Tracking 477409 as yet unmatched pairs. 51359 records in RAM. INFO 2026-06-08 08:41:00 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:06:30s. Time for last 1,000,000: 2s. Last read position: chr11:8,683,206 INFO 2026-06-08 08:41:00 MarkDuplicates Tracking 474612 as yet unmatched pairs. 48562 records in RAM. INFO 2026-06-08 08:41:01 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 1s. Last read position: chr11:14,458,667 INFO 2026-06-08 08:41:01 MarkDuplicates Tracking 472406 as yet unmatched pairs. 46355 records in RAM. INFO 2026-06-08 08:41:03 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:06:33s. Time for last 1,000,000: 1s. Last read position: chr11:33,710,129 INFO 2026-06-08 08:41:03 MarkDuplicates Tracking 470873 as yet unmatched pairs. 44821 records in RAM. INFO 2026-06-08 08:41:05 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:06:35s. Time for last 1,000,000: 1s. Last read position: chr11:46,347,753 INFO 2026-06-08 08:41:05 MarkDuplicates Tracking 467749 as yet unmatched pairs. 41697 records in RAM. INFO 2026-06-08 08:41:06 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 1s. Last read position: chr11:57,334,485 INFO 2026-06-08 08:41:06 MarkDuplicates Tracking 465403 as yet unmatched pairs. 39350 records in RAM. INFO 2026-06-08 08:41:08 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 1s. Last read position: chr11:61,368,624 INFO 2026-06-08 08:41:08 MarkDuplicates Tracking 463201 as yet unmatched pairs. 37148 records in RAM. INFO 2026-06-08 08:41:10 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 1s. Last read position: chr11:62,273,013 INFO 2026-06-08 08:41:10 MarkDuplicates Tracking 461288 as yet unmatched pairs. 35230 records in RAM. INFO 2026-06-08 08:41:11 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 1s. Last read position: chr11:62,525,073 INFO 2026-06-08 08:41:11 MarkDuplicates Tracking 460185 as yet unmatched pairs. 34127 records in RAM. INFO 2026-06-08 08:41:13 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 1s. Last read position: chr11:62,532,256 INFO 2026-06-08 08:41:13 MarkDuplicates Tracking 458162 as yet unmatched pairs. 32104 records in RAM. INFO 2026-06-08 08:41:14 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:06:44s. Time for last 1,000,000: 1s. Last read position: chr11:63,766,078 INFO 2026-06-08 08:41:14 MarkDuplicates Tracking 455152 as yet unmatched pairs. 29094 records in RAM. INFO 2026-06-08 08:41:16 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:06:46s. Time for last 1,000,000: 1s. Last read position: chr11:65,122,372 INFO 2026-06-08 08:41:16 MarkDuplicates Tracking 452802 as yet unmatched pairs. 26743 records in RAM. INFO 2026-06-08 08:41:17 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 1s. Last read position: chr11:65,870,639 INFO 2026-06-08 08:41:17 MarkDuplicates Tracking 450087 as yet unmatched pairs. 24019 records in RAM. INFO 2026-06-08 08:41:19 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 1s. Last read position: chr11:67,464,677 INFO 2026-06-08 08:41:19 MarkDuplicates Tracking 447812 as yet unmatched pairs. 21744 records in RAM. INFO 2026-06-08 08:41:21 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:06:51s. Time for last 1,000,000: 1s. Last read position: chr11:70,473,185 INFO 2026-06-08 08:41:21 MarkDuplicates Tracking 445374 as yet unmatched pairs. 19305 records in RAM. INFO 2026-06-08 08:41:22 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 1s. Last read position: chr11:72,757,813 INFO 2026-06-08 08:41:22 MarkDuplicates Tracking 443371 as yet unmatched pairs. 17302 records in RAM. INFO 2026-06-08 08:41:24 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 2s. Last read position: chr11:75,401,707 INFO 2026-06-08 08:41:24 MarkDuplicates Tracking 441912 as yet unmatched pairs. 15841 records in RAM. INFO 2026-06-08 08:41:26 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 1s. Last read position: chr11:77,332,730 INFO 2026-06-08 08:41:26 MarkDuplicates Tracking 438672 as yet unmatched pairs. 12600 records in RAM. INFO 2026-06-08 08:41:28 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 2s. Last read position: chr11:78,121,068 INFO 2026-06-08 08:41:28 MarkDuplicates Tracking 436945 as yet unmatched pairs. 10873 records in RAM. INFO 2026-06-08 08:41:30 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:07:00s. Time for last 1,000,000: 1s. Last read position: chr11:93,738,361 INFO 2026-06-08 08:41:30 MarkDuplicates Tracking 434017 as yet unmatched pairs. 7945 records in RAM. INFO 2026-06-08 08:41:32 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 1s. Last read position: chr11:114,312,307 INFO 2026-06-08 08:41:32 MarkDuplicates Tracking 431785 as yet unmatched pairs. 5712 records in RAM. INFO 2026-06-08 08:41:34 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:07:04s. Time for last 1,000,000: 1s. Last read position: chr11:119,127,066 INFO 2026-06-08 08:41:34 MarkDuplicates Tracking 429534 as yet unmatched pairs. 3461 records in RAM. INFO 2026-06-08 08:41:35 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 1s. Last read position: chr11:126,406,487 INFO 2026-06-08 08:41:35 MarkDuplicates Tracking 427416 as yet unmatched pairs. 1343 records in RAM. INFO 2026-06-08 08:41:37 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 2s. Last read position: chr12:900,570 INFO 2026-06-08 08:41:37 MarkDuplicates Tracking 425337 as yet unmatched pairs. 56101 records in RAM. INFO 2026-06-08 08:41:39 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 1s. Last read position: chr12:6,385,297 INFO 2026-06-08 08:41:39 MarkDuplicates Tracking 423113 as yet unmatched pairs. 53871 records in RAM. INFO 2026-06-08 08:41:41 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:07:11s. Time for last 1,000,000: 1s. Last read position: chr12:7,065,200 INFO 2026-06-08 08:41:41 MarkDuplicates Tracking 420841 as yet unmatched pairs. 51599 records in RAM. INFO 2026-06-08 08:41:43 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 1s. Last read position: chr12:12,477,294 INFO 2026-06-08 08:41:43 MarkDuplicates Tracking 418643 as yet unmatched pairs. 49398 records in RAM. INFO 2026-06-08 08:41:45 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:07:15s. Time for last 1,000,000: 1s. Last read position: chr12:26,064,707 INFO 2026-06-08 08:41:45 MarkDuplicates Tracking 416685 as yet unmatched pairs. 47440 records in RAM. INFO 2026-06-08 08:42:48 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:08:18s. Time for last 1,000,000: 63s. Last read position: chr12:40,432,730 INFO 2026-06-08 08:42:48 MarkDuplicates Tracking 415699 as yet unmatched pairs. 46451 records in RAM. INFO 2026-06-08 08:42:50 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:08:20s. Time for last 1,000,000: 1s. Last read position: chr12:40,486,548 INFO 2026-06-08 08:42:50 MarkDuplicates Tracking 413478 as yet unmatched pairs. 44228 records in RAM. INFO 2026-06-08 08:42:52 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:08:22s. Time for last 1,000,000: 1s. Last read position: chr12:40,490,148 INFO 2026-06-08 08:42:52 MarkDuplicates Tracking 411005 as yet unmatched pairs. 41755 records in RAM. INFO 2026-06-08 08:42:53 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:08:24s. Time for last 1,000,000: 1s. Last read position: chr12:40,570,495 INFO 2026-06-08 08:42:53 MarkDuplicates Tracking 408860 as yet unmatched pairs. 39610 records in RAM. INFO 2026-06-08 08:42:55 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 1s. Last read position: chr12:48,775,054 INFO 2026-06-08 08:42:55 MarkDuplicates Tracking 406284 as yet unmatched pairs. 37034 records in RAM. INFO 2026-06-08 08:42:57 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:08:27s. Time for last 1,000,000: 1s. Last read position: chr12:49,185,817 INFO 2026-06-08 08:42:57 MarkDuplicates Tracking 404559 as yet unmatched pairs. 35308 records in RAM. INFO 2026-06-08 08:42:58 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 1s. Last read position: chr12:51,458,640 INFO 2026-06-08 08:42:58 MarkDuplicates Tracking 402178 as yet unmatched pairs. 32925 records in RAM. INFO 2026-06-08 08:43:01 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:08:31s. Time for last 1,000,000: 2s. Last read position: chr12:53,459,328 INFO 2026-06-08 08:43:01 MarkDuplicates Tracking 400486 as yet unmatched pairs. 31232 records in RAM. INFO 2026-06-08 08:43:03 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:08:33s. Time for last 1,000,000: 2s. Last read position: chr12:55,954,203 INFO 2026-06-08 08:43:03 MarkDuplicates Tracking 397960 as yet unmatched pairs. 28705 records in RAM. INFO 2026-06-08 08:43:05 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 1s. Last read position: chr12:56,276,009 INFO 2026-06-08 08:43:05 MarkDuplicates Tracking 395817 as yet unmatched pairs. 26562 records in RAM. INFO 2026-06-08 08:43:07 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 1s. Last read position: chr12:57,096,722 INFO 2026-06-08 08:43:07 MarkDuplicates Tracking 395262 as yet unmatched pairs. 26007 records in RAM. INFO 2026-06-08 08:43:08 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:08:39s. Time for last 1,000,000: 1s. Last read position: chr12:57,258,066 INFO 2026-06-08 08:43:08 MarkDuplicates Tracking 391609 as yet unmatched pairs. 22354 records in RAM. INFO 2026-06-08 08:43:10 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 1s. Last read position: chr12:65,170,445 INFO 2026-06-08 08:43:10 MarkDuplicates Tracking 389382 as yet unmatched pairs. 20126 records in RAM. INFO 2026-06-08 08:43:12 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:08:42s. Time for last 1,000,000: 1s. Last read position: chr12:79,781,816 INFO 2026-06-08 08:43:12 MarkDuplicates Tracking 387319 as yet unmatched pairs. 18063 records in RAM. INFO 2026-06-08 08:43:13 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:08:44s. Time for last 1,000,000: 1s. Last read position: chr12:98,533,604 INFO 2026-06-08 08:43:13 MarkDuplicates Tracking 385443 as yet unmatched pairs. 16187 records in RAM. INFO 2026-06-08 08:43:15 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:08:45s. Time for last 1,000,000: 1s. Last read position: chr12:103,982,821 INFO 2026-06-08 08:43:15 MarkDuplicates Tracking 383052 as yet unmatched pairs. 13796 records in RAM. INFO 2026-06-08 08:43:17 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:08:47s. Time for last 1,000,000: 1s. Last read position: chr12:110,436,120 INFO 2026-06-08 08:43:17 MarkDuplicates Tracking 380883 as yet unmatched pairs. 11625 records in RAM. INFO 2026-06-08 08:43:19 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 1s. Last read position: chr12:112,970,006 INFO 2026-06-08 08:43:19 MarkDuplicates Tracking 379112 as yet unmatched pairs. 9853 records in RAM. INFO 2026-06-08 08:43:20 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 1s. Last read position: chr12:120,144,971 INFO 2026-06-08 08:43:20 MarkDuplicates Tracking 376310 as yet unmatched pairs. 7048 records in RAM. INFO 2026-06-08 08:43:23 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:08:53s. Time for last 1,000,000: 2s. Last read position: chr12:122,333,126 INFO 2026-06-08 08:43:23 MarkDuplicates Tracking 374013 as yet unmatched pairs. 4751 records in RAM. INFO 2026-06-08 08:43:25 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:08:55s. Time for last 1,000,000: 2s. Last read position: chr12:124,466,173 INFO 2026-06-08 08:43:25 MarkDuplicates Tracking 371775 as yet unmatched pairs. 2510 records in RAM. INFO 2026-06-08 08:43:26 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:08:57s. Time for last 1,000,000: 1s. Last read position: chr12:132,816,548 INFO 2026-06-08 08:43:26 MarkDuplicates Tracking 369734 as yet unmatched pairs. 468 records in RAM. INFO 2026-06-08 08:43:28 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:08:58s. Time for last 1,000,000: 1s. Last read position: chr13:31,145,577 INFO 2026-06-08 08:43:28 MarkDuplicates Tracking 367541 as yet unmatched pairs. 8319 records in RAM. INFO 2026-06-08 08:43:30 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:09:00s. Time for last 1,000,000: 1s. Last read position: chr13:44,436,681 INFO 2026-06-08 08:43:30 MarkDuplicates Tracking 365413 as yet unmatched pairs. 6190 records in RAM. INFO 2026-06-08 08:43:32 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:09:02s. Time for last 1,000,000: 1s. Last read position: chr13:75,760,984 INFO 2026-06-08 08:43:32 MarkDuplicates Tracking 363550 as yet unmatched pairs. 4325 records in RAM. INFO 2026-06-08 08:43:33 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:09:03s. Time for last 1,000,000: 1s. Last read position: chr13:110,176,627 INFO 2026-06-08 08:43:33 MarkDuplicates Tracking 361273 as yet unmatched pairs. 2044 records in RAM. INFO 2026-06-08 08:43:35 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 1s. Last read position: chr14:20,460,244 INFO 2026-06-08 08:43:35 MarkDuplicates Tracking 358826 as yet unmatched pairs. 27983 records in RAM. INFO 2026-06-08 08:43:36 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:09:07s. Time for last 1,000,000: 1s. Last read position: chr14:23,061,116 INFO 2026-06-08 08:43:36 MarkDuplicates Tracking 356784 as yet unmatched pairs. 25941 records in RAM. INFO 2026-06-08 08:43:38 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 1s. Last read position: chr14:24,267,763 INFO 2026-06-08 08:43:38 MarkDuplicates Tracking 354561 as yet unmatched pairs. 23717 records in RAM. INFO 2026-06-08 08:43:40 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:09:10s. Time for last 1,000,000: 1s. Last read position: chr14:35,683,861 INFO 2026-06-08 08:43:40 MarkDuplicates Tracking 352251 as yet unmatched pairs. 21406 records in RAM. INFO 2026-06-08 08:43:42 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:09:12s. Time for last 1,000,000: 1s. Last read position: chr14:50,772,963 INFO 2026-06-08 08:43:42 MarkDuplicates Tracking 350229 as yet unmatched pairs. 19383 records in RAM. INFO 2026-06-08 08:43:44 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 2s. Last read position: chr14:60,124,910 INFO 2026-06-08 08:43:44 MarkDuplicates Tracking 348176 as yet unmatched pairs. 17326 records in RAM. INFO 2026-06-08 08:43:46 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 1s. Last read position: chr14:67,659,795 INFO 2026-06-08 08:43:46 MarkDuplicates Tracking 346177 as yet unmatched pairs. 15327 records in RAM. INFO 2026-06-08 08:43:47 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:09:17s. Time for last 1,000,000: 1s. Last read position: chr14:73,595,183 INFO 2026-06-08 08:43:47 MarkDuplicates Tracking 343946 as yet unmatched pairs. 13095 records in RAM. INFO 2026-06-08 08:43:49 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:09:19s. Time for last 1,000,000: 1s. Last read position: chr14:77,433,842 INFO 2026-06-08 08:43:49 MarkDuplicates Tracking 341662 as yet unmatched pairs. 10809 records in RAM. INFO 2026-06-08 08:43:50 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:09:21s. Time for last 1,000,000: 1s. Last read position: chr14:93,220,257 INFO 2026-06-08 08:43:50 MarkDuplicates Tracking 339588 as yet unmatched pairs. 8733 records in RAM. INFO 2026-06-08 08:43:52 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 1s. Last read position: chr14:99,917,817 INFO 2026-06-08 08:43:52 MarkDuplicates Tracking 337274 as yet unmatched pairs. 6417 records in RAM. INFO 2026-06-08 08:43:53 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:09:24s. Time for last 1,000,000: 1s. Last read position: chr14:102,083,875 INFO 2026-06-08 08:43:53 MarkDuplicates Tracking 335335 as yet unmatched pairs. 4478 records in RAM. INFO 2026-06-08 08:43:55 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 1s. Last read position: chr14:104,941,207 INFO 2026-06-08 08:43:55 MarkDuplicates Tracking 332664 as yet unmatched pairs. 1806 records in RAM. INFO 2026-06-08 08:43:57 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:09:27s. Time for last 1,000,000: 1s. Last read position: chr15:20,466,208 INFO 2026-06-08 08:43:57 MarkDuplicates Tracking 330868 as yet unmatched pairs. 21393 records in RAM. INFO 2026-06-08 08:43:58 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:09:28s. Time for last 1,000,000: 1s. Last read position: chr15:32,603,852 INFO 2026-06-08 08:43:58 MarkDuplicates Tracking 329158 as yet unmatched pairs. 19682 records in RAM. INFO 2026-06-08 08:44:00 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:09:30s. Time for last 1,000,000: 1s. Last read position: chr15:40,569,361 INFO 2026-06-08 08:44:00 MarkDuplicates Tracking 327082 as yet unmatched pairs. 17605 records in RAM. INFO 2026-06-08 08:44:02 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:09:32s. Time for last 1,000,000: 1s. Last read position: chr15:43,185,561 INFO 2026-06-08 08:44:02 MarkDuplicates Tracking 324905 as yet unmatched pairs. 15426 records in RAM. INFO 2026-06-08 08:44:03 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:09:34s. Time for last 1,000,000: 1s. Last read position: chr15:48,425,428 INFO 2026-06-08 08:44:03 MarkDuplicates Tracking 322964 as yet unmatched pairs. 13485 records in RAM. INFO 2026-06-08 08:44:05 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 1s. Last read position: chr15:57,231,166 INFO 2026-06-08 08:44:05 MarkDuplicates Tracking 321609 as yet unmatched pairs. 12130 records in RAM. INFO 2026-06-08 08:44:07 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 1s. Last read position: chr15:64,123,516 INFO 2026-06-08 08:44:07 MarkDuplicates Tracking 318682 as yet unmatched pairs. 9203 records in RAM. INFO 2026-06-08 08:44:09 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:09:39s. Time for last 1,000,000: 2s. Last read position: chr15:71,341,546 INFO 2026-06-08 08:44:09 MarkDuplicates Tracking 316350 as yet unmatched pairs. 6871 records in RAM. INFO 2026-06-08 08:44:11 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:09:41s. Time for last 1,000,000: 1s. Last read position: chr15:75,598,606 INFO 2026-06-08 08:44:11 MarkDuplicates Tracking 313966 as yet unmatched pairs. 4484 records in RAM. INFO 2026-06-08 08:44:12 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:09:43s. Time for last 1,000,000: 1s. Last read position: chr15:85,707,962 INFO 2026-06-08 08:44:12 MarkDuplicates Tracking 312034 as yet unmatched pairs. 2551 records in RAM. INFO 2026-06-08 08:44:14 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 1s. Last read position: chr15:101,065,723 INFO 2026-06-08 08:44:14 MarkDuplicates Tracking 309764 as yet unmatched pairs. 281 records in RAM. INFO 2026-06-08 08:44:16 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:09:46s. Time for last 1,000,000: 1s. Last read position: chr16:676,695 INFO 2026-06-08 08:44:16 MarkDuplicates Tracking 307085 as yet unmatched pairs. 46699 records in RAM. INFO 2026-06-08 08:44:17 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:09:48s. Time for last 1,000,000: 1s. Last read position: chr16:1,675,302 INFO 2026-06-08 08:44:17 MarkDuplicates Tracking 304207 as yet unmatched pairs. 43820 records in RAM. INFO 2026-06-08 08:44:19 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:09:49s. Time for last 1,000,000: 1s. Last read position: chr16:2,113,238 INFO 2026-06-08 08:44:19 MarkDuplicates Tracking 301524 as yet unmatched pairs. 41137 records in RAM. INFO 2026-06-08 08:44:20 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:09:51s. Time for last 1,000,000: 1s. Last read position: chr16:2,764,991 INFO 2026-06-08 08:44:20 MarkDuplicates Tracking 299301 as yet unmatched pairs. 38914 records in RAM. INFO 2026-06-08 08:44:22 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:09:52s. Time for last 1,000,000: 1s. Last read position: chr16:3,728,634 INFO 2026-06-08 08:44:22 MarkDuplicates Tracking 296701 as yet unmatched pairs. 36314 records in RAM. INFO 2026-06-08 08:44:24 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:09:54s. Time for last 1,000,000: 1s. Last read position: chr16:8,897,023 INFO 2026-06-08 08:44:24 MarkDuplicates Tracking 294571 as yet unmatched pairs. 34184 records in RAM. INFO 2026-06-08 08:44:26 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:09:56s. Time for last 1,000,000: 1s. Last read position: chr16:14,261,003 INFO 2026-06-08 08:44:26 MarkDuplicates Tracking 292436 as yet unmatched pairs. 32047 records in RAM. INFO 2026-06-08 08:44:27 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:09:57s. Time for last 1,000,000: 1s. Last read position: chr16:15,016,200 INFO 2026-06-08 08:44:27 MarkDuplicates Tracking 291703 as yet unmatched pairs. 31314 records in RAM. INFO 2026-06-08 08:44:28 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 1s. Last read position: chr16:16,318,851 INFO 2026-06-08 08:44:28 MarkDuplicates Tracking 290296 as yet unmatched pairs. 29906 records in RAM. INFO 2026-06-08 08:44:30 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:10:00s. Time for last 1,000,000: 1s. Last read position: chr16:18,318,009 INFO 2026-06-08 08:44:30 MarkDuplicates Tracking 289572 as yet unmatched pairs. 29182 records in RAM. INFO 2026-06-08 08:44:32 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:10:02s. Time for last 1,000,000: 1s. Last read position: chr16:18,391,082 INFO 2026-06-08 08:44:32 MarkDuplicates Tracking 288641 as yet unmatched pairs. 28251 records in RAM. INFO 2026-06-08 08:44:34 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:10:04s. Time for last 1,000,000: 1s. Last read position: chr16:19,503,473 INFO 2026-06-08 08:44:34 MarkDuplicates Tracking 286904 as yet unmatched pairs. 26514 records in RAM. INFO 2026-06-08 08:44:35 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 1s. Last read position: chr16:21,833,487 INFO 2026-06-08 08:44:35 MarkDuplicates Tracking 285363 as yet unmatched pairs. 24973 records in RAM. INFO 2026-06-08 08:44:37 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:10:07s. Time for last 1,000,000: 1s. Last read position: chr16:22,519,971 INFO 2026-06-08 08:44:37 MarkDuplicates Tracking 284736 as yet unmatched pairs. 24345 records in RAM. INFO 2026-06-08 08:44:38 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:10:08s. Time for last 1,000,000: 1s. Last read position: chr16:27,363,538 INFO 2026-06-08 08:44:38 MarkDuplicates Tracking 283360 as yet unmatched pairs. 22968 records in RAM. INFO 2026-06-08 08:44:39 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:10:10s. Time for last 1,000,000: 1s. Last read position: chr16:28,888,918 INFO 2026-06-08 08:44:39 MarkDuplicates Tracking 281491 as yet unmatched pairs. 21099 records in RAM. INFO 2026-06-08 08:44:41 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:10:11s. Time for last 1,000,000: 1s. Last read position: chr16:29,548,648 INFO 2026-06-08 08:44:41 MarkDuplicates Tracking 280611 as yet unmatched pairs. 20217 records in RAM. INFO 2026-06-08 08:44:42 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 1s. Last read position: chr16:30,194,246 INFO 2026-06-08 08:44:42 MarkDuplicates Tracking 278201 as yet unmatched pairs. 17807 records in RAM. INFO 2026-06-08 08:44:44 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:10:14s. Time for last 1,000,000: 1s. Last read position: chr16:30,711,983 INFO 2026-06-08 08:44:44 MarkDuplicates Tracking 276648 as yet unmatched pairs. 16254 records in RAM. INFO 2026-06-08 08:44:45 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:10:15s. Time for last 1,000,000: 1s. Last read position: chr16:31,189,184 INFO 2026-06-08 08:44:45 MarkDuplicates Tracking 275292 as yet unmatched pairs. 14898 records in RAM. INFO 2026-06-08 08:44:47 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:10:17s. Time for last 1,000,000: 1s. Last read position: chr16:53,461,603 INFO 2026-06-08 08:44:47 MarkDuplicates Tracking 272445 as yet unmatched pairs. 12048 records in RAM. INFO 2026-06-08 08:44:48 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:10:19s. Time for last 1,000,000: 1s. Last read position: chr16:64,992,992 INFO 2026-06-08 08:44:48 MarkDuplicates Tracking 270228 as yet unmatched pairs. 9831 records in RAM. INFO 2026-06-08 08:44:50 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:10:20s. Time for last 1,000,000: 1s. Last read position: chr16:69,143,256 INFO 2026-06-08 08:44:50 MarkDuplicates Tracking 267566 as yet unmatched pairs. 7169 records in RAM. INFO 2026-06-08 08:44:52 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:10:22s. Time for last 1,000,000: 1s. Last read position: chr16:74,606,661 INFO 2026-06-08 08:44:52 MarkDuplicates Tracking 265394 as yet unmatched pairs. 4992 records in RAM. INFO 2026-06-08 08:44:54 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:10:24s. Time for last 1,000,000: 1s. Last read position: chr16:88,432,265 INFO 2026-06-08 08:44:54 MarkDuplicates Tracking 262863 as yet unmatched pairs. 2457 records in RAM. INFO 2026-06-08 08:44:57 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:10:27s. Time for last 1,000,000: 3s. Last read position: chr17:769,915 INFO 2026-06-08 08:44:57 MarkDuplicates Tracking 260346 as yet unmatched pairs. 108867 records in RAM. INFO 2026-06-08 08:44:59 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:10:29s. Time for last 1,000,000: 1s. Last read position: chr17:3,942,680 INFO 2026-06-08 08:44:59 MarkDuplicates Tracking 258112 as yet unmatched pairs. 106633 records in RAM. INFO 2026-06-08 08:45:01 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:10:31s. Time for last 1,000,000: 2s. Last read position: chr17:7,224,642 INFO 2026-06-08 08:45:01 MarkDuplicates Tracking 255715 as yet unmatched pairs. 104236 records in RAM. INFO 2026-06-08 08:45:03 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:10:33s. Time for last 1,000,000: 1s. Last read position: chr17:7,849,814 INFO 2026-06-08 08:45:03 MarkDuplicates Tracking 253606 as yet unmatched pairs. 102127 records in RAM. INFO 2026-06-08 08:45:05 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:10:35s. Time for last 1,000,000: 2s. Last read position: chr17:16,057,934 INFO 2026-06-08 08:45:05 MarkDuplicates Tracking 251532 as yet unmatched pairs. 100050 records in RAM. INFO 2026-06-08 08:45:07 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:10:37s. Time for last 1,000,000: 2s. Last read position: chr17:20,204,425 INFO 2026-06-08 08:45:07 MarkDuplicates Tracking 249305 as yet unmatched pairs. 97822 records in RAM. INFO 2026-06-08 08:45:09 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:10:39s. Time for last 1,000,000: 2s. Last read position: chr17:29,287,638 INFO 2026-06-08 08:45:09 MarkDuplicates Tracking 247088 as yet unmatched pairs. 95605 records in RAM. INFO 2026-06-08 08:45:11 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:10:41s. Time for last 1,000,000: 1s. Last read position: chr17:32,369,306 INFO 2026-06-08 08:45:11 MarkDuplicates Tracking 245074 as yet unmatched pairs. 93590 records in RAM. INFO 2026-06-08 08:45:13 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:10:43s. Time for last 1,000,000: 1s. Last read position: chr17:37,161,899 INFO 2026-06-08 08:45:13 MarkDuplicates Tracking 243134 as yet unmatched pairs. 91650 records in RAM. INFO 2026-06-08 08:45:14 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:10:44s. Time for last 1,000,000: 1s. Last read position: chr17:38,850,423 INFO 2026-06-08 08:45:14 MarkDuplicates Tracking 243098 as yet unmatched pairs. 91614 records in RAM. INFO 2026-06-08 08:45:16 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 1s. Last read position: chr17:39,709,395 INFO 2026-06-08 08:45:16 MarkDuplicates Tracking 240041 as yet unmatched pairs. 88557 records in RAM. INFO 2026-06-08 08:45:18 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:10:48s. Time for last 1,000,000: 1s. Last read position: chr17:39,723,448 INFO 2026-06-08 08:45:18 MarkDuplicates Tracking 238068 as yet unmatched pairs. 86584 records in RAM. INFO 2026-06-08 08:45:19 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:10:50s. Time for last 1,000,000: 1s. Last read position: chr17:40,094,120 INFO 2026-06-08 08:45:19 MarkDuplicates Tracking 233718 as yet unmatched pairs. 82234 records in RAM. INFO 2026-06-08 08:45:21 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:10:52s. Time for last 1,000,000: 1s. Last read position: chr17:41,524,875 INFO 2026-06-08 08:45:21 MarkDuplicates Tracking 233411 as yet unmatched pairs. 81926 records in RAM. INFO 2026-06-08 08:45:24 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:10:54s. Time for last 1,000,000: 2s. Last read position: chr17:42,128,369 INFO 2026-06-08 08:45:24 MarkDuplicates Tracking 228694 as yet unmatched pairs. 77208 records in RAM. INFO 2026-06-08 08:45:26 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:10:56s. Time for last 1,000,000: 1s. Last read position: chr17:43,018,599 INFO 2026-06-08 08:45:26 MarkDuplicates Tracking 226520 as yet unmatched pairs. 75034 records in RAM. INFO 2026-06-08 08:45:27 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 1s. Last read position: chr17:44,853,555 INFO 2026-06-08 08:45:27 MarkDuplicates Tracking 224167 as yet unmatched pairs. 72680 records in RAM. INFO 2026-06-08 08:45:29 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:10:59s. Time for last 1,000,000: 1s. Last read position: chr17:47,569,399 INFO 2026-06-08 08:45:29 MarkDuplicates Tracking 222337 as yet unmatched pairs. 70850 records in RAM. INFO 2026-06-08 08:45:31 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:11:01s. Time for last 1,000,000: 1s. Last read position: chr17:50,089,175 INFO 2026-06-08 08:45:31 MarkDuplicates Tracking 220247 as yet unmatched pairs. 68760 records in RAM. INFO 2026-06-08 08:45:32 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:11:02s. Time for last 1,000,000: 1s. Last read position: chr17:50,186,367 INFO 2026-06-08 08:45:32 MarkDuplicates Tracking 223875 as yet unmatched pairs. 72388 records in RAM. INFO 2026-06-08 08:45:34 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:11:04s. Time for last 1,000,000: 1s. Last read position: chr17:50,187,015 INFO 2026-06-08 08:45:34 MarkDuplicates Tracking 238726 as yet unmatched pairs. 87239 records in RAM. INFO 2026-06-08 08:45:36 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:11:06s. Time for last 1,000,000: 1s. Last read position: chr17:50,187,936 INFO 2026-06-08 08:45:36 MarkDuplicates Tracking 223236 as yet unmatched pairs. 71748 records in RAM. INFO 2026-06-08 08:45:37 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:11:08s. Time for last 1,000,000: 1s. Last read position: chr17:50,188,617 INFO 2026-06-08 08:45:37 MarkDuplicates Tracking 222367 as yet unmatched pairs. 70879 records in RAM. INFO 2026-06-08 08:45:39 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:11:09s. Time for last 1,000,000: 1s. Last read position: chr17:50,189,229 INFO 2026-06-08 08:45:39 MarkDuplicates Tracking 216528 as yet unmatched pairs. 65040 records in RAM. INFO 2026-06-08 08:45:42 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:11:12s. Time for last 1,000,000: 2s. Last read position: chr17:50,189,695 INFO 2026-06-08 08:45:42 MarkDuplicates Tracking 222127 as yet unmatched pairs. 70639 records in RAM. INFO 2026-06-08 08:45:44 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:11:14s. Time for last 1,000,000: 2s. Last read position: chr17:50,190,333 INFO 2026-06-08 08:45:44 MarkDuplicates Tracking 226524 as yet unmatched pairs. 75035 records in RAM. INFO 2026-06-08 08:45:46 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:11:16s. Time for last 1,000,000: 1s. Last read position: chr17:50,191,477 INFO 2026-06-08 08:45:46 MarkDuplicates Tracking 208059 as yet unmatched pairs. 56570 records in RAM. INFO 2026-06-08 08:45:47 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:11:18s. Time for last 1,000,000: 1s. Last read position: chr17:50,192,664 INFO 2026-06-08 08:45:47 MarkDuplicates Tracking 211341 as yet unmatched pairs. 59852 records in RAM. INFO 2026-06-08 08:45:49 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:11:19s. Time for last 1,000,000: 1s. Last read position: chr17:50,193,976 INFO 2026-06-08 08:45:49 MarkDuplicates Tracking 209413 as yet unmatched pairs. 57924 records in RAM. INFO 2026-06-08 08:45:51 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:11:21s. Time for last 1,000,000: 1s. Last read position: chr17:50,194,409 INFO 2026-06-08 08:45:51 MarkDuplicates Tracking 208252 as yet unmatched pairs. 56763 records in RAM. INFO 2026-06-08 08:45:53 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:11:23s. Time for last 1,000,000: 1s. Last read position: chr17:50,195,061 INFO 2026-06-08 08:45:53 MarkDuplicates Tracking 200941 as yet unmatched pairs. 49452 records in RAM. INFO 2026-06-08 08:45:55 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:11:25s. Time for last 1,000,000: 1s. Last read position: chr17:50,195,613 INFO 2026-06-08 08:45:55 MarkDuplicates Tracking 207357 as yet unmatched pairs. 55868 records in RAM. INFO 2026-06-08 08:45:57 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:11:27s. Time for last 1,000,000: 1s. Last read position: chr17:50,196,330 INFO 2026-06-08 08:45:57 MarkDuplicates Tracking 202667 as yet unmatched pairs. 51178 records in RAM. INFO 2026-06-08 08:45:59 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:11:30s. Time for last 1,000,000: 2s. Last read position: chr17:50,197,045 INFO 2026-06-08 08:45:59 MarkDuplicates Tracking 201921 as yet unmatched pairs. 50432 records in RAM. INFO 2026-06-08 08:46:01 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:11:32s. Time for last 1,000,000: 2s. Last read position: chr17:50,198,177 INFO 2026-06-08 08:46:01 MarkDuplicates Tracking 190879 as yet unmatched pairs. 39389 records in RAM. INFO 2026-06-08 08:46:03 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:11:34s. Time for last 1,000,000: 1s. Last read position: chr17:50,199,443 INFO 2026-06-08 08:46:03 MarkDuplicates Tracking 183743 as yet unmatched pairs. 32253 records in RAM. INFO 2026-06-08 08:46:05 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:11:35s. Time for last 1,000,000: 1s. Last read position: chr17:50,541,599 INFO 2026-06-08 08:46:05 MarkDuplicates Tracking 176410 as yet unmatched pairs. 24920 records in RAM. INFO 2026-06-08 08:46:07 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:11:37s. Time for last 1,000,000: 1s. Last read position: chr17:59,647,495 INFO 2026-06-08 08:46:07 MarkDuplicates Tracking 174688 as yet unmatched pairs. 23198 records in RAM. INFO 2026-06-08 08:46:08 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:11:39s. Time for last 1,000,000: 1s. Last read position: chr17:61,961,007 INFO 2026-06-08 08:46:08 MarkDuplicates Tracking 172201 as yet unmatched pairs. 20711 records in RAM. INFO 2026-06-08 08:46:10 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:11:40s. Time for last 1,000,000: 1s. Last read position: chr17:64,213,654 INFO 2026-06-08 08:46:10 MarkDuplicates Tracking 170048 as yet unmatched pairs. 18558 records in RAM. INFO 2026-06-08 08:46:12 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:11:42s. Time for last 1,000,000: 1s. Last read position: chr17:68,042,155 INFO 2026-06-08 08:46:12 MarkDuplicates Tracking 167911 as yet unmatched pairs. 16421 records in RAM. INFO 2026-06-08 08:46:13 MarkDuplicates Read 368,000,000 records. Elapsed time: 00:11:43s. Time for last 1,000,000: 1s. Last read position: chr17:74,204,156 INFO 2026-06-08 08:46:13 MarkDuplicates Tracking 166480 as yet unmatched pairs. 14990 records in RAM. INFO 2026-06-08 08:46:15 MarkDuplicates Read 369,000,000 records. Elapsed time: 00:11:45s. Time for last 1,000,000: 1s. Last read position: chr17:75,757,255 INFO 2026-06-08 08:46:15 MarkDuplicates Tracking 163419 as yet unmatched pairs. 11928 records in RAM. INFO 2026-06-08 08:46:17 MarkDuplicates Read 370,000,000 records. Elapsed time: 00:11:47s. Time for last 1,000,000: 1s. Last read position: chr17:78,398,275 INFO 2026-06-08 08:46:17 MarkDuplicates Tracking 160863 as yet unmatched pairs. 9370 records in RAM. INFO 2026-06-08 08:46:19 MarkDuplicates Read 371,000,000 records. Elapsed time: 00:11:49s. Time for last 1,000,000: 2s. Last read position: chr17:80,334,154 INFO 2026-06-08 08:46:19 MarkDuplicates Tracking 158673 as yet unmatched pairs. 7180 records in RAM. INFO 2026-06-08 08:46:21 MarkDuplicates Read 372,000,000 records. Elapsed time: 00:11:51s. Time for last 1,000,000: 1s. Last read position: chr17:81,511,999 INFO 2026-06-08 08:46:21 MarkDuplicates Tracking 156377 as yet unmatched pairs. 4884 records in RAM. INFO 2026-06-08 08:46:22 MarkDuplicates Read 373,000,000 records. Elapsed time: 00:11:53s. Time for last 1,000,000: 1s. Last read position: chr17:82,083,096 INFO 2026-06-08 08:46:22 MarkDuplicates Tracking 153742 as yet unmatched pairs. 2248 records in RAM. INFO 2026-06-08 08:46:24 MarkDuplicates Read 374,000,000 records. Elapsed time: 00:11:54s. Time for last 1,000,000: 1s. Last read position: chr18:3,075,720 INFO 2026-06-08 08:46:24 MarkDuplicates Tracking 150898 as yet unmatched pairs. 7782 records in RAM. INFO 2026-06-08 08:46:26 MarkDuplicates Read 375,000,000 records. Elapsed time: 00:11:56s. Time for last 1,000,000: 1s. Last read position: chr18:23,533,418 INFO 2026-06-08 08:46:26 MarkDuplicates Tracking 148911 as yet unmatched pairs. 5795 records in RAM. INFO 2026-06-08 08:46:27 MarkDuplicates Read 376,000,000 records. Elapsed time: 00:11:58s. Time for last 1,000,000: 1s. Last read position: chr18:47,130,281 INFO 2026-06-08 08:46:27 MarkDuplicates Tracking 146807 as yet unmatched pairs. 3691 records in RAM. INFO 2026-06-08 08:46:29 MarkDuplicates Read 377,000,000 records. Elapsed time: 00:11:59s. Time for last 1,000,000: 1s. Last read position: chr18:63,128,611 INFO 2026-06-08 08:46:29 MarkDuplicates Tracking 144932 as yet unmatched pairs. 1816 records in RAM. INFO 2026-06-08 08:46:31 MarkDuplicates Read 378,000,000 records. Elapsed time: 00:12:01s. Time for last 1,000,000: 2s. Last read position: chr19:1,056,929 INFO 2026-06-08 08:46:31 MarkDuplicates Tracking 141975 as yet unmatched pairs. 57339 records in RAM. INFO 2026-06-08 08:46:33 MarkDuplicates Read 379,000,000 records. Elapsed time: 00:12:03s. Time for last 1,000,000: 1s. Last read position: chr19:2,339,857 INFO 2026-06-08 08:46:33 MarkDuplicates Tracking 139270 as yet unmatched pairs. 54634 records in RAM. INFO 2026-06-08 08:46:34 MarkDuplicates Read 380,000,000 records. Elapsed time: 00:12:05s. Time for last 1,000,000: 1s. Last read position: chr19:5,245,818 INFO 2026-06-08 08:46:34 MarkDuplicates Tracking 136545 as yet unmatched pairs. 51909 records in RAM. INFO 2026-06-08 08:46:36 MarkDuplicates Read 381,000,000 records. Elapsed time: 00:12:07s. Time for last 1,000,000: 1s. Last read position: chr19:7,871,639 INFO 2026-06-08 08:46:36 MarkDuplicates Tracking 134400 as yet unmatched pairs. 49764 records in RAM. INFO 2026-06-08 08:46:38 MarkDuplicates Read 382,000,000 records. Elapsed time: 00:12:08s. Time for last 1,000,000: 1s. Last read position: chr19:10,368,055 INFO 2026-06-08 08:46:38 MarkDuplicates Tracking 131859 as yet unmatched pairs. 47222 records in RAM. INFO 2026-06-08 08:46:40 MarkDuplicates Read 383,000,000 records. Elapsed time: 00:12:10s. Time for last 1,000,000: 1s. Last read position: chr19:12,433,113 INFO 2026-06-08 08:46:40 MarkDuplicates Tracking 129584 as yet unmatched pairs. 44947 records in RAM. INFO 2026-06-08 08:46:42 MarkDuplicates Read 384,000,000 records. Elapsed time: 00:12:12s. Time for last 1,000,000: 1s. Last read position: chr19:14,155,487 INFO 2026-06-08 08:46:42 MarkDuplicates Tracking 126986 as yet unmatched pairs. 42349 records in RAM. INFO 2026-06-08 08:46:44 MarkDuplicates Read 385,000,000 records. Elapsed time: 00:12:14s. Time for last 1,000,000: 2s. Last read position: chr19:15,265,391 INFO 2026-06-08 08:46:44 MarkDuplicates Tracking 125079 as yet unmatched pairs. 40442 records in RAM. INFO 2026-06-08 08:46:46 MarkDuplicates Read 386,000,000 records. Elapsed time: 00:12:16s. Time for last 1,000,000: 1s. Last read position: chr19:17,726,001 INFO 2026-06-08 08:46:46 MarkDuplicates Tracking 122047 as yet unmatched pairs. 37409 records in RAM. INFO 2026-06-08 08:46:47 MarkDuplicates Read 387,000,000 records. Elapsed time: 00:12:18s. Time for last 1,000,000: 1s. Last read position: chr19:19,180,653 INFO 2026-06-08 08:46:47 MarkDuplicates Tracking 119536 as yet unmatched pairs. 34898 records in RAM. INFO 2026-06-08 08:46:49 MarkDuplicates Read 388,000,000 records. Elapsed time: 00:12:19s. Time for last 1,000,000: 1s. Last read position: chr19:35,060,760 INFO 2026-06-08 08:46:49 MarkDuplicates Tracking 117177 as yet unmatched pairs. 32539 records in RAM. INFO 2026-06-08 08:46:51 MarkDuplicates Read 389,000,000 records. Elapsed time: 00:12:21s. Time for last 1,000,000: 1s. Last read position: chr19:38,081,893 INFO 2026-06-08 08:46:51 MarkDuplicates Tracking 114651 as yet unmatched pairs. 30013 records in RAM. INFO 2026-06-08 08:46:52 MarkDuplicates Read 390,000,000 records. Elapsed time: 00:12:22s. Time for last 1,000,000: 1s. Last read position: chr19:39,433,558 INFO 2026-06-08 08:46:52 MarkDuplicates Tracking 112656 as yet unmatched pairs. 28018 records in RAM. INFO 2026-06-08 08:46:54 MarkDuplicates Read 391,000,000 records. Elapsed time: 00:12:24s. Time for last 1,000,000: 1s. Last read position: chr19:39,972,542 INFO 2026-06-08 08:46:54 MarkDuplicates Tracking 110027 as yet unmatched pairs. 25389 records in RAM. INFO 2026-06-08 08:46:55 MarkDuplicates Read 392,000,000 records. Elapsed time: 00:12:26s. Time for last 1,000,000: 1s. Last read position: chr19:41,720,017 INFO 2026-06-08 08:46:55 MarkDuplicates Tracking 107950 as yet unmatched pairs. 23293 records in RAM. INFO 2026-06-08 08:46:57 MarkDuplicates Read 393,000,000 records. Elapsed time: 00:12:27s. Time for last 1,000,000: 1s. Last read position: chr19:42,316,522 INFO 2026-06-08 08:46:57 MarkDuplicates Tracking 105641 as yet unmatched pairs. 20984 records in RAM. INFO 2026-06-08 08:46:59 MarkDuplicates Read 394,000,000 records. Elapsed time: 00:12:29s. Time for last 1,000,000: 1s. Last read position: chr19:45,052,817 INFO 2026-06-08 08:46:59 MarkDuplicates Tracking 103006 as yet unmatched pairs. 18348 records in RAM. INFO 2026-06-08 08:47:01 MarkDuplicates Read 395,000,000 records. Elapsed time: 00:12:31s. Time for last 1,000,000: 2s. Last read position: chr19:46,724,915 INFO 2026-06-08 08:47:01 MarkDuplicates Tracking 100556 as yet unmatched pairs. 15898 records in RAM. INFO 2026-06-08 08:47:03 MarkDuplicates Read 396,000,000 records. Elapsed time: 00:12:33s. Time for last 1,000,000: 2s. Last read position: chr19:48,613,010 INFO 2026-06-08 08:47:03 MarkDuplicates Tracking 98099 as yet unmatched pairs. 13441 records in RAM. INFO 2026-06-08 08:47:05 MarkDuplicates Read 397,000,000 records. Elapsed time: 00:12:35s. Time for last 1,000,000: 1s. Last read position: chr19:49,594,764 INFO 2026-06-08 08:47:05 MarkDuplicates Tracking 95730 as yet unmatched pairs. 11072 records in RAM. INFO 2026-06-08 08:47:07 MarkDuplicates Read 398,000,000 records. Elapsed time: 00:12:37s. Time for last 1,000,000: 1s. Last read position: chr19:51,416,313 INFO 2026-06-08 08:47:07 MarkDuplicates Tracking 93294 as yet unmatched pairs. 8636 records in RAM. INFO 2026-06-08 08:47:08 MarkDuplicates Read 399,000,000 records. Elapsed time: 00:12:38s. Time for last 1,000,000: 1s. Last read position: chr19:54,456,662 INFO 2026-06-08 08:47:08 MarkDuplicates Tracking 91302 as yet unmatched pairs. 6644 records in RAM. INFO 2026-06-08 08:47:10 MarkDuplicates Read 400,000,000 records. Elapsed time: 00:12:40s. Time for last 1,000,000: 1s. Last read position: chr19:55,616,437 INFO 2026-06-08 08:47:10 MarkDuplicates Tracking 88524 as yet unmatched pairs. 3866 records in RAM. INFO 2026-06-08 08:47:11 MarkDuplicates Read 401,000,000 records. Elapsed time: 00:12:42s. Time for last 1,000,000: 1s. Last read position: chr19:57,858,648 INFO 2026-06-08 08:47:11 MarkDuplicates Tracking 86798 as yet unmatched pairs. 2140 records in RAM. INFO 2026-06-08 08:47:13 MarkDuplicates Read 402,000,000 records. Elapsed time: 00:12:44s. Time for last 1,000,000: 1s. Last read position: chr20:1,372,219 INFO 2026-06-08 08:47:13 MarkDuplicates Tracking 84397 as yet unmatched pairs. 22059 records in RAM. INFO 2026-06-08 08:47:15 MarkDuplicates Read 403,000,000 records. Elapsed time: 00:12:45s. Time for last 1,000,000: 1s. Last read position: chr20:5,547,654 INFO 2026-06-08 08:47:15 MarkDuplicates Tracking 81659 as yet unmatched pairs. 19320 records in RAM. INFO 2026-06-08 08:47:17 MarkDuplicates Read 404,000,000 records. Elapsed time: 00:12:47s. Time for last 1,000,000: 2s. Last read position: chr20:21,340,730 INFO 2026-06-08 08:47:17 MarkDuplicates Tracking 79367 as yet unmatched pairs. 17028 records in RAM. INFO 2026-06-08 08:47:19 MarkDuplicates Read 405,000,000 records. Elapsed time: 00:12:49s. Time for last 1,000,000: 2s. Last read position: chr20:33,789,522 INFO 2026-06-08 08:47:19 MarkDuplicates Tracking 76982 as yet unmatched pairs. 14643 records in RAM. INFO 2026-06-08 08:47:22 MarkDuplicates Read 406,000,000 records. Elapsed time: 00:12:52s. Time for last 1,000,000: 2s. Last read position: chr20:36,525,940 INFO 2026-06-08 08:47:22 MarkDuplicates Tracking 74702 as yet unmatched pairs. 12363 records in RAM. INFO 2026-06-08 08:47:24 MarkDuplicates Read 407,000,000 records. Elapsed time: 00:12:55s. Time for last 1,000,000: 2s. Last read position: chr20:43,460,933 INFO 2026-06-08 08:47:24 MarkDuplicates Tracking 72679 as yet unmatched pairs. 10340 records in RAM. INFO 2026-06-08 08:47:26 MarkDuplicates Read 408,000,000 records. Elapsed time: 00:12:56s. Time for last 1,000,000: 1s. Last read position: chr20:47,663,526 INFO 2026-06-08 08:47:26 MarkDuplicates Tracking 70219 as yet unmatched pairs. 7880 records in RAM. INFO 2026-06-08 08:47:28 MarkDuplicates Read 409,000,000 records. Elapsed time: 00:12:58s. Time for last 1,000,000: 1s. Last read position: chr20:54,028,551 INFO 2026-06-08 08:47:28 MarkDuplicates Tracking 68067 as yet unmatched pairs. 5727 records in RAM. INFO 2026-06-08 08:47:29 MarkDuplicates Read 410,000,000 records. Elapsed time: 00:13:00s. Time for last 1,000,000: 1s. Last read position: chr20:62,323,592 INFO 2026-06-08 08:47:29 MarkDuplicates Tracking 65827 as yet unmatched pairs. 3487 records in RAM. INFO 2026-06-08 08:47:31 MarkDuplicates Read 411,000,000 records. Elapsed time: 00:13:01s. Time for last 1,000,000: 1s. Last read position: chr20:63,697,039 INFO 2026-06-08 08:47:31 MarkDuplicates Tracking 63170 as yet unmatched pairs. 830 records in RAM. INFO 2026-06-08 08:47:32 MarkDuplicates Read 412,000,000 records. Elapsed time: 00:13:03s. Time for last 1,000,000: 1s. Last read position: chr21:8,258,926 INFO 2026-06-08 08:47:32 MarkDuplicates Tracking 61649 as yet unmatched pairs. 11334 records in RAM. INFO 2026-06-08 08:47:34 MarkDuplicates Read 413,000,000 records. Elapsed time: 00:13:04s. Time for last 1,000,000: 1s. Last read position: chr21:13,936,917 INFO 2026-06-08 08:47:34 MarkDuplicates Tracking 60545 as yet unmatched pairs. 10230 records in RAM. INFO 2026-06-08 08:47:35 MarkDuplicates Read 414,000,000 records. Elapsed time: 00:13:06s. Time for last 1,000,000: 1s. Last read position: chr21:33,552,915 INFO 2026-06-08 08:47:35 MarkDuplicates Tracking 58467 as yet unmatched pairs. 8152 records in RAM. INFO 2026-06-08 08:47:38 MarkDuplicates Read 415,000,000 records. Elapsed time: 00:13:09s. Time for last 1,000,000: 3s. Last read position: chr21:39,348,912 INFO 2026-06-08 08:47:38 MarkDuplicates Tracking 56187 as yet unmatched pairs. 5871 records in RAM. INFO 2026-06-08 08:47:40 MarkDuplicates Read 416,000,000 records. Elapsed time: 00:13:10s. Time for last 1,000,000: 1s. Last read position: chr21:44,777,285 INFO 2026-06-08 08:47:40 MarkDuplicates Tracking 54043 as yet unmatched pairs. 3727 records in RAM. INFO 2026-06-08 08:47:42 MarkDuplicates Read 417,000,000 records. Elapsed time: 00:13:12s. Time for last 1,000,000: 1s. Last read position: chr21:46,126,044 INFO 2026-06-08 08:47:42 MarkDuplicates Tracking 51403 as yet unmatched pairs. 1087 records in RAM. INFO 2026-06-08 08:47:44 MarkDuplicates Read 418,000,000 records. Elapsed time: 00:13:15s. Time for last 1,000,000: 2s. Last read position: chr22:20,086,173 INFO 2026-06-08 08:47:44 MarkDuplicates Tracking 49011 as yet unmatched pairs. 22802 records in RAM. INFO 2026-06-08 08:47:46 MarkDuplicates Read 419,000,000 records. Elapsed time: 00:13:16s. Time for last 1,000,000: 1s. Last read position: chr22:23,766,191 INFO 2026-06-08 08:47:46 MarkDuplicates Tracking 46942 as yet unmatched pairs. 20733 records in RAM. INFO 2026-06-08 08:47:48 MarkDuplicates Read 420,000,000 records. Elapsed time: 00:13:18s. Time for last 1,000,000: 1s. Last read position: chr22:28,795,329 INFO 2026-06-08 08:47:48 MarkDuplicates Tracking 46770 as yet unmatched pairs. 20561 records in RAM. INFO 2026-06-08 08:47:49 MarkDuplicates Read 421,000,000 records. Elapsed time: 00:13:20s. Time for last 1,000,000: 1s. Last read position: chr22:29,825,705 INFO 2026-06-08 08:47:49 MarkDuplicates Tracking 42023 as yet unmatched pairs. 15814 records in RAM. INFO 2026-06-08 08:47:51 MarkDuplicates Read 422,000,000 records. Elapsed time: 00:13:22s. Time for last 1,000,000: 2s. Last read position: chr22:35,744,203 INFO 2026-06-08 08:47:51 MarkDuplicates Tracking 39656 as yet unmatched pairs. 13446 records in RAM. INFO 2026-06-08 08:47:53 MarkDuplicates Read 423,000,000 records. Elapsed time: 00:13:24s. Time for last 1,000,000: 1s. Last read position: chr22:37,282,581 INFO 2026-06-08 08:47:53 MarkDuplicates Tracking 37194 as yet unmatched pairs. 10984 records in RAM. INFO 2026-06-08 08:47:55 MarkDuplicates Read 424,000,000 records. Elapsed time: 00:13:25s. Time for last 1,000,000: 1s. Last read position: chr22:38,699,862 INFO 2026-06-08 08:47:55 MarkDuplicates Tracking 34565 as yet unmatched pairs. 8355 records in RAM. INFO 2026-06-08 08:47:57 MarkDuplicates Read 425,000,000 records. Elapsed time: 00:13:27s. Time for last 1,000,000: 1s. Last read position: chr22:41,249,307 INFO 2026-06-08 08:47:57 MarkDuplicates Tracking 32356 as yet unmatched pairs. 6146 records in RAM. INFO 2026-06-08 08:47:59 MarkDuplicates Read 426,000,000 records. Elapsed time: 00:13:29s. Time for last 1,000,000: 1s. Last read position: chr22:46,364,512 INFO 2026-06-08 08:47:59 MarkDuplicates Tracking 30491 as yet unmatched pairs. 4280 records in RAM. INFO 2026-06-08 08:48:00 MarkDuplicates Read 427,000,000 records. Elapsed time: 00:13:30s. Time for last 1,000,000: 1s. Last read position: chr22:50,462,925 INFO 2026-06-08 08:48:00 MarkDuplicates Tracking 27415 as yet unmatched pairs. 1204 records in RAM. INFO 2026-06-08 08:48:02 MarkDuplicates Read 428,000,000 records. Elapsed time: 00:13:32s. Time for last 1,000,000: 1s. Last read position: chrX:3,323,597 INFO 2026-06-08 08:48:02 MarkDuplicates Tracking 24920 as yet unmatched pairs. 21501 records in RAM. INFO 2026-06-08 08:48:04 MarkDuplicates Read 429,000,000 records. Elapsed time: 00:13:34s. Time for last 1,000,000: 1s. Last read position: chrX:21,977,002 INFO 2026-06-08 08:48:04 MarkDuplicates Tracking 22782 as yet unmatched pairs. 19363 records in RAM. INFO 2026-06-08 08:48:05 MarkDuplicates Read 430,000,000 records. Elapsed time: 00:13:35s. Time for last 1,000,000: 1s. Last read position: chrX:41,229,701 INFO 2026-06-08 08:48:05 MarkDuplicates Tracking 21035 as yet unmatched pairs. 17616 records in RAM. INFO 2026-06-08 08:48:07 MarkDuplicates Read 431,000,000 records. Elapsed time: 00:13:37s. Time for last 1,000,000: 1s. Last read position: chrX:48,906,517 INFO 2026-06-08 08:48:07 MarkDuplicates Tracking 18745 as yet unmatched pairs. 15326 records in RAM. INFO 2026-06-08 08:48:08 MarkDuplicates Read 432,000,000 records. Elapsed time: 00:13:39s. Time for last 1,000,000: 1s. Last read position: chrX:53,607,528 INFO 2026-06-08 08:48:08 MarkDuplicates Tracking 16755 as yet unmatched pairs. 13336 records in RAM. INFO 2026-06-08 08:48:10 MarkDuplicates Read 433,000,000 records. Elapsed time: 00:13:40s. Time for last 1,000,000: 1s. Last read position: chrX:71,247,733 INFO 2026-06-08 08:48:10 MarkDuplicates Tracking 14373 as yet unmatched pairs. 10954 records in RAM. INFO 2026-06-08 08:48:11 MarkDuplicates Read 434,000,000 records. Elapsed time: 00:13:42s. Time for last 1,000,000: 1s. Last read position: chrX:77,853,919 INFO 2026-06-08 08:48:11 MarkDuplicates Tracking 12528 as yet unmatched pairs. 9109 records in RAM. INFO 2026-06-08 08:48:13 MarkDuplicates Read 435,000,000 records. Elapsed time: 00:13:43s. Time for last 1,000,000: 1s. Last read position: chrX:107,759,599 INFO 2026-06-08 08:48:13 MarkDuplicates Tracking 10493 as yet unmatched pairs. 7074 records in RAM. INFO 2026-06-08 08:48:14 MarkDuplicates Read 436,000,000 records. Elapsed time: 00:13:45s. Time for last 1,000,000: 1s. Last read position: chrX:129,911,006 INFO 2026-06-08 08:48:14 MarkDuplicates Tracking 8467 as yet unmatched pairs. 5048 records in RAM. INFO 2026-06-08 08:48:16 MarkDuplicates Read 437,000,000 records. Elapsed time: 00:13:46s. Time for last 1,000,000: 1s. Last read position: chrX:153,797,493 INFO 2026-06-08 08:48:16 MarkDuplicates Tracking 6467 as yet unmatched pairs. 3047 records in RAM. INFO 2026-06-08 08:48:18 MarkDuplicates Read 438,000,000 records. Elapsed time: 00:13:48s. Time for last 1,000,000: 1s. Last read position: chrX:154,488,682 INFO 2026-06-08 08:48:18 MarkDuplicates Tracking 3851 as yet unmatched pairs. 431 records in RAM. INFO 2026-06-08 08:48:19 MarkDuplicates Read 439,000,000 records. Elapsed time: 00:13:49s. Time for last 1,000,000: 1s. Last read position: GL000220.1:159,472 INFO 2026-06-08 08:48:19 MarkDuplicates Tracking 2450 as yet unmatched pairs. 24 records in RAM. INFO 2026-06-08 08:48:20 MarkDuplicates Read 440,000,000 records. Elapsed time: 00:13:50s. Time for last 1,000,000: 1s. Last read position: KI270733.1:177,457 INFO 2026-06-08 08:48:20 MarkDuplicates Tracking 79 as yet unmatched pairs. 21 records in RAM. INFO 2026-06-08 08:48:20 MarkDuplicates Read 440255791 records. 0 pairs never matched. INFO 2026-06-08 08:49:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 38302428712; totalMemory: 54693724160; maxMemory: 63585648640 INFO 2026-06-08 08:49:14 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk. INFO 2026-06-08 08:49:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2026-06-08 08:49:52 OpticalDuplicateFinder Large duplicate set. size = 1869 INFO 2026-06-08 08:49:52 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-18,819 INFO 2026-06-08 08:49:52 OpticalDuplicateFinder Large duplicate set. size = 1380 INFO 2026-06-08 08:49:52 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,283 INFO 2026-06-08 08:49:58 OpticalDuplicateFinder Large duplicate set. size = 1134 INFO 2026-06-08 08:49:58 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:7,836 INFO 2026-06-08 08:49:58 OpticalDuplicateFinder Large duplicate set. size = 1157 INFO 2026-06-08 08:49:58 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:1,073 INFO 2026-06-08 08:49:58 OpticalDuplicateFinder Large duplicate set. size = 1129 INFO 2026-06-08 08:49:58 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:2,270 INFO 2026-06-08 08:49:58 OpticalDuplicateFinder Large duplicate set. size = 1903 INFO 2026-06-08 08:49:58 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:14,607 INFO 2026-06-08 08:49:58 OpticalDuplicateFinder Large duplicate set. size = 1091 INFO 2026-06-08 08:49:58 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,709 INFO 2026-06-08 08:50:21 OpticalDuplicateFinder Large duplicate set. size = 1031 INFO 2026-06-08 08:50:21 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-13,682 INFO 2026-06-08 08:50:21 OpticalDuplicateFinder Large duplicate set. size = 1440 INFO 2026-06-08 08:50:21 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:10,570 INFO 2026-06-08 08:50:21 OpticalDuplicateFinder Large duplicate set. size = 1288 INFO 2026-06-08 08:50:21 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:17,010 INFO 2026-06-08 08:50:21 OpticalDuplicateFinder Large duplicate set. size = 1292 INFO 2026-06-08 08:50:21 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,188 INFO 2026-06-08 08:50:21 OpticalDuplicateFinder Large duplicate set. size = 1013 INFO 2026-06-08 08:50:21 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,465 INFO 2026-06-08 08:50:21 OpticalDuplicateFinder Large duplicate set. size = 1192 INFO 2026-06-08 08:50:21 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,754 INFO 2026-06-08 08:50:21 OpticalDuplicateFinder Large duplicate set. size = 1486 INFO 2026-06-08 08:50:21 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,500 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder Large duplicate set. size = 1176 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:25,553 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder Large duplicate set. size = 1011 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-14,985 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder Large duplicate set. size = 1741 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:26,176 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder Large duplicate set. size = 1176 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,308 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder Large duplicate set. size = 1048 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,025 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder Large duplicate set. size = 1149 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,462 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder Large duplicate set. size = 1476 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:14,915 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder Large duplicate set. size = 1058 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:15,441 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder Large duplicate set. size = 1089 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,014 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder Large duplicate set. size = 1295 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-25,688 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder Large duplicate set. size = 1163 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-14,580 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder Large duplicate set. size = 1100 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,121 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder Large duplicate set. size = 1140 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,579 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder Large duplicate set. size = 1166 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-19,863 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder Large duplicate set. size = 1300 INFO 2026-06-08 08:50:22 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,359 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder Large duplicate set. size = 1177 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:25,246 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder Large duplicate set. size = 1401 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:10,554 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder Large duplicate set. size = 1516 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-19,159 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder Large duplicate set. size = 1235 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,433 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder Large duplicate set. size = 1046 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,830 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder Large duplicate set. size = 1507 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,559 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder Large duplicate set. size = 1377 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,774 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder Large duplicate set. size = 1603 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:21,888 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder Large duplicate set. size = 1299 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,723 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder Large duplicate set. size = 2445 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-27,937 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:10,312 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder Large duplicate set. size = 1363 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:23,280 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder Large duplicate set. size = 1516 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:24,688 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder Large duplicate set. size = 1627 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,342 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder Large duplicate set. size = 1015 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:26,184 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder Large duplicate set. size = 1013 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:7,820 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder Large duplicate set. size = 1216 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,127 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder Large duplicate set. size = 1955 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:23,070 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder Large duplicate set. size = 1062 INFO 2026-06-08 08:50:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:7,213 INFO 2026-06-08 08:50:24 OpticalDuplicateFinder Large duplicate set. size = 1626 INFO 2026-06-08 08:50:24 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,190 INFO 2026-06-08 08:50:24 OpticalDuplicateFinder Large duplicate set. size = 1372 INFO 2026-06-08 08:50:24 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:6,145 INFO 2026-06-08 08:50:48 MarkDuplicates Traversing fragment information and detecting duplicates. WARNING 2026-06-08 08:50:48 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered. INFO 2026-06-08 08:51:34 MarkDuplicates Sorting list of duplicate records. INFO 2026-06-08 08:51:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 204602368; totalMemory: 234881024; maxMemory: 63585648640 INFO 2026-06-08 08:51:35 MarkDuplicates Marking 290686890 records as duplicates. INFO 2026-06-08 08:51:35 MarkDuplicates Found 7162613 optical duplicate clusters. INFO 2026-06-08 08:51:35 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2026-06-08 08:51:53 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:17s. Time for last 10,000,000: 17s. Last read position: chr1:45,511,379 INFO 2026-06-08 08:52:09 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:33s. Time for last 10,000,000: 16s. Last read position: chr1:149,463,915 INFO 2026-06-08 08:52:26 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:50s. Time for last 10,000,000: 16s. Last read position: chr1:161,542,655 INFO 2026-06-08 08:52:43 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:07s. Time for last 10,000,000: 17s. Last read position: chr1:225,652,694 INFO 2026-06-08 08:53:00 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:24s. Time for last 10,000,000: 16s. Last read position: chr2:47,162,287 INFO 2026-06-08 08:53:17 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:42s. Time for last 10,000,000: 17s. Last read position: chr2:151,655,920 INFO 2026-06-08 08:53:34 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:01:59s. Time for last 10,000,000: 17s. Last read position: chr2:189,034,122 INFO 2026-06-08 08:53:52 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:17s. Time for last 10,000,000: 17s. Last read position: chr2:215,419,320 INFO 2026-06-08 08:54:14 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:38s. Time for last 10,000,000: 21s. Last read position: chr3:42,620,037 INFO 2026-06-08 08:54:33 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:57s. Time for last 10,000,000: 18s. Last read position: chr3:129,561,670 INFO 2026-06-08 08:54:54 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:03:18s. Time for last 10,000,000: 21s. Last read position: chr4:39,898,389 INFO 2026-06-08 08:55:12 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:36s. Time for last 10,000,000: 17s. Last read position: chr5:36,984,671 INFO 2026-06-08 08:55:31 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:55s. Time for last 10,000,000: 19s. Last read position: chr5:138,164,889 INFO 2026-06-08 08:55:48 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:04:12s. Time for last 10,000,000: 17s. Last read position: chr5:179,873,119 INFO 2026-06-08 08:56:05 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:04:29s. Time for last 10,000,000: 16s. Last read position: chr6:33,417,517 INFO 2026-06-08 08:56:22 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:47s. Time for last 10,000,000: 17s. Last read position: chr6:169,723,999 INFO 2026-06-08 08:56:39 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:05:03s. Time for last 10,000,000: 16s. Last read position: chr7:93,131,216 INFO 2026-06-08 08:56:56 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:05:20s. Time for last 10,000,000: 16s. Last read position: chr7:152,230,309 INFO 2026-06-08 08:57:13 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:05:37s. Time for last 10,000,000: 17s. Last read position: chr8:123,768,731 INFO 2026-06-08 08:57:29 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:05:54s. Time for last 10,000,000: 16s. Last read position: chr9:88,475,476 INFO 2026-06-08 08:57:45 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:06:10s. Time for last 10,000,000: 16s. Last read position: chr10:13,666,086 INFO 2026-06-08 08:58:01 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:06:26s. Time for last 10,000,000: 16s. Last read position: chr10:116,906,669 INFO 2026-06-08 08:58:18 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:06:42s. Time for last 10,000,000: 16s. Last read position: chr11:61,368,624 INFO 2026-06-08 08:58:34 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:06:58s. Time for last 10,000,000: 16s. Last read position: chr11:75,401,707 INFO 2026-06-08 08:58:50 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:07:14s. Time for last 10,000,000: 16s. Last read position: chr12:12,477,294 INFO 2026-06-08 08:59:07 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:07:31s. Time for last 10,000,000: 16s. Last read position: chr12:55,954,203 INFO 2026-06-08 08:59:23 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:07:48s. Time for last 10,000,000: 16s. Last read position: chr12:120,144,971 INFO 2026-06-08 08:59:41 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:08:05s. Time for last 10,000,000: 17s. Last read position: chr14:24,267,763 INFO 2026-06-08 08:59:57 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:08:22s. Time for last 10,000,000: 16s. Last read position: chr14:104,941,207 INFO 2026-06-08 09:00:14 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:08:39s. Time for last 10,000,000: 16s. Last read position: chr15:85,707,962 INFO 2026-06-08 09:00:31 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:08:55s. Time for last 10,000,000: 16s. Last read position: chr16:16,318,851 INFO 2026-06-08 09:00:48 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:09:12s. Time for last 10,000,000: 16s. Last read position: chr16:30,711,983 INFO 2026-06-08 09:01:05 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:09:29s. Time for last 10,000,000: 16s. Last read position: chr17:7,849,814 INFO 2026-06-08 09:01:22 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:09:46s. Time for last 10,000,000: 16s. Last read position: chr17:41,524,875 INFO 2026-06-08 09:01:38 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:10:03s. Time for last 10,000,000: 16s. Last read position: chr17:50,189,229 INFO 2026-06-08 09:01:55 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:10:19s. Time for last 10,000,000: 16s. Last read position: chr17:50,197,045 INFO 2026-06-08 09:02:11 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:10:35s. Time for last 10,000,000: 16s. Last read position: chr17:78,398,275 INFO 2026-06-08 09:02:27 MarkDuplicates Written 380,000,000 records. Elapsed time: 00:10:51s. Time for last 10,000,000: 15s. Last read position: chr19:5,245,818 INFO 2026-06-08 09:02:43 MarkDuplicates Written 390,000,000 records. Elapsed time: 00:11:07s. Time for last 10,000,000: 16s. Last read position: chr19:39,433,558 INFO 2026-06-08 09:02:59 MarkDuplicates Written 400,000,000 records. Elapsed time: 00:11:23s. Time for last 10,000,000: 16s. Last read position: chr19:55,616,437 INFO 2026-06-08 09:03:16 MarkDuplicates Written 410,000,000 records. Elapsed time: 00:11:40s. Time for last 10,000,000: 16s. Last read position: chr20:62,323,592 INFO 2026-06-08 09:03:32 MarkDuplicates Written 420,000,000 records. Elapsed time: 00:11:57s. Time for last 10,000,000: 16s. Last read position: chr22:28,795,329 INFO 2026-06-08 09:03:49 MarkDuplicates Written 430,000,000 records. Elapsed time: 00:12:13s. Time for last 10,000,000: 16s. Last read position: chrX:41,229,701 INFO 2026-06-08 09:04:05 MarkDuplicates Written 440,000,000 records. Elapsed time: 00:12:29s. Time for last 10,000,000: 16s. Last read position: KI270733.1:177,457 INFO 2026-06-08 09:04:13 MarkDuplicates Writing complete. Closing input iterator. INFO 2026-06-08 09:04:13 MarkDuplicates Duplicate Index cleanup. INFO 2026-06-08 09:04:13 MarkDuplicates Getting Memory Stats. INFO 2026-06-08 09:04:13 MarkDuplicates Before output close freeMemory: 204578272; totalMemory: 234881024; maxMemory: 63585648640 INFO 2026-06-08 09:04:13 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2026-06-08 09:04:13 MarkDuplicates After output close freeMemory: 104815696; totalMemory: 134217728; maxMemory: 63585648640 [Mon Jun 08 09:04:13 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 29.75 minutes. Runtime.totalMemory()=134217728 ls: *cram: No such file or directory ls: *.crai: No such file or directory