Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/0d7ee4cf82c2695950ec1366afa6f4/.command.sh Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/0d7ee4cf82c2695950ec1366afa6f4/.command.run Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/c82f3abe66dde4df84f5b367dc575a/aih-tih-sc-33eb27-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam ==> STAGING COMPLETE (5 inputs) Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT aih-tih-sc-33eb27-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-33eb27-R1_A23WJ53LT4_1.md.bam --METRICS_FILE aih-tih-sc-33eb27-R1_A23WJ53LT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT 08:42:22.141 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 08:42:22 GMT 2026] MarkDuplicates --INPUT aih-tih-sc-33eb27-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-33eb27-R1_A23WJ53LT4_1.md.bam --METRICS_FILE aih-tih-sc-33eb27-R1_A23WJ53LT4_1.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Mon Jun 08 08:42:22 GMT 2026] Executing as ?@nf-0d0d7ee4cf82c2695950ec1366afa6f4-aa278-t7dd9 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 08:42:22 MarkDuplicates Start of doWork freeMemory: 105829376; totalMemory: 134217728; maxMemory: 63585648640 INFO 2026-06-08 08:42:22 MarkDuplicates Reading input file and constructing read end information. INFO 2026-06-08 08:42:22 MarkDuplicates Will retain up to 230382784 data points before spilling to disk. INFO 2026-06-08 08:42:26 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:1,319,403 INFO 2026-06-08 08:42:26 MarkDuplicates Tracking 1740 as yet unmatched pairs. 114 records in RAM. INFO 2026-06-08 08:42:28 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 2s. Last read position: chr1:2,556,677 INFO 2026-06-08 08:42:28 MarkDuplicates Tracking 3626 as yet unmatched pairs. 274 records in RAM. INFO 2026-06-08 08:42:30 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: chr1:8,656,161 INFO 2026-06-08 08:42:30 MarkDuplicates Tracking 5024 as yet unmatched pairs. 9 records in RAM. INFO 2026-06-08 08:42:32 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: chr1:11,922,779 INFO 2026-06-08 08:42:32 MarkDuplicates Tracking 6787 as yet unmatched pairs. 184 records in RAM. INFO 2026-06-08 08:42:34 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: chr1:16,148,976 INFO 2026-06-08 08:42:34 MarkDuplicates Tracking 8272 as yet unmatched pairs. 101 records in RAM. INFO 2026-06-08 08:42:36 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 2s. Last read position: chr1:19,244,984 INFO 2026-06-08 08:42:36 MarkDuplicates Tracking 9751 as yet unmatched pairs. 7 records in RAM. INFO 2026-06-08 08:42:38 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: chr1:21,834,881 INFO 2026-06-08 08:42:38 MarkDuplicates Tracking 11356 as yet unmatched pairs. 147 records in RAM. INFO 2026-06-08 08:42:40 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr1:22,639,231 INFO 2026-06-08 08:42:40 MarkDuplicates Tracking 13368 as yet unmatched pairs. 543 records in RAM. INFO 2026-06-08 08:42:41 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: chr1:24,651,355 INFO 2026-06-08 08:42:41 MarkDuplicates Tracking 14441 as yet unmatched pairs. 79 records in RAM. INFO 2026-06-08 08:42:43 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: chr1:26,921,801 INFO 2026-06-08 08:42:43 MarkDuplicates Tracking 15889 as yet unmatched pairs. 27 records in RAM. INFO 2026-06-08 08:42:45 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 1s. Last read position: chr1:31,261,538 INFO 2026-06-08 08:42:45 MarkDuplicates Tracking 17499 as yet unmatched pairs. 152 records in RAM. INFO 2026-06-08 08:42:47 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 2s. Last read position: chr1:32,332,729 INFO 2026-06-08 08:42:47 MarkDuplicates Tracking 18959 as yet unmatched pairs. 75 records in RAM. INFO 2026-06-08 08:42:49 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 2s. Last read position: chr1:33,330,085 INFO 2026-06-08 08:42:49 MarkDuplicates Tracking 20563 as yet unmatched pairs. 143 records in RAM. INFO 2026-06-08 08:42:52 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 2s. Last read position: chr1:36,178,693 INFO 2026-06-08 08:42:52 MarkDuplicates Tracking 22101 as yet unmatched pairs. 48 records in RAM. INFO 2026-06-08 08:42:53 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 1s. Last read position: chr1:39,388,322 INFO 2026-06-08 08:42:53 MarkDuplicates Tracking 23647 as yet unmatched pairs. 202 records in RAM. INFO 2026-06-08 08:42:55 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 1s. Last read position: chr1:41,570,473 INFO 2026-06-08 08:42:55 MarkDuplicates Tracking 24903 as yet unmatched pairs. 13 records in RAM. INFO 2026-06-08 08:42:57 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 1s. Last read position: chr1:43,569,621 INFO 2026-06-08 08:42:57 MarkDuplicates Tracking 26827 as yet unmatched pairs. 355 records in RAM. INFO 2026-06-08 08:42:59 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 1s. Last read position: chr1:44,778,604 INFO 2026-06-08 08:42:59 MarkDuplicates Tracking 28083 as yet unmatched pairs. 14 records in RAM. INFO 2026-06-08 08:43:00 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 1s. Last read position: chr1:46,286,100 INFO 2026-06-08 08:43:00 MarkDuplicates Tracking 29790 as yet unmatched pairs. 257 records in RAM. INFO 2026-06-08 08:43:02 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 1s. Last read position: chr1:52,687,891 INFO 2026-06-08 08:43:02 MarkDuplicates Tracking 31254 as yet unmatched pairs. 118 records in RAM. INFO 2026-06-08 08:43:03 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 1s. Last read position: chr1:55,178,054 INFO 2026-06-08 08:43:03 MarkDuplicates Tracking 32543 as yet unmatched pairs. 9 records in RAM. INFO 2026-06-08 08:43:05 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 1s. Last read position: chr1:67,042,267 INFO 2026-06-08 08:43:05 MarkDuplicates Tracking 34129 as yet unmatched pairs. 111 records in RAM. INFO 2026-06-08 08:43:06 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 1s. Last read position: chr1:86,880,695 INFO 2026-06-08 08:43:06 MarkDuplicates Tracking 35774 as yet unmatched pairs. 391 records in RAM. INFO 2026-06-08 08:43:08 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 1s. Last read position: chr1:94,983,233 INFO 2026-06-08 08:43:08 MarkDuplicates Tracking 36706 as yet unmatched pairs. 94 records in RAM. INFO 2026-06-08 08:43:10 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 2s. Last read position: chr1:109,355,444 INFO 2026-06-08 08:43:10 MarkDuplicates Tracking 38016 as yet unmatched pairs. 164 records in RAM. INFO 2026-06-08 08:43:11 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 1s. Last read position: chr1:112,520,738 INFO 2026-06-08 08:43:11 MarkDuplicates Tracking 39423 as yet unmatched pairs. 66 records in RAM. INFO 2026-06-08 08:43:13 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 1s. Last read position: chr1:114,708,027 INFO 2026-06-08 08:43:13 MarkDuplicates Tracking 40808 as yet unmatched pairs. 94 records in RAM. INFO 2026-06-08 08:43:15 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 1s. Last read position: chr1:117,025,599 INFO 2026-06-08 08:43:15 MarkDuplicates Tracking 42012 as yet unmatched pairs. 24 records in RAM. INFO 2026-06-08 08:43:16 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 1s. Last read position: chr1:119,997,158 INFO 2026-06-08 08:43:16 MarkDuplicates Tracking 44120 as yet unmatched pairs. 686 records in RAM. INFO 2026-06-08 08:43:18 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 1s. Last read position: chr1:146,068,810 INFO 2026-06-08 08:43:18 MarkDuplicates Tracking 44314 as yet unmatched pairs. 112 records in RAM. INFO 2026-06-08 08:43:20 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 1s. Last read position: chr1:148,590,839 INFO 2026-06-08 08:43:20 MarkDuplicates Tracking 44706 as yet unmatched pairs. 55 records in RAM. INFO 2026-06-08 08:43:21 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 1s. Last read position: chr1:149,842,379 INFO 2026-06-08 08:43:21 MarkDuplicates Tracking 47393 as yet unmatched pairs. 1596 records in RAM. INFO 2026-06-08 08:43:22 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 1s. Last read position: chr1:150,267,460 INFO 2026-06-08 08:43:22 MarkDuplicates Tracking 47226 as yet unmatched pairs. 527 records in RAM. INFO 2026-06-08 08:43:24 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 1s. Last read position: chr1:151,232,550 INFO 2026-06-08 08:43:24 MarkDuplicates Tracking 48308 as yet unmatched pairs. 113 records in RAM. INFO 2026-06-08 08:43:26 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 1s. Last read position: chr1:151,838,842 INFO 2026-06-08 08:43:26 MarkDuplicates Tracking 49913 as yet unmatched pairs. 29 records in RAM. INFO 2026-06-08 08:43:27 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 1s. Last read position: chr1:154,157,623 INFO 2026-06-08 08:43:27 MarkDuplicates Tracking 55030 as yet unmatched pairs. 3728 records in RAM. INFO 2026-06-08 08:43:29 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 1s. Last read position: chr1:154,449,962 INFO 2026-06-08 08:43:29 MarkDuplicates Tracking 52599 as yet unmatched pairs. 10 records in RAM. INFO 2026-06-08 08:43:31 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 1s. Last read position: chr1:155,135,920 INFO 2026-06-08 08:43:31 MarkDuplicates Tracking 54239 as yet unmatched pairs. 204 records in RAM. INFO 2026-06-08 08:43:32 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 1s. Last read position: chr1:155,688,071 INFO 2026-06-08 08:43:32 MarkDuplicates Tracking 55658 as yet unmatched pairs. 332 records in RAM. INFO 2026-06-08 08:43:34 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 1s. Last read position: chr1:156,135,218 INFO 2026-06-08 08:43:34 MarkDuplicates Tracking 59505 as yet unmatched pairs. 2588 records in RAM. INFO 2026-06-08 08:43:35 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 1s. Last read position: chr1:156,533,017 INFO 2026-06-08 08:43:35 MarkDuplicates Tracking 58932 as yet unmatched pairs. 300 records in RAM. INFO 2026-06-08 08:43:37 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 1s. Last read position: chr1:159,942,985 INFO 2026-06-08 08:43:37 MarkDuplicates Tracking 60230 as yet unmatched pairs. 96 records in RAM. INFO 2026-06-08 08:43:38 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 1s. Last read position: chr1:161,454,637 INFO 2026-06-08 08:43:38 MarkDuplicates Tracking 61602 as yet unmatched pairs. 4 records in RAM. INFO 2026-06-08 08:43:39 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 1s. Last read position: chr1:169,106,826 INFO 2026-06-08 08:43:39 MarkDuplicates Tracking 65155 as yet unmatched pairs. 2040 records in RAM. INFO 2026-06-08 08:43:41 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 1s. Last read position: chr1:171,589,476 INFO 2026-06-08 08:43:41 MarkDuplicates Tracking 64636 as yet unmatched pairs. 217 records in RAM. INFO 2026-06-08 08:43:43 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 1s. Last read position: chr1:180,196,596 INFO 2026-06-08 08:43:43 MarkDuplicates Tracking 66207 as yet unmatched pairs. 279 records in RAM. INFO 2026-06-08 08:43:44 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 1s. Last read position: chr1:185,297,978 INFO 2026-06-08 08:43:44 MarkDuplicates Tracking 67552 as yet unmatched pairs. 73 records in RAM. INFO 2026-06-08 08:43:46 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 1s. Last read position: chr1:198,731,694 INFO 2026-06-08 08:43:46 MarkDuplicates Tracking 68724 as yet unmatched pairs. 64 records in RAM. INFO 2026-06-08 08:43:48 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 1s. Last read position: chr1:202,134,453 INFO 2026-06-08 08:43:48 MarkDuplicates Tracking 70480 as yet unmatched pairs. 257 records in RAM. INFO 2026-06-08 08:43:49 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 1s. Last read position: chr1:204,261,455 INFO 2026-06-08 08:43:49 MarkDuplicates Tracking 71723 as yet unmatched pairs. 222 records in RAM. INFO 2026-06-08 08:43:50 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 1s. Last read position: chr1:206,933,038 INFO 2026-06-08 08:43:50 MarkDuplicates Tracking 73171 as yet unmatched pairs. 283 records in RAM. INFO 2026-06-08 08:43:52 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 1s. Last read position: chr1:209,628,143 INFO 2026-06-08 08:43:52 MarkDuplicates Tracking 74534 as yet unmatched pairs. 240 records in RAM. INFO 2026-06-08 08:43:53 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 1s. Last read position: chr1:220,105,959 INFO 2026-06-08 08:43:53 MarkDuplicates Tracking 75744 as yet unmatched pairs. 105 records in RAM. INFO 2026-06-08 08:43:55 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 1s. Last read position: chr1:225,846,906 INFO 2026-06-08 08:43:55 MarkDuplicates Tracking 77197 as yet unmatched pairs. 146 records in RAM. INFO 2026-06-08 08:43:56 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 1s. Last read position: chr1:228,147,647 INFO 2026-06-08 08:43:56 MarkDuplicates Tracking 79307 as yet unmatched pairs. 683 records in RAM. INFO 2026-06-08 08:43:58 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 1s. Last read position: chr1:233,379,653 INFO 2026-06-08 08:43:58 MarkDuplicates Tracking 80251 as yet unmatched pairs. 49 records in RAM. INFO 2026-06-08 08:43:59 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 1s. Last read position: chr1:236,550,831 INFO 2026-06-08 08:43:59 MarkDuplicates Tracking 81966 as yet unmatched pairs. 95 records in RAM. INFO 2026-06-08 08:44:01 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 1s. Last read position: chr1:246,916,246 INFO 2026-06-08 08:44:01 MarkDuplicates Tracking 83393 as yet unmatched pairs. 152 records in RAM. INFO 2026-06-08 08:44:04 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 2s. Last read position: chr2:9,588,298 INFO 2026-06-08 08:44:04 MarkDuplicates Tracking 85294 as yet unmatched pairs. 85187 records in RAM. INFO 2026-06-08 08:44:05 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 1s. Last read position: chr2:17,683,751 INFO 2026-06-08 08:44:05 MarkDuplicates Tracking 86506 as yet unmatched pairs. 86398 records in RAM. INFO 2026-06-08 08:44:07 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 1s. Last read position: chr2:24,710,953 INFO 2026-06-08 08:44:07 MarkDuplicates Tracking 88117 as yet unmatched pairs. 88007 records in RAM. INFO 2026-06-08 08:44:09 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 1s. Last read position: chr2:27,128,930 INFO 2026-06-08 08:44:09 MarkDuplicates Tracking 89425 as yet unmatched pairs. 89315 records in RAM. INFO 2026-06-08 08:44:10 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 1s. Last read position: chr2:28,752,161 INFO 2026-06-08 08:44:10 MarkDuplicates Tracking 93273 as yet unmatched pairs. 93163 records in RAM. INFO 2026-06-08 08:44:12 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,255 INFO 2026-06-08 08:44:12 MarkDuplicates Tracking 121779 as yet unmatched pairs. 90315 records in RAM. INFO 2026-06-08 08:44:14 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,264 INFO 2026-06-08 08:44:14 MarkDuplicates Tracking 597955 as yet unmatched pairs. 62633 records in RAM. INFO 2026-06-08 08:44:16 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,406 INFO 2026-06-08 08:44:16 MarkDuplicates Tracking 787289 as yet unmatched pairs. 51869 records in RAM. INFO 2026-06-08 08:44:17 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 1s. Last read position: chr2:37,020,821 INFO 2026-06-08 08:44:17 MarkDuplicates Tracking 836595 as yet unmatched pairs. 48186 records in RAM. INFO 2026-06-08 08:44:19 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 1s. Last read position: chr2:43,224,353 INFO 2026-06-08 08:44:19 MarkDuplicates Tracking 835965 as yet unmatched pairs. 47555 records in RAM. INFO 2026-06-08 08:44:21 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 1s. Last read position: chr2:47,011,329 INFO 2026-06-08 08:44:21 MarkDuplicates Tracking 833397 as yet unmatched pairs. 44986 records in RAM. INFO 2026-06-08 08:44:23 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 1s. Last read position: chr2:54,629,350 INFO 2026-06-08 08:44:23 MarkDuplicates Tracking 832661 as yet unmatched pairs. 44248 records in RAM. INFO 2026-06-08 08:44:24 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 1s. Last read position: chr2:58,251,644 INFO 2026-06-08 08:44:24 MarkDuplicates Tracking 830411 as yet unmatched pairs. 41996 records in RAM. INFO 2026-06-08 08:44:26 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 1s. Last read position: chr2:65,255,577 INFO 2026-06-08 08:44:26 MarkDuplicates Tracking 829381 as yet unmatched pairs. 40966 records in RAM. INFO 2026-06-08 08:44:27 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 1s. Last read position: chr2:71,481,926 INFO 2026-06-08 08:44:27 MarkDuplicates Tracking 827729 as yet unmatched pairs. 39312 records in RAM. INFO 2026-06-08 08:44:29 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 1s. Last read position: chr2:74,460,424 INFO 2026-06-08 08:44:29 MarkDuplicates Tracking 826343 as yet unmatched pairs. 37926 records in RAM. INFO 2026-06-08 08:44:30 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 1s. Last read position: chr2:85,539,333 INFO 2026-06-08 08:44:30 MarkDuplicates Tracking 825056 as yet unmatched pairs. 36636 records in RAM. INFO 2026-06-08 08:44:32 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 1s. Last read position: chr2:88,738,015 INFO 2026-06-08 08:44:32 MarkDuplicates Tracking 823667 as yet unmatched pairs. 35247 records in RAM. INFO 2026-06-08 08:44:34 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 1s. Last read position: chr2:96,860,773 INFO 2026-06-08 08:44:34 MarkDuplicates Tracking 822117 as yet unmatched pairs. 33695 records in RAM. INFO 2026-06-08 08:44:35 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 1s. Last read position: chr2:101,842,612 INFO 2026-06-08 08:44:35 MarkDuplicates Tracking 820687 as yet unmatched pairs. 32258 records in RAM. INFO 2026-06-08 08:44:37 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 1s. Last read position: chr2:108,764,884 INFO 2026-06-08 08:44:37 MarkDuplicates Tracking 819864 as yet unmatched pairs. 31435 records in RAM. INFO 2026-06-08 08:44:38 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 1s. Last read position: chr2:110,534,615 INFO 2026-06-08 08:44:38 MarkDuplicates Tracking 818494 as yet unmatched pairs. 30064 records in RAM. INFO 2026-06-08 08:44:40 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 1s. Last read position: chr2:113,890,140 INFO 2026-06-08 08:44:40 MarkDuplicates Tracking 817653 as yet unmatched pairs. 29222 records in RAM. INFO 2026-06-08 08:44:42 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 1s. Last read position: chr2:127,713,923 INFO 2026-06-08 08:44:42 MarkDuplicates Tracking 816176 as yet unmatched pairs. 27741 records in RAM. INFO 2026-06-08 08:44:43 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 1s. Last read position: chr2:135,163,046 INFO 2026-06-08 08:44:43 MarkDuplicates Tracking 814780 as yet unmatched pairs. 26344 records in RAM. INFO 2026-06-08 08:44:44 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 1s. Last read position: chr2:158,642,593 INFO 2026-06-08 08:44:44 MarkDuplicates Tracking 813542 as yet unmatched pairs. 25106 records in RAM. INFO 2026-06-08 08:44:46 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr2:170,080,556 INFO 2026-06-08 08:44:46 MarkDuplicates Tracking 812165 as yet unmatched pairs. 23729 records in RAM. INFO 2026-06-08 08:44:48 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 1s. Last read position: chr2:174,720,207 INFO 2026-06-08 08:44:48 MarkDuplicates Tracking 811140 as yet unmatched pairs. 22693 records in RAM. INFO 2026-06-08 08:44:49 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 1s. Last read position: chr2:181,921,993 INFO 2026-06-08 08:44:49 MarkDuplicates Tracking 809587 as yet unmatched pairs. 21140 records in RAM. INFO 2026-06-08 08:44:50 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 1s. Last read position: chr2:189,010,235 INFO 2026-06-08 08:44:50 MarkDuplicates Tracking 808378 as yet unmatched pairs. 19930 records in RAM. INFO 2026-06-08 08:44:52 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 1s. Last read position: chr2:197,121,440 INFO 2026-06-08 08:44:52 MarkDuplicates Tracking 806567 as yet unmatched pairs. 18113 records in RAM. INFO 2026-06-08 08:44:54 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 1s. Last read position: chr2:201,160,841 INFO 2026-06-08 08:44:54 MarkDuplicates Tracking 805306 as yet unmatched pairs. 16850 records in RAM. INFO 2026-06-08 08:44:55 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 1s. Last read position: chr2:207,560,229 INFO 2026-06-08 08:44:55 MarkDuplicates Tracking 804385 as yet unmatched pairs. 15927 records in RAM. INFO 2026-06-08 08:44:56 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 1s. Last read position: chr2:215,375,241 INFO 2026-06-08 08:44:56 MarkDuplicates Tracking 803605 as yet unmatched pairs. 15145 records in RAM. INFO 2026-06-08 08:44:59 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 2s. Last read position: chr2:215,407,143 INFO 2026-06-08 08:44:59 MarkDuplicates Tracking 802796 as yet unmatched pairs. 14333 records in RAM. INFO 2026-06-08 08:45:01 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 1s. Last read position: chr2:216,499,369 INFO 2026-06-08 08:45:01 MarkDuplicates Tracking 802976 as yet unmatched pairs. 14512 records in RAM. INFO 2026-06-08 08:45:02 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 1s. Last read position: chr2:218,594,159 INFO 2026-06-08 08:45:02 MarkDuplicates Tracking 798363 as yet unmatched pairs. 9899 records in RAM. INFO 2026-06-08 08:45:04 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 1s. Last read position: chr2:219,492,138 INFO 2026-06-08 08:45:04 MarkDuplicates Tracking 796721 as yet unmatched pairs. 8257 records in RAM. INFO 2026-06-08 08:45:05 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 1s. Last read position: chr2:230,172,127 INFO 2026-06-08 08:45:05 MarkDuplicates Tracking 795117 as yet unmatched pairs. 6626 records in RAM. INFO 2026-06-08 08:45:07 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 1s. Last read position: chr2:231,807,530 INFO 2026-06-08 08:45:07 MarkDuplicates Tracking 793819 as yet unmatched pairs. 5328 records in RAM. INFO 2026-06-08 08:45:09 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 2s. Last read position: chr2:237,363,264 INFO 2026-06-08 08:45:09 MarkDuplicates Tracking 792361 as yet unmatched pairs. 3867 records in RAM. INFO 2026-06-08 08:45:11 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 1s. Last read position: chr2:240,589,399 INFO 2026-06-08 08:45:11 MarkDuplicates Tracking 790558 as yet unmatched pairs. 2064 records in RAM. INFO 2026-06-08 08:45:13 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 1s. Last read position: chr2:241,668,621 INFO 2026-06-08 08:45:13 MarkDuplicates Tracking 788946 as yet unmatched pairs. 448 records in RAM. INFO 2026-06-08 08:45:15 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 2s. Last read position: chr3:9,940,961 INFO 2026-06-08 08:45:15 MarkDuplicates Tracking 787242 as yet unmatched pairs. 40602 records in RAM. INFO 2026-06-08 08:45:16 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 1s. Last read position: chr3:14,131,619 INFO 2026-06-08 08:45:16 MarkDuplicates Tracking 785749 as yet unmatched pairs. 39108 records in RAM. INFO 2026-06-08 08:45:18 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 1s. Last read position: chr3:31,533,245 INFO 2026-06-08 08:45:18 MarkDuplicates Tracking 784937 as yet unmatched pairs. 38294 records in RAM. INFO 2026-06-08 08:45:19 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 1s. Last read position: chr3:38,008,013 INFO 2026-06-08 08:45:19 MarkDuplicates Tracking 782870 as yet unmatched pairs. 36226 records in RAM. INFO 2026-06-08 08:45:21 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 1s. Last read position: chr3:41,236,405 INFO 2026-06-08 08:45:21 MarkDuplicates Tracking 781931 as yet unmatched pairs. 35287 records in RAM. INFO 2026-06-08 08:45:23 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 1s. Last read position: chr3:46,995,145 INFO 2026-06-08 08:45:23 MarkDuplicates Tracking 780128 as yet unmatched pairs. 33483 records in RAM. INFO 2026-06-08 08:45:24 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 1s. Last read position: chr3:47,916,031 INFO 2026-06-08 08:45:24 MarkDuplicates Tracking 778682 as yet unmatched pairs. 32037 records in RAM. INFO 2026-06-08 08:45:26 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 1s. Last read position: chr3:48,640,057 INFO 2026-06-08 08:45:26 MarkDuplicates Tracking 776882 as yet unmatched pairs. 30236 records in RAM. INFO 2026-06-08 08:45:27 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 1s. Last read position: chr3:49,357,337 INFO 2026-06-08 08:45:27 MarkDuplicates Tracking 775382 as yet unmatched pairs. 28736 records in RAM. INFO 2026-06-08 08:45:29 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 1s. Last read position: chr3:50,188,033 INFO 2026-06-08 08:45:29 MarkDuplicates Tracking 773750 as yet unmatched pairs. 27101 records in RAM. INFO 2026-06-08 08:45:30 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 1s. Last read position: chr3:52,259,717 INFO 2026-06-08 08:45:30 MarkDuplicates Tracking 772341 as yet unmatched pairs. 25692 records in RAM. INFO 2026-06-08 08:45:32 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 1s. Last read position: chr3:53,860,194 INFO 2026-06-08 08:45:32 MarkDuplicates Tracking 770728 as yet unmatched pairs. 24069 records in RAM. INFO 2026-06-08 08:45:34 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 1s. Last read position: chr3:63,982,194 INFO 2026-06-08 08:45:34 MarkDuplicates Tracking 769344 as yet unmatched pairs. 22684 records in RAM. INFO 2026-06-08 08:45:35 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 1s. Last read position: chr3:98,593,024 INFO 2026-06-08 08:45:35 MarkDuplicates Tracking 767990 as yet unmatched pairs. 21330 records in RAM. INFO 2026-06-08 08:45:37 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 1s. Last read position: chr3:108,351,787 INFO 2026-06-08 08:45:37 MarkDuplicates Tracking 766879 as yet unmatched pairs. 20218 records in RAM. INFO 2026-06-08 08:45:38 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 1s. Last read position: chr3:120,404,852 INFO 2026-06-08 08:45:38 MarkDuplicates Tracking 765534 as yet unmatched pairs. 18872 records in RAM. INFO 2026-06-08 08:45:40 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 1s. Last read position: chr3:123,946,947 INFO 2026-06-08 08:45:40 MarkDuplicates Tracking 764198 as yet unmatched pairs. 17535 records in RAM. INFO 2026-06-08 08:45:41 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 1s. Last read position: chr3:127,604,919 INFO 2026-06-08 08:45:41 MarkDuplicates Tracking 762738 as yet unmatched pairs. 16075 records in RAM. INFO 2026-06-08 08:45:43 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 1s. Last read position: chr3:129,171,252 INFO 2026-06-08 08:45:43 MarkDuplicates Tracking 763452 as yet unmatched pairs. 16785 records in RAM. INFO 2026-06-08 08:45:44 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 1s. Last read position: chr3:133,620,261 INFO 2026-06-08 08:45:44 MarkDuplicates Tracking 759520 as yet unmatched pairs. 12853 records in RAM. INFO 2026-06-08 08:45:46 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: chr3:142,498,748 INFO 2026-06-08 08:45:46 MarkDuplicates Tracking 758068 as yet unmatched pairs. 11400 records in RAM. INFO 2026-06-08 08:45:47 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 1s. Last read position: chr3:155,853,777 INFO 2026-06-08 08:45:47 MarkDuplicates Tracking 756470 as yet unmatched pairs. 9802 records in RAM. INFO 2026-06-08 08:45:49 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 1s. Last read position: chr3:170,360,394 INFO 2026-06-08 08:45:49 MarkDuplicates Tracking 755320 as yet unmatched pairs. 8648 records in RAM. INFO 2026-06-08 08:45:51 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 1s. Last read position: chr3:183,086,733 INFO 2026-06-08 08:45:51 MarkDuplicates Tracking 753837 as yet unmatched pairs. 7165 records in RAM. INFO 2026-06-08 08:45:53 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 2s. Last read position: chr3:184,323,203 INFO 2026-06-08 08:45:53 MarkDuplicates Tracking 752521 as yet unmatched pairs. 5849 records in RAM. INFO 2026-06-08 08:45:54 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 1s. Last read position: chr3:188,153,340 INFO 2026-06-08 08:45:54 MarkDuplicates Tracking 750867 as yet unmatched pairs. 4195 records in RAM. INFO 2026-06-08 08:45:56 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 1s. Last read position: chr3:195,635,301 INFO 2026-06-08 08:45:56 MarkDuplicates Tracking 749436 as yet unmatched pairs. 2763 records in RAM. INFO 2026-06-08 08:45:57 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 1s. Last read position: chr3:195,783,234 INFO 2026-06-08 08:45:57 MarkDuplicates Tracking 749479 as yet unmatched pairs. 2805 records in RAM. INFO 2026-06-08 08:45:59 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 1s. Last read position: chr3:196,075,288 INFO 2026-06-08 08:45:59 MarkDuplicates Tracking 748012 as yet unmatched pairs. 1338 records in RAM. INFO 2026-06-08 08:46:01 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 1s. Last read position: chr4:957,922 INFO 2026-06-08 08:46:01 MarkDuplicates Tracking 746109 as yet unmatched pairs. 23157 records in RAM. INFO 2026-06-08 08:46:03 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 2s. Last read position: chr4:1,735,760 INFO 2026-06-08 08:46:03 MarkDuplicates Tracking 744586 as yet unmatched pairs. 21634 records in RAM. INFO 2026-06-08 08:46:05 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 1s. Last read position: chr4:2,931,090 INFO 2026-06-08 08:46:05 MarkDuplicates Tracking 743054 as yet unmatched pairs. 20102 records in RAM. INFO 2026-06-08 08:46:06 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 1s. Last read position: chr4:7,703,282 INFO 2026-06-08 08:46:06 MarkDuplicates Tracking 741155 as yet unmatched pairs. 18201 records in RAM. INFO 2026-06-08 08:46:08 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 1s. Last read position: chr4:17,874,092 INFO 2026-06-08 08:46:08 MarkDuplicates Tracking 739834 as yet unmatched pairs. 16873 records in RAM. INFO 2026-06-08 08:46:09 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 1s. Last read position: chr4:41,935,487 INFO 2026-06-08 08:46:09 MarkDuplicates Tracking 738596 as yet unmatched pairs. 15633 records in RAM. INFO 2026-06-08 08:46:11 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 1s. Last read position: chr4:56,315,400 INFO 2026-06-08 08:46:11 MarkDuplicates Tracking 737178 as yet unmatched pairs. 14212 records in RAM. INFO 2026-06-08 08:46:13 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 1s. Last read position: chr4:74,365,278 INFO 2026-06-08 08:46:13 MarkDuplicates Tracking 736180 as yet unmatched pairs. 13212 records in RAM. INFO 2026-06-08 08:46:14 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 1s. Last read position: chr4:82,875,740 INFO 2026-06-08 08:46:14 MarkDuplicates Tracking 734265 as yet unmatched pairs. 11297 records in RAM. INFO 2026-06-08 08:46:15 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 1s. Last read position: chr4:101,025,904 INFO 2026-06-08 08:46:15 MarkDuplicates Tracking 732814 as yet unmatched pairs. 9845 records in RAM. INFO 2026-06-08 08:46:17 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 1s. Last read position: chr4:113,292,423 INFO 2026-06-08 08:46:17 MarkDuplicates Tracking 731406 as yet unmatched pairs. 8437 records in RAM. INFO 2026-06-08 08:46:19 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 1s. Last read position: chr4:128,271,308 INFO 2026-06-08 08:46:19 MarkDuplicates Tracking 730248 as yet unmatched pairs. 7279 records in RAM. INFO 2026-06-08 08:46:20 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 1s. Last read position: chr4:150,265,748 INFO 2026-06-08 08:46:20 MarkDuplicates Tracking 729065 as yet unmatched pairs. 6095 records in RAM. INFO 2026-06-08 08:46:21 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 1s. Last read position: chr4:153,293,111 INFO 2026-06-08 08:46:21 MarkDuplicates Tracking 727981 as yet unmatched pairs. 5006 records in RAM. INFO 2026-06-08 08:46:23 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 1s. Last read position: chr4:169,707,119 INFO 2026-06-08 08:46:23 MarkDuplicates Tracking 726372 as yet unmatched pairs. 3394 records in RAM. INFO 2026-06-08 08:46:25 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 1s. Last read position: chr4:186,603,650 INFO 2026-06-08 08:46:25 MarkDuplicates Tracking 725067 as yet unmatched pairs. 2089 records in RAM. INFO 2026-06-08 08:46:26 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 1s. Last read position: chr4:186,707,883 INFO 2026-06-08 08:46:26 MarkDuplicates Tracking 724134 as yet unmatched pairs. 1156 records in RAM. INFO 2026-06-08 08:46:28 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 1s. Last read position: chr5:1,337,913 INFO 2026-06-08 08:46:28 MarkDuplicates Tracking 722587 as yet unmatched pairs. 44648 records in RAM. INFO 2026-06-08 08:46:31 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 2s. Last read position: chr5:14,286,925 INFO 2026-06-08 08:46:31 MarkDuplicates Tracking 721118 as yet unmatched pairs. 43176 records in RAM. INFO 2026-06-08 08:46:32 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 1s. Last read position: chr5:14,481,271 INFO 2026-06-08 08:46:32 MarkDuplicates Tracking 718475 as yet unmatched pairs. 40533 records in RAM. INFO 2026-06-08 08:46:34 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 1s. Last read position: chr5:25,827,875 INFO 2026-06-08 08:46:34 MarkDuplicates Tracking 716977 as yet unmatched pairs. 39034 records in RAM. INFO 2026-06-08 08:46:36 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 1s. Last read position: chr5:37,318,024 INFO 2026-06-08 08:46:36 MarkDuplicates Tracking 715918 as yet unmatched pairs. 37970 records in RAM. INFO 2026-06-08 08:46:38 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 1s. Last read position: chr5:55,534,588 INFO 2026-06-08 08:46:38 MarkDuplicates Tracking 714453 as yet unmatched pairs. 36505 records in RAM. INFO 2026-06-08 08:46:39 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 1s. Last read position: chr5:71,123,657 INFO 2026-06-08 08:46:39 MarkDuplicates Tracking 713329 as yet unmatched pairs. 35381 records in RAM. INFO 2026-06-08 08:46:41 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 1s. Last read position: chr5:77,708,279 INFO 2026-06-08 08:46:41 MarkDuplicates Tracking 712211 as yet unmatched pairs. 34262 records in RAM. INFO 2026-06-08 08:46:42 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 1s. Last read position: chr5:87,331,348 INFO 2026-06-08 08:46:42 MarkDuplicates Tracking 710662 as yet unmatched pairs. 32712 records in RAM. INFO 2026-06-08 08:46:44 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 1s. Last read position: chr5:100,535,853 INFO 2026-06-08 08:46:44 MarkDuplicates Tracking 709322 as yet unmatched pairs. 31359 records in RAM. INFO 2026-06-08 08:46:45 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 1s. Last read position: chr5:123,028,776 INFO 2026-06-08 08:46:45 MarkDuplicates Tracking 708046 as yet unmatched pairs. 30082 records in RAM. INFO 2026-06-08 08:46:47 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 1s. Last read position: chr5:128,174,637 INFO 2026-06-08 08:46:47 MarkDuplicates Tracking 707394 as yet unmatched pairs. 29430 records in RAM. INFO 2026-06-08 08:46:49 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 1s. Last read position: chr5:133,956,906 INFO 2026-06-08 08:46:49 MarkDuplicates Tracking 704926 as yet unmatched pairs. 26961 records in RAM. INFO 2026-06-08 08:46:50 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr5:135,578,769 INFO 2026-06-08 08:46:50 MarkDuplicates Tracking 704744 as yet unmatched pairs. 26777 records in RAM. INFO 2026-06-08 08:46:52 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr5:138,391,562 INFO 2026-06-08 08:46:52 MarkDuplicates Tracking 702105 as yet unmatched pairs. 24137 records in RAM. INFO 2026-06-08 08:46:53 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 1s. Last read position: chr5:139,680,991 INFO 2026-06-08 08:46:53 MarkDuplicates Tracking 700795 as yet unmatched pairs. 22827 records in RAM. INFO 2026-06-08 08:46:56 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 2s. Last read position: chr5:141,303,561 INFO 2026-06-08 08:46:56 MarkDuplicates Tracking 699092 as yet unmatched pairs. 21099 records in RAM. INFO 2026-06-08 08:46:58 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 1s. Last read position: chr5:141,868,871 INFO 2026-06-08 08:46:58 MarkDuplicates Tracking 697841 as yet unmatched pairs. 19848 records in RAM. INFO 2026-06-08 08:46:59 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 1s. Last read position: chr5:149,550,051 INFO 2026-06-08 08:46:59 MarkDuplicates Tracking 696556 as yet unmatched pairs. 18560 records in RAM. INFO 2026-06-08 08:47:01 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 1s. Last read position: chr5:150,183,554 INFO 2026-06-08 08:47:01 MarkDuplicates Tracking 694862 as yet unmatched pairs. 16866 records in RAM. INFO 2026-06-08 08:47:02 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 1s. Last read position: chr5:150,405,122 INFO 2026-06-08 08:47:02 MarkDuplicates Tracking 700906 as yet unmatched pairs. 22909 records in RAM. INFO 2026-06-08 08:47:04 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 1s. Last read position: chr5:150,649,377 INFO 2026-06-08 08:47:04 MarkDuplicates Tracking 691701 as yet unmatched pairs. 13703 records in RAM. INFO 2026-06-08 08:47:05 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 1s. Last read position: chr5:154,792,785 INFO 2026-06-08 08:47:05 MarkDuplicates Tracking 690619 as yet unmatched pairs. 12616 records in RAM. INFO 2026-06-08 08:47:07 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 1s. Last read position: chr5:163,441,148 INFO 2026-06-08 08:47:07 MarkDuplicates Tracking 688698 as yet unmatched pairs. 10695 records in RAM. INFO 2026-06-08 08:47:08 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 1s. Last read position: chr5:171,392,763 INFO 2026-06-08 08:47:08 MarkDuplicates Tracking 692398 as yet unmatched pairs. 14391 records in RAM. INFO 2026-06-08 08:47:10 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 1s. Last read position: chr5:176,290,661 INFO 2026-06-08 08:47:10 MarkDuplicates Tracking 686189 as yet unmatched pairs. 8181 records in RAM. INFO 2026-06-08 08:47:12 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 1s. Last read position: chr5:177,332,115 INFO 2026-06-08 08:47:12 MarkDuplicates Tracking 685452 as yet unmatched pairs. 7444 records in RAM. INFO 2026-06-08 08:47:13 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 1s. Last read position: chr5:179,129,952 INFO 2026-06-08 08:47:13 MarkDuplicates Tracking 682998 as yet unmatched pairs. 4989 records in RAM. INFO 2026-06-08 08:47:14 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 1s. Last read position: chr5:179,801,924 INFO 2026-06-08 08:47:14 MarkDuplicates Tracking 681908 as yet unmatched pairs. 3890 records in RAM. INFO 2026-06-08 08:47:16 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 1s. Last read position: chr5:179,836,499 INFO 2026-06-08 08:47:16 MarkDuplicates Tracking 682710 as yet unmatched pairs. 4692 records in RAM. INFO 2026-06-08 08:47:17 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 1s. Last read position: chr5:181,241,545 INFO 2026-06-08 08:47:17 MarkDuplicates Tracking 678929 as yet unmatched pairs. 910 records in RAM. INFO 2026-06-08 08:47:19 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 1s. Last read position: chr6:7,189,209 INFO 2026-06-08 08:47:19 MarkDuplicates Tracking 677052 as yet unmatched pairs. 44954 records in RAM. INFO 2026-06-08 08:47:21 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 1s. Last read position: chr6:7,910,531 INFO 2026-06-08 08:47:21 MarkDuplicates Tracking 674959 as yet unmatched pairs. 42861 records in RAM. INFO 2026-06-08 08:47:22 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 1s. Last read position: chr6:19,837,470 INFO 2026-06-08 08:47:22 MarkDuplicates Tracking 673481 as yet unmatched pairs. 41381 records in RAM. INFO 2026-06-08 08:47:24 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 1s. Last read position: chr6:26,158,172 INFO 2026-06-08 08:47:24 MarkDuplicates Tracking 672409 as yet unmatched pairs. 40309 records in RAM. INFO 2026-06-08 08:47:26 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 2s. Last read position: chr6:27,146,487 INFO 2026-06-08 08:47:26 MarkDuplicates Tracking 671746 as yet unmatched pairs. 39645 records in RAM. INFO 2026-06-08 08:47:28 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 1s. Last read position: chr6:28,390,527 INFO 2026-06-08 08:47:28 MarkDuplicates Tracking 669034 as yet unmatched pairs. 36932 records in RAM. INFO 2026-06-08 08:47:29 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 1s. Last read position: chr6:30,491,189 INFO 2026-06-08 08:47:29 MarkDuplicates Tracking 668162 as yet unmatched pairs. 36060 records in RAM. INFO 2026-06-08 08:47:31 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 2s. Last read position: chr6:30,913,336 INFO 2026-06-08 08:47:31 MarkDuplicates Tracking 666172 as yet unmatched pairs. 34067 records in RAM. INFO 2026-06-08 08:47:33 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr6:31,625,483 INFO 2026-06-08 08:47:33 MarkDuplicates Tracking 665329 as yet unmatched pairs. 33224 records in RAM. INFO 2026-06-08 08:47:35 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 1s. Last read position: chr6:31,669,420 INFO 2026-06-08 08:47:35 MarkDuplicates Tracking 663892 as yet unmatched pairs. 31787 records in RAM. INFO 2026-06-08 08:47:36 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 1s. Last read position: chr6:31,828,570 INFO 2026-06-08 08:47:36 MarkDuplicates Tracking 662276 as yet unmatched pairs. 30168 records in RAM. INFO 2026-06-08 08:47:38 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 1s. Last read position: chr6:32,027,435 INFO 2026-06-08 08:47:38 MarkDuplicates Tracking 660946 as yet unmatched pairs. 28838 records in RAM. INFO 2026-06-08 08:47:39 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 1s. Last read position: chr6:32,853,521 INFO 2026-06-08 08:47:39 MarkDuplicates Tracking 659958 as yet unmatched pairs. 27850 records in RAM. INFO 2026-06-08 08:47:41 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 1s. Last read position: chr6:33,313,353 INFO 2026-06-08 08:47:41 MarkDuplicates Tracking 658884 as yet unmatched pairs. 26776 records in RAM. INFO 2026-06-08 08:47:43 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 1s. Last read position: chr6:34,242,786 INFO 2026-06-08 08:47:43 MarkDuplicates Tracking 656470 as yet unmatched pairs. 24361 records in RAM. INFO 2026-06-08 08:47:44 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:05:20s. Time for last 1,000,000: 1s. Last read position: chr6:36,507,511 INFO 2026-06-08 08:47:44 MarkDuplicates Tracking 654986 as yet unmatched pairs. 22877 records in RAM. INFO 2026-06-08 08:47:45 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 1s. Last read position: chr6:42,106,422 INFO 2026-06-08 08:47:45 MarkDuplicates Tracking 653586 as yet unmatched pairs. 21475 records in RAM. INFO 2026-06-08 08:47:47 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 1s. Last read position: chr6:43,369,067 INFO 2026-06-08 08:47:47 MarkDuplicates Tracking 652140 as yet unmatched pairs. 20029 records in RAM. INFO 2026-06-08 08:47:49 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 1s. Last read position: chr6:44,255,156 INFO 2026-06-08 08:47:49 MarkDuplicates Tracking 650703 as yet unmatched pairs. 18591 records in RAM. INFO 2026-06-08 08:47:50 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 1s. Last read position: chr6:56,492,964 INFO 2026-06-08 08:47:50 MarkDuplicates Tracking 649150 as yet unmatched pairs. 17033 records in RAM. INFO 2026-06-08 08:47:52 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 1s. Last read position: chr6:75,130,964 INFO 2026-06-08 08:47:52 MarkDuplicates Tracking 647851 as yet unmatched pairs. 15733 records in RAM. INFO 2026-06-08 08:47:53 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 1s. Last read position: chr6:85,640,231 INFO 2026-06-08 08:47:53 MarkDuplicates Tracking 646621 as yet unmatched pairs. 14502 records in RAM. INFO 2026-06-08 08:47:54 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 1s. Last read position: chr6:106,360,796 INFO 2026-06-08 08:47:54 MarkDuplicates Tracking 645027 as yet unmatched pairs. 12908 records in RAM. INFO 2026-06-08 08:47:56 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 1s. Last read position: chr6:111,266,662 INFO 2026-06-08 08:47:56 MarkDuplicates Tracking 643609 as yet unmatched pairs. 11489 records in RAM. INFO 2026-06-08 08:47:57 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 1s. Last read position: chr6:126,643,857 INFO 2026-06-08 08:47:57 MarkDuplicates Tracking 642096 as yet unmatched pairs. 9973 records in RAM. INFO 2026-06-08 08:47:59 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 1s. Last read position: chr6:135,181,491 INFO 2026-06-08 08:47:59 MarkDuplicates Tracking 641389 as yet unmatched pairs. 9265 records in RAM. INFO 2026-06-08 08:48:00 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 1s. Last read position: chr6:138,431,847 INFO 2026-06-08 08:48:00 MarkDuplicates Tracking 639448 as yet unmatched pairs. 7323 records in RAM. INFO 2026-06-08 08:48:02 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 1s. Last read position: chr6:149,676,611 INFO 2026-06-08 08:48:02 MarkDuplicates Tracking 637968 as yet unmatched pairs. 5842 records in RAM. INFO 2026-06-08 08:48:03 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 1s. Last read position: chr6:157,672,880 INFO 2026-06-08 08:48:03 MarkDuplicates Tracking 636598 as yet unmatched pairs. 4470 records in RAM. INFO 2026-06-08 08:48:05 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 1s. Last read position: chr6:158,787,135 INFO 2026-06-08 08:48:05 MarkDuplicates Tracking 636337 as yet unmatched pairs. 4209 records in RAM. INFO 2026-06-08 08:48:06 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 1s. Last read position: chr6:163,570,747 INFO 2026-06-08 08:48:06 MarkDuplicates Tracking 633674 as yet unmatched pairs. 1546 records in RAM. INFO 2026-06-08 08:48:08 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 2s. Last read position: chr7:726,762 INFO 2026-06-08 08:48:08 MarkDuplicates Tracking 632084 as yet unmatched pairs. 60698 records in RAM. INFO 2026-06-08 08:48:10 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 1s. Last read position: chr7:2,366,999 INFO 2026-06-08 08:48:10 MarkDuplicates Tracking 630157 as yet unmatched pairs. 58763 records in RAM. INFO 2026-06-08 08:48:11 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 1s. Last read position: chr7:5,315,074 INFO 2026-06-08 08:48:11 MarkDuplicates Tracking 628769 as yet unmatched pairs. 57374 records in RAM. INFO 2026-06-08 08:48:13 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 1s. Last read position: chr7:5,527,778 INFO 2026-06-08 08:48:13 MarkDuplicates Tracking 634372 as yet unmatched pairs. 62975 records in RAM. INFO 2026-06-08 08:48:15 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 1s. Last read position: chr7:5,529,177 INFO 2026-06-08 08:48:15 MarkDuplicates Tracking 630531 as yet unmatched pairs. 59134 records in RAM. INFO 2026-06-08 08:48:16 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 1s. Last read position: chr7:6,642,599 INFO 2026-06-08 08:48:16 MarkDuplicates Tracking 623556 as yet unmatched pairs. 52158 records in RAM. INFO 2026-06-08 08:48:18 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 1s. Last read position: chr7:26,152,692 INFO 2026-06-08 08:48:18 MarkDuplicates Tracking 622419 as yet unmatched pairs. 51021 records in RAM. INFO 2026-06-08 08:48:19 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 1s. Last read position: chr7:30,599,945 INFO 2026-06-08 08:48:19 MarkDuplicates Tracking 620829 as yet unmatched pairs. 49431 records in RAM. INFO 2026-06-08 08:48:21 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 1s. Last read position: chr7:43,877,691 INFO 2026-06-08 08:48:21 MarkDuplicates Tracking 619312 as yet unmatched pairs. 47913 records in RAM. INFO 2026-06-08 08:48:22 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 1s. Last read position: chr7:44,799,427 INFO 2026-06-08 08:48:22 MarkDuplicates Tracking 618107 as yet unmatched pairs. 46705 records in RAM. INFO 2026-06-08 08:48:24 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 1s. Last read position: chr7:55,171,177 INFO 2026-06-08 08:48:24 MarkDuplicates Tracking 616268 as yet unmatched pairs. 44866 records in RAM. INFO 2026-06-08 08:48:25 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 1s. Last read position: chr7:70,766,189 INFO 2026-06-08 08:48:25 MarkDuplicates Tracking 614739 as yet unmatched pairs. 43336 records in RAM. INFO 2026-06-08 08:48:27 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 1s. Last read position: chr7:73,508,326 INFO 2026-06-08 08:48:27 MarkDuplicates Tracking 614155 as yet unmatched pairs. 42750 records in RAM. INFO 2026-06-08 08:48:28 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 1s. Last read position: chr7:74,508,098 INFO 2026-06-08 08:48:28 MarkDuplicates Tracking 612544 as yet unmatched pairs. 41137 records in RAM. INFO 2026-06-08 08:48:29 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 1s. Last read position: chr7:75,496,852 INFO 2026-06-08 08:48:29 MarkDuplicates Tracking 611445 as yet unmatched pairs. 40038 records in RAM. INFO 2026-06-08 08:48:31 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 1s. Last read position: chr7:76,503,500 INFO 2026-06-08 08:48:31 MarkDuplicates Tracking 609854 as yet unmatched pairs. 38446 records in RAM. INFO 2026-06-08 08:48:32 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 1s. Last read position: chr7:91,973,939 INFO 2026-06-08 08:48:32 MarkDuplicates Tracking 608917 as yet unmatched pairs. 37509 records in RAM. INFO 2026-06-08 08:48:34 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 1s. Last read position: chr7:94,422,965 INFO 2026-06-08 08:48:34 MarkDuplicates Tracking 607687 as yet unmatched pairs. 36278 records in RAM. INFO 2026-06-08 08:48:35 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 1s. Last read position: chr7:99,325,993 INFO 2026-06-08 08:48:35 MarkDuplicates Tracking 605974 as yet unmatched pairs. 34560 records in RAM. INFO 2026-06-08 08:48:37 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 1s. Last read position: chr7:100,156,643 INFO 2026-06-08 08:48:37 MarkDuplicates Tracking 604454 as yet unmatched pairs. 33039 records in RAM. INFO 2026-06-08 08:48:39 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 1s. Last read position: chr7:100,822,284 INFO 2026-06-08 08:48:39 MarkDuplicates Tracking 603484 as yet unmatched pairs. 32066 records in RAM. INFO 2026-06-08 08:48:40 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 1s. Last read position: chr7:100,991,636 INFO 2026-06-08 08:48:40 MarkDuplicates Tracking 601832 as yet unmatched pairs. 30414 records in RAM. INFO 2026-06-08 08:48:42 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 1s. Last read position: chr7:100,992,926 INFO 2026-06-08 08:48:42 MarkDuplicates Tracking 602021 as yet unmatched pairs. 30603 records in RAM. INFO 2026-06-08 08:48:44 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 1s. Last read position: chr7:100,993,410 INFO 2026-06-08 08:48:44 MarkDuplicates Tracking 601536 as yet unmatched pairs. 30118 records in RAM. INFO 2026-06-08 08:48:45 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 1s. Last read position: chr7:100,993,763 INFO 2026-06-08 08:48:45 MarkDuplicates Tracking 601461 as yet unmatched pairs. 30043 records in RAM. INFO 2026-06-08 08:48:46 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 1s. Last read position: chr7:100,994,427 INFO 2026-06-08 08:48:46 MarkDuplicates Tracking 600617 as yet unmatched pairs. 29199 records in RAM. INFO 2026-06-08 08:48:47 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 0s. Last read position: chr7:100,994,957 INFO 2026-06-08 08:48:47 MarkDuplicates Tracking 600548 as yet unmatched pairs. 29130 records in RAM. INFO 2026-06-08 08:48:48 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 0s. Last read position: chr7:100,995,264 INFO 2026-06-08 08:48:48 MarkDuplicates Tracking 602224 as yet unmatched pairs. 30806 records in RAM. INFO 2026-06-08 08:48:49 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 1s. Last read position: chr7:100,996,058 INFO 2026-06-08 08:48:49 MarkDuplicates Tracking 600781 as yet unmatched pairs. 29363 records in RAM. INFO 2026-06-08 08:48:50 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 0s. Last read position: chr7:100,996,337 INFO 2026-06-08 08:48:50 MarkDuplicates Tracking 602525 as yet unmatched pairs. 31107 records in RAM. INFO 2026-06-08 08:48:51 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 1s. Last read position: chr7:100,996,522 INFO 2026-06-08 08:48:51 MarkDuplicates Tracking 599849 as yet unmatched pairs. 28431 records in RAM. INFO 2026-06-08 08:48:53 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 1s. Last read position: chr7:100,996,890 INFO 2026-06-08 08:48:53 MarkDuplicates Tracking 607898 as yet unmatched pairs. 36480 records in RAM. INFO 2026-06-08 08:48:54 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:06:30s. Time for last 1,000,000: 1s. Last read position: chr7:100,997,162 INFO 2026-06-08 08:48:54 MarkDuplicates Tracking 605656 as yet unmatched pairs. 34238 records in RAM. INFO 2026-06-08 08:48:55 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 1s. Last read position: chr7:100,997,516 INFO 2026-06-08 08:48:55 MarkDuplicates Tracking 603209 as yet unmatched pairs. 31790 records in RAM. INFO 2026-06-08 08:48:56 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:06:33s. Time for last 1,000,000: 1s. Last read position: chr7:100,997,894 INFO 2026-06-08 08:48:56 MarkDuplicates Tracking 602721 as yet unmatched pairs. 31301 records in RAM. INFO 2026-06-08 08:48:58 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 1s. Last read position: chr7:100,998,118 INFO 2026-06-08 08:48:58 MarkDuplicates Tracking 597928 as yet unmatched pairs. 26508 records in RAM. INFO 2026-06-08 08:48:59 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:06:35s. Time for last 1,000,000: 0s. Last read position: chr7:100,998,421 INFO 2026-06-08 08:48:59 MarkDuplicates Tracking 596545 as yet unmatched pairs. 25124 records in RAM. INFO 2026-06-08 08:49:00 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 0s. Last read position: chr7:100,998,680 INFO 2026-06-08 08:49:00 MarkDuplicates Tracking 603583 as yet unmatched pairs. 32162 records in RAM. INFO 2026-06-08 08:49:01 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 1s. Last read position: chr7:100,998,987 INFO 2026-06-08 08:49:01 MarkDuplicates Tracking 596171 as yet unmatched pairs. 24750 records in RAM. INFO 2026-06-08 08:49:02 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 1s. Last read position: chr7:100,999,621 INFO 2026-06-08 08:49:02 MarkDuplicates Tracking 600260 as yet unmatched pairs. 28839 records in RAM. INFO 2026-06-08 08:49:03 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 1s. Last read position: chr7:100,999,923 INFO 2026-06-08 08:49:03 MarkDuplicates Tracking 599122 as yet unmatched pairs. 27701 records in RAM. INFO 2026-06-08 08:49:05 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 1s. Last read position: chr7:101,000,402 INFO 2026-06-08 08:49:05 MarkDuplicates Tracking 600416 as yet unmatched pairs. 28995 records in RAM. INFO 2026-06-08 08:49:06 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 1s. Last read position: chr7:101,000,768 INFO 2026-06-08 08:49:06 MarkDuplicates Tracking 603928 as yet unmatched pairs. 32507 records in RAM. INFO 2026-06-08 08:49:07 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 1s. Last read position: chr7:101,001,055 INFO 2026-06-08 08:49:07 MarkDuplicates Tracking 595929 as yet unmatched pairs. 24508 records in RAM. INFO 2026-06-08 08:49:09 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 1s. Last read position: chr7:101,001,357 INFO 2026-06-08 08:49:09 MarkDuplicates Tracking 594146 as yet unmatched pairs. 22725 records in RAM. INFO 2026-06-08 08:49:10 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:06:46s. Time for last 1,000,000: 1s. Last read position: chr7:101,001,632 INFO 2026-06-08 08:49:10 MarkDuplicates Tracking 592725 as yet unmatched pairs. 21304 records in RAM. INFO 2026-06-08 08:49:11 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:06:47s. Time for last 1,000,000: 1s. Last read position: chr7:101,001,922 INFO 2026-06-08 08:49:11 MarkDuplicates Tracking 592720 as yet unmatched pairs. 21299 records in RAM. INFO 2026-06-08 08:49:13 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 1s. Last read position: chr7:101,002,557 INFO 2026-06-08 08:49:13 MarkDuplicates Tracking 596304 as yet unmatched pairs. 24883 records in RAM. INFO 2026-06-08 08:49:14 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 1s. Last read position: chr7:101,003,232 INFO 2026-06-08 08:49:14 MarkDuplicates Tracking 591204 as yet unmatched pairs. 19783 records in RAM. INFO 2026-06-08 08:49:15 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:06:51s. Time for last 1,000,000: 1s. Last read position: chr7:101,004,000 INFO 2026-06-08 08:49:15 MarkDuplicates Tracking 589534 as yet unmatched pairs. 18113 records in RAM. INFO 2026-06-08 08:49:16 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 1s. Last read position: chr7:101,013,967 INFO 2026-06-08 08:49:16 MarkDuplicates Tracking 589773 as yet unmatched pairs. 18352 records in RAM. INFO 2026-06-08 08:49:18 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 1s. Last read position: chr7:102,493,943 INFO 2026-06-08 08:49:18 MarkDuplicates Tracking 587536 as yet unmatched pairs. 16115 records in RAM. INFO 2026-06-08 08:49:20 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 1s. Last read position: chr7:105,107,751 INFO 2026-06-08 08:49:20 MarkDuplicates Tracking 587004 as yet unmatched pairs. 15583 records in RAM. INFO 2026-06-08 08:49:21 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 1s. Last read position: chr7:116,249,135 INFO 2026-06-08 08:49:21 MarkDuplicates Tracking 585686 as yet unmatched pairs. 14256 records in RAM. INFO 2026-06-08 08:49:23 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 1s. Last read position: chr7:116,782,027 INFO 2026-06-08 08:49:23 MarkDuplicates Tracking 585007 as yet unmatched pairs. 13577 records in RAM. INFO 2026-06-08 08:50:27 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:08:03s. Time for last 1,000,000: 63s. Last read position: chr7:127,701,176 INFO 2026-06-08 08:50:27 MarkDuplicates Tracking 584173 as yet unmatched pairs. 12743 records in RAM. INFO 2026-06-08 08:50:29 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 1s. Last read position: chr7:128,758,873 INFO 2026-06-08 08:50:29 MarkDuplicates Tracking 581535 as yet unmatched pairs. 10105 records in RAM. INFO 2026-06-08 08:50:30 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:08:06s. Time for last 1,000,000: 1s. Last read position: chr7:135,594,656 INFO 2026-06-08 08:50:30 MarkDuplicates Tracking 580320 as yet unmatched pairs. 8890 records in RAM. INFO 2026-06-08 08:50:32 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:08:08s. Time for last 1,000,000: 1s. Last read position: chr7:139,614,329 INFO 2026-06-08 08:50:32 MarkDuplicates Tracking 578574 as yet unmatched pairs. 7144 records in RAM. INFO 2026-06-08 08:50:33 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:08:09s. Time for last 1,000,000: 1s. Last read position: chr7:143,382,983 INFO 2026-06-08 08:50:33 MarkDuplicates Tracking 577443 as yet unmatched pairs. 6009 records in RAM. INFO 2026-06-08 08:50:35 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:08:11s. Time for last 1,000,000: 1s. Last read position: chr7:144,363,357 INFO 2026-06-08 08:50:35 MarkDuplicates Tracking 576185 as yet unmatched pairs. 4751 records in RAM. INFO 2026-06-08 08:50:36 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:08:12s. Time for last 1,000,000: 1s. Last read position: chr7:150,371,697 INFO 2026-06-08 08:50:36 MarkDuplicates Tracking 575146 as yet unmatched pairs. 3712 records in RAM. INFO 2026-06-08 08:50:38 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:08:14s. Time for last 1,000,000: 2s. Last read position: chr7:151,234,062 INFO 2026-06-08 08:50:38 MarkDuplicates Tracking 573456 as yet unmatched pairs. 2022 records in RAM. INFO 2026-06-08 08:50:40 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 1s. Last read position: chr7:157,409,824 INFO 2026-06-08 08:50:40 MarkDuplicates Tracking 571992 as yet unmatched pairs. 558 records in RAM. INFO 2026-06-08 08:50:42 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:08:18s. Time for last 1,000,000: 1s. Last read position: chr8:12,186,395 INFO 2026-06-08 08:50:42 MarkDuplicates Tracking 570252 as yet unmatched pairs. 31515 records in RAM. INFO 2026-06-08 08:50:43 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 1s. Last read position: chr8:22,614,285 INFO 2026-06-08 08:50:43 MarkDuplicates Tracking 569119 as yet unmatched pairs. 30381 records in RAM. INFO 2026-06-08 08:50:45 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 1s. Last read position: chr8:29,337,310 INFO 2026-06-08 08:50:45 MarkDuplicates Tracking 567332 as yet unmatched pairs. 28593 records in RAM. INFO 2026-06-08 08:50:46 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 1s. Last read position: chr8:38,207,689 INFO 2026-06-08 08:50:46 MarkDuplicates Tracking 566020 as yet unmatched pairs. 27279 records in RAM. INFO 2026-06-08 08:50:48 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:08:24s. Time for last 1,000,000: 1s. Last read position: chr8:42,187,493 INFO 2026-06-08 08:50:48 MarkDuplicates Tracking 564820 as yet unmatched pairs. 26079 records in RAM. INFO 2026-06-08 08:50:49 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 1s. Last read position: chr8:47,966,372 INFO 2026-06-08 08:50:49 MarkDuplicates Tracking 563605 as yet unmatched pairs. 24862 records in RAM. INFO 2026-06-08 08:50:51 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:08:28s. Time for last 1,000,000: 2s. Last read position: chr8:63,038,662 INFO 2026-06-08 08:50:51 MarkDuplicates Tracking 561901 as yet unmatched pairs. 23158 records in RAM. INFO 2026-06-08 08:50:53 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 1s. Last read position: chr8:73,322,693 INFO 2026-06-08 08:50:53 MarkDuplicates Tracking 560648 as yet unmatched pairs. 21904 records in RAM. INFO 2026-06-08 08:50:54 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:08:31s. Time for last 1,000,000: 1s. Last read position: chr8:94,380,159 INFO 2026-06-08 08:50:54 MarkDuplicates Tracking 559341 as yet unmatched pairs. 20597 records in RAM. INFO 2026-06-08 08:50:56 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 1s. Last read position: chr8:100,704,935 INFO 2026-06-08 08:50:56 MarkDuplicates Tracking 559823 as yet unmatched pairs. 21079 records in RAM. INFO 2026-06-08 08:50:58 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 2s. Last read position: chr8:102,289,535 INFO 2026-06-08 08:50:58 MarkDuplicates Tracking 556366 as yet unmatched pairs. 17622 records in RAM. INFO 2026-06-08 08:51:00 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:08:36s. Time for last 1,000,000: 1s. Last read position: chr8:120,255,321 INFO 2026-06-08 08:51:00 MarkDuplicates Tracking 554918 as yet unmatched pairs. 16173 records in RAM. INFO 2026-06-08 08:51:01 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 1s. Last read position: chr8:127,738,885 INFO 2026-06-08 08:51:01 MarkDuplicates Tracking 554236 as yet unmatched pairs. 15491 records in RAM. INFO 2026-06-08 08:51:02 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:08:39s. Time for last 1,000,000: 1s. Last read position: chr8:143,020,901 INFO 2026-06-08 08:51:02 MarkDuplicates Tracking 552898 as yet unmatched pairs. 14153 records in RAM. INFO 2026-06-08 08:51:04 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 1s. Last read position: chr8:143,791,168 INFO 2026-06-08 08:51:04 MarkDuplicates Tracking 550256 as yet unmatched pairs. 11510 records in RAM. INFO 2026-06-08 08:51:05 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:08:41s. Time for last 1,000,000: 1s. Last read position: chr8:143,858,884 INFO 2026-06-08 08:51:05 MarkDuplicates Tracking 549500 as yet unmatched pairs. 10754 records in RAM. INFO 2026-06-08 08:51:06 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:08:42s. Time for last 1,000,000: 1s. Last read position: chr8:143,860,606 INFO 2026-06-08 08:51:06 MarkDuplicates Tracking 549722 as yet unmatched pairs. 10974 records in RAM. INFO 2026-06-08 08:51:07 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:08:43s. Time for last 1,000,000: 1s. Last read position: chr8:143,861,972 INFO 2026-06-08 08:51:07 MarkDuplicates Tracking 548477 as yet unmatched pairs. 9729 records in RAM. INFO 2026-06-08 08:51:08 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:08:45s. Time for last 1,000,000: 1s. Last read position: chr8:143,863,335 INFO 2026-06-08 08:51:08 MarkDuplicates Tracking 548325 as yet unmatched pairs. 9577 records in RAM. INFO 2026-06-08 08:51:10 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:08:46s. Time for last 1,000,000: 1s. Last read position: chr8:143,864,933 INFO 2026-06-08 08:51:10 MarkDuplicates Tracking 547174 as yet unmatched pairs. 8426 records in RAM. INFO 2026-06-08 08:51:11 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:08:47s. Time for last 1,000,000: 1s. Last read position: chr8:143,866,423 INFO 2026-06-08 08:51:11 MarkDuplicates Tracking 546661 as yet unmatched pairs. 7913 records in RAM. INFO 2026-06-08 08:51:12 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 1s. Last read position: chr8:143,919,180 INFO 2026-06-08 08:51:12 MarkDuplicates Tracking 545278 as yet unmatched pairs. 6523 records in RAM. INFO 2026-06-08 08:51:14 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:08:50s. Time for last 1,000,000: 1s. Last read position: chr8:143,934,426 INFO 2026-06-08 08:51:14 MarkDuplicates Tracking 543030 as yet unmatched pairs. 4274 records in RAM. INFO 2026-06-08 08:51:15 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 1s. Last read position: chr8:144,313,866 INFO 2026-06-08 08:51:15 MarkDuplicates Tracking 541454 as yet unmatched pairs. 2693 records in RAM. INFO 2026-06-08 08:51:16 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:08:53s. Time for last 1,000,000: 1s. Last read position: chr8:144,547,682 INFO 2026-06-08 08:51:16 MarkDuplicates Tracking 539287 as yet unmatched pairs. 526 records in RAM. INFO 2026-06-08 08:51:18 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 1s. Last read position: chr9:5,418,627 INFO 2026-06-08 08:51:18 MarkDuplicates Tracking 538042 as yet unmatched pairs. 37849 records in RAM. INFO 2026-06-08 08:51:20 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:08:56s. Time for last 1,000,000: 1s. Last read position: chr9:19,120,937 INFO 2026-06-08 08:51:20 MarkDuplicates Tracking 536649 as yet unmatched pairs. 36454 records in RAM. INFO 2026-06-08 08:51:21 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:08:57s. Time for last 1,000,000: 1s. Last read position: chr9:33,265,169 INFO 2026-06-08 08:51:21 MarkDuplicates Tracking 535302 as yet unmatched pairs. 35107 records in RAM. INFO 2026-06-08 08:51:23 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:08:59s. Time for last 1,000,000: 1s. Last read position: chr9:35,093,464 INFO 2026-06-08 08:51:23 MarkDuplicates Tracking 533615 as yet unmatched pairs. 33407 records in RAM. INFO 2026-06-08 08:51:24 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:09:00s. Time for last 1,000,000: 1s. Last read position: chr9:35,841,590 INFO 2026-06-08 08:51:24 MarkDuplicates Tracking 532048 as yet unmatched pairs. 31840 records in RAM. INFO 2026-06-08 08:51:26 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:09:02s. Time for last 1,000,000: 1s. Last read position: chr9:69,221,226 INFO 2026-06-08 08:51:26 MarkDuplicates Tracking 531040 as yet unmatched pairs. 30821 records in RAM. INFO 2026-06-08 08:51:27 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:09:04s. Time for last 1,000,000: 1s. Last read position: chr9:83,661,742 INFO 2026-06-08 08:51:27 MarkDuplicates Tracking 529586 as yet unmatched pairs. 29365 records in RAM. INFO 2026-06-08 08:51:29 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 1s. Last read position: chr9:92,265,513 INFO 2026-06-08 08:51:29 MarkDuplicates Tracking 528165 as yet unmatched pairs. 27943 records in RAM. INFO 2026-06-08 08:51:30 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:09:06s. Time for last 1,000,000: 1s. Last read position: chr9:93,576,805 INFO 2026-06-08 08:51:30 MarkDuplicates Tracking 526497 as yet unmatched pairs. 26275 records in RAM. INFO 2026-06-08 08:51:32 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 1s. Last read position: chr9:98,943,999 INFO 2026-06-08 08:51:32 MarkDuplicates Tracking 525520 as yet unmatched pairs. 25298 records in RAM. INFO 2026-06-08 08:51:34 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:09:10s. Time for last 1,000,000: 1s. Last read position: chr9:107,487,620 INFO 2026-06-08 08:51:34 MarkDuplicates Tracking 523644 as yet unmatched pairs. 23422 records in RAM. INFO 2026-06-08 08:51:36 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:09:12s. Time for last 1,000,000: 1s. Last read position: chr9:113,169,406 INFO 2026-06-08 08:51:36 MarkDuplicates Tracking 522185 as yet unmatched pairs. 21963 records in RAM. INFO 2026-06-08 08:51:38 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 2s. Last read position: chr9:121,138,553 INFO 2026-06-08 08:51:38 MarkDuplicates Tracking 520687 as yet unmatched pairs. 20457 records in RAM. INFO 2026-06-08 08:51:40 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 1s. Last read position: chr9:124,858,031 INFO 2026-06-08 08:51:40 MarkDuplicates Tracking 519774 as yet unmatched pairs. 19543 records in RAM. INFO 2026-06-08 08:51:41 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:09:17s. Time for last 1,000,000: 1s. Last read position: chr9:127,517,870 INFO 2026-06-08 08:51:41 MarkDuplicates Tracking 517946 as yet unmatched pairs. 17715 records in RAM. INFO 2026-06-08 08:51:43 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:09:19s. Time for last 1,000,000: 1s. Last read position: chr9:128,260,688 INFO 2026-06-08 08:51:43 MarkDuplicates Tracking 516118 as yet unmatched pairs. 15887 records in RAM. INFO 2026-06-08 08:51:44 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 1s. Last read position: chr9:128,721,341 INFO 2026-06-08 08:51:44 MarkDuplicates Tracking 515298 as yet unmatched pairs. 15067 records in RAM. INFO 2026-06-08 08:51:46 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 1s. Last read position: chr9:130,476,939 INFO 2026-06-08 08:51:46 MarkDuplicates Tracking 513986 as yet unmatched pairs. 13755 records in RAM. INFO 2026-06-08 08:51:47 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:09:23s. Time for last 1,000,000: 1s. Last read position: chr9:131,464,991 INFO 2026-06-08 08:51:47 MarkDuplicates Tracking 511764 as yet unmatched pairs. 11530 records in RAM. INFO 2026-06-08 08:51:49 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 1s. Last read position: chr9:133,341,508 INFO 2026-06-08 08:51:49 MarkDuplicates Tracking 510040 as yet unmatched pairs. 9802 records in RAM. INFO 2026-06-08 08:51:50 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:09:26s. Time for last 1,000,000: 1s. Last read position: chr9:134,815,604 INFO 2026-06-08 08:51:50 MarkDuplicates Tracking 508555 as yet unmatched pairs. 8317 records in RAM. INFO 2026-06-08 08:51:52 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:09:28s. Time for last 1,000,000: 1s. Last read position: chr9:136,496,293 INFO 2026-06-08 08:51:52 MarkDuplicates Tracking 507204 as yet unmatched pairs. 6966 records in RAM. INFO 2026-06-08 08:51:53 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:09:29s. Time for last 1,000,000: 1s. Last read position: chr9:136,839,075 INFO 2026-06-08 08:51:53 MarkDuplicates Tracking 505419 as yet unmatched pairs. 5179 records in RAM. INFO 2026-06-08 08:51:55 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:09:31s. Time for last 1,000,000: 1s. Last read position: chr9:137,082,659 INFO 2026-06-08 08:51:55 MarkDuplicates Tracking 503049 as yet unmatched pairs. 2808 records in RAM. INFO 2026-06-08 08:51:56 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:09:32s. Time for last 1,000,000: 1s. Last read position: chr9:137,301,659 INFO 2026-06-08 08:51:56 MarkDuplicates Tracking 501729 as yet unmatched pairs. 1487 records in RAM. INFO 2026-06-08 08:51:58 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:09:34s. Time for last 1,000,000: 1s. Last read position: chr10:5,456,895 INFO 2026-06-08 08:51:58 MarkDuplicates Tracking 499638 as yet unmatched pairs. 27324 records in RAM. INFO 2026-06-08 08:51:59 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:09:36s. Time for last 1,000,000: 1s. Last read position: chr10:20,812,874 INFO 2026-06-08 08:51:59 MarkDuplicates Tracking 498254 as yet unmatched pairs. 25939 records in RAM. INFO 2026-06-08 08:52:01 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 1s. Last read position: chr10:32,017,205 INFO 2026-06-08 08:52:01 MarkDuplicates Tracking 499395 as yet unmatched pairs. 27079 records in RAM. INFO 2026-06-08 08:52:02 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:09:39s. Time for last 1,000,000: 1s. Last read position: chr10:32,346,790 INFO 2026-06-08 08:52:02 MarkDuplicates Tracking 495828 as yet unmatched pairs. 23511 records in RAM. INFO 2026-06-08 08:52:04 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:09:40s. Time for last 1,000,000: 1s. Last read position: chr10:45,826,233 INFO 2026-06-08 08:52:04 MarkDuplicates Tracking 494222 as yet unmatched pairs. 21904 records in RAM. INFO 2026-06-08 08:52:06 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:09:42s. Time for last 1,000,000: 1s. Last read position: chr10:50,093,305 INFO 2026-06-08 08:52:06 MarkDuplicates Tracking 493215 as yet unmatched pairs. 20897 records in RAM. INFO 2026-06-08 08:52:07 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 1s. Last read position: chr10:68,338,633 INFO 2026-06-08 08:52:07 MarkDuplicates Tracking 491816 as yet unmatched pairs. 19495 records in RAM. INFO 2026-06-08 08:52:10 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:09:46s. Time for last 1,000,000: 2s. Last read position: chr10:71,299,194 INFO 2026-06-08 08:52:10 MarkDuplicates Tracking 490306 as yet unmatched pairs. 17984 records in RAM. INFO 2026-06-08 08:52:12 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:09:48s. Time for last 1,000,000: 1s. Last read position: chr10:73,998,211 INFO 2026-06-08 08:52:12 MarkDuplicates Tracking 488994 as yet unmatched pairs. 16672 records in RAM. INFO 2026-06-08 08:52:13 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:09:49s. Time for last 1,000,000: 1s. Last read position: chr10:79,706,081 INFO 2026-06-08 08:52:13 MarkDuplicates Tracking 487498 as yet unmatched pairs. 15175 records in RAM. INFO 2026-06-08 08:52:15 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:09:51s. Time for last 1,000,000: 1s. Last read position: chr10:87,214,075 INFO 2026-06-08 08:52:15 MarkDuplicates Tracking 486335 as yet unmatched pairs. 14012 records in RAM. INFO 2026-06-08 08:52:16 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:09:52s. Time for last 1,000,000: 1s. Last read position: chr10:93,356,699 INFO 2026-06-08 08:52:16 MarkDuplicates Tracking 484936 as yet unmatched pairs. 12613 records in RAM. INFO 2026-06-08 08:52:18 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:09:54s. Time for last 1,000,000: 1s. Last read position: chr10:96,955,118 INFO 2026-06-08 08:52:18 MarkDuplicates Tracking 483648 as yet unmatched pairs. 11324 records in RAM. INFO 2026-06-08 08:52:19 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:09:55s. Time for last 1,000,000: 1s. Last read position: chr10:100,360,840 INFO 2026-06-08 08:52:19 MarkDuplicates Tracking 482416 as yet unmatched pairs. 10091 records in RAM. INFO 2026-06-08 08:52:21 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:09:57s. Time for last 1,000,000: 1s. Last read position: chr10:102,344,048 INFO 2026-06-08 08:52:21 MarkDuplicates Tracking 480542 as yet unmatched pairs. 8217 records in RAM. INFO 2026-06-08 08:52:22 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:09:58s. Time for last 1,000,000: 1s. Last read position: chr10:104,034,627 INFO 2026-06-08 08:52:22 MarkDuplicates Tracking 479126 as yet unmatched pairs. 6801 records in RAM. INFO 2026-06-08 08:52:24 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:10:00s. Time for last 1,000,000: 1s. Last read position: chr10:113,158,043 INFO 2026-06-08 08:52:24 MarkDuplicates Tracking 477420 as yet unmatched pairs. 5093 records in RAM. INFO 2026-06-08 08:52:25 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:10:01s. Time for last 1,000,000: 1s. Last read position: chr10:119,073,789 INFO 2026-06-08 08:52:25 MarkDuplicates Tracking 476347 as yet unmatched pairs. 4020 records in RAM. INFO 2026-06-08 08:52:27 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:10:03s. Time for last 1,000,000: 1s. Last read position: chr10:123,160,519 INFO 2026-06-08 08:52:27 MarkDuplicates Tracking 474845 as yet unmatched pairs. 2518 records in RAM. INFO 2026-06-08 08:52:28 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:10:04s. Time for last 1,000,000: 1s. Last read position: chr10:128,108,851 INFO 2026-06-08 08:52:28 MarkDuplicates Tracking 473384 as yet unmatched pairs. 1056 records in RAM. INFO 2026-06-08 08:52:30 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 1s. Last read position: chr11:314,245 INFO 2026-06-08 08:52:30 MarkDuplicates Tracking 473708 as yet unmatched pairs. 60381 records in RAM. INFO 2026-06-08 08:52:32 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:10:08s. Time for last 1,000,000: 1s. Last read position: chr11:409,869 INFO 2026-06-08 08:52:32 MarkDuplicates Tracking 470640 as yet unmatched pairs. 57310 records in RAM. INFO 2026-06-08 08:52:33 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 1s. Last read position: chr11:771,329 INFO 2026-06-08 08:52:33 MarkDuplicates Tracking 468890 as yet unmatched pairs. 55558 records in RAM. INFO 2026-06-08 08:52:35 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:10:11s. Time for last 1,000,000: 1s. Last read position: chr11:1,083,751 INFO 2026-06-08 08:52:35 MarkDuplicates Tracking 467504 as yet unmatched pairs. 54172 records in RAM. INFO 2026-06-08 08:52:36 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 1s. Last read position: chr11:1,245,400 INFO 2026-06-08 08:52:36 MarkDuplicates Tracking 465959 as yet unmatched pairs. 52627 records in RAM. INFO 2026-06-08 08:52:38 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:10:14s. Time for last 1,000,000: 1s. Last read position: chr11:1,761,309 INFO 2026-06-08 08:52:38 MarkDuplicates Tracking 466571 as yet unmatched pairs. 53238 records in RAM. INFO 2026-06-08 08:52:40 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:10:16s. Time for last 1,000,000: 2s. Last read position: chr11:3,706,506 INFO 2026-06-08 08:52:40 MarkDuplicates Tracking 463069 as yet unmatched pairs. 49735 records in RAM. INFO 2026-06-08 08:52:42 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:10:18s. Time for last 1,000,000: 1s. Last read position: chr11:6,682,775 INFO 2026-06-08 08:52:42 MarkDuplicates Tracking 461476 as yet unmatched pairs. 48142 records in RAM. INFO 2026-06-08 08:52:44 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:10:20s. Time for last 1,000,000: 1s. Last read position: chr11:10,799,329 INFO 2026-06-08 08:52:44 MarkDuplicates Tracking 460574 as yet unmatched pairs. 47239 records in RAM. INFO 2026-06-08 08:52:46 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:10:22s. Time for last 1,000,000: 1s. Last read position: chr11:14,867,583 INFO 2026-06-08 08:52:46 MarkDuplicates Tracking 458537 as yet unmatched pairs. 45202 records in RAM. INFO 2026-06-08 08:52:47 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:10:23s. Time for last 1,000,000: 1s. Last read position: chr11:22,625,277 INFO 2026-06-08 08:52:47 MarkDuplicates Tracking 457158 as yet unmatched pairs. 43823 records in RAM. INFO 2026-06-08 08:52:49 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:10:25s. Time for last 1,000,000: 1s. Last read position: chr11:34,621,142 INFO 2026-06-08 08:52:49 MarkDuplicates Tracking 456958 as yet unmatched pairs. 43621 records in RAM. INFO 2026-06-08 08:52:50 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:10:27s. Time for last 1,000,000: 1s. Last read position: chr11:45,913,889 INFO 2026-06-08 08:52:50 MarkDuplicates Tracking 454462 as yet unmatched pairs. 41124 records in RAM. INFO 2026-06-08 08:52:52 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:10:28s. Time for last 1,000,000: 1s. Last read position: chr11:46,818,433 INFO 2026-06-08 08:52:52 MarkDuplicates Tracking 453084 as yet unmatched pairs. 39746 records in RAM. INFO 2026-06-08 08:52:54 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:10:30s. Time for last 1,000,000: 1s. Last read position: chr11:57,302,601 INFO 2026-06-08 08:52:54 MarkDuplicates Tracking 451622 as yet unmatched pairs. 38284 records in RAM. INFO 2026-06-08 08:52:55 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:10:31s. Time for last 1,000,000: 1s. Last read position: chr11:57,815,462 INFO 2026-06-08 08:52:55 MarkDuplicates Tracking 451390 as yet unmatched pairs. 38051 records in RAM. INFO 2026-06-08 08:52:56 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:10:33s. Time for last 1,000,000: 1s. Last read position: chr11:61,313,673 INFO 2026-06-08 08:52:56 MarkDuplicates Tracking 448840 as yet unmatched pairs. 35501 records in RAM. INFO 2026-06-08 08:52:58 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:10:34s. Time for last 1,000,000: 1s. Last read position: chr11:62,518,932 INFO 2026-06-08 08:52:58 MarkDuplicates Tracking 447461 as yet unmatched pairs. 34117 records in RAM. INFO 2026-06-08 08:52:59 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:10:36s. Time for last 1,000,000: 1s. Last read position: chr11:62,559,753 INFO 2026-06-08 08:52:59 MarkDuplicates Tracking 447370 as yet unmatched pairs. 34024 records in RAM. INFO 2026-06-08 08:53:01 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:10:37s. Time for last 1,000,000: 1s. Last read position: chr11:62,752,092 INFO 2026-06-08 08:53:01 MarkDuplicates Tracking 444216 as yet unmatched pairs. 30870 records in RAM. INFO 2026-06-08 08:53:03 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:10:39s. Time for last 1,000,000: 1s. Last read position: chr11:64,223,924 INFO 2026-06-08 08:53:03 MarkDuplicates Tracking 442749 as yet unmatched pairs. 29403 records in RAM. INFO 2026-06-08 08:53:04 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:10:40s. Time for last 1,000,000: 1s. Last read position: chr11:64,354,114 INFO 2026-06-08 08:53:04 MarkDuplicates Tracking 440718 as yet unmatched pairs. 27372 records in RAM. INFO 2026-06-08 08:53:06 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:10:42s. Time for last 1,000,000: 1s. Last read position: chr11:65,109,350 INFO 2026-06-08 08:53:06 MarkDuplicates Tracking 439046 as yet unmatched pairs. 25700 records in RAM. INFO 2026-06-08 08:53:07 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:10:43s. Time for last 1,000,000: 1s. Last read position: chr11:65,573,386 INFO 2026-06-08 08:53:07 MarkDuplicates Tracking 437481 as yet unmatched pairs. 24135 records in RAM. INFO 2026-06-08 08:53:09 MarkDuplicates Read 368,000,000 records. Elapsed time: 00:10:45s. Time for last 1,000,000: 1s. Last read position: chr11:65,712,432 INFO 2026-06-08 08:53:09 MarkDuplicates Tracking 435449 as yet unmatched pairs. 22103 records in RAM. INFO 2026-06-08 08:53:10 MarkDuplicates Read 369,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 1s. Last read position: chr11:66,315,727 INFO 2026-06-08 08:53:10 MarkDuplicates Tracking 433895 as yet unmatched pairs. 20549 records in RAM. INFO 2026-06-08 08:53:12 MarkDuplicates Read 370,000,000 records. Elapsed time: 00:10:48s. Time for last 1,000,000: 1s. Last read position: chr11:67,279,420 INFO 2026-06-08 08:53:12 MarkDuplicates Tracking 432389 as yet unmatched pairs. 19043 records in RAM. INFO 2026-06-08 08:53:15 MarkDuplicates Read 371,000,000 records. Elapsed time: 00:10:51s. Time for last 1,000,000: 2s. Last read position: chr11:67,586,185 INFO 2026-06-08 08:53:15 MarkDuplicates Tracking 432276 as yet unmatched pairs. 18930 records in RAM. INFO 2026-06-08 08:53:17 MarkDuplicates Read 372,000,000 records. Elapsed time: 00:10:53s. Time for last 1,000,000: 1s. Last read position: chr11:68,750,604 INFO 2026-06-08 08:53:17 MarkDuplicates Tracking 428588 as yet unmatched pairs. 15240 records in RAM. INFO 2026-06-08 08:53:18 MarkDuplicates Read 373,000,000 records. Elapsed time: 00:10:54s. Time for last 1,000,000: 1s. Last read position: chr11:71,435,403 INFO 2026-06-08 08:53:18 MarkDuplicates Tracking 427153 as yet unmatched pairs. 13805 records in RAM. INFO 2026-06-08 08:53:20 MarkDuplicates Read 374,000,000 records. Elapsed time: 00:10:56s. Time for last 1,000,000: 1s. Last read position: chr11:72,329,720 INFO 2026-06-08 08:53:20 MarkDuplicates Tracking 425544 as yet unmatched pairs. 12195 records in RAM. INFO 2026-06-08 08:53:21 MarkDuplicates Read 375,000,000 records. Elapsed time: 00:10:57s. Time for last 1,000,000: 1s. Last read position: chr11:75,443,239 INFO 2026-06-08 08:53:21 MarkDuplicates Tracking 423905 as yet unmatched pairs. 10553 records in RAM. INFO 2026-06-08 08:53:23 MarkDuplicates Read 376,000,000 records. Elapsed time: 00:10:59s. Time for last 1,000,000: 1s. Last read position: chr11:85,974,732 INFO 2026-06-08 08:53:23 MarkDuplicates Tracking 422601 as yet unmatched pairs. 9248 records in RAM. INFO 2026-06-08 08:53:24 MarkDuplicates Read 377,000,000 records. Elapsed time: 00:11:00s. Time for last 1,000,000: 1s. Last read position: chr11:102,110,974 INFO 2026-06-08 08:53:24 MarkDuplicates Tracking 422137 as yet unmatched pairs. 8783 records in RAM. INFO 2026-06-08 08:53:26 MarkDuplicates Read 378,000,000 records. Elapsed time: 00:11:02s. Time for last 1,000,000: 1s. Last read position: chr11:112,082,889 INFO 2026-06-08 08:53:26 MarkDuplicates Tracking 419570 as yet unmatched pairs. 6216 records in RAM. INFO 2026-06-08 08:53:27 MarkDuplicates Read 379,000,000 records. Elapsed time: 00:11:03s. Time for last 1,000,000: 1s. Last read position: chr11:118,545,691 INFO 2026-06-08 08:53:27 MarkDuplicates Tracking 418099 as yet unmatched pairs. 4745 records in RAM. INFO 2026-06-08 08:53:29 MarkDuplicates Read 380,000,000 records. Elapsed time: 00:11:05s. Time for last 1,000,000: 1s. Last read position: chr11:120,337,250 INFO 2026-06-08 08:53:29 MarkDuplicates Tracking 416515 as yet unmatched pairs. 3154 records in RAM. INFO 2026-06-08 08:53:30 MarkDuplicates Read 381,000,000 records. Elapsed time: 00:11:06s. Time for last 1,000,000: 1s. Last read position: chr11:125,637,484 INFO 2026-06-08 08:53:30 MarkDuplicates Tracking 415037 as yet unmatched pairs. 1676 records in RAM. INFO 2026-06-08 08:53:32 MarkDuplicates Read 382,000,000 records. Elapsed time: 00:11:08s. Time for last 1,000,000: 1s. Last read position: chr11:134,194,044 INFO 2026-06-08 08:53:32 MarkDuplicates Tracking 413527 as yet unmatched pairs. 166 records in RAM. INFO 2026-06-08 08:53:34 MarkDuplicates Read 383,000,000 records. Elapsed time: 00:11:10s. Time for last 1,000,000: 1s. Last read position: chr12:890,465 INFO 2026-06-08 08:53:34 MarkDuplicates Tracking 412474 as yet unmatched pairs. 57052 records in RAM. INFO 2026-06-08 08:53:35 MarkDuplicates Read 384,000,000 records. Elapsed time: 00:11:11s. Time for last 1,000,000: 1s. Last read position: chr12:2,888,525 INFO 2026-06-08 08:53:35 MarkDuplicates Tracking 410615 as yet unmatched pairs. 55193 records in RAM. INFO 2026-06-08 08:53:37 MarkDuplicates Read 385,000,000 records. Elapsed time: 00:11:13s. Time for last 1,000,000: 1s. Last read position: chr12:4,288,892 INFO 2026-06-08 08:53:37 MarkDuplicates Tracking 415059 as yet unmatched pairs. 59637 records in RAM. INFO 2026-06-08 08:53:39 MarkDuplicates Read 386,000,000 records. Elapsed time: 00:11:15s. Time for last 1,000,000: 1s. Last read position: chr12:4,686,937 INFO 2026-06-08 08:53:39 MarkDuplicates Tracking 411518 as yet unmatched pairs. 56096 records in RAM. INFO 2026-06-08 08:53:40 MarkDuplicates Read 387,000,000 records. Elapsed time: 00:11:16s. Time for last 1,000,000: 1s. Last read position: chr12:6,374,417 INFO 2026-06-08 08:53:40 MarkDuplicates Tracking 407030 as yet unmatched pairs. 51608 records in RAM. INFO 2026-06-08 08:53:42 MarkDuplicates Read 388,000,000 records. Elapsed time: 00:11:18s. Time for last 1,000,000: 2s. Last read position: chr12:6,653,248 INFO 2026-06-08 08:53:42 MarkDuplicates Tracking 404510 as yet unmatched pairs. 49088 records in RAM. INFO 2026-06-08 08:53:45 MarkDuplicates Read 389,000,000 records. Elapsed time: 00:11:21s. Time for last 1,000,000: 2s. Last read position: chr12:7,070,072 INFO 2026-06-08 08:53:45 MarkDuplicates Tracking 402937 as yet unmatched pairs. 47515 records in RAM. INFO 2026-06-08 08:53:47 MarkDuplicates Read 390,000,000 records. Elapsed time: 00:11:23s. Time for last 1,000,000: 1s. Last read position: chr12:10,723,017 INFO 2026-06-08 08:53:47 MarkDuplicates Tracking 401859 as yet unmatched pairs. 46434 records in RAM. INFO 2026-06-08 08:53:48 MarkDuplicates Read 391,000,000 records. Elapsed time: 00:11:24s. Time for last 1,000,000: 1s. Last read position: chr12:12,912,470 INFO 2026-06-08 08:53:48 MarkDuplicates Tracking 401318 as yet unmatched pairs. 45893 records in RAM. INFO 2026-06-08 08:53:50 MarkDuplicates Read 392,000,000 records. Elapsed time: 00:11:26s. Time for last 1,000,000: 1s. Last read position: chr12:21,646,937 INFO 2026-06-08 08:53:50 MarkDuplicates Tracking 399423 as yet unmatched pairs. 43998 records in RAM. INFO 2026-06-08 08:53:51 MarkDuplicates Read 393,000,000 records. Elapsed time: 00:11:27s. Time for last 1,000,000: 1s. Last read position: chr12:32,640,469 INFO 2026-06-08 08:53:51 MarkDuplicates Tracking 397256 as yet unmatched pairs. 41831 records in RAM. INFO 2026-06-08 08:53:53 MarkDuplicates Read 394,000,000 records. Elapsed time: 00:11:29s. Time for last 1,000,000: 1s. Last read position: chr12:47,964,369 INFO 2026-06-08 08:53:53 MarkDuplicates Tracking 396614 as yet unmatched pairs. 41181 records in RAM. INFO 2026-06-08 08:53:54 MarkDuplicates Read 395,000,000 records. Elapsed time: 00:11:30s. Time for last 1,000,000: 1s. Last read position: chr12:49,044,220 INFO 2026-06-08 08:53:54 MarkDuplicates Tracking 394541 as yet unmatched pairs. 39108 records in RAM. INFO 2026-06-08 08:53:56 MarkDuplicates Read 396,000,000 records. Elapsed time: 00:11:32s. Time for last 1,000,000: 1s. Last read position: chr12:49,186,694 INFO 2026-06-08 08:53:56 MarkDuplicates Tracking 393350 as yet unmatched pairs. 37917 records in RAM. INFO 2026-06-08 08:53:57 MarkDuplicates Read 397,000,000 records. Elapsed time: 00:11:33s. Time for last 1,000,000: 1s. Last read position: chr12:50,090,387 INFO 2026-06-08 08:53:57 MarkDuplicates Tracking 391922 as yet unmatched pairs. 36489 records in RAM. INFO 2026-06-08 08:53:59 MarkDuplicates Read 398,000,000 records. Elapsed time: 00:11:35s. Time for last 1,000,000: 1s. Last read position: chr12:52,897,481 INFO 2026-06-08 08:53:59 MarkDuplicates Tracking 391645 as yet unmatched pairs. 36212 records in RAM. INFO 2026-06-08 08:54:00 MarkDuplicates Read 399,000,000 records. Elapsed time: 00:11:36s. Time for last 1,000,000: 1s. Last read position: chr12:52,952,723 INFO 2026-06-08 08:54:00 MarkDuplicates Tracking 391182 as yet unmatched pairs. 35747 records in RAM. INFO 2026-06-08 08:54:02 MarkDuplicates Read 400,000,000 records. Elapsed time: 00:11:38s. Time for last 1,000,000: 1s. Last read position: chr12:53,455,987 INFO 2026-06-08 08:54:02 MarkDuplicates Tracking 387989 as yet unmatched pairs. 32554 records in RAM. INFO 2026-06-08 08:54:03 MarkDuplicates Read 401,000,000 records. Elapsed time: 00:11:39s. Time for last 1,000,000: 1s. Last read position: chr12:54,347,767 INFO 2026-06-08 08:54:03 MarkDuplicates Tracking 386413 as yet unmatched pairs. 30978 records in RAM. INFO 2026-06-08 08:54:05 MarkDuplicates Read 402,000,000 records. Elapsed time: 00:11:41s. Time for last 1,000,000: 1s. Last read position: chr12:56,101,195 INFO 2026-06-08 08:54:05 MarkDuplicates Tracking 385232 as yet unmatched pairs. 29797 records in RAM. INFO 2026-06-08 08:54:06 MarkDuplicates Read 403,000,000 records. Elapsed time: 00:11:42s. Time for last 1,000,000: 1s. Last read position: chr12:56,314,926 INFO 2026-06-08 08:54:06 MarkDuplicates Tracking 383682 as yet unmatched pairs. 28247 records in RAM. INFO 2026-06-08 08:54:08 MarkDuplicates Read 404,000,000 records. Elapsed time: 00:11:44s. Time for last 1,000,000: 1s. Last read position: chr12:56,717,852 INFO 2026-06-08 08:54:08 MarkDuplicates Tracking 382048 as yet unmatched pairs. 26613 records in RAM. INFO 2026-06-08 08:54:10 MarkDuplicates Read 405,000,000 records. Elapsed time: 00:11:46s. Time for last 1,000,000: 2s. Last read position: chr12:57,106,701 INFO 2026-06-08 08:54:10 MarkDuplicates Tracking 380884 as yet unmatched pairs. 25449 records in RAM. INFO 2026-06-08 08:54:12 MarkDuplicates Read 406,000,000 records. Elapsed time: 00:11:48s. Time for last 1,000,000: 1s. Last read position: chr12:57,210,306 INFO 2026-06-08 08:54:12 MarkDuplicates Tracking 379044 as yet unmatched pairs. 23609 records in RAM. INFO 2026-06-08 08:54:13 MarkDuplicates Read 407,000,000 records. Elapsed time: 00:11:49s. Time for last 1,000,000: 1s. Last read position: chr12:57,751,033 INFO 2026-06-08 08:54:13 MarkDuplicates Tracking 377622 as yet unmatched pairs. 22187 records in RAM. INFO 2026-06-08 08:54:15 MarkDuplicates Read 408,000,000 records. Elapsed time: 00:11:51s. Time for last 1,000,000: 2s. Last read position: chr12:67,657,630 INFO 2026-06-08 08:54:15 MarkDuplicates Tracking 376063 as yet unmatched pairs. 20628 records in RAM. INFO 2026-06-08 08:54:17 MarkDuplicates Read 409,000,000 records. Elapsed time: 00:11:53s. Time for last 1,000,000: 1s. Last read position: chr12:71,638,455 INFO 2026-06-08 08:54:17 MarkDuplicates Tracking 374691 as yet unmatched pairs. 19256 records in RAM. INFO 2026-06-08 08:54:19 MarkDuplicates Read 410,000,000 records. Elapsed time: 00:11:55s. Time for last 1,000,000: 1s. Last read position: chr12:93,378,120 INFO 2026-06-08 08:54:19 MarkDuplicates Tracking 373159 as yet unmatched pairs. 17723 records in RAM. INFO 2026-06-08 08:54:20 MarkDuplicates Read 411,000,000 records. Elapsed time: 00:11:56s. Time for last 1,000,000: 1s. Last read position: chr12:100,312,558 INFO 2026-06-08 08:54:20 MarkDuplicates Tracking 371749 as yet unmatched pairs. 16310 records in RAM. INFO 2026-06-08 08:54:22 MarkDuplicates Read 412,000,000 records. Elapsed time: 00:11:58s. Time for last 1,000,000: 1s. Last read position: chr12:105,330,837 INFO 2026-06-08 08:54:22 MarkDuplicates Tracking 371093 as yet unmatched pairs. 15653 records in RAM. INFO 2026-06-08 08:54:23 MarkDuplicates Read 413,000,000 records. Elapsed time: 00:11:59s. Time for last 1,000,000: 1s. Last read position: chr12:110,333,249 INFO 2026-06-08 08:54:23 MarkDuplicates Tracking 369484 as yet unmatched pairs. 14042 records in RAM. INFO 2026-06-08 08:54:25 MarkDuplicates Read 414,000,000 records. Elapsed time: 00:12:01s. Time for last 1,000,000: 1s. Last read position: chr12:112,171,160 INFO 2026-06-08 08:54:25 MarkDuplicates Tracking 367594 as yet unmatched pairs. 12151 records in RAM. INFO 2026-06-08 08:54:26 MarkDuplicates Read 415,000,000 records. Elapsed time: 00:12:02s. Time for last 1,000,000: 1s. Last read position: chr12:113,372,753 INFO 2026-06-08 08:54:26 MarkDuplicates Tracking 365954 as yet unmatched pairs. 10511 records in RAM. INFO 2026-06-08 08:54:28 MarkDuplicates Read 416,000,000 records. Elapsed time: 00:12:04s. Time for last 1,000,000: 1s. Last read position: chr12:120,129,372 INFO 2026-06-08 08:54:28 MarkDuplicates Tracking 364557 as yet unmatched pairs. 9107 records in RAM. INFO 2026-06-08 08:54:29 MarkDuplicates Read 417,000,000 records. Elapsed time: 00:12:05s. Time for last 1,000,000: 1s. Last read position: chr12:120,575,874 INFO 2026-06-08 08:54:29 MarkDuplicates Tracking 363344 as yet unmatched pairs. 7894 records in RAM. INFO 2026-06-08 08:54:31 MarkDuplicates Read 418,000,000 records. Elapsed time: 00:12:07s. Time for last 1,000,000: 1s. Last read position: chr12:122,133,761 INFO 2026-06-08 08:54:31 MarkDuplicates Tracking 361915 as yet unmatched pairs. 6464 records in RAM. INFO 2026-06-08 08:54:32 MarkDuplicates Read 419,000,000 records. Elapsed time: 00:12:08s. Time for last 1,000,000: 1s. Last read position: chr12:123,690,582 INFO 2026-06-08 08:54:32 MarkDuplicates Tracking 359739 as yet unmatched pairs. 4287 records in RAM. INFO 2026-06-08 08:54:34 MarkDuplicates Read 420,000,000 records. Elapsed time: 00:12:10s. Time for last 1,000,000: 1s. Last read position: chr12:124,949,985 INFO 2026-06-08 08:54:34 MarkDuplicates Tracking 358188 as yet unmatched pairs. 2735 records in RAM. INFO 2026-06-08 08:54:35 MarkDuplicates Read 421,000,000 records. Elapsed time: 00:12:11s. Time for last 1,000,000: 1s. Last read position: chr12:132,571,355 INFO 2026-06-08 08:54:35 MarkDuplicates Tracking 356654 as yet unmatched pairs. 1200 records in RAM. INFO 2026-06-08 08:54:37 MarkDuplicates Read 422,000,000 records. Elapsed time: 00:12:13s. Time for last 1,000,000: 1s. Last read position: chr13:20,006,542 INFO 2026-06-08 08:54:37 MarkDuplicates Tracking 355690 as yet unmatched pairs. 17280 records in RAM. INFO 2026-06-08 08:54:39 MarkDuplicates Read 423,000,000 records. Elapsed time: 00:12:15s. Time for last 1,000,000: 1s. Last read position: chr13:24,892,750 INFO 2026-06-08 08:54:39 MarkDuplicates Tracking 353776 as yet unmatched pairs. 15366 records in RAM. INFO 2026-06-08 08:54:40 MarkDuplicates Read 424,000,000 records. Elapsed time: 00:12:16s. Time for last 1,000,000: 1s. Last read position: chr13:29,767,636 INFO 2026-06-08 08:54:40 MarkDuplicates Tracking 352295 as yet unmatched pairs. 13884 records in RAM. INFO 2026-06-08 08:54:42 MarkDuplicates Read 425,000,000 records. Elapsed time: 00:12:18s. Time for last 1,000,000: 1s. Last read position: chr13:40,904,758 INFO 2026-06-08 08:54:42 MarkDuplicates Tracking 350879 as yet unmatched pairs. 12468 records in RAM. INFO 2026-06-08 08:54:44 MarkDuplicates Read 426,000,000 records. Elapsed time: 00:12:20s. Time for last 1,000,000: 2s. Last read position: chr13:46,343,369 INFO 2026-06-08 08:54:44 MarkDuplicates Tracking 349988 as yet unmatched pairs. 11577 records in RAM. INFO 2026-06-08 08:54:46 MarkDuplicates Read 427,000,000 records. Elapsed time: 00:12:22s. Time for last 1,000,000: 2s. Last read position: chr13:52,680,071 INFO 2026-06-08 08:54:46 MarkDuplicates Tracking 348388 as yet unmatched pairs. 9977 records in RAM. INFO 2026-06-08 08:54:48 MarkDuplicates Read 428,000,000 records. Elapsed time: 00:12:24s. Time for last 1,000,000: 1s. Last read position: chr13:77,021,757 INFO 2026-06-08 08:54:48 MarkDuplicates Tracking 346700 as yet unmatched pairs. 8285 records in RAM. INFO 2026-06-08 08:54:49 MarkDuplicates Read 429,000,000 records. Elapsed time: 00:12:26s. Time for last 1,000,000: 1s. Last read position: chr13:98,446,144 INFO 2026-06-08 08:54:49 MarkDuplicates Tracking 345527 as yet unmatched pairs. 7112 records in RAM. INFO 2026-06-08 08:54:51 MarkDuplicates Read 430,000,000 records. Elapsed time: 00:12:27s. Time for last 1,000,000: 1s. Last read position: chr13:106,544,100 INFO 2026-06-08 08:54:51 MarkDuplicates Tracking 343637 as yet unmatched pairs. 5222 records in RAM. INFO 2026-06-08 08:54:53 MarkDuplicates Read 431,000,000 records. Elapsed time: 00:12:29s. Time for last 1,000,000: 1s. Last read position: chr13:110,424,995 INFO 2026-06-08 08:54:53 MarkDuplicates Tracking 342365 as yet unmatched pairs. 3950 records in RAM. INFO 2026-06-08 08:54:54 MarkDuplicates Read 432,000,000 records. Elapsed time: 00:12:30s. Time for last 1,000,000: 1s. Last read position: chr13:112,565,146 INFO 2026-06-08 08:54:54 MarkDuplicates Tracking 340370 as yet unmatched pairs. 1953 records in RAM. INFO 2026-06-08 08:54:55 MarkDuplicates Read 433,000,000 records. Elapsed time: 00:12:32s. Time for last 1,000,000: 1s. Last read position: chr13:114,282,030 INFO 2026-06-08 08:54:55 MarkDuplicates Tracking 338678 as yet unmatched pairs. 260 records in RAM. INFO 2026-06-08 08:54:57 MarkDuplicates Read 434,000,000 records. Elapsed time: 00:12:33s. Time for last 1,000,000: 1s. Last read position: chr14:22,771,285 INFO 2026-06-08 08:54:57 MarkDuplicates Tracking 337101 as yet unmatched pairs. 17446 records in RAM. INFO 2026-06-08 08:54:59 MarkDuplicates Read 435,000,000 records. Elapsed time: 00:12:35s. Time for last 1,000,000: 1s. Last read position: chr14:24,138,475 INFO 2026-06-08 08:54:59 MarkDuplicates Tracking 335957 as yet unmatched pairs. 16302 records in RAM. INFO 2026-06-08 08:55:00 MarkDuplicates Read 436,000,000 records. Elapsed time: 00:12:36s. Time for last 1,000,000: 1s. Last read position: chr14:32,149,931 INFO 2026-06-08 08:55:00 MarkDuplicates Tracking 334209 as yet unmatched pairs. 14554 records in RAM. INFO 2026-06-08 08:55:02 MarkDuplicates Read 437,000,000 records. Elapsed time: 00:12:38s. Time for last 1,000,000: 1s. Last read position: chr14:52,053,654 INFO 2026-06-08 08:55:02 MarkDuplicates Tracking 332946 as yet unmatched pairs. 13288 records in RAM. INFO 2026-06-08 08:55:03 MarkDuplicates Read 438,000,000 records. Elapsed time: 00:12:39s. Time for last 1,000,000: 1s. Last read position: chr14:62,618,156 INFO 2026-06-08 08:55:03 MarkDuplicates Tracking 331570 as yet unmatched pairs. 11912 records in RAM. INFO 2026-06-08 08:55:05 MarkDuplicates Read 439,000,000 records. Elapsed time: 00:12:41s. Time for last 1,000,000: 1s. Last read position: chr14:67,807,903 INFO 2026-06-08 08:55:05 MarkDuplicates Tracking 330218 as yet unmatched pairs. 10560 records in RAM. INFO 2026-06-08 08:55:06 MarkDuplicates Read 440,000,000 records. Elapsed time: 00:12:42s. Time for last 1,000,000: 1s. Last read position: chr14:73,941,034 INFO 2026-06-08 08:55:06 MarkDuplicates Tracking 328736 as yet unmatched pairs. 9076 records in RAM. INFO 2026-06-08 08:55:08 MarkDuplicates Read 441,000,000 records. Elapsed time: 00:12:44s. Time for last 1,000,000: 1s. Last read position: chr14:81,270,748 INFO 2026-06-08 08:55:08 MarkDuplicates Tracking 327383 as yet unmatched pairs. 7722 records in RAM. INFO 2026-06-08 08:55:09 MarkDuplicates Read 442,000,000 records. Elapsed time: 00:12:45s. Time for last 1,000,000: 1s. Last read position: chr14:95,191,488 INFO 2026-06-08 08:55:09 MarkDuplicates Tracking 325940 as yet unmatched pairs. 6279 records in RAM. INFO 2026-06-08 08:55:11 MarkDuplicates Read 443,000,000 records. Elapsed time: 00:12:47s. Time for last 1,000,000: 1s. Last read position: chr14:102,050,484 INFO 2026-06-08 08:55:11 MarkDuplicates Tracking 324940 as yet unmatched pairs. 5268 records in RAM. INFO 2026-06-08 08:55:12 MarkDuplicates Read 444,000,000 records. Elapsed time: 00:12:48s. Time for last 1,000,000: 1s. Last read position: chr14:104,701,453 INFO 2026-06-08 08:55:12 MarkDuplicates Tracking 323098 as yet unmatched pairs. 3425 records in RAM. INFO 2026-06-08 08:55:14 MarkDuplicates Read 445,000,000 records. Elapsed time: 00:12:50s. Time for last 1,000,000: 1s. Last read position: chr14:105,587,762 INFO 2026-06-08 08:55:14 MarkDuplicates Tracking 321345 as yet unmatched pairs. 1672 records in RAM. INFO 2026-06-08 08:55:15 MarkDuplicates Read 446,000,000 records. Elapsed time: 00:12:52s. Time for last 1,000,000: 1s. Last read position: chr14:105,742,341 INFO 2026-06-08 08:55:15 MarkDuplicates Tracking 320501 as yet unmatched pairs. 828 records in RAM. INFO 2026-06-08 08:55:17 MarkDuplicates Read 447,000,000 records. Elapsed time: 00:12:53s. Time for last 1,000,000: 1s. Last read position: chr15:29,718,020 INFO 2026-06-08 08:55:17 MarkDuplicates Tracking 319007 as yet unmatched pairs. 18145 records in RAM. INFO 2026-06-08 08:55:19 MarkDuplicates Read 448,000,000 records. Elapsed time: 00:12:55s. Time for last 1,000,000: 2s. Last read position: chr15:39,595,360 INFO 2026-06-08 08:55:19 MarkDuplicates Tracking 317849 as yet unmatched pairs. 16986 records in RAM. INFO 2026-06-08 08:55:21 MarkDuplicates Read 449,000,000 records. Elapsed time: 00:12:57s. Time for last 1,000,000: 1s. Last read position: chr15:41,748,762 INFO 2026-06-08 08:55:21 MarkDuplicates Tracking 316410 as yet unmatched pairs. 15544 records in RAM. INFO 2026-06-08 08:55:22 MarkDuplicates Read 450,000,000 records. Elapsed time: 00:12:59s. Time for last 1,000,000: 1s. Last read position: chr15:43,698,990 INFO 2026-06-08 08:55:22 MarkDuplicates Tracking 315029 as yet unmatched pairs. 14163 records in RAM. INFO 2026-06-08 08:55:24 MarkDuplicates Read 451,000,000 records. Elapsed time: 00:13:00s. Time for last 1,000,000: 1s. Last read position: chr15:47,771,069 INFO 2026-06-08 08:55:24 MarkDuplicates Tracking 313606 as yet unmatched pairs. 12740 records in RAM. INFO 2026-06-08 08:55:25 MarkDuplicates Read 452,000,000 records. Elapsed time: 00:13:02s. Time for last 1,000,000: 1s. Last read position: chr15:57,282,530 INFO 2026-06-08 08:55:25 MarkDuplicates Tracking 312182 as yet unmatched pairs. 11316 records in RAM. INFO 2026-06-08 08:55:27 MarkDuplicates Read 453,000,000 records. Elapsed time: 00:13:03s. Time for last 1,000,000: 1s. Last read position: chr15:63,971,473 INFO 2026-06-08 08:55:27 MarkDuplicates Tracking 310778 as yet unmatched pairs. 9909 records in RAM. INFO 2026-06-08 08:55:28 MarkDuplicates Read 454,000,000 records. Elapsed time: 00:13:05s. Time for last 1,000,000: 1s. Last read position: chr15:69,417,490 INFO 2026-06-08 08:55:28 MarkDuplicates Tracking 309285 as yet unmatched pairs. 8415 records in RAM. INFO 2026-06-08 08:55:30 MarkDuplicates Read 455,000,000 records. Elapsed time: 00:13:06s. Time for last 1,000,000: 1s. Last read position: chr15:74,023,050 INFO 2026-06-08 08:55:30 MarkDuplicates Tracking 307937 as yet unmatched pairs. 7067 records in RAM. INFO 2026-06-08 08:55:31 MarkDuplicates Read 456,000,000 records. Elapsed time: 00:13:07s. Time for last 1,000,000: 1s. Last read position: chr15:75,649,918 INFO 2026-06-08 08:55:31 MarkDuplicates Tracking 306192 as yet unmatched pairs. 5322 records in RAM. INFO 2026-06-08 08:55:33 MarkDuplicates Read 457,000,000 records. Elapsed time: 00:13:09s. Time for last 1,000,000: 1s. Last read position: chr15:80,948,828 INFO 2026-06-08 08:55:33 MarkDuplicates Tracking 304790 as yet unmatched pairs. 3916 records in RAM. INFO 2026-06-08 08:55:34 MarkDuplicates Read 458,000,000 records. Elapsed time: 00:13:10s. Time for last 1,000,000: 1s. Last read position: chr15:88,856,478 INFO 2026-06-08 08:55:34 MarkDuplicates Tracking 303681 as yet unmatched pairs. 2807 records in RAM. INFO 2026-06-08 08:55:36 MarkDuplicates Read 459,000,000 records. Elapsed time: 00:13:12s. Time for last 1,000,000: 1s. Last read position: chr15:90,761,145 INFO 2026-06-08 08:55:36 MarkDuplicates Tracking 302275 as yet unmatched pairs. 1401 records in RAM. INFO 2026-06-08 08:55:37 MarkDuplicates Read 460,000,000 records. Elapsed time: 00:13:14s. Time for last 1,000,000: 1s. Last read position: chr16:58,386 INFO 2026-06-08 08:55:37 MarkDuplicates Tracking 300995 as yet unmatched pairs. 56029 records in RAM. INFO 2026-06-08 08:55:39 MarkDuplicates Read 461,000,000 records. Elapsed time: 00:13:15s. Time for last 1,000,000: 1s. Last read position: chr16:635,745 INFO 2026-06-08 08:55:39 MarkDuplicates Tracking 299267 as yet unmatched pairs. 54301 records in RAM. INFO 2026-06-08 08:55:41 MarkDuplicates Read 462,000,000 records. Elapsed time: 00:13:17s. Time for last 1,000,000: 1s. Last read position: chr16:1,452,793 INFO 2026-06-08 08:55:41 MarkDuplicates Tracking 297451 as yet unmatched pairs. 52481 records in RAM. INFO 2026-06-08 08:55:43 MarkDuplicates Read 463,000,000 records. Elapsed time: 00:13:19s. Time for last 1,000,000: 2s. Last read position: chr16:2,037,562 INFO 2026-06-08 08:55:43 MarkDuplicates Tracking 295728 as yet unmatched pairs. 50755 records in RAM. INFO 2026-06-08 08:55:44 MarkDuplicates Read 464,000,000 records. Elapsed time: 00:13:20s. Time for last 1,000,000: 1s. Last read position: chr16:2,448,947 INFO 2026-06-08 08:55:44 MarkDuplicates Tracking 293756 as yet unmatched pairs. 48783 records in RAM. INFO 2026-06-08 08:55:46 MarkDuplicates Read 465,000,000 records. Elapsed time: 00:13:22s. Time for last 1,000,000: 1s. Last read position: chr16:2,766,977 INFO 2026-06-08 08:55:46 MarkDuplicates Tracking 293018 as yet unmatched pairs. 48045 records in RAM. INFO 2026-06-08 08:55:48 MarkDuplicates Read 466,000,000 records. Elapsed time: 00:13:24s. Time for last 1,000,000: 2s. Last read position: chr16:3,141,155 INFO 2026-06-08 08:55:48 MarkDuplicates Tracking 290451 as yet unmatched pairs. 45477 records in RAM. INFO 2026-06-08 08:55:50 MarkDuplicates Read 467,000,000 records. Elapsed time: 00:13:26s. Time for last 1,000,000: 1s. Last read position: chr16:4,609,832 INFO 2026-06-08 08:55:50 MarkDuplicates Tracking 288789 as yet unmatched pairs. 43815 records in RAM. INFO 2026-06-08 08:55:51 MarkDuplicates Read 468,000,000 records. Elapsed time: 00:13:27s. Time for last 1,000,000: 1s. Last read position: chr16:10,922,478 INFO 2026-06-08 08:55:51 MarkDuplicates Tracking 287177 as yet unmatched pairs. 42202 records in RAM. INFO 2026-06-08 08:55:53 MarkDuplicates Read 469,000,000 records. Elapsed time: 00:13:29s. Time for last 1,000,000: 1s. Last read position: chr16:14,872,295 INFO 2026-06-08 08:55:53 MarkDuplicates Tracking 285870 as yet unmatched pairs. 40893 records in RAM. INFO 2026-06-08 08:55:54 MarkDuplicates Read 470,000,000 records. Elapsed time: 00:13:30s. Time for last 1,000,000: 1s. Last read position: chr16:15,703,944 INFO 2026-06-08 08:55:54 MarkDuplicates Tracking 285144 as yet unmatched pairs. 40167 records in RAM. INFO 2026-06-08 08:55:55 MarkDuplicates Read 471,000,000 records. Elapsed time: 00:13:31s. Time for last 1,000,000: 1s. Last read position: chr16:16,357,397 INFO 2026-06-08 08:55:55 MarkDuplicates Tracking 284543 as yet unmatched pairs. 39566 records in RAM. INFO 2026-06-08 08:55:56 MarkDuplicates Read 472,000,000 records. Elapsed time: 00:13:33s. Time for last 1,000,000: 1s. Last read position: chr16:18,431,823 INFO 2026-06-08 08:55:56 MarkDuplicates Tracking 283863 as yet unmatched pairs. 38885 records in RAM. INFO 2026-06-08 08:55:58 MarkDuplicates Read 473,000,000 records. Elapsed time: 00:13:34s. Time for last 1,000,000: 1s. Last read position: chr16:19,788,884 INFO 2026-06-08 08:55:58 MarkDuplicates Tracking 282599 as yet unmatched pairs. 37615 records in RAM. INFO 2026-06-08 08:55:59 MarkDuplicates Read 474,000,000 records. Elapsed time: 00:13:35s. Time for last 1,000,000: 1s. Last read position: chr16:21,834,955 INFO 2026-06-08 08:55:59 MarkDuplicates Tracking 282032 as yet unmatched pairs. 37048 records in RAM. INFO 2026-06-08 08:56:00 MarkDuplicates Read 475,000,000 records. Elapsed time: 00:13:36s. Time for last 1,000,000: 1s. Last read position: chr16:22,527,612 INFO 2026-06-08 08:56:00 MarkDuplicates Tracking 281480 as yet unmatched pairs. 36496 records in RAM. INFO 2026-06-08 08:56:02 MarkDuplicates Read 476,000,000 records. Elapsed time: 00:13:38s. Time for last 1,000,000: 1s. Last read position: chr16:24,823,705 INFO 2026-06-08 08:56:02 MarkDuplicates Tracking 280649 as yet unmatched pairs. 35665 records in RAM. INFO 2026-06-08 08:56:03 MarkDuplicates Read 477,000,000 records. Elapsed time: 00:13:39s. Time for last 1,000,000: 1s. Last read position: chr16:28,388,551 INFO 2026-06-08 08:56:03 MarkDuplicates Tracking 279762 as yet unmatched pairs. 34776 records in RAM. INFO 2026-06-08 08:56:05 MarkDuplicates Read 478,000,000 records. Elapsed time: 00:13:41s. Time for last 1,000,000: 1s. Last read position: chr16:28,829,427 INFO 2026-06-08 08:56:05 MarkDuplicates Tracking 278668 as yet unmatched pairs. 33682 records in RAM. INFO 2026-06-08 08:56:06 MarkDuplicates Read 479,000,000 records. Elapsed time: 00:13:42s. Time for last 1,000,000: 1s. Last read position: chr16:29,383,702 INFO 2026-06-08 08:56:06 MarkDuplicates Tracking 277129 as yet unmatched pairs. 32143 records in RAM. INFO 2026-06-08 08:56:07 MarkDuplicates Read 480,000,000 records. Elapsed time: 00:13:43s. Time for last 1,000,000: 1s. Last read position: chr16:29,491,646 INFO 2026-06-08 08:56:07 MarkDuplicates Tracking 276847 as yet unmatched pairs. 31861 records in RAM. INFO 2026-06-08 08:56:09 MarkDuplicates Read 481,000,000 records. Elapsed time: 00:13:45s. Time for last 1,000,000: 1s. Last read position: chr16:29,808,730 INFO 2026-06-08 08:56:09 MarkDuplicates Tracking 276030 as yet unmatched pairs. 31044 records in RAM. INFO 2026-06-08 08:56:11 MarkDuplicates Read 482,000,000 records. Elapsed time: 00:13:47s. Time for last 1,000,000: 2s. Last read position: chr16:29,887,733 INFO 2026-06-08 08:56:11 MarkDuplicates Tracking 273377 as yet unmatched pairs. 28388 records in RAM. INFO 2026-06-08 08:56:13 MarkDuplicates Read 483,000,000 records. Elapsed time: 00:13:49s. Time for last 1,000,000: 1s. Last read position: chr16:30,069,302 INFO 2026-06-08 08:56:13 MarkDuplicates Tracking 274510 as yet unmatched pairs. 29521 records in RAM. INFO 2026-06-08 08:56:14 MarkDuplicates Read 484,000,000 records. Elapsed time: 00:13:51s. Time for last 1,000,000: 1s. Last read position: chr16:30,193,043 INFO 2026-06-08 08:56:14 MarkDuplicates Tracking 270454 as yet unmatched pairs. 25465 records in RAM. INFO 2026-06-08 08:56:16 MarkDuplicates Read 485,000,000 records. Elapsed time: 00:13:52s. Time for last 1,000,000: 1s. Last read position: chr16:30,358,426 INFO 2026-06-08 08:56:16 MarkDuplicates Tracking 269986 as yet unmatched pairs. 24997 records in RAM. INFO 2026-06-08 08:56:17 MarkDuplicates Read 486,000,000 records. Elapsed time: 00:13:53s. Time for last 1,000,000: 1s. Last read position: chr16:30,662,657 INFO 2026-06-08 08:56:17 MarkDuplicates Tracking 268189 as yet unmatched pairs. 23200 records in RAM. INFO 2026-06-08 08:56:19 MarkDuplicates Read 487,000,000 records. Elapsed time: 00:13:55s. Time for last 1,000,000: 1s. Last read position: chr16:30,737,270 INFO 2026-06-08 08:56:19 MarkDuplicates Tracking 266827 as yet unmatched pairs. 21838 records in RAM. INFO 2026-06-08 08:56:20 MarkDuplicates Read 488,000,000 records. Elapsed time: 00:13:57s. Time for last 1,000,000: 1s. Last read position: chr16:30,961,415 INFO 2026-06-08 08:56:20 MarkDuplicates Tracking 264837 as yet unmatched pairs. 19847 records in RAM. INFO 2026-06-08 08:56:22 MarkDuplicates Read 489,000,000 records. Elapsed time: 00:13:58s. Time for last 1,000,000: 1s. Last read position: chr16:31,142,730 INFO 2026-06-08 08:56:22 MarkDuplicates Tracking 263051 as yet unmatched pairs. 18061 records in RAM. INFO 2026-06-08 08:56:23 MarkDuplicates Read 490,000,000 records. Elapsed time: 00:14:00s. Time for last 1,000,000: 1s. Last read position: chr16:31,191,396 INFO 2026-06-08 08:56:23 MarkDuplicates Tracking 264585 as yet unmatched pairs. 19595 records in RAM. INFO 2026-06-08 08:56:25 MarkDuplicates Read 491,000,000 records. Elapsed time: 00:14:01s. Time for last 1,000,000: 1s. Last read position: chr16:48,361,713 INFO 2026-06-08 08:56:25 MarkDuplicates Tracking 260299 as yet unmatched pairs. 15308 records in RAM. INFO 2026-06-08 08:56:26 MarkDuplicates Read 492,000,000 records. Elapsed time: 00:14:02s. Time for last 1,000,000: 1s. Last read position: chr16:51,646,727 INFO 2026-06-08 08:56:26 MarkDuplicates Tracking 258675 as yet unmatched pairs. 13684 records in RAM. INFO 2026-06-08 08:56:28 MarkDuplicates Read 493,000,000 records. Elapsed time: 00:14:04s. Time for last 1,000,000: 1s. Last read position: chr16:57,026,909 INFO 2026-06-08 08:56:28 MarkDuplicates Tracking 257310 as yet unmatched pairs. 12319 records in RAM. INFO 2026-06-08 08:56:30 MarkDuplicates Read 494,000,000 records. Elapsed time: 00:14:06s. Time for last 1,000,000: 1s. Last read position: chr16:58,599,248 INFO 2026-06-08 08:56:30 MarkDuplicates Tracking 255893 as yet unmatched pairs. 10901 records in RAM. INFO 2026-06-08 08:56:31 MarkDuplicates Read 495,000,000 records. Elapsed time: 00:14:07s. Time for last 1,000,000: 1s. Last read position: chr16:67,877,355 INFO 2026-06-08 08:56:31 MarkDuplicates Tracking 254098 as yet unmatched pairs. 9105 records in RAM. INFO 2026-06-08 08:56:33 MarkDuplicates Read 496,000,000 records. Elapsed time: 00:14:09s. Time for last 1,000,000: 1s. Last read position: chr16:69,713,059 INFO 2026-06-08 08:56:33 MarkDuplicates Tracking 253046 as yet unmatched pairs. 8053 records in RAM. INFO 2026-06-08 08:56:34 MarkDuplicates Read 497,000,000 records. Elapsed time: 00:14:10s. Time for last 1,000,000: 1s. Last read position: chr16:72,794,490 INFO 2026-06-08 08:56:34 MarkDuplicates Tracking 251268 as yet unmatched pairs. 6272 records in RAM. INFO 2026-06-08 08:56:36 MarkDuplicates Read 498,000,000 records. Elapsed time: 00:14:12s. Time for last 1,000,000: 1s. Last read position: chr16:82,164,122 INFO 2026-06-08 08:56:36 MarkDuplicates Tracking 249741 as yet unmatched pairs. 4744 records in RAM. INFO 2026-06-08 08:56:38 MarkDuplicates Read 499,000,000 records. Elapsed time: 00:14:14s. Time for last 1,000,000: 2s. Last read position: chr16:88,431,816 INFO 2026-06-08 08:56:38 MarkDuplicates Tracking 248324 as yet unmatched pairs. 3325 records in RAM. INFO 2026-06-08 08:56:40 MarkDuplicates Read 500,000,000 records. Elapsed time: 00:14:16s. Time for last 1,000,000: 1s. Last read position: chr16:89,508,443 INFO 2026-06-08 08:56:40 MarkDuplicates Tracking 246749 as yet unmatched pairs. 1750 records in RAM. INFO 2026-06-08 08:56:42 MarkDuplicates Read 501,000,000 records. Elapsed time: 00:14:18s. Time for last 1,000,000: 1s. Last read position: chr17:655,843 INFO 2026-06-08 08:56:42 MarkDuplicates Tracking 245043 as yet unmatched pairs. 73226 records in RAM. INFO 2026-06-08 08:56:43 MarkDuplicates Read 502,000,000 records. Elapsed time: 00:14:19s. Time for last 1,000,000: 1s. Last read position: chr17:1,676,000 INFO 2026-06-08 08:56:43 MarkDuplicates Tracking 243509 as yet unmatched pairs. 71692 records in RAM. INFO 2026-06-08 08:56:45 MarkDuplicates Read 503,000,000 records. Elapsed time: 00:14:21s. Time for last 1,000,000: 1s. Last read position: chr17:4,183,812 INFO 2026-06-08 08:56:45 MarkDuplicates Tracking 241799 as yet unmatched pairs. 69982 records in RAM. INFO 2026-06-08 08:56:46 MarkDuplicates Read 504,000,000 records. Elapsed time: 00:14:22s. Time for last 1,000,000: 1s. Last read position: chr17:5,391,601 INFO 2026-06-08 08:56:46 MarkDuplicates Tracking 240300 as yet unmatched pairs. 68483 records in RAM. INFO 2026-06-08 08:56:48 MarkDuplicates Read 505,000,000 records. Elapsed time: 00:14:24s. Time for last 1,000,000: 1s. Last read position: chr17:7,462,180 INFO 2026-06-08 08:56:48 MarkDuplicates Tracking 238741 as yet unmatched pairs. 66924 records in RAM. INFO 2026-06-08 08:56:50 MarkDuplicates Read 506,000,000 records. Elapsed time: 00:14:26s. Time for last 1,000,000: 1s. Last read position: chr17:7,859,412 INFO 2026-06-08 08:56:50 MarkDuplicates Tracking 237307 as yet unmatched pairs. 65490 records in RAM. INFO 2026-06-08 08:56:51 MarkDuplicates Read 507,000,000 records. Elapsed time: 00:14:27s. Time for last 1,000,000: 1s. Last read position: chr17:16,080,718 INFO 2026-06-08 08:56:51 MarkDuplicates Tracking 236028 as yet unmatched pairs. 64211 records in RAM. INFO 2026-06-08 08:56:53 MarkDuplicates Read 508,000,000 records. Elapsed time: 00:14:29s. Time for last 1,000,000: 1s. Last read position: chr17:18,247,249 INFO 2026-06-08 08:56:53 MarkDuplicates Tracking 234420 as yet unmatched pairs. 62603 records in RAM. INFO 2026-06-08 08:56:54 MarkDuplicates Read 509,000,000 records. Elapsed time: 00:14:30s. Time for last 1,000,000: 1s. Last read position: chr17:28,043,272 INFO 2026-06-08 08:56:54 MarkDuplicates Tracking 232896 as yet unmatched pairs. 61078 records in RAM. INFO 2026-06-08 08:56:56 MarkDuplicates Read 510,000,000 records. Elapsed time: 00:14:32s. Time for last 1,000,000: 1s. Last read position: chr17:28,748,932 INFO 2026-06-08 08:56:56 MarkDuplicates Tracking 231698 as yet unmatched pairs. 59880 records in RAM. INFO 2026-06-08 08:56:57 MarkDuplicates Read 511,000,000 records. Elapsed time: 00:14:33s. Time for last 1,000,000: 1s. Last read position: chr17:30,893,782 INFO 2026-06-08 08:56:57 MarkDuplicates Tracking 229981 as yet unmatched pairs. 58161 records in RAM. INFO 2026-06-08 08:56:59 MarkDuplicates Read 512,000,000 records. Elapsed time: 00:14:36s. Time for last 1,000,000: 2s. Last read position: chr17:35,012,016 INFO 2026-06-08 08:56:59 MarkDuplicates Tracking 228830 as yet unmatched pairs. 57010 records in RAM. INFO 2026-06-08 08:57:01 MarkDuplicates Read 513,000,000 records. Elapsed time: 00:14:37s. Time for last 1,000,000: 1s. Last read position: chr17:36,537,106 INFO 2026-06-08 08:57:01 MarkDuplicates Tracking 227435 as yet unmatched pairs. 55615 records in RAM. INFO 2026-06-08 08:57:03 MarkDuplicates Read 514,000,000 records. Elapsed time: 00:14:39s. Time for last 1,000,000: 1s. Last read position: chr17:38,720,546 INFO 2026-06-08 08:57:03 MarkDuplicates Tracking 226689 as yet unmatched pairs. 54869 records in RAM. INFO 2026-06-08 08:57:05 MarkDuplicates Read 515,000,000 records. Elapsed time: 00:14:41s. Time for last 1,000,000: 1s. Last read position: chr17:39,629,169 INFO 2026-06-08 08:57:05 MarkDuplicates Tracking 225004 as yet unmatched pairs. 53184 records in RAM. INFO 2026-06-08 08:57:06 MarkDuplicates Read 516,000,000 records. Elapsed time: 00:14:42s. Time for last 1,000,000: 1s. Last read position: chr17:39,723,442 INFO 2026-06-08 08:57:06 MarkDuplicates Tracking 224549 as yet unmatched pairs. 52729 records in RAM. INFO 2026-06-08 08:57:08 MarkDuplicates Read 517,000,000 records. Elapsed time: 00:14:44s. Time for last 1,000,000: 1s. Last read position: chr17:40,163,786 INFO 2026-06-08 08:57:08 MarkDuplicates Tracking 221568 as yet unmatched pairs. 49748 records in RAM. INFO 2026-06-08 08:59:13 MarkDuplicates Read 518,000,000 records. Elapsed time: 00:16:49s. Time for last 1,000,000: 125s. Last read position: chr17:41,524,965 INFO 2026-06-08 08:59:13 MarkDuplicates Tracking 220176 as yet unmatched pairs. 48356 records in RAM. INFO 2026-06-08 08:59:15 MarkDuplicates Read 519,000,000 records. Elapsed time: 00:16:51s. Time for last 1,000,000: 2s. Last read position: chr17:42,021,543 INFO 2026-06-08 08:59:15 MarkDuplicates Tracking 218250 as yet unmatched pairs. 46429 records in RAM. INFO 2026-06-08 08:59:17 MarkDuplicates Read 520,000,000 records. Elapsed time: 00:16:53s. Time for last 1,000,000: 1s. Last read position: chr17:42,795,019 INFO 2026-06-08 08:59:17 MarkDuplicates Tracking 216610 as yet unmatched pairs. 44789 records in RAM. INFO 2026-06-08 08:59:18 MarkDuplicates Read 521,000,000 records. Elapsed time: 00:16:54s. Time for last 1,000,000: 1s. Last read position: chr17:43,825,749 INFO 2026-06-08 08:59:18 MarkDuplicates Tracking 215122 as yet unmatched pairs. 43301 records in RAM. INFO 2026-06-08 08:59:20 MarkDuplicates Read 522,000,000 records. Elapsed time: 00:16:56s. Time for last 1,000,000: 1s. Last read position: chr17:44,880,590 INFO 2026-06-08 08:59:20 MarkDuplicates Tracking 213861 as yet unmatched pairs. 42036 records in RAM. INFO 2026-06-08 08:59:21 MarkDuplicates Read 523,000,000 records. Elapsed time: 00:16:57s. Time for last 1,000,000: 1s. Last read position: chr17:46,513,667 INFO 2026-06-08 08:59:21 MarkDuplicates Tracking 212282 as yet unmatched pairs. 40456 records in RAM. INFO 2026-06-08 08:59:23 MarkDuplicates Read 524,000,000 records. Elapsed time: 00:16:59s. Time for last 1,000,000: 1s. Last read position: chr17:48,076,877 INFO 2026-06-08 08:59:23 MarkDuplicates Tracking 210967 as yet unmatched pairs. 39140 records in RAM. INFO 2026-06-08 08:59:25 MarkDuplicates Read 525,000,000 records. Elapsed time: 00:17:01s. Time for last 1,000,000: 1s. Last read position: chr17:50,095,537 INFO 2026-06-08 08:59:25 MarkDuplicates Tracking 209424 as yet unmatched pairs. 37597 records in RAM. INFO 2026-06-08 08:59:26 MarkDuplicates Read 526,000,000 records. Elapsed time: 00:17:02s. Time for last 1,000,000: 1s. Last read position: chr17:50,187,946 INFO 2026-06-08 08:59:26 MarkDuplicates Tracking 214673 as yet unmatched pairs. 42846 records in RAM. INFO 2026-06-08 08:59:28 MarkDuplicates Read 527,000,000 records. Elapsed time: 00:17:05s. Time for last 1,000,000: 2s. Last read position: chr17:50,189,689 INFO 2026-06-08 08:59:28 MarkDuplicates Tracking 215391 as yet unmatched pairs. 43563 records in RAM. INFO 2026-06-08 08:59:30 MarkDuplicates Read 528,000,000 records. Elapsed time: 00:17:06s. Time for last 1,000,000: 1s. Last read position: chr17:50,192,475 INFO 2026-06-08 08:59:30 MarkDuplicates Tracking 209343 as yet unmatched pairs. 37515 records in RAM. INFO 2026-06-08 08:59:32 MarkDuplicates Read 529,000,000 records. Elapsed time: 00:17:08s. Time for last 1,000,000: 1s. Last read position: chr17:50,194,738 INFO 2026-06-08 08:59:32 MarkDuplicates Tracking 207721 as yet unmatched pairs. 35893 records in RAM. INFO 2026-06-08 08:59:33 MarkDuplicates Read 530,000,000 records. Elapsed time: 00:17:09s. Time for last 1,000,000: 1s. Last read position: chr17:50,196,616 INFO 2026-06-08 08:59:33 MarkDuplicates Tracking 206342 as yet unmatched pairs. 34514 records in RAM. INFO 2026-06-08 08:59:35 MarkDuplicates Read 531,000,000 records. Elapsed time: 00:17:11s. Time for last 1,000,000: 1s. Last read position: chr17:50,199,900 INFO 2026-06-08 08:59:35 MarkDuplicates Tracking 201153 as yet unmatched pairs. 29325 records in RAM. INFO 2026-06-08 08:59:36 MarkDuplicates Read 532,000,000 records. Elapsed time: 00:17:12s. Time for last 1,000,000: 1s. Last read position: chr17:54,930,117 INFO 2026-06-08 08:59:36 MarkDuplicates Tracking 198261 as yet unmatched pairs. 26432 records in RAM. INFO 2026-06-08 08:59:38 MarkDuplicates Read 533,000,000 records. Elapsed time: 00:17:14s. Time for last 1,000,000: 1s. Last read position: chr17:58,357,995 INFO 2026-06-08 08:59:38 MarkDuplicates Tracking 197825 as yet unmatched pairs. 25996 records in RAM. INFO 2026-06-08 08:59:40 MarkDuplicates Read 534,000,000 records. Elapsed time: 00:17:16s. Time for last 1,000,000: 1s. Last read position: chr17:59,660,445 INFO 2026-06-08 08:59:40 MarkDuplicates Tracking 196654 as yet unmatched pairs. 24825 records in RAM. INFO 2026-06-08 08:59:41 MarkDuplicates Read 535,000,000 records. Elapsed time: 00:17:17s. Time for last 1,000,000: 1s. Last read position: chr17:59,685,728 INFO 2026-06-08 08:59:41 MarkDuplicates Tracking 195643 as yet unmatched pairs. 23814 records in RAM. INFO 2026-06-08 08:59:43 MarkDuplicates Read 536,000,000 records. Elapsed time: 00:17:19s. Time for last 1,000,000: 2s. Last read position: chr17:63,579,840 INFO 2026-06-08 08:59:43 MarkDuplicates Tracking 192222 as yet unmatched pairs. 20393 records in RAM. INFO 2026-06-08 08:59:45 MarkDuplicates Read 537,000,000 records. Elapsed time: 00:17:21s. Time for last 1,000,000: 1s. Last read position: chr17:65,053,643 INFO 2026-06-08 08:59:45 MarkDuplicates Tracking 190814 as yet unmatched pairs. 18984 records in RAM. INFO 2026-06-08 08:59:47 MarkDuplicates Read 538,000,000 records. Elapsed time: 00:17:23s. Time for last 1,000,000: 1s. Last read position: chr17:68,433,501 INFO 2026-06-08 08:59:47 MarkDuplicates Tracking 189146 as yet unmatched pairs. 17316 records in RAM. INFO 2026-06-08 08:59:48 MarkDuplicates Read 539,000,000 records. Elapsed time: 00:17:24s. Time for last 1,000,000: 1s. Last read position: chr17:74,836,431 INFO 2026-06-08 08:59:48 MarkDuplicates Tracking 187686 as yet unmatched pairs. 15856 records in RAM. INFO 2026-06-08 08:59:50 MarkDuplicates Read 540,000,000 records. Elapsed time: 00:17:26s. Time for last 1,000,000: 1s. Last read position: chr17:75,573,106 INFO 2026-06-08 08:59:50 MarkDuplicates Tracking 187079 as yet unmatched pairs. 15249 records in RAM. INFO 2026-06-08 08:59:51 MarkDuplicates Read 541,000,000 records. Elapsed time: 00:17:27s. Time for last 1,000,000: 1s. Last read position: chr17:75,778,829 INFO 2026-06-08 08:59:51 MarkDuplicates Tracking 185320 as yet unmatched pairs. 13490 records in RAM. INFO 2026-06-08 08:59:53 MarkDuplicates Read 542,000,000 records. Elapsed time: 00:17:29s. Time for last 1,000,000: 1s. Last read position: chr17:76,479,104 INFO 2026-06-08 08:59:53 MarkDuplicates Tracking 182509 as yet unmatched pairs. 10679 records in RAM. INFO 2026-06-08 08:59:54 MarkDuplicates Read 543,000,000 records. Elapsed time: 00:17:30s. Time for last 1,000,000: 1s. Last read position: chr17:78,427,002 INFO 2026-06-08 08:59:54 MarkDuplicates Tracking 180859 as yet unmatched pairs. 9029 records in RAM. INFO 2026-06-08 08:59:56 MarkDuplicates Read 544,000,000 records. Elapsed time: 00:17:32s. Time for last 1,000,000: 1s. Last read position: chr17:80,278,794 INFO 2026-06-08 08:59:56 MarkDuplicates Tracking 179664 as yet unmatched pairs. 7834 records in RAM. INFO 2026-06-08 08:59:57 MarkDuplicates Read 545,000,000 records. Elapsed time: 00:17:33s. Time for last 1,000,000: 1s. Last read position: chr17:80,883,916 INFO 2026-06-08 08:59:57 MarkDuplicates Tracking 177844 as yet unmatched pairs. 6014 records in RAM. INFO 2026-06-08 08:59:59 MarkDuplicates Read 546,000,000 records. Elapsed time: 00:17:35s. Time for last 1,000,000: 1s. Last read position: chr17:81,666,370 INFO 2026-06-08 08:59:59 MarkDuplicates Tracking 176323 as yet unmatched pairs. 4493 records in RAM. INFO 2026-06-08 09:00:00 MarkDuplicates Read 547,000,000 records. Elapsed time: 00:17:37s. Time for last 1,000,000: 1s. Last read position: chr17:81,934,974 INFO 2026-06-08 09:00:00 MarkDuplicates Tracking 174777 as yet unmatched pairs. 2947 records in RAM. INFO 2026-06-08 09:00:02 MarkDuplicates Read 548,000,000 records. Elapsed time: 00:17:38s. Time for last 1,000,000: 1s. Last read position: chr17:82,237,397 INFO 2026-06-08 09:00:02 MarkDuplicates Tracking 173264 as yet unmatched pairs. 1434 records in RAM. INFO 2026-06-08 09:00:04 MarkDuplicates Read 549,000,000 records. Elapsed time: 00:17:40s. Time for last 1,000,000: 1s. Last read position: chr18:6,462,200 INFO 2026-06-08 09:00:04 MarkDuplicates Tracking 171250 as yet unmatched pairs. 6381 records in RAM. INFO 2026-06-08 09:00:05 MarkDuplicates Read 550,000,000 records. Elapsed time: 00:17:41s. Time for last 1,000,000: 1s. Last read position: chr18:23,463,063 INFO 2026-06-08 09:00:05 MarkDuplicates Tracking 169796 as yet unmatched pairs. 4924 records in RAM. INFO 2026-06-08 09:00:06 MarkDuplicates Read 551,000,000 records. Elapsed time: 00:17:42s. Time for last 1,000,000: 1s. Last read position: chr18:36,138,320 INFO 2026-06-08 09:00:06 MarkDuplicates Tracking 168411 as yet unmatched pairs. 3539 records in RAM. INFO 2026-06-08 09:00:08 MarkDuplicates Read 552,000,000 records. Elapsed time: 00:17:44s. Time for last 1,000,000: 1s. Last read position: chr18:55,228,011 INFO 2026-06-08 09:00:08 MarkDuplicates Tracking 166975 as yet unmatched pairs. 2102 records in RAM. INFO 2026-06-08 09:00:10 MarkDuplicates Read 553,000,000 records. Elapsed time: 00:17:46s. Time for last 1,000,000: 1s. Last read position: chr18:75,249,970 INFO 2026-06-08 09:00:10 MarkDuplicates Tracking 165389 as yet unmatched pairs. 516 records in RAM. INFO 2026-06-08 09:00:12 MarkDuplicates Read 554,000,000 records. Elapsed time: 00:17:48s. Time for last 1,000,000: 2s. Last read position: chr19:757,253 INFO 2026-06-08 09:00:12 MarkDuplicates Tracking 164323 as yet unmatched pairs. 78478 records in RAM. INFO 2026-06-08 09:00:13 MarkDuplicates Read 555,000,000 records. Elapsed time: 00:17:49s. Time for last 1,000,000: 1s. Last read position: chr19:1,052,058 INFO 2026-06-08 09:00:13 MarkDuplicates Tracking 162015 as yet unmatched pairs. 76170 records in RAM. INFO 2026-06-08 09:00:15 MarkDuplicates Read 556,000,000 records. Elapsed time: 00:17:51s. Time for last 1,000,000: 1s. Last read position: chr19:1,390,992 INFO 2026-06-08 09:00:15 MarkDuplicates Tracking 160446 as yet unmatched pairs. 74601 records in RAM. INFO 2026-06-08 09:00:17 MarkDuplicates Read 557,000,000 records. Elapsed time: 00:17:53s. Time for last 1,000,000: 1s. Last read position: chr19:1,877,510 INFO 2026-06-08 09:00:17 MarkDuplicates Tracking 158338 as yet unmatched pairs. 72492 records in RAM. INFO 2026-06-08 09:00:18 MarkDuplicates Read 558,000,000 records. Elapsed time: 00:17:54s. Time for last 1,000,000: 1s. Last read position: chr19:2,271,449 INFO 2026-06-08 09:00:18 MarkDuplicates Tracking 157574 as yet unmatched pairs. 71728 records in RAM. INFO 2026-06-08 09:00:20 MarkDuplicates Read 559,000,000 records. Elapsed time: 00:17:56s. Time for last 1,000,000: 2s. Last read position: chr19:3,532,037 INFO 2026-06-08 09:00:20 MarkDuplicates Tracking 154690 as yet unmatched pairs. 68842 records in RAM. INFO 2026-06-08 09:00:22 MarkDuplicates Read 560,000,000 records. Elapsed time: 00:17:59s. Time for last 1,000,000: 2s. Last read position: chr19:4,362,695 INFO 2026-06-08 09:00:22 MarkDuplicates Tracking 152844 as yet unmatched pairs. 66996 records in RAM. INFO 2026-06-08 09:00:24 MarkDuplicates Read 561,000,000 records. Elapsed time: 00:18:00s. Time for last 1,000,000: 1s. Last read position: chr19:5,657,287 INFO 2026-06-08 09:00:24 MarkDuplicates Tracking 151180 as yet unmatched pairs. 65332 records in RAM. INFO 2026-06-08 09:00:25 MarkDuplicates Read 562,000,000 records. Elapsed time: 00:18:01s. Time for last 1,000,000: 1s. Last read position: chr19:6,387,450 INFO 2026-06-08 09:00:25 MarkDuplicates Tracking 149592 as yet unmatched pairs. 63744 records in RAM. INFO 2026-06-08 09:00:27 MarkDuplicates Read 563,000,000 records. Elapsed time: 00:18:03s. Time for last 1,000,000: 1s. Last read position: chr19:7,477,194 INFO 2026-06-08 09:00:27 MarkDuplicates Tracking 147870 as yet unmatched pairs. 62022 records in RAM. INFO 2026-06-08 09:00:28 MarkDuplicates Read 564,000,000 records. Elapsed time: 00:18:05s. Time for last 1,000,000: 1s. Last read position: chr19:8,468,800 INFO 2026-06-08 09:00:28 MarkDuplicates Tracking 146759 as yet unmatched pairs. 60911 records in RAM. INFO 2026-06-08 09:00:30 MarkDuplicates Read 565,000,000 records. Elapsed time: 00:18:06s. Time for last 1,000,000: 1s. Last read position: chr19:10,320,798 INFO 2026-06-08 09:00:30 MarkDuplicates Tracking 144627 as yet unmatched pairs. 58779 records in RAM. INFO 2026-06-08 09:00:31 MarkDuplicates Read 566,000,000 records. Elapsed time: 00:18:08s. Time for last 1,000,000: 1s. Last read position: chr19:10,798,545 INFO 2026-06-08 09:00:31 MarkDuplicates Tracking 143205 as yet unmatched pairs. 57357 records in RAM. INFO 2026-06-08 09:00:34 MarkDuplicates Read 567,000,000 records. Elapsed time: 00:18:10s. Time for last 1,000,000: 2s. Last read position: chr19:11,252,907 INFO 2026-06-08 09:00:34 MarkDuplicates Tracking 141563 as yet unmatched pairs. 55715 records in RAM. INFO 2026-06-08 09:00:35 MarkDuplicates Read 568,000,000 records. Elapsed time: 00:18:11s. Time for last 1,000,000: 1s. Last read position: chr19:12,734,355 INFO 2026-06-08 09:00:35 MarkDuplicates Tracking 140434 as yet unmatched pairs. 54586 records in RAM. INFO 2026-06-08 09:00:37 MarkDuplicates Read 569,000,000 records. Elapsed time: 00:18:13s. Time for last 1,000,000: 1s. Last read position: chr19:13,136,143 INFO 2026-06-08 09:00:37 MarkDuplicates Tracking 138164 as yet unmatched pairs. 52316 records in RAM. INFO 2026-06-08 09:00:38 MarkDuplicates Read 570,000,000 records. Elapsed time: 00:18:15s. Time for last 1,000,000: 1s. Last read position: chr19:14,409,847 INFO 2026-06-08 09:00:38 MarkDuplicates Tracking 136525 as yet unmatched pairs. 50677 records in RAM. INFO 2026-06-08 09:00:40 MarkDuplicates Read 571,000,000 records. Elapsed time: 00:18:16s. Time for last 1,000,000: 1s. Last read position: chr19:15,161,461 INFO 2026-06-08 09:00:40 MarkDuplicates Tracking 135166 as yet unmatched pairs. 49318 records in RAM. INFO 2026-06-08 09:00:41 MarkDuplicates Read 572,000,000 records. Elapsed time: 00:18:18s. Time for last 1,000,000: 1s. Last read position: chr19:15,267,526 INFO 2026-06-08 09:00:41 MarkDuplicates Tracking 133525 as yet unmatched pairs. 47677 records in RAM. INFO 2026-06-08 09:00:43 MarkDuplicates Read 573,000,000 records. Elapsed time: 00:18:20s. Time for last 1,000,000: 2s. Last read position: chr19:17,168,017 INFO 2026-06-08 09:00:43 MarkDuplicates Tracking 131683 as yet unmatched pairs. 45835 records in RAM. INFO 2026-06-08 09:00:45 MarkDuplicates Read 574,000,000 records. Elapsed time: 00:18:21s. Time for last 1,000,000: 1s. Last read position: chr19:17,843,479 INFO 2026-06-08 09:00:45 MarkDuplicates Tracking 130021 as yet unmatched pairs. 44172 records in RAM. INFO 2026-06-08 09:00:47 MarkDuplicates Read 575,000,000 records. Elapsed time: 00:18:23s. Time for last 1,000,000: 1s. Last read position: chr19:18,538,347 INFO 2026-06-08 09:00:47 MarkDuplicates Tracking 128660 as yet unmatched pairs. 42811 records in RAM. INFO 2026-06-08 09:00:49 MarkDuplicates Read 576,000,000 records. Elapsed time: 00:18:25s. Time for last 1,000,000: 1s. Last read position: chr19:19,498,595 INFO 2026-06-08 09:00:49 MarkDuplicates Tracking 127024 as yet unmatched pairs. 41175 records in RAM. INFO 2026-06-08 09:00:50 MarkDuplicates Read 577,000,000 records. Elapsed time: 00:18:26s. Time for last 1,000,000: 1s. Last read position: chr19:33,301,571 INFO 2026-06-08 09:00:50 MarkDuplicates Tracking 125439 as yet unmatched pairs. 39590 records in RAM. INFO 2026-06-08 09:00:52 MarkDuplicates Read 578,000,000 records. Elapsed time: 00:18:28s. Time for last 1,000,000: 1s. Last read position: chr19:35,259,039 INFO 2026-06-08 09:00:52 MarkDuplicates Tracking 124171 as yet unmatched pairs. 38322 records in RAM. INFO 2026-06-08 09:00:53 MarkDuplicates Read 579,000,000 records. Elapsed time: 00:18:29s. Time for last 1,000,000: 1s. Last read position: chr19:36,011,403 INFO 2026-06-08 09:00:53 MarkDuplicates Tracking 121497 as yet unmatched pairs. 35648 records in RAM. INFO 2026-06-08 09:00:54 MarkDuplicates Read 580,000,000 records. Elapsed time: 00:18:31s. Time for last 1,000,000: 1s. Last read position: chr19:38,620,376 INFO 2026-06-08 09:00:54 MarkDuplicates Tracking 120891 as yet unmatched pairs. 35042 records in RAM. INFO 2026-06-08 09:00:56 MarkDuplicates Read 581,000,000 records. Elapsed time: 00:18:32s. Time for last 1,000,000: 1s. Last read position: chr19:38,838,511 INFO 2026-06-08 09:00:56 MarkDuplicates Tracking 118909 as yet unmatched pairs. 33060 records in RAM. INFO 2026-06-08 09:00:58 MarkDuplicates Read 582,000,000 records. Elapsed time: 00:18:34s. Time for last 1,000,000: 1s. Last read position: chr19:39,836,610 INFO 2026-06-08 09:00:58 MarkDuplicates Tracking 117198 as yet unmatched pairs. 31349 records in RAM. INFO 2026-06-08 09:00:59 MarkDuplicates Read 583,000,000 records. Elapsed time: 00:18:35s. Time for last 1,000,000: 1s. Last read position: chr19:39,886,281 INFO 2026-06-08 09:00:59 MarkDuplicates Tracking 116640 as yet unmatched pairs. 30791 records in RAM. INFO 2026-06-08 09:01:01 MarkDuplicates Read 584,000,000 records. Elapsed time: 00:18:37s. Time for last 1,000,000: 2s. Last read position: chr19:39,902,462 INFO 2026-06-08 09:01:01 MarkDuplicates Tracking 114729 as yet unmatched pairs. 28880 records in RAM. INFO 2026-06-08 09:01:03 MarkDuplicates Read 585,000,000 records. Elapsed time: 00:18:39s. Time for last 1,000,000: 1s. Last read position: chr19:40,242,031 INFO 2026-06-08 09:01:03 MarkDuplicates Tracking 113138 as yet unmatched pairs. 27289 records in RAM. INFO 2026-06-08 09:01:04 MarkDuplicates Read 586,000,000 records. Elapsed time: 00:18:40s. Time for last 1,000,000: 1s. Last read position: chr19:41,292,410 INFO 2026-06-08 09:01:04 MarkDuplicates Tracking 111276 as yet unmatched pairs. 25426 records in RAM. INFO 2026-06-08 09:01:06 MarkDuplicates Read 587,000,000 records. Elapsed time: 00:18:42s. Time for last 1,000,000: 1s. Last read position: chr19:41,715,550 INFO 2026-06-08 09:01:06 MarkDuplicates Tracking 112275 as yet unmatched pairs. 26425 records in RAM. INFO 2026-06-08 09:01:07 MarkDuplicates Read 588,000,000 records. Elapsed time: 00:18:43s. Time for last 1,000,000: 1s. Last read position: chr19:41,756,939 INFO 2026-06-08 09:01:07 MarkDuplicates Tracking 109470 as yet unmatched pairs. 23620 records in RAM. INFO 2026-06-08 09:01:09 MarkDuplicates Read 589,000,000 records. Elapsed time: 00:18:45s. Time for last 1,000,000: 1s. Last read position: chr19:42,274,282 INFO 2026-06-08 09:01:09 MarkDuplicates Tracking 107468 as yet unmatched pairs. 21618 records in RAM. INFO 2026-06-08 09:01:10 MarkDuplicates Read 590,000,000 records. Elapsed time: 00:18:46s. Time for last 1,000,000: 1s. Last read position: chr19:43,738,117 INFO 2026-06-08 09:01:10 MarkDuplicates Tracking 104952 as yet unmatched pairs. 19101 records in RAM. INFO 2026-06-08 09:01:11 MarkDuplicates Read 591,000,000 records. Elapsed time: 00:18:48s. Time for last 1,000,000: 1s. Last read position: chr19:45,386,099 INFO 2026-06-08 09:01:11 MarkDuplicates Tracking 103357 as yet unmatched pairs. 17506 records in RAM. INFO 2026-06-08 09:01:13 MarkDuplicates Read 592,000,000 records. Elapsed time: 00:18:49s. Time for last 1,000,000: 1s. Last read position: chr19:46,608,232 INFO 2026-06-08 09:01:13 MarkDuplicates Tracking 102105 as yet unmatched pairs. 16254 records in RAM. INFO 2026-06-08 09:01:15 MarkDuplicates Read 593,000,000 records. Elapsed time: 00:18:51s. Time for last 1,000,000: 1s. Last read position: chr19:47,726,121 INFO 2026-06-08 09:01:15 MarkDuplicates Tracking 99883 as yet unmatched pairs. 14032 records in RAM. INFO 2026-06-08 09:01:16 MarkDuplicates Read 594,000,000 records. Elapsed time: 00:18:52s. Time for last 1,000,000: 1s. Last read position: chr19:48,841,240 INFO 2026-06-08 09:01:16 MarkDuplicates Tracking 98238 as yet unmatched pairs. 12387 records in RAM. INFO 2026-06-08 09:01:18 MarkDuplicates Read 595,000,000 records. Elapsed time: 00:18:54s. Time for last 1,000,000: 1s. Last read position: chr19:49,496,449 INFO 2026-06-08 09:01:18 MarkDuplicates Tracking 96533 as yet unmatched pairs. 10681 records in RAM. INFO 2026-06-08 09:01:19 MarkDuplicates Read 596,000,000 records. Elapsed time: 00:18:56s. Time for last 1,000,000: 1s. Last read position: chr19:49,805,464 INFO 2026-06-08 09:01:19 MarkDuplicates Tracking 95242 as yet unmatched pairs. 9389 records in RAM. INFO 2026-06-08 09:01:21 MarkDuplicates Read 597,000,000 records. Elapsed time: 00:18:57s. Time for last 1,000,000: 1s. Last read position: chr19:50,290,962 INFO 2026-06-08 09:01:21 MarkDuplicates Tracking 93377 as yet unmatched pairs. 7524 records in RAM. INFO 2026-06-08 09:01:23 MarkDuplicates Read 598,000,000 records. Elapsed time: 00:18:59s. Time for last 1,000,000: 1s. Last read position: chr19:53,874,341 INFO 2026-06-08 09:01:23 MarkDuplicates Tracking 91789 as yet unmatched pairs. 5935 records in RAM. INFO 2026-06-08 09:01:25 MarkDuplicates Read 599,000,000 records. Elapsed time: 00:19:01s. Time for last 1,000,000: 2s. Last read position: chr19:55,198,679 INFO 2026-06-08 09:01:25 MarkDuplicates Tracking 89913 as yet unmatched pairs. 4059 records in RAM. INFO 2026-06-08 09:01:27 MarkDuplicates Read 600,000,000 records. Elapsed time: 00:19:03s. Time for last 1,000,000: 1s. Last read position: chr19:55,694,842 INFO 2026-06-08 09:01:27 MarkDuplicates Tracking 88658 as yet unmatched pairs. 2803 records in RAM. INFO 2026-06-08 09:01:28 MarkDuplicates Read 601,000,000 records. Elapsed time: 00:19:04s. Time for last 1,000,000: 1s. Last read position: chr19:58,544,984 INFO 2026-06-08 09:01:28 MarkDuplicates Tracking 86837 as yet unmatched pairs. 981 records in RAM. INFO 2026-06-08 09:01:30 MarkDuplicates Read 602,000,000 records. Elapsed time: 00:19:06s. Time for last 1,000,000: 1s. Last read position: chr20:1,375,513 INFO 2026-06-08 09:01:30 MarkDuplicates Tracking 85858 as yet unmatched pairs. 28121 records in RAM. INFO 2026-06-08 09:01:31 MarkDuplicates Read 603,000,000 records. Elapsed time: 00:19:07s. Time for last 1,000,000: 1s. Last read position: chr20:3,786,019 INFO 2026-06-08 09:01:31 MarkDuplicates Tracking 83373 as yet unmatched pairs. 25636 records in RAM. INFO 2026-06-08 09:01:33 MarkDuplicates Read 604,000,000 records. Elapsed time: 00:19:09s. Time for last 1,000,000: 1s. Last read position: chr20:6,112,552 INFO 2026-06-08 09:01:33 MarkDuplicates Tracking 81889 as yet unmatched pairs. 24152 records in RAM. INFO 2026-06-08 09:01:34 MarkDuplicates Read 605,000,000 records. Elapsed time: 00:19:11s. Time for last 1,000,000: 1s. Last read position: chr20:17,636,633 INFO 2026-06-08 09:01:34 MarkDuplicates Tracking 80403 as yet unmatched pairs. 22666 records in RAM. INFO 2026-06-08 09:01:36 MarkDuplicates Read 606,000,000 records. Elapsed time: 00:19:12s. Time for last 1,000,000: 1s. Last read position: chr20:22,582,525 INFO 2026-06-08 09:01:36 MarkDuplicates Tracking 78880 as yet unmatched pairs. 21143 records in RAM. INFO 2026-06-08 09:01:37 MarkDuplicates Read 607,000,000 records. Elapsed time: 00:19:13s. Time for last 1,000,000: 1s. Last read position: chr20:31,561,718 INFO 2026-06-08 09:01:37 MarkDuplicates Tracking 77529 as yet unmatched pairs. 19792 records in RAM. INFO 2026-06-08 09:01:39 MarkDuplicates Read 608,000,000 records. Elapsed time: 00:19:15s. Time for last 1,000,000: 1s. Last read position: chr20:33,397,005 INFO 2026-06-08 09:01:39 MarkDuplicates Tracking 75652 as yet unmatched pairs. 17915 records in RAM. INFO 2026-06-08 09:01:40 MarkDuplicates Read 609,000,000 records. Elapsed time: 00:19:16s. Time for last 1,000,000: 1s. Last read position: chr20:35,176,204 INFO 2026-06-08 09:01:40 MarkDuplicates Tracking 74145 as yet unmatched pairs. 16408 records in RAM. INFO 2026-06-08 09:01:42 MarkDuplicates Read 610,000,000 records. Elapsed time: 00:19:18s. Time for last 1,000,000: 1s. Last read position: chr20:36,500,208 INFO 2026-06-08 09:01:42 MarkDuplicates Tracking 73128 as yet unmatched pairs. 15391 records in RAM. INFO 2026-06-08 09:01:44 MarkDuplicates Read 611,000,000 records. Elapsed time: 00:19:20s. Time for last 1,000,000: 1s. Last read position: chr20:38,766,278 INFO 2026-06-08 09:01:44 MarkDuplicates Tracking 71102 as yet unmatched pairs. 13365 records in RAM. INFO 2026-06-08 09:01:45 MarkDuplicates Read 612,000,000 records. Elapsed time: 00:19:21s. Time for last 1,000,000: 1s. Last read position: chr20:44,503,907 INFO 2026-06-08 09:01:45 MarkDuplicates Tracking 69690 as yet unmatched pairs. 11953 records in RAM. INFO 2026-06-08 09:01:47 MarkDuplicates Read 613,000,000 records. Elapsed time: 00:19:23s. Time for last 1,000,000: 1s. Last read position: chr20:45,898,074 INFO 2026-06-08 09:01:47 MarkDuplicates Tracking 68636 as yet unmatched pairs. 10899 records in RAM. INFO 2026-06-08 09:01:49 MarkDuplicates Read 614,000,000 records. Elapsed time: 00:19:25s. Time for last 1,000,000: 1s. Last read position: chr20:49,248,004 INFO 2026-06-08 09:01:49 MarkDuplicates Tracking 66761 as yet unmatched pairs. 9024 records in RAM. INFO 2026-06-08 09:01:50 MarkDuplicates Read 615,000,000 records. Elapsed time: 00:19:26s. Time for last 1,000,000: 1s. Last read position: chr20:53,253,795 INFO 2026-06-08 09:01:50 MarkDuplicates Tracking 65206 as yet unmatched pairs. 7469 records in RAM. INFO 2026-06-08 09:01:51 MarkDuplicates Read 616,000,000 records. Elapsed time: 00:19:27s. Time for last 1,000,000: 1s. Last read position: chr20:58,909,392 INFO 2026-06-08 09:01:51 MarkDuplicates Tracking 65184 as yet unmatched pairs. 7447 records in RAM. INFO 2026-06-08 09:01:54 MarkDuplicates Read 617,000,000 records. Elapsed time: 00:19:30s. Time for last 1,000,000: 2s. Last read position: chr20:62,327,307 INFO 2026-06-08 09:01:54 MarkDuplicates Tracking 61955 as yet unmatched pairs. 4218 records in RAM. INFO 2026-06-08 09:01:55 MarkDuplicates Read 618,000,000 records. Elapsed time: 00:19:31s. Time for last 1,000,000: 1s. Last read position: chr20:63,520,821 INFO 2026-06-08 09:01:55 MarkDuplicates Tracking 61627 as yet unmatched pairs. 3890 records in RAM. INFO 2026-06-08 09:01:57 MarkDuplicates Read 619,000,000 records. Elapsed time: 00:19:33s. Time for last 1,000,000: 1s. Last read position: chr20:63,742,546 INFO 2026-06-08 09:01:57 MarkDuplicates Tracking 58811 as yet unmatched pairs. 1074 records in RAM. INFO 2026-06-08 09:01:58 MarkDuplicates Read 620,000,000 records. Elapsed time: 00:19:35s. Time for last 1,000,000: 1s. Last read position: chr21:8,216,084 INFO 2026-06-08 09:01:58 MarkDuplicates Tracking 56848 as yet unmatched pairs. 9972 records in RAM. INFO 2026-06-08 09:02:00 MarkDuplicates Read 621,000,000 records. Elapsed time: 00:19:36s. Time for last 1,000,000: 1s. Last read position: chr21:8,400,302 INFO 2026-06-08 09:02:00 MarkDuplicates Tracking 56540 as yet unmatched pairs. 9660 records in RAM. INFO 2026-06-08 09:02:01 MarkDuplicates Read 622,000,000 records. Elapsed time: 00:19:37s. Time for last 1,000,000: 1s. Last read position: chr21:15,833,361 INFO 2026-06-08 09:02:01 MarkDuplicates Tracking 55213 as yet unmatched pairs. 8333 records in RAM. INFO 2026-06-08 09:02:02 MarkDuplicates Read 623,000,000 records. Elapsed time: 00:19:38s. Time for last 1,000,000: 1s. Last read position: chr21:33,549,767 INFO 2026-06-08 09:02:02 MarkDuplicates Tracking 54110 as yet unmatched pairs. 7230 records in RAM. INFO 2026-06-08 09:02:04 MarkDuplicates Read 624,000,000 records. Elapsed time: 00:19:40s. Time for last 1,000,000: 1s. Last read position: chr21:37,164,060 INFO 2026-06-08 09:02:04 MarkDuplicates Tracking 52370 as yet unmatched pairs. 5490 records in RAM. INFO 2026-06-08 09:02:06 MarkDuplicates Read 625,000,000 records. Elapsed time: 00:19:42s. Time for last 1,000,000: 1s. Last read position: chr21:42,312,199 INFO 2026-06-08 09:02:06 MarkDuplicates Tracking 52417 as yet unmatched pairs. 5537 records in RAM. INFO 2026-06-08 09:02:07 MarkDuplicates Read 626,000,000 records. Elapsed time: 00:19:43s. Time for last 1,000,000: 1s. Last read position: chr21:44,330,180 INFO 2026-06-08 09:02:07 MarkDuplicates Tracking 49323 as yet unmatched pairs. 2443 records in RAM. INFO 2026-06-08 09:02:08 MarkDuplicates Read 627,000,000 records. Elapsed time: 00:19:45s. Time for last 1,000,000: 1s. Last read position: chr21:46,124,908 INFO 2026-06-08 09:02:08 MarkDuplicates Tracking 47918 as yet unmatched pairs. 1038 records in RAM. INFO 2026-06-08 09:02:10 MarkDuplicates Read 628,000,000 records. Elapsed time: 00:19:46s. Time for last 1,000,000: 1s. Last read position: chr22:19,851,292 INFO 2026-06-08 09:02:10 MarkDuplicates Tracking 46149 as yet unmatched pairs. 19736 records in RAM. INFO 2026-06-08 09:02:11 MarkDuplicates Read 629,000,000 records. Elapsed time: 00:19:48s. Time for last 1,000,000: 1s. Last read position: chr22:23,182,212 INFO 2026-06-08 09:02:11 MarkDuplicates Tracking 44604 as yet unmatched pairs. 18191 records in RAM. INFO 2026-06-08 09:02:13 MarkDuplicates Read 630,000,000 records. Elapsed time: 00:19:49s. Time for last 1,000,000: 1s. Last read position: chr22:25,181,742 INFO 2026-06-08 09:02:13 MarkDuplicates Tracking 42884 as yet unmatched pairs. 16471 records in RAM. INFO 2026-06-08 09:02:15 MarkDuplicates Read 631,000,000 records. Elapsed time: 00:19:51s. Time for last 1,000,000: 1s. Last read position: chr22:29,299,691 INFO 2026-06-08 09:02:15 MarkDuplicates Tracking 41764 as yet unmatched pairs. 15351 records in RAM. INFO 2026-06-08 09:02:16 MarkDuplicates Read 632,000,000 records. Elapsed time: 00:19:52s. Time for last 1,000,000: 1s. Last read position: chr22:31,821,493 INFO 2026-06-08 09:02:16 MarkDuplicates Tracking 39795 as yet unmatched pairs. 13382 records in RAM. INFO 2026-06-08 09:02:17 MarkDuplicates Read 633,000,000 records. Elapsed time: 00:19:53s. Time for last 1,000,000: 1s. Last read position: chr22:36,312,201 INFO 2026-06-08 09:02:17 MarkDuplicates Tracking 38261 as yet unmatched pairs. 11848 records in RAM. INFO 2026-06-08 09:02:19 MarkDuplicates Read 634,000,000 records. Elapsed time: 00:19:55s. Time for last 1,000,000: 1s. Last read position: chr22:37,888,459 INFO 2026-06-08 09:02:19 MarkDuplicates Tracking 36638 as yet unmatched pairs. 10225 records in RAM. INFO 2026-06-08 09:02:21 MarkDuplicates Read 635,000,000 records. Elapsed time: 00:19:57s. Time for last 1,000,000: 1s. Last read position: chr22:39,529,564 INFO 2026-06-08 09:02:21 MarkDuplicates Tracking 34947 as yet unmatched pairs. 8534 records in RAM. INFO 2026-06-08 09:02:22 MarkDuplicates Read 636,000,000 records. Elapsed time: 00:19:58s. Time for last 1,000,000: 1s. Last read position: chr22:41,875,618 INFO 2026-06-08 09:02:22 MarkDuplicates Tracking 33758 as yet unmatched pairs. 7345 records in RAM. INFO 2026-06-08 09:02:23 MarkDuplicates Read 637,000,000 records. Elapsed time: 00:19:59s. Time for last 1,000,000: 1s. Last read position: chr22:45,922,073 INFO 2026-06-08 09:02:23 MarkDuplicates Tracking 31864 as yet unmatched pairs. 5451 records in RAM. INFO 2026-06-08 09:02:26 MarkDuplicates Read 638,000,000 records. Elapsed time: 00:20:02s. Time for last 1,000,000: 2s. Last read position: chr22:50,247,996 INFO 2026-06-08 09:02:26 MarkDuplicates Tracking 30343 as yet unmatched pairs. 3930 records in RAM. INFO 2026-06-08 09:02:27 MarkDuplicates Read 639,000,000 records. Elapsed time: 00:20:03s. Time for last 1,000,000: 1s. Last read position: chr22:50,455,124 INFO 2026-06-08 09:02:27 MarkDuplicates Tracking 28963 as yet unmatched pairs. 2546 records in RAM. INFO 2026-06-08 09:02:29 MarkDuplicates Read 640,000,000 records. Elapsed time: 00:20:05s. Time for last 1,000,000: 1s. Last read position: chr22:50,720,197 INFO 2026-06-08 09:02:29 MarkDuplicates Tracking 26723 as yet unmatched pairs. 301 records in RAM. INFO 2026-06-08 09:02:31 MarkDuplicates Read 641,000,000 records. Elapsed time: 00:20:07s. Time for last 1,000,000: 1s. Last read position: chrX:10,449,386 INFO 2026-06-08 09:02:31 MarkDuplicates Tracking 25113 as yet unmatched pairs. 20057 records in RAM. INFO 2026-06-08 09:02:32 MarkDuplicates Read 642,000,000 records. Elapsed time: 00:20:09s. Time for last 1,000,000: 1s. Last read position: chrX:23,783,230 INFO 2026-06-08 09:02:32 MarkDuplicates Tracking 24061 as yet unmatched pairs. 19001 records in RAM. INFO 2026-06-08 09:02:34 MarkDuplicates Read 643,000,000 records. Elapsed time: 00:20:10s. Time for last 1,000,000: 1s. Last read position: chrX:41,151,041 INFO 2026-06-08 09:02:34 MarkDuplicates Tracking 22533 as yet unmatched pairs. 17473 records in RAM. INFO 2026-06-08 09:02:35 MarkDuplicates Read 644,000,000 records. Elapsed time: 00:20:11s. Time for last 1,000,000: 1s. Last read position: chrX:47,567,288 INFO 2026-06-08 09:02:35 MarkDuplicates Tracking 21096 as yet unmatched pairs. 16036 records in RAM. INFO 2026-06-08 09:02:37 MarkDuplicates Read 645,000,000 records. Elapsed time: 00:20:13s. Time for last 1,000,000: 1s. Last read position: chrX:49,071,921 INFO 2026-06-08 09:02:37 MarkDuplicates Tracking 19487 as yet unmatched pairs. 14427 records in RAM. INFO 2026-06-08 09:02:38 MarkDuplicates Read 646,000,000 records. Elapsed time: 00:20:14s. Time for last 1,000,000: 1s. Last read position: chrX:53,548,016 INFO 2026-06-08 09:02:38 MarkDuplicates Tracking 18222 as yet unmatched pairs. 13162 records in RAM. INFO 2026-06-08 09:02:40 MarkDuplicates Read 647,000,000 records. Elapsed time: 00:20:16s. Time for last 1,000,000: 1s. Last read position: chrX:65,529,594 INFO 2026-06-08 09:02:40 MarkDuplicates Tracking 16528 as yet unmatched pairs. 11468 records in RAM. INFO 2026-06-08 09:02:41 MarkDuplicates Read 648,000,000 records. Elapsed time: 00:20:17s. Time for last 1,000,000: 1s. Last read position: chrX:71,298,498 INFO 2026-06-08 09:02:41 MarkDuplicates Tracking 15719 as yet unmatched pairs. 10658 records in RAM. INFO 2026-06-08 09:02:43 MarkDuplicates Read 649,000,000 records. Elapsed time: 00:20:19s. Time for last 1,000,000: 1s. Last read position: chrX:77,969,274 INFO 2026-06-08 09:02:43 MarkDuplicates Tracking 14178 as yet unmatched pairs. 9117 records in RAM. INFO 2026-06-08 09:02:44 MarkDuplicates Read 650,000,000 records. Elapsed time: 00:20:20s. Time for last 1,000,000: 1s. Last read position: chrX:103,676,494 INFO 2026-06-08 09:02:44 MarkDuplicates Tracking 12758 as yet unmatched pairs. 7697 records in RAM. INFO 2026-06-08 09:02:46 MarkDuplicates Read 651,000,000 records. Elapsed time: 00:20:22s. Time for last 1,000,000: 1s. Last read position: chrX:120,608,341 INFO 2026-06-08 09:02:46 MarkDuplicates Tracking 11271 as yet unmatched pairs. 6210 records in RAM. INFO 2026-06-08 09:02:47 MarkDuplicates Read 652,000,000 records. Elapsed time: 00:20:24s. Time for last 1,000,000: 1s. Last read position: chrX:139,762,019 INFO 2026-06-08 09:02:47 MarkDuplicates Tracking 9746 as yet unmatched pairs. 4685 records in RAM. INFO 2026-06-08 09:02:49 MarkDuplicates Read 653,000,000 records. Elapsed time: 00:20:25s. Time for last 1,000,000: 1s. Last read position: chrX:153,952,034 INFO 2026-06-08 09:02:49 MarkDuplicates Tracking 8421 as yet unmatched pairs. 3360 records in RAM. INFO 2026-06-08 09:02:50 MarkDuplicates Read 654,000,000 records. Elapsed time: 00:20:26s. Time for last 1,000,000: 1s. Last read position: chrX:154,361,389 INFO 2026-06-08 09:02:50 MarkDuplicates Tracking 7404 as yet unmatched pairs. 2343 records in RAM. INFO 2026-06-08 09:02:52 MarkDuplicates Read 655,000,000 records. Elapsed time: 00:20:28s. Time for last 1,000,000: 1s. Last read position: chrX:155,120,029 INFO 2026-06-08 09:02:52 MarkDuplicates Tracking 5164 as yet unmatched pairs. 103 records in RAM. INFO 2026-06-08 09:02:54 MarkDuplicates Read 656,000,000 records. Elapsed time: 00:20:31s. Time for last 1,000,000: 2s. Last read position: GL000220.1:116,388 INFO 2026-06-08 09:02:54 MarkDuplicates Tracking 2498 as yet unmatched pairs. 91 records in RAM. INFO 2026-06-08 09:02:56 MarkDuplicates Read 657,000,000 records. Elapsed time: 00:20:32s. Time for last 1,000,000: 1s. Last read position: KI270713.1:21,894 INFO 2026-06-08 09:02:56 MarkDuplicates Tracking 2383 as yet unmatched pairs. 0 records in RAM. INFO 2026-06-08 09:02:57 MarkDuplicates Read 658,000,000 records. Elapsed time: 00:20:33s. Time for last 1,000,000: 1s. Last read position: KI270733.1:176,401 INFO 2026-06-08 09:02:57 MarkDuplicates Tracking 25 as yet unmatched pairs. 23 records in RAM. INFO 2026-06-08 09:02:57 MarkDuplicates Read 658356355 records. 0 pairs never matched. INFO 2026-06-08 09:03:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 204142048; totalMemory: 234881024; maxMemory: 63585648640 INFO 2026-06-08 09:03:46 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk. INFO 2026-06-08 09:03:51 MarkDuplicates Traversing read pair information and detecting duplicates. WARNING 2026-06-08 09:03:51 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered. INFO 2026-06-08 09:04:14 OpticalDuplicateFinder Large duplicate set. size = 1110 INFO 2026-06-08 09:04:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,521 INFO 2026-06-08 09:04:19 OpticalDuplicateFinder Large duplicate set. size = 1573 INFO 2026-06-08 09:04:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:6,639 INFO 2026-06-08 09:04:22 OpticalDuplicateFinder Large duplicate set. size = 1003 INFO 2026-06-08 09:04:22 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,338 INFO 2026-06-08 09:04:22 OpticalDuplicateFinder Large duplicate set. size = 1065 INFO 2026-06-08 09:04:22 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,201 INFO 2026-06-08 09:04:22 OpticalDuplicateFinder Large duplicate set. size = 1261 INFO 2026-06-08 09:04:22 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,218 INFO 2026-06-08 09:04:22 OpticalDuplicateFinder Large duplicate set. size = 1241 INFO 2026-06-08 09:04:22 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-13,990 INFO 2026-06-08 09:04:22 OpticalDuplicateFinder Large duplicate set. size = 1401 INFO 2026-06-08 09:04:22 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,225 INFO 2026-06-08 09:04:22 OpticalDuplicateFinder Large duplicate set. size = 1723 INFO 2026-06-08 09:04:22 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-14,734 INFO 2026-06-08 09:04:22 OpticalDuplicateFinder Large duplicate set. size = 1025 INFO 2026-06-08 09:04:22 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:7,448 INFO 2026-06-08 09:04:22 OpticalDuplicateFinder Large duplicate set. size = 1012 INFO 2026-06-08 09:04:22 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,785 INFO 2026-06-08 09:04:22 OpticalDuplicateFinder Large duplicate set. size = 1095 INFO 2026-06-08 09:04:22 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,985 INFO 2026-06-08 09:04:23 OpticalDuplicateFinder Large duplicate set. size = 1135 INFO 2026-06-08 09:04:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,484 INFO 2026-06-08 09:04:23 OpticalDuplicateFinder Large duplicate set. size = 1289 INFO 2026-06-08 09:04:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,641 INFO 2026-06-08 09:04:23 OpticalDuplicateFinder Large duplicate set. size = 1372 INFO 2026-06-08 09:04:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:6,801 INFO 2026-06-08 09:04:23 OpticalDuplicateFinder Large duplicate set. size = 1065 INFO 2026-06-08 09:04:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,017 INFO 2026-06-08 09:04:23 OpticalDuplicateFinder Large duplicate set. size = 1434 INFO 2026-06-08 09:04:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-19,548 INFO 2026-06-08 09:04:23 OpticalDuplicateFinder Large duplicate set. size = 2261 INFO 2026-06-08 09:04:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,082 INFO 2026-06-08 09:04:23 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:31,904 INFO 2026-06-08 09:04:24 OpticalDuplicateFinder Large duplicate set. size = 1579 INFO 2026-06-08 09:04:24 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:10,910 INFO 2026-06-08 09:04:24 OpticalDuplicateFinder Large duplicate set. size = 1408 INFO 2026-06-08 09:04:24 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,382 INFO 2026-06-08 09:05:31 MarkDuplicates Traversing fragment information and detecting duplicates. WARNING 2026-06-08 09:05:31 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered. INFO 2026-06-08 09:06:35 MarkDuplicates Sorting list of duplicate records. INFO 2026-06-08 09:06:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 203974984; totalMemory: 234881024; maxMemory: 63585648640 INFO 2026-06-08 09:06:42 MarkDuplicates Marking 408459345 records as duplicates. INFO 2026-06-08 09:06:42 MarkDuplicates Found 10729935 optical duplicate clusters. INFO 2026-06-08 09:06:42 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2026-06-08 09:07:01 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:18s. Time for last 10,000,000: 18s. Last read position: chr1:26,921,801 INFO 2026-06-08 09:07:19 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:36s. Time for last 10,000,000: 17s. Last read position: chr1:52,687,891 INFO 2026-06-08 09:07:37 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:54s. Time for last 10,000,000: 17s. Last read position: chr1:146,068,810 INFO 2026-06-08 09:07:55 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:12s. Time for last 10,000,000: 17s. Last read position: chr1:156,135,218 INFO 2026-06-08 09:08:13 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:30s. Time for last 10,000,000: 18s. Last read position: chr1:204,261,455 INFO 2026-06-08 09:08:31 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:48s. Time for last 10,000,000: 18s. Last read position: chr2:17,683,751 INFO 2026-06-08 09:08:48 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:06s. Time for last 10,000,000: 17s. Last read position: chr2:54,629,350 INFO 2026-06-08 09:09:06 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:23s. Time for last 10,000,000: 17s. Last read position: chr2:110,534,615 INFO 2026-06-08 09:09:24 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:41s. Time for last 10,000,000: 18s. Last read position: chr2:201,160,841 INFO 2026-06-08 09:09:42 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:59s. Time for last 10,000,000: 17s. Last read position: chr2:240,589,399 INFO 2026-06-08 09:10:00 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:03:17s. Time for last 10,000,000: 17s. Last read position: chr3:49,357,337 INFO 2026-06-08 09:10:17 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:34s. Time for last 10,000,000: 17s. Last read position: chr3:129,171,252 INFO 2026-06-08 09:10:35 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:52s. Time for last 10,000,000: 17s. Last read position: chr3:196,075,288 INFO 2026-06-08 09:10:53 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:04:10s. Time for last 10,000,000: 17s. Last read position: chr4:101,025,904 INFO 2026-06-08 09:11:11 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:04:28s. Time for last 10,000,000: 17s. Last read position: chr5:14,481,271 INFO 2026-06-08 09:11:29 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:46s. Time for last 10,000,000: 18s. Last read position: chr5:133,956,906 INFO 2026-06-08 09:11:46 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:05:04s. Time for last 10,000,000: 17s. Last read position: chr5:154,792,785 INFO 2026-06-08 09:12:04 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:05:21s. Time for last 10,000,000: 17s. Last read position: chr6:7,910,531 INFO 2026-06-08 09:12:21 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:05:39s. Time for last 10,000,000: 17s. Last read position: chr6:32,027,435 INFO 2026-06-08 09:12:39 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:05:56s. Time for last 10,000,000: 17s. Last read position: chr6:85,640,231 INFO 2026-06-08 09:12:57 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:06:14s. Time for last 10,000,000: 17s. Last read position: chr7:726,762 INFO 2026-06-08 09:13:14 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:06:31s. Time for last 10,000,000: 17s. Last read position: chr7:55,171,177 INFO 2026-06-08 09:13:32 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:06:49s. Time for last 10,000,000: 17s. Last read position: chr7:100,822,284 INFO 2026-06-08 09:13:49 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:07:06s. Time for last 10,000,000: 16s. Last read position: chr7:100,996,522 INFO 2026-06-08 09:14:06 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:07:23s. Time for last 10,000,000: 17s. Last read position: chr7:100,999,923 INFO 2026-06-08 09:14:22 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:07:39s. Time for last 10,000,000: 16s. Last read position: chr7:101,013,967 INFO 2026-06-08 09:14:40 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:07:57s. Time for last 10,000,000: 17s. Last read position: chr7:144,363,357 INFO 2026-06-08 09:14:57 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:08:14s. Time for last 10,000,000: 17s. Last read position: chr8:63,038,662 INFO 2026-06-08 09:15:15 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:08:32s. Time for last 10,000,000: 17s. Last read position: chr8:143,860,606 INFO 2026-06-08 09:15:32 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:08:49s. Time for last 10,000,000: 16s. Last read position: chr9:19,120,937 INFO 2026-06-08 09:15:49 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:09:06s. Time for last 10,000,000: 17s. Last read position: chr9:113,169,406 INFO 2026-06-08 09:16:06 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:09:24s. Time for last 10,000,000: 17s. Last read position: chr9:136,496,293 INFO 2026-06-08 09:16:24 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:09:41s. Time for last 10,000,000: 17s. Last read position: chr10:68,338,633 INFO 2026-06-08 09:16:42 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:09:59s. Time for last 10,000,000: 17s. Last read position: chr10:113,158,043 INFO 2026-06-08 09:16:59 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:10:16s. Time for last 10,000,000: 17s. Last read position: chr11:3,706,506 INFO 2026-06-08 09:17:16 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:10:34s. Time for last 10,000,000: 17s. Last read position: chr11:61,313,673 INFO 2026-06-08 09:17:34 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:10:51s. Time for last 10,000,000: 17s. Last read position: chr11:67,279,420 INFO 2026-06-08 09:17:51 MarkDuplicates Written 380,000,000 records. Elapsed time: 00:11:08s. Time for last 10,000,000: 17s. Last read position: chr11:120,337,250 INFO 2026-06-08 09:18:09 MarkDuplicates Written 390,000,000 records. Elapsed time: 00:11:26s. Time for last 10,000,000: 17s. Last read position: chr12:10,723,017 INFO 2026-06-08 09:18:26 MarkDuplicates Written 400,000,000 records. Elapsed time: 00:11:43s. Time for last 10,000,000: 17s. Last read position: chr12:53,455,987 INFO 2026-06-08 09:18:44 MarkDuplicates Written 410,000,000 records. Elapsed time: 00:12:01s. Time for last 10,000,000: 17s. Last read position: chr12:93,378,120 INFO 2026-06-08 09:19:01 MarkDuplicates Written 420,000,000 records. Elapsed time: 00:12:18s. Time for last 10,000,000: 17s. Last read position: chr12:124,949,985 INFO 2026-06-08 09:19:19 MarkDuplicates Written 430,000,000 records. Elapsed time: 00:12:36s. Time for last 10,000,000: 17s. Last read position: chr13:106,544,100 INFO 2026-06-08 09:19:36 MarkDuplicates Written 440,000,000 records. Elapsed time: 00:12:53s. Time for last 10,000,000: 17s. Last read position: chr14:73,941,034 INFO 2026-06-08 09:19:54 MarkDuplicates Written 450,000,000 records. Elapsed time: 00:13:11s. Time for last 10,000,000: 17s. Last read position: chr15:43,698,990 INFO 2026-06-08 09:20:11 MarkDuplicates Written 460,000,000 records. Elapsed time: 00:13:28s. Time for last 10,000,000: 17s. Last read position: chr16:58,386 INFO 2026-06-08 09:20:28 MarkDuplicates Written 470,000,000 records. Elapsed time: 00:13:46s. Time for last 10,000,000: 17s. Last read position: chr16:15,703,944 INFO 2026-06-08 09:20:46 MarkDuplicates Written 480,000,000 records. Elapsed time: 00:14:03s. Time for last 10,000,000: 17s. Last read position: chr16:29,491,646 INFO 2026-06-08 09:21:03 MarkDuplicates Written 490,000,000 records. Elapsed time: 00:14:20s. Time for last 10,000,000: 17s. Last read position: chr16:31,191,396 INFO 2026-06-08 09:21:21 MarkDuplicates Written 500,000,000 records. Elapsed time: 00:14:38s. Time for last 10,000,000: 17s. Last read position: chr16:89,508,443 INFO 2026-06-08 09:21:38 MarkDuplicates Written 510,000,000 records. Elapsed time: 00:14:55s. Time for last 10,000,000: 17s. Last read position: chr17:28,748,932 INFO 2026-06-08 09:21:56 MarkDuplicates Written 520,000,000 records. Elapsed time: 00:15:13s. Time for last 10,000,000: 17s. Last read position: chr17:42,795,019 INFO 2026-06-08 09:22:13 MarkDuplicates Written 530,000,000 records. Elapsed time: 00:15:30s. Time for last 10,000,000: 17s. Last read position: chr17:50,196,616 INFO 2026-06-08 09:22:30 MarkDuplicates Written 540,000,000 records. Elapsed time: 00:15:47s. Time for last 10,000,000: 17s. Last read position: chr17:75,573,106 INFO 2026-06-08 09:22:48 MarkDuplicates Written 550,000,000 records. Elapsed time: 00:16:05s. Time for last 10,000,000: 17s. Last read position: chr18:23,463,063 INFO 2026-06-08 09:23:05 MarkDuplicates Written 560,000,000 records. Elapsed time: 00:16:22s. Time for last 10,000,000: 17s. Last read position: chr19:4,362,695 INFO 2026-06-08 09:23:22 MarkDuplicates Written 570,000,000 records. Elapsed time: 00:16:39s. Time for last 10,000,000: 17s. Last read position: chr19:14,409,847 INFO 2026-06-08 09:23:39 MarkDuplicates Written 580,000,000 records. Elapsed time: 00:16:57s. Time for last 10,000,000: 17s. Last read position: chr19:38,620,376 INFO 2026-06-08 09:23:57 MarkDuplicates Written 590,000,000 records. Elapsed time: 00:17:14s. Time for last 10,000,000: 17s. Last read position: chr19:43,738,117 INFO 2026-06-08 09:24:14 MarkDuplicates Written 600,000,000 records. Elapsed time: 00:17:31s. Time for last 10,000,000: 17s. Last read position: chr19:55,694,842 INFO 2026-06-08 09:24:31 MarkDuplicates Written 610,000,000 records. Elapsed time: 00:17:48s. Time for last 10,000,000: 17s. Last read position: chr20:36,500,208 INFO 2026-06-08 09:24:49 MarkDuplicates Written 620,000,000 records. Elapsed time: 00:18:06s. Time for last 10,000,000: 17s. Last read position: chr21:8,216,084 INFO 2026-06-08 09:25:05 MarkDuplicates Written 630,000,000 records. Elapsed time: 00:18:23s. Time for last 10,000,000: 16s. Last read position: chr22:25,181,742 INFO 2026-06-08 09:25:23 MarkDuplicates Written 640,000,000 records. Elapsed time: 00:18:40s. Time for last 10,000,000: 17s. Last read position: chr22:50,720,197 INFO 2026-06-08 09:25:40 MarkDuplicates Written 650,000,000 records. Elapsed time: 00:18:57s. Time for last 10,000,000: 17s. Last read position: chrX:103,676,494 INFO 2026-06-08 09:25:58 MarkDuplicates Written 660,000,000 records. Elapsed time: 00:19:15s. Time for last 10,000,000: 17s. Last read position: */* INFO 2026-06-08 09:26:01 MarkDuplicates Writing complete. Closing input iterator. INFO 2026-06-08 09:26:01 MarkDuplicates Duplicate Index cleanup. INFO 2026-06-08 09:26:01 MarkDuplicates Getting Memory Stats. INFO 2026-06-08 09:26:01 MarkDuplicates Before output close freeMemory: 203360136; totalMemory: 234881024; maxMemory: 63585648640 INFO 2026-06-08 09:26:01 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2026-06-08 09:26:01 MarkDuplicates After output close freeMemory: 104192608; totalMemory: 134217728; maxMemory: 63585648640 [Mon Jun 08 09:26:01 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 43.66 minutes. Runtime.totalMemory()=134217728 Tool returned: 0 ls: *cram: No such file or directory ls: *.crai: No such file or directory