Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/f23bb31e470587dfe008557f43d6da/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/31d014da57bf3d6810accc6e29f56a/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/31d014da57bf3d6810accc6e29f56a/.command.run Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai ==> STAGING COMPLETE (5 inputs) Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bam --METRICS_FILE aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT 20:22:59.432 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Wed Jun 03 20:22:59 GMT 2026] MarkDuplicates --INPUT aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bam --METRICS_FILE aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Wed Jun 03 20:22:59 GMT 2026] Executing as ?@nf-9931d014da57bf3d6810accc6e29f56a-a9388-mx55d on Linux 6.12.88 amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0 INFO 2026-06-03 20:22:59 MarkDuplicates Start of doWork freeMemory: 105828128; totalMemory: 134217728; maxMemory: 63585648640 INFO 2026-06-03 20:22:59 MarkDuplicates Reading input file and constructing read end information. INFO 2026-06-03 20:22:59 MarkDuplicates Will retain up to 230382784 data points before spilling to disk. INFO 2026-06-03 20:23:03 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:1,353,871 INFO 2026-06-03 20:23:03 MarkDuplicates Tracking 2000 as yet unmatched pairs. 295 records in RAM. INFO 2026-06-03 20:23:05 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: chr1:2,406,582 INFO 2026-06-03 20:23:05 MarkDuplicates Tracking 3469 as yet unmatched pairs. 114 records in RAM. INFO 2026-06-03 20:23:06 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: chr1:8,359,785 INFO 2026-06-03 20:23:06 MarkDuplicates Tracking 5197 as yet unmatched pairs. 204 records in RAM. INFO 2026-06-03 20:23:08 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: chr1:11,020,517 INFO 2026-06-03 20:23:08 MarkDuplicates Tracking 7267 as yet unmatched pairs. 784 records in RAM. INFO 2026-06-03 20:23:10 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: chr1:13,779,467 INFO 2026-06-03 20:23:10 MarkDuplicates Tracking 8251 as yet unmatched pairs. 234 records in RAM. INFO 2026-06-03 20:23:12 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: chr1:16,579,270 INFO 2026-06-03 20:23:12 MarkDuplicates Tracking 10261 as yet unmatched pairs. 908 records in RAM. INFO 2026-06-03 20:23:13 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: chr1:19,155,635 INFO 2026-06-03 20:23:13 MarkDuplicates Tracking 11118 as yet unmatched pairs. 274 records in RAM. INFO 2026-06-03 20:23:15 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: chr1:20,773,496 INFO 2026-06-03 20:23:15 MarkDuplicates Tracking 12632 as yet unmatched pairs. 310 records in RAM. INFO 2026-06-03 20:23:17 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: chr1:21,846,448 INFO 2026-06-03 20:23:17 MarkDuplicates Tracking 14276 as yet unmatched pairs. 405 records in RAM. INFO 2026-06-03 20:23:19 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: chr1:22,120,038 INFO 2026-06-03 20:23:19 MarkDuplicates Tracking 15577 as yet unmatched pairs. 119 records in RAM. INFO 2026-06-03 20:23:20 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: chr1:23,429,856 INFO 2026-06-03 20:23:20 MarkDuplicates Tracking 17081 as yet unmatched pairs. 190 records in RAM. INFO 2026-06-03 20:23:23 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 2s. Last read position: chr1:25,901,611 INFO 2026-06-03 20:23:23 MarkDuplicates Tracking 18664 as yet unmatched pairs. 416 records in RAM. INFO 2026-06-03 20:23:25 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 2s. Last read position: chr1:27,345,386 INFO 2026-06-03 20:23:25 MarkDuplicates Tracking 19876 as yet unmatched pairs. 109 records in RAM. INFO 2026-06-03 20:23:26 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 1s. Last read position: chr1:30,936,746 INFO 2026-06-03 20:23:26 MarkDuplicates Tracking 21589 as yet unmatched pairs. 291 records in RAM. INFO 2026-06-03 20:23:27 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 1s. Last read position: chr1:32,203,901 INFO 2026-06-03 20:23:27 MarkDuplicates Tracking 22943 as yet unmatched pairs. 91 records in RAM. INFO 2026-06-03 20:23:29 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 1s. Last read position: chr1:34,757,537 INFO 2026-06-03 20:23:29 MarkDuplicates Tracking 24530 as yet unmatched pairs. 68 records in RAM. INFO 2026-06-03 20:23:30 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 1s. Last read position: chr1:37,501,882 INFO 2026-06-03 20:23:30 MarkDuplicates Tracking 26217 as yet unmatched pairs. 260 records in RAM. INFO 2026-06-03 20:23:32 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 1s. Last read position: chr1:39,485,642 INFO 2026-06-03 20:23:32 MarkDuplicates Tracking 27844 as yet unmatched pairs. 484 records in RAM. INFO 2026-06-03 20:23:33 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 1s. Last read position: chr1:42,929,990 INFO 2026-06-03 20:23:33 MarkDuplicates Tracking 29107 as yet unmatched pairs. 281 records in RAM. INFO 2026-06-03 20:23:34 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 1s. Last read position: chr1:43,984,948 INFO 2026-06-03 20:23:34 MarkDuplicates Tracking 30528 as yet unmatched pairs. 95 records in RAM. INFO 2026-06-03 20:23:36 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 1s. Last read position: chr1:46,184,650 INFO 2026-06-03 20:23:36 MarkDuplicates Tracking 40146 as yet unmatched pairs. 8328 records in RAM. INFO 2026-06-03 20:23:38 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 1s. Last read position: chr1:51,819,849 INFO 2026-06-03 20:23:38 MarkDuplicates Tracking 33549 as yet unmatched pairs. 324 records in RAM. INFO 2026-06-03 20:23:40 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 2s. Last read position: chr1:55,162,247 INFO 2026-06-03 20:23:40 MarkDuplicates Tracking 35049 as yet unmatched pairs. 308 records in RAM. INFO 2026-06-03 20:23:42 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 1s. Last read position: chr1:67,049,801 INFO 2026-06-03 20:23:42 MarkDuplicates Tracking 36713 as yet unmatched pairs. 559 records in RAM. INFO 2026-06-03 20:23:43 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 1s. Last read position: chr1:85,582,170 INFO 2026-06-03 20:23:43 MarkDuplicates Tracking 37637 as yet unmatched pairs. 214 records in RAM. INFO 2026-06-03 20:23:45 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 1s. Last read position: chr1:89,117,658 INFO 2026-06-03 20:23:45 MarkDuplicates Tracking 38795 as yet unmatched pairs. 211 records in RAM. INFO 2026-06-03 20:23:47 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 2s. Last read position: chr1:100,015,319 INFO 2026-06-03 20:23:47 MarkDuplicates Tracking 40117 as yet unmatched pairs. 303 records in RAM. INFO 2026-06-03 20:23:48 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 1s. Last read position: chr1:109,752,041 INFO 2026-06-03 20:23:48 MarkDuplicates Tracking 41684 as yet unmatched pairs. 522 records in RAM. INFO 2026-06-03 20:23:50 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 1s. Last read position: chr1:112,702,569 INFO 2026-06-03 20:23:50 MarkDuplicates Tracking 44903 as yet unmatched pairs. 2419 records in RAM. INFO 2026-06-03 20:23:52 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 1s. Last read position: chr1:114,739,769 INFO 2026-06-03 20:23:52 MarkDuplicates Tracking 44649 as yet unmatched pairs. 861 records in RAM. INFO 2026-06-03 20:23:54 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 2s. Last read position: chr1:119,798,574 INFO 2026-06-03 20:23:54 MarkDuplicates Tracking 48062 as yet unmatched pairs. 2898 records in RAM. INFO 2026-06-03 20:23:55 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 1s. Last read position: chr1:120,511,713 INFO 2026-06-03 20:23:55 MarkDuplicates Tracking 46676 as yet unmatched pairs. 232 records in RAM. INFO 2026-06-03 20:23:57 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 1s. Last read position: chr1:146,066,326 INFO 2026-06-03 20:23:57 MarkDuplicates Tracking 47633 as yet unmatched pairs. 405 records in RAM. INFO 2026-06-03 20:23:58 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 1s. Last read position: chr1:148,558,381 INFO 2026-06-03 20:23:58 MarkDuplicates Tracking 47978 as yet unmatched pairs. 180 records in RAM. INFO 2026-06-03 20:23:59 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 1s. Last read position: chr1:149,852,653 INFO 2026-06-03 20:23:59 MarkDuplicates Tracking 48602 as yet unmatched pairs. 132 records in RAM. INFO 2026-06-03 20:24:01 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 1s. Last read position: chr1:150,627,555 INFO 2026-06-03 20:24:01 MarkDuplicates Tracking 51136 as yet unmatched pairs. 1224 records in RAM. INFO 2026-06-03 20:24:02 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 1s. Last read position: chr1:151,518,505 INFO 2026-06-03 20:24:02 MarkDuplicates Tracking 51470 as yet unmatched pairs. 224 records in RAM. INFO 2026-06-03 20:24:04 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 1s. Last read position: chr1:153,813,376 INFO 2026-06-03 20:24:04 MarkDuplicates Tracking 52823 as yet unmatched pairs. 202 records in RAM. INFO 2026-06-03 20:24:05 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 1s. Last read position: chr1:154,272,722 INFO 2026-06-03 20:24:05 MarkDuplicates Tracking 54248 as yet unmatched pairs. 342 records in RAM. INFO 2026-06-03 20:24:07 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 1s. Last read position: chr1:155,187,290 INFO 2026-06-03 20:24:07 MarkDuplicates Tracking 56360 as yet unmatched pairs. 882 records in RAM. INFO 2026-06-03 20:24:08 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 1s. Last read position: chr1:155,915,858 INFO 2026-06-03 20:24:08 MarkDuplicates Tracking 56932 as yet unmatched pairs. 253 records in RAM. INFO 2026-06-03 20:24:09 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 1s. Last read position: chr1:156,137,190 INFO 2026-06-03 20:24:09 MarkDuplicates Tracking 61845 as yet unmatched pairs. 3335 records in RAM. INFO 2026-06-03 20:24:12 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 2s. Last read position: chr1:156,677,193 INFO 2026-06-03 20:24:12 MarkDuplicates Tracking 61173 as yet unmatched pairs. 897 records in RAM. INFO 2026-06-03 20:24:13 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 1s. Last read position: chr1:160,296,076 INFO 2026-06-03 20:24:13 MarkDuplicates Tracking 62008 as yet unmatched pairs. 347 records in RAM. INFO 2026-06-03 20:24:15 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 1s. Last read position: chr1:161,581,370 INFO 2026-06-03 20:24:15 MarkDuplicates Tracking 63374 as yet unmatched pairs. 313 records in RAM. INFO 2026-06-03 20:24:16 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 1s. Last read position: chr1:167,722,161 INFO 2026-06-03 20:24:16 MarkDuplicates Tracking 64413 as yet unmatched pairs. 135 records in RAM. INFO 2026-06-03 20:24:18 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 1s. Last read position: chr1:171,584,411 INFO 2026-06-03 20:24:18 MarkDuplicates Tracking 65938 as yet unmatched pairs. 255 records in RAM. INFO 2026-06-03 20:24:19 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 1s. Last read position: chr1:180,175,320 INFO 2026-06-03 20:24:19 MarkDuplicates Tracking 67818 as yet unmatched pairs. 781 records in RAM. INFO 2026-06-03 20:24:20 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 1s. Last read position: chr1:184,706,749 INFO 2026-06-03 20:24:20 MarkDuplicates Tracking 68843 as yet unmatched pairs. 394 records in RAM. INFO 2026-06-03 20:24:22 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 1s. Last read position: chr1:186,679,170 INFO 2026-06-03 20:24:22 MarkDuplicates Tracking 69637 as yet unmatched pairs. 47 records in RAM. INFO 2026-06-03 20:24:23 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 1s. Last read position: chr1:201,623,402 INFO 2026-06-03 20:24:23 MarkDuplicates Tracking 71288 as yet unmatched pairs. 351 records in RAM. INFO 2026-06-03 20:24:25 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 1s. Last read position: chr1:203,483,318 INFO 2026-06-03 20:24:25 MarkDuplicates Tracking 72555 as yet unmatched pairs. 254 records in RAM. INFO 2026-06-03 20:24:26 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 1s. Last read position: chr1:205,592,210 INFO 2026-06-03 20:24:26 MarkDuplicates Tracking 73797 as yet unmatched pairs. 195 records in RAM. INFO 2026-06-03 20:24:28 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 1s. Last read position: chr1:206,932,476 INFO 2026-06-03 20:24:28 MarkDuplicates Tracking 81539 as yet unmatched pairs. 6695 records in RAM. INFO 2026-06-03 20:24:29 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 1s. Last read position: chr1:206,937,237 INFO 2026-06-03 20:24:29 MarkDuplicates Tracking 80699 as yet unmatched pairs. 4319 records in RAM. INFO 2026-06-03 20:24:30 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 1s. Last read position: chr1:208,042,123 INFO 2026-06-03 20:24:30 MarkDuplicates Tracking 77939 as yet unmatched pairs. 175 records in RAM. INFO 2026-06-03 20:24:32 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 1s. Last read position: chr1:222,628,168 INFO 2026-06-03 20:24:32 MarkDuplicates Tracking 79304 as yet unmatched pairs. 187 records in RAM. INFO 2026-06-03 20:24:34 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 1s. Last read position: chr1:225,887,399 INFO 2026-06-03 20:24:34 MarkDuplicates Tracking 80702 as yet unmatched pairs. 325 records in RAM. INFO 2026-06-03 20:24:36 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 1s. Last read position: chr1:228,401,178 INFO 2026-06-03 20:24:36 MarkDuplicates Tracking 82062 as yet unmatched pairs. 97 records in RAM. INFO 2026-06-03 20:24:37 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 1s. Last read position: chr1:235,335,283 INFO 2026-06-03 20:24:37 MarkDuplicates Tracking 83677 as yet unmatched pairs. 154 records in RAM. INFO 2026-06-03 20:24:39 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 1s. Last read position: chr1:244,055,033 INFO 2026-06-03 20:24:39 MarkDuplicates Tracking 84968 as yet unmatched pairs. 93 records in RAM. INFO 2026-06-03 20:24:41 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 2s. Last read position: chr2:6,861,209 INFO 2026-06-03 20:24:41 MarkDuplicates Tracking 86479 as yet unmatched pairs. 85424 records in RAM. INFO 2026-06-03 20:24:42 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 1s. Last read position: chr2:15,556,783 INFO 2026-06-03 20:24:42 MarkDuplicates Tracking 87991 as yet unmatched pairs. 86913 records in RAM. INFO 2026-06-03 20:24:44 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 1s. Last read position: chr2:24,644,093 INFO 2026-06-03 20:24:44 MarkDuplicates Tracking 89774 as yet unmatched pairs. 88674 records in RAM. INFO 2026-06-03 20:24:46 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 2s. Last read position: chr2:27,085,226 INFO 2026-06-03 20:24:46 MarkDuplicates Tracking 91355 as yet unmatched pairs. 90233 records in RAM. INFO 2026-06-03 20:24:47 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 1s. Last read position: chr2:28,793,943 INFO 2026-06-03 20:24:47 MarkDuplicates Tracking 96151 as yet unmatched pairs. 95009 records in RAM. INFO 2026-06-03 20:24:49 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,258 INFO 2026-06-03 20:24:49 MarkDuplicates Tracking 137205 as yet unmatched pairs. 88675 records in RAM. INFO 2026-06-03 20:24:51 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,264 INFO 2026-06-03 20:24:51 MarkDuplicates Tracking 621856 as yet unmatched pairs. 58136 records in RAM. INFO 2026-06-03 20:24:52 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,406 INFO 2026-06-03 20:24:52 MarkDuplicates Tracking 727066 as yet unmatched pairs. 50787 records in RAM. INFO 2026-06-03 20:24:54 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 1s. Last read position: chr2:37,671,620 INFO 2026-06-03 20:24:54 MarkDuplicates Tracking 776375 as yet unmatched pairs. 46696 records in RAM. INFO 2026-06-03 20:24:55 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 1s. Last read position: chr2:43,974,623 INFO 2026-06-03 20:24:55 MarkDuplicates Tracking 775065 as yet unmatched pairs. 45369 records in RAM. INFO 2026-06-03 20:24:57 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 1s. Last read position: chr2:49,922,127 INFO 2026-06-03 20:24:57 MarkDuplicates Tracking 773771 as yet unmatched pairs. 44053 records in RAM. INFO 2026-06-03 20:24:58 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 1s. Last read position: chr2:54,646,352 INFO 2026-06-03 20:24:58 MarkDuplicates Tracking 772627 as yet unmatched pairs. 42891 records in RAM. INFO 2026-06-03 20:25:00 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 1s. Last read position: chr2:61,222,618 INFO 2026-06-03 20:25:00 MarkDuplicates Tracking 770914 as yet unmatched pairs. 41165 records in RAM. INFO 2026-06-03 20:25:01 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 1s. Last read position: chr2:69,102,847 INFO 2026-06-03 20:25:01 MarkDuplicates Tracking 769953 as yet unmatched pairs. 40187 records in RAM. INFO 2026-06-03 20:25:03 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 2s. Last read position: chr2:72,944,963 INFO 2026-06-03 20:25:03 MarkDuplicates Tracking 768214 as yet unmatched pairs. 38427 records in RAM. INFO 2026-06-03 20:25:05 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 1s. Last read position: chr2:74,461,308 INFO 2026-06-03 20:25:05 MarkDuplicates Tracking 767187 as yet unmatched pairs. 37382 records in RAM. INFO 2026-06-03 20:25:07 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 1s. Last read position: chr2:85,541,254 INFO 2026-06-03 20:25:07 MarkDuplicates Tracking 766211 as yet unmatched pairs. 36386 records in RAM. INFO 2026-06-03 20:25:09 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 1s. Last read position: chr2:88,857,503 INFO 2026-06-03 20:25:09 MarkDuplicates Tracking 767252 as yet unmatched pairs. 37407 records in RAM. INFO 2026-06-03 20:25:10 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 1s. Last read position: chr2:97,557,111 INFO 2026-06-03 20:25:10 MarkDuplicates Tracking 763133 as yet unmatched pairs. 33270 records in RAM. INFO 2026-06-03 20:25:12 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 1s. Last read position: chr2:105,386,430 INFO 2026-06-03 20:25:12 MarkDuplicates Tracking 762225 as yet unmatched pairs. 32343 records in RAM. INFO 2026-06-03 20:25:13 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 1s. Last read position: chr2:109,347,729 INFO 2026-06-03 20:25:13 MarkDuplicates Tracking 760901 as yet unmatched pairs. 31005 records in RAM. INFO 2026-06-03 20:25:14 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 1s. Last read position: chr2:111,772,383 INFO 2026-06-03 20:25:14 MarkDuplicates Tracking 760209 as yet unmatched pairs. 30307 records in RAM. INFO 2026-06-03 20:25:16 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 1s. Last read position: chr2:120,289,731 INFO 2026-06-03 20:25:16 MarkDuplicates Tracking 759473 as yet unmatched pairs. 29551 records in RAM. INFO 2026-06-03 20:25:17 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 1s. Last read position: chr2:130,152,610 INFO 2026-06-03 20:25:17 MarkDuplicates Tracking 758073 as yet unmatched pairs. 28132 records in RAM. INFO 2026-06-03 20:25:18 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 1s. Last read position: chr2:144,424,817 INFO 2026-06-03 20:25:18 MarkDuplicates Tracking 757061 as yet unmatched pairs. 27095 records in RAM. INFO 2026-06-03 20:25:20 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 1s. Last read position: chr2:159,881,123 INFO 2026-06-03 20:25:20 MarkDuplicates Tracking 755385 as yet unmatched pairs. 25387 records in RAM. INFO 2026-06-03 20:25:21 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 1s. Last read position: chr2:171,553,345 INFO 2026-06-03 20:25:21 MarkDuplicates Tracking 754956 as yet unmatched pairs. 24935 records in RAM. INFO 2026-06-03 20:25:23 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr2:177,231,747 INFO 2026-06-03 20:25:23 MarkDuplicates Tracking 753136 as yet unmatched pairs. 23104 records in RAM. INFO 2026-06-03 20:25:25 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 2s. Last read position: chr2:186,659,046 INFO 2026-06-03 20:25:25 MarkDuplicates Tracking 751818 as yet unmatched pairs. 21771 records in RAM. INFO 2026-06-03 20:25:26 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 1s. Last read position: chr2:189,064,023 INFO 2026-06-03 20:25:26 MarkDuplicates Tracking 750230 as yet unmatched pairs. 20172 records in RAM. INFO 2026-06-03 20:25:28 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 1s. Last read position: chr2:197,398,460 INFO 2026-06-03 20:25:28 MarkDuplicates Tracking 749119 as yet unmatched pairs. 19049 records in RAM. INFO 2026-06-03 20:25:29 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 1s. Last read position: chr2:202,523,983 INFO 2026-06-03 20:25:29 MarkDuplicates Tracking 747283 as yet unmatched pairs. 17195 records in RAM. INFO 2026-06-03 20:25:31 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 1s. Last read position: chr2:208,248,562 INFO 2026-06-03 20:25:31 MarkDuplicates Tracking 746421 as yet unmatched pairs. 16316 records in RAM. INFO 2026-06-03 20:25:32 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 1s. Last read position: chr2:215,376,635 INFO 2026-06-03 20:25:32 MarkDuplicates Tracking 749002 as yet unmatched pairs. 18893 records in RAM. INFO 2026-06-03 20:25:33 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 1s. Last read position: chr2:215,408,333 INFO 2026-06-03 20:25:33 MarkDuplicates Tracking 746770 as yet unmatched pairs. 16660 records in RAM. INFO 2026-06-03 20:25:35 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 1s. Last read position: chr2:216,676,742 INFO 2026-06-03 20:25:35 MarkDuplicates Tracking 743227 as yet unmatched pairs. 13102 records in RAM. INFO 2026-06-03 20:25:36 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 1s. Last read position: chr2:218,269,962 INFO 2026-06-03 20:25:36 MarkDuplicates Tracking 740921 as yet unmatched pairs. 10779 records in RAM. INFO 2026-06-03 20:25:38 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 1s. Last read position: chr2:219,418,401 INFO 2026-06-03 20:25:38 MarkDuplicates Tracking 740156 as yet unmatched pairs. 10000 records in RAM. INFO 2026-06-03 20:25:39 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 1s. Last read position: chr2:223,975,772 INFO 2026-06-03 20:25:39 MarkDuplicates Tracking 737956 as yet unmatched pairs. 7784 records in RAM. INFO 2026-06-03 20:25:41 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 1s. Last read position: chr2:230,875,714 INFO 2026-06-03 20:25:41 MarkDuplicates Tracking 738216 as yet unmatched pairs. 8024 records in RAM. INFO 2026-06-03 20:25:42 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 1s. Last read position: chr2:232,549,510 INFO 2026-06-03 20:25:42 MarkDuplicates Tracking 735051 as yet unmatched pairs. 4844 records in RAM. INFO 2026-06-03 20:25:44 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 1s. Last read position: chr2:237,366,909 INFO 2026-06-03 20:25:44 MarkDuplicates Tracking 734221 as yet unmatched pairs. 3983 records in RAM. INFO 2026-06-03 20:25:45 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 1s. Last read position: chr2:240,462,289 INFO 2026-06-03 20:25:45 MarkDuplicates Tracking 732389 as yet unmatched pairs. 2119 records in RAM. INFO 2026-06-03 20:25:46 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 1s. Last read position: chr2:241,719,935 INFO 2026-06-03 20:25:46 MarkDuplicates Tracking 730642 as yet unmatched pairs. 356 records in RAM. INFO 2026-06-03 20:25:49 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 2s. Last read position: chr3:9,930,075 INFO 2026-06-03 20:25:49 MarkDuplicates Tracking 729293 as yet unmatched pairs. 43156 records in RAM. INFO 2026-06-03 20:25:51 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 1s. Last read position: chr3:14,402,748 INFO 2026-06-03 20:25:51 MarkDuplicates Tracking 727738 as yet unmatched pairs. 41587 records in RAM. INFO 2026-06-03 20:25:52 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 1s. Last read position: chr3:30,671,975 INFO 2026-06-03 20:25:52 MarkDuplicates Tracking 727336 as yet unmatched pairs. 41168 records in RAM. INFO 2026-06-03 20:25:54 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 1s. Last read position: chr3:37,324,755 INFO 2026-06-03 20:25:54 MarkDuplicates Tracking 725172 as yet unmatched pairs. 38996 records in RAM. INFO 2026-06-03 20:25:56 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 1s. Last read position: chr3:41,225,079 INFO 2026-06-03 20:25:56 MarkDuplicates Tracking 724467 as yet unmatched pairs. 38278 records in RAM. INFO 2026-06-03 20:25:57 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 1s. Last read position: chr3:45,676,945 INFO 2026-06-03 20:25:57 MarkDuplicates Tracking 722257 as yet unmatched pairs. 36055 records in RAM. INFO 2026-06-03 20:25:59 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 1s. Last read position: chr3:47,852,851 INFO 2026-06-03 20:25:59 MarkDuplicates Tracking 721675 as yet unmatched pairs. 35459 records in RAM. INFO 2026-06-03 20:26:01 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 1s. Last read position: chr3:48,628,451 INFO 2026-06-03 20:26:01 MarkDuplicates Tracking 719639 as yet unmatched pairs. 33414 records in RAM. INFO 2026-06-03 20:26:02 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 1s. Last read position: chr3:49,132,371 INFO 2026-06-03 20:26:02 MarkDuplicates Tracking 718296 as yet unmatched pairs. 32050 records in RAM. INFO 2026-06-03 20:26:04 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 1s. Last read position: chr3:49,902,667 INFO 2026-06-03 20:26:04 MarkDuplicates Tracking 716691 as yet unmatched pairs. 30434 records in RAM. INFO 2026-06-03 20:26:05 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 1s. Last read position: chr3:51,414,816 INFO 2026-06-03 20:26:05 MarkDuplicates Tracking 714642 as yet unmatched pairs. 28359 records in RAM. INFO 2026-06-03 20:26:07 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 1s. Last read position: chr3:52,513,240 INFO 2026-06-03 20:26:07 MarkDuplicates Tracking 713547 as yet unmatched pairs. 27253 records in RAM. INFO 2026-06-03 20:26:08 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 1s. Last read position: chr3:57,912,416 INFO 2026-06-03 20:26:08 MarkDuplicates Tracking 711735 as yet unmatched pairs. 25431 records in RAM. INFO 2026-06-03 20:26:10 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 1s. Last read position: chr3:63,999,455 INFO 2026-06-03 20:26:10 MarkDuplicates Tracking 710417 as yet unmatched pairs. 24097 records in RAM. INFO 2026-06-03 20:26:11 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 1s. Last read position: chr3:87,227,496 INFO 2026-06-03 20:26:11 MarkDuplicates Tracking 709351 as yet unmatched pairs. 22994 records in RAM. INFO 2026-06-03 20:26:13 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 1s. Last read position: chr3:100,842,021 INFO 2026-06-03 20:26:13 MarkDuplicates Tracking 707977 as yet unmatched pairs. 21609 records in RAM. INFO 2026-06-03 20:26:14 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 1s. Last read position: chr3:113,465,664 INFO 2026-06-03 20:26:14 MarkDuplicates Tracking 706837 as yet unmatched pairs. 20453 records in RAM. INFO 2026-06-03 20:26:16 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 1s. Last read position: chr3:122,536,071 INFO 2026-06-03 20:26:16 MarkDuplicates Tracking 705663 as yet unmatched pairs. 19252 records in RAM. INFO 2026-06-03 20:26:17 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 1s. Last read position: chr3:124,712,936 INFO 2026-06-03 20:26:17 MarkDuplicates Tracking 704175 as yet unmatched pairs. 17752 records in RAM. INFO 2026-06-03 20:26:19 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 1s. Last read position: chr3:128,065,001 INFO 2026-06-03 20:26:19 MarkDuplicates Tracking 703173 as yet unmatched pairs. 16728 records in RAM. INFO 2026-06-03 20:26:20 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 1s. Last read position: chr3:130,932,112 INFO 2026-06-03 20:26:20 MarkDuplicates Tracking 702090 as yet unmatched pairs. 15635 records in RAM. INFO 2026-06-03 20:26:22 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 1s. Last read position: chr3:139,379,046 INFO 2026-06-03 20:26:22 MarkDuplicates Tracking 700743 as yet unmatched pairs. 14274 records in RAM. INFO 2026-06-03 20:26:23 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: chr3:149,657,085 INFO 2026-06-03 20:26:23 MarkDuplicates Tracking 699621 as yet unmatched pairs. 13136 records in RAM. INFO 2026-06-03 20:26:25 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 1s. Last read position: chr3:165,007,939 INFO 2026-06-03 20:26:25 MarkDuplicates Tracking 697636 as yet unmatched pairs. 11131 records in RAM. INFO 2026-06-03 20:26:26 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 1s. Last read position: chr3:179,221,018 INFO 2026-06-03 20:26:26 MarkDuplicates Tracking 696166 as yet unmatched pairs. 9630 records in RAM. INFO 2026-06-03 20:26:28 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 1s. Last read position: chr3:184,321,416 INFO 2026-06-03 20:26:28 MarkDuplicates Tracking 694997 as yet unmatched pairs. 8441 records in RAM. INFO 2026-06-03 20:26:29 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 1s. Last read position: chr3:188,406,268 INFO 2026-06-03 20:26:29 MarkDuplicates Tracking 694631 as yet unmatched pairs. 8046 records in RAM. INFO 2026-06-03 20:26:31 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 1s. Last read position: chr3:195,524,837 INFO 2026-06-03 20:26:31 MarkDuplicates Tracking 692342 as yet unmatched pairs. 5727 records in RAM. INFO 2026-06-03 20:26:32 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 1s. Last read position: chr3:195,778,947 INFO 2026-06-03 20:26:32 MarkDuplicates Tracking 694459 as yet unmatched pairs. 7838 records in RAM. INFO 2026-06-03 20:26:34 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 1s. Last read position: chr3:195,780,748 INFO 2026-06-03 20:26:34 MarkDuplicates Tracking 699061 as yet unmatched pairs. 12438 records in RAM. INFO 2026-06-03 20:26:35 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 1s. Last read position: chr3:195,782,384 INFO 2026-06-03 20:26:35 MarkDuplicates Tracking 698634 as yet unmatched pairs. 12004 records in RAM. INFO 2026-06-03 20:26:36 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 1s. Last read position: chr3:195,784,441 INFO 2026-06-03 20:26:36 MarkDuplicates Tracking 698422 as yet unmatched pairs. 11786 records in RAM. INFO 2026-06-03 20:26:37 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 1s. Last read position: chr3:195,786,503 INFO 2026-06-03 20:26:37 MarkDuplicates Tracking 693160 as yet unmatched pairs. 6507 records in RAM. INFO 2026-06-03 20:26:39 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 1s. Last read position: chr3:195,789,530 INFO 2026-06-03 20:26:39 MarkDuplicates Tracking 688770 as yet unmatched pairs. 2115 records in RAM. INFO 2026-06-03 20:26:41 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 2s. Last read position: chr3:197,913,779 INFO 2026-06-03 20:26:41 MarkDuplicates Tracking 686703 as yet unmatched pairs. 38 records in RAM. INFO 2026-06-03 20:26:43 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 1s. Last read position: chr4:1,801,931 INFO 2026-06-03 20:26:43 MarkDuplicates Tracking 685022 as yet unmatched pairs. 22583 records in RAM. INFO 2026-06-03 20:26:44 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 1s. Last read position: chr4:4,376,146 INFO 2026-06-03 20:26:44 MarkDuplicates Tracking 683435 as yet unmatched pairs. 20976 records in RAM. INFO 2026-06-03 20:26:46 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 1s. Last read position: chr4:10,116,123 INFO 2026-06-03 20:26:46 MarkDuplicates Tracking 682479 as yet unmatched pairs. 20010 records in RAM. INFO 2026-06-03 20:26:48 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 1s. Last read position: chr4:26,739,962 INFO 2026-06-03 20:26:48 MarkDuplicates Tracking 680597 as yet unmatched pairs. 18109 records in RAM. INFO 2026-06-03 20:26:49 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 1s. Last read position: chr4:42,543,956 INFO 2026-06-03 20:26:49 MarkDuplicates Tracking 679380 as yet unmatched pairs. 16863 records in RAM. INFO 2026-06-03 20:26:51 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 1s. Last read position: chr4:54,274,912 INFO 2026-06-03 20:26:51 MarkDuplicates Tracking 680278 as yet unmatched pairs. 17746 records in RAM. INFO 2026-06-03 20:26:53 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 1s. Last read position: chr4:57,110,151 INFO 2026-06-03 20:26:53 MarkDuplicates Tracking 677024 as yet unmatched pairs. 14482 records in RAM. INFO 2026-06-03 20:26:54 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 1s. Last read position: chr4:74,445,276 INFO 2026-06-03 20:26:54 MarkDuplicates Tracking 675394 as yet unmatched pairs. 12841 records in RAM. INFO 2026-06-03 20:26:56 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 1s. Last read position: chr4:78,833,663 INFO 2026-06-03 20:26:56 MarkDuplicates Tracking 674068 as yet unmatched pairs. 11489 records in RAM. INFO 2026-06-03 20:26:57 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 1s. Last read position: chr4:86,359,649 INFO 2026-06-03 20:26:57 MarkDuplicates Tracking 672720 as yet unmatched pairs. 10128 records in RAM. INFO 2026-06-03 20:26:59 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 1s. Last read position: chr4:98,587,747 INFO 2026-06-03 20:26:59 MarkDuplicates Tracking 671429 as yet unmatched pairs. 8813 records in RAM. INFO 2026-06-03 20:27:00 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 1s. Last read position: chr4:110,559,713 INFO 2026-06-03 20:27:00 MarkDuplicates Tracking 670226 as yet unmatched pairs. 7598 records in RAM. INFO 2026-06-03 20:27:02 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 1s. Last read position: chr4:119,300,390 INFO 2026-06-03 20:27:02 MarkDuplicates Tracking 669349 as yet unmatched pairs. 6698 records in RAM. INFO 2026-06-03 20:27:03 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 1s. Last read position: chr4:137,529,636 INFO 2026-06-03 20:27:03 MarkDuplicates Tracking 668275 as yet unmatched pairs. 5615 records in RAM. INFO 2026-06-03 20:27:05 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 1s. Last read position: chr4:150,350,046 INFO 2026-06-03 20:27:05 MarkDuplicates Tracking 666671 as yet unmatched pairs. 3972 records in RAM. INFO 2026-06-03 20:27:06 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 1s. Last read position: chr4:158,171,021 INFO 2026-06-03 20:27:06 MarkDuplicates Tracking 665624 as yet unmatched pairs. 2913 records in RAM. INFO 2026-06-03 20:27:07 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 1s. Last read position: chr4:176,320,104 INFO 2026-06-03 20:27:07 MarkDuplicates Tracking 664216 as yet unmatched pairs. 1477 records in RAM. INFO 2026-06-03 20:27:09 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 1s. Last read position: chr5:223,559 INFO 2026-06-03 20:27:09 MarkDuplicates Tracking 662941 as yet unmatched pairs. 34010 records in RAM. INFO 2026-06-03 20:27:11 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 1s. Last read position: chr5:10,681,080 INFO 2026-06-03 20:27:11 MarkDuplicates Tracking 661621 as yet unmatched pairs. 32673 records in RAM. INFO 2026-06-03 20:27:12 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 1s. Last read position: chr5:16,465,434 INFO 2026-06-03 20:27:12 MarkDuplicates Tracking 659738 as yet unmatched pairs. 30774 records in RAM. INFO 2026-06-03 20:27:14 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 1s. Last read position: chr5:37,364,320 INFO 2026-06-03 20:27:14 MarkDuplicates Tracking 658543 as yet unmatched pairs. 29560 records in RAM. INFO 2026-06-03 20:27:16 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 2s. Last read position: chr5:43,379,652 INFO 2026-06-03 20:27:16 MarkDuplicates Tracking 657854 as yet unmatched pairs. 28861 records in RAM. INFO 2026-06-03 20:27:18 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 1s. Last read position: chr5:58,459,072 INFO 2026-06-03 20:27:18 MarkDuplicates Tracking 656120 as yet unmatched pairs. 27109 records in RAM. INFO 2026-06-03 20:27:19 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 1s. Last read position: chr5:70,925,131 INFO 2026-06-03 20:27:19 MarkDuplicates Tracking 655099 as yet unmatched pairs. 26074 records in RAM. INFO 2026-06-03 20:27:21 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 2s. Last read position: chr5:75,511,268 INFO 2026-06-03 20:27:21 MarkDuplicates Tracking 653835 as yet unmatched pairs. 24804 records in RAM. INFO 2026-06-03 20:27:23 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 1s. Last read position: chr5:83,539,556 INFO 2026-06-03 20:27:23 MarkDuplicates Tracking 652841 as yet unmatched pairs. 23790 records in RAM. INFO 2026-06-03 20:27:24 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 1s. Last read position: chr5:97,022,450 INFO 2026-06-03 20:27:24 MarkDuplicates Tracking 651401 as yet unmatched pairs. 22338 records in RAM. INFO 2026-06-03 20:27:26 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 1s. Last read position: chr5:116,447,441 INFO 2026-06-03 20:27:26 MarkDuplicates Tracking 650097 as yet unmatched pairs. 21022 records in RAM. INFO 2026-06-03 20:27:28 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 1s. Last read position: chr5:132,322,276 INFO 2026-06-03 20:27:28 MarkDuplicates Tracking 648684 as yet unmatched pairs. 19566 records in RAM. INFO 2026-06-03 20:27:29 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr5:135,571,383 INFO 2026-06-03 20:27:29 MarkDuplicates Tracking 647771 as yet unmatched pairs. 18623 records in RAM. INFO 2026-06-03 20:27:31 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 1s. Last read position: chr5:138,930,549 INFO 2026-06-03 20:27:31 MarkDuplicates Tracking 646584 as yet unmatched pairs. 17419 records in RAM. INFO 2026-06-03 20:27:32 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 1s. Last read position: chr5:141,201,274 INFO 2026-06-03 20:27:32 MarkDuplicates Tracking 644759 as yet unmatched pairs. 15549 records in RAM. INFO 2026-06-03 20:27:34 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 1s. Last read position: chr5:141,878,299 INFO 2026-06-03 20:27:34 MarkDuplicates Tracking 643264 as yet unmatched pairs. 14041 records in RAM. INFO 2026-06-03 20:27:35 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 1s. Last read position: chr5:150,061,491 INFO 2026-06-03 20:27:35 MarkDuplicates Tracking 642100 as yet unmatched pairs. 12861 records in RAM. INFO 2026-06-03 20:27:37 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 1s. Last read position: chr5:150,402,580 INFO 2026-06-03 20:27:37 MarkDuplicates Tracking 658092 as yet unmatched pairs. 28835 records in RAM. INFO 2026-06-03 20:27:38 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 1s. Last read position: chr5:150,407,213 INFO 2026-06-03 20:27:38 MarkDuplicates Tracking 645017 as yet unmatched pairs. 15753 records in RAM. INFO 2026-06-03 20:27:39 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 1s. Last read position: chr5:151,671,652 INFO 2026-06-03 20:27:39 MarkDuplicates Tracking 638192 as yet unmatched pairs. 8920 records in RAM. INFO 2026-06-03 20:27:41 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 1s. Last read position: chr5:163,814,744 INFO 2026-06-03 20:27:41 MarkDuplicates Tracking 636278 as yet unmatched pairs. 6985 records in RAM. INFO 2026-06-03 20:27:42 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 1s. Last read position: chr5:172,924,036 INFO 2026-06-03 20:27:42 MarkDuplicates Tracking 635406 as yet unmatched pairs. 6104 records in RAM. INFO 2026-06-03 20:27:44 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 1s. Last read position: chr5:177,332,117 INFO 2026-06-03 20:27:44 MarkDuplicates Tracking 634684 as yet unmatched pairs. 5373 records in RAM. INFO 2026-06-03 20:27:46 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 1s. Last read position: chr5:179,621,309 INFO 2026-06-03 20:27:46 MarkDuplicates Tracking 632844 as yet unmatched pairs. 3518 records in RAM. INFO 2026-06-03 20:27:47 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 1s. Last read position: chr5:179,833,669 INFO 2026-06-03 20:27:47 MarkDuplicates Tracking 632828 as yet unmatched pairs. 3495 records in RAM. INFO 2026-06-03 20:27:49 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 1s. Last read position: chr6:1,389,903 INFO 2026-06-03 20:27:49 MarkDuplicates Tracking 629204 as yet unmatched pairs. 41519 records in RAM. INFO 2026-06-03 20:27:50 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 1s. Last read position: chr6:7,226,592 INFO 2026-06-03 20:27:50 MarkDuplicates Tracking 628352 as yet unmatched pairs. 40642 records in RAM. INFO 2026-06-03 20:27:52 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 1s. Last read position: chr6:11,213,527 INFO 2026-06-03 20:27:52 MarkDuplicates Tracking 626621 as yet unmatched pairs. 38898 records in RAM. INFO 2026-06-03 20:27:54 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 1s. Last read position: chr6:24,706,143 INFO 2026-06-03 20:27:54 MarkDuplicates Tracking 625393 as yet unmatched pairs. 37644 records in RAM. INFO 2026-06-03 20:27:56 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 2s. Last read position: chr6:27,808,311 INFO 2026-06-03 20:27:56 MarkDuplicates Tracking 623942 as yet unmatched pairs. 36180 records in RAM. INFO 2026-06-03 20:27:57 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 1s. Last read position: chr6:30,071,640 INFO 2026-06-03 20:27:57 MarkDuplicates Tracking 622495 as yet unmatched pairs. 34726 records in RAM. INFO 2026-06-03 20:27:59 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 1s. Last read position: chr6:30,892,061 INFO 2026-06-03 20:27:59 MarkDuplicates Tracking 621323 as yet unmatched pairs. 33546 records in RAM. INFO 2026-06-03 20:28:01 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 1s. Last read position: chr6:31,627,987 INFO 2026-06-03 20:28:01 MarkDuplicates Tracking 620047 as yet unmatched pairs. 32265 records in RAM. INFO 2026-06-03 20:28:02 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 1s. Last read position: chr6:31,816,415 INFO 2026-06-03 20:28:02 MarkDuplicates Tracking 618354 as yet unmatched pairs. 30554 records in RAM. INFO 2026-06-03 20:28:04 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 1s. Last read position: chr6:31,934,268 INFO 2026-06-03 20:28:04 MarkDuplicates Tracking 617305 as yet unmatched pairs. 29495 records in RAM. INFO 2026-06-03 20:28:05 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 1s. Last read position: chr6:32,067,812 INFO 2026-06-03 20:28:05 MarkDuplicates Tracking 616811 as yet unmatched pairs. 28986 records in RAM. INFO 2026-06-03 20:28:07 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 1s. Last read position: chr6:32,443,809 INFO 2026-06-03 20:28:07 MarkDuplicates Tracking 615227 as yet unmatched pairs. 27389 records in RAM. INFO 2026-06-03 20:28:08 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 1s. Last read position: chr6:33,201,605 INFO 2026-06-03 20:28:08 MarkDuplicates Tracking 613239 as yet unmatched pairs. 25397 records in RAM. INFO 2026-06-03 20:28:10 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr6:33,667,126 INFO 2026-06-03 20:28:10 MarkDuplicates Tracking 611461 as yet unmatched pairs. 23603 records in RAM. INFO 2026-06-03 20:28:11 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 1s. Last read position: chr6:36,322,394 INFO 2026-06-03 20:28:11 MarkDuplicates Tracking 609780 as yet unmatched pairs. 21910 records in RAM. INFO 2026-06-03 20:28:13 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 1s. Last read position: chr6:42,564,349 INFO 2026-06-03 20:28:13 MarkDuplicates Tracking 608367 as yet unmatched pairs. 20470 records in RAM. INFO 2026-06-03 20:28:14 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 1s. Last read position: chr6:44,082,743 INFO 2026-06-03 20:28:14 MarkDuplicates Tracking 606586 as yet unmatched pairs. 18677 records in RAM. INFO 2026-06-03 20:28:16 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 1s. Last read position: chr6:52,509,528 INFO 2026-06-03 20:28:16 MarkDuplicates Tracking 605422 as yet unmatched pairs. 17498 records in RAM. INFO 2026-06-03 20:28:17 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 1s. Last read position: chr6:56,601,463 INFO 2026-06-03 20:28:17 MarkDuplicates Tracking 604530 as yet unmatched pairs. 16566 records in RAM. INFO 2026-06-03 20:28:19 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 1s. Last read position: chr6:73,518,735 INFO 2026-06-03 20:28:19 MarkDuplicates Tracking 602943 as yet unmatched pairs. 14958 records in RAM. INFO 2026-06-03 20:28:20 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 1s. Last read position: chr6:85,574,317 INFO 2026-06-03 20:28:20 MarkDuplicates Tracking 602551 as yet unmatched pairs. 14538 records in RAM. INFO 2026-06-03 20:28:22 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 2s. Last read position: chr6:105,397,876 INFO 2026-06-03 20:28:22 MarkDuplicates Tracking 600641 as yet unmatched pairs. 12618 records in RAM. INFO 2026-06-03 20:28:24 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 1s. Last read position: chr6:111,694,679 INFO 2026-06-03 20:28:24 MarkDuplicates Tracking 599234 as yet unmatched pairs. 11188 records in RAM. INFO 2026-06-03 20:28:25 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 1s. Last read position: chr6:119,348,624 INFO 2026-06-03 20:28:25 MarkDuplicates Tracking 598083 as yet unmatched pairs. 10021 records in RAM. INFO 2026-06-03 20:28:27 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 1s. Last read position: chr6:132,374,729 INFO 2026-06-03 20:28:27 MarkDuplicates Tracking 597038 as yet unmatched pairs. 8956 records in RAM. INFO 2026-06-03 20:28:29 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 1s. Last read position: chr6:138,905,053 INFO 2026-06-03 20:28:29 MarkDuplicates Tracking 595064 as yet unmatched pairs. 6966 records in RAM. INFO 2026-06-03 20:28:31 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 1s. Last read position: chr6:149,378,671 INFO 2026-06-03 20:28:31 MarkDuplicates Tracking 593958 as yet unmatched pairs. 5837 records in RAM. INFO 2026-06-03 20:28:32 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 1s. Last read position: chr6:154,450,133 INFO 2026-06-03 20:28:32 MarkDuplicates Tracking 592630 as yet unmatched pairs. 4497 records in RAM. INFO 2026-06-03 20:28:33 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 1s. Last read position: chr6:158,783,651 INFO 2026-06-03 20:28:33 MarkDuplicates Tracking 592683 as yet unmatched pairs. 4535 records in RAM. INFO 2026-06-03 20:28:35 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 1s. Last read position: chr6:163,563,674 INFO 2026-06-03 20:28:35 MarkDuplicates Tracking 591769 as yet unmatched pairs. 3615 records in RAM. INFO 2026-06-03 20:28:37 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 1s. Last read position: chr7:849,574 INFO 2026-06-03 20:28:37 MarkDuplicates Tracking 588079 as yet unmatched pairs. 59399 records in RAM. INFO 2026-06-03 20:28:38 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 1s. Last read position: chr7:4,762,217 INFO 2026-06-03 20:28:38 MarkDuplicates Tracking 586182 as yet unmatched pairs. 57487 records in RAM. INFO 2026-06-03 20:28:40 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 1s. Last read position: chr7:5,528,036 INFO 2026-06-03 20:28:40 MarkDuplicates Tracking 597676 as yet unmatched pairs. 68967 records in RAM. INFO 2026-06-03 20:28:42 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 1s. Last read position: chr7:5,529,645 INFO 2026-06-03 20:28:42 MarkDuplicates Tracking 583073 as yet unmatched pairs. 54357 records in RAM. INFO 2026-06-03 20:28:43 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 1s. Last read position: chr7:16,792,924 INFO 2026-06-03 20:28:43 MarkDuplicates Tracking 586690 as yet unmatched pairs. 57954 records in RAM. INFO 2026-06-03 20:28:44 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 1s. Last read position: chr7:26,197,641 INFO 2026-06-03 20:28:44 MarkDuplicates Tracking 582560 as yet unmatched pairs. 53812 records in RAM. INFO 2026-06-03 20:28:46 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 1s. Last read position: chr7:36,673,993 INFO 2026-06-03 20:28:46 MarkDuplicates Tracking 579355 as yet unmatched pairs. 50584 records in RAM. INFO 2026-06-03 20:28:48 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 1s. Last read position: chr7:44,112,182 INFO 2026-06-03 20:28:48 MarkDuplicates Tracking 578173 as yet unmatched pairs. 49391 records in RAM. INFO 2026-06-03 20:28:49 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 1s. Last read position: chr7:47,413,940 INFO 2026-06-03 20:28:49 MarkDuplicates Tracking 576469 as yet unmatched pairs. 47674 records in RAM. INFO 2026-06-03 20:28:50 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 1s. Last read position: chr7:65,970,338 INFO 2026-06-03 20:28:50 MarkDuplicates Tracking 575144 as yet unmatched pairs. 46331 records in RAM. INFO 2026-06-03 20:28:52 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 1s. Last read position: chr7:73,489,274 INFO 2026-06-03 20:28:52 MarkDuplicates Tracking 574032 as yet unmatched pairs. 45199 records in RAM. INFO 2026-06-03 20:28:54 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 1s. Last read position: chr7:75,148,976 INFO 2026-06-03 20:28:54 MarkDuplicates Tracking 572638 as yet unmatched pairs. 43786 records in RAM. INFO 2026-06-03 20:28:56 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 2s. Last read position: chr7:76,480,512 INFO 2026-06-03 20:28:56 MarkDuplicates Tracking 571555 as yet unmatched pairs. 42694 records in RAM. INFO 2026-06-03 20:28:58 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 1s. Last read position: chr7:87,907,244 INFO 2026-06-03 20:28:58 MarkDuplicates Tracking 570233 as yet unmatched pairs. 41357 records in RAM. INFO 2026-06-03 20:28:59 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 1s. Last read position: chr7:93,134,595 INFO 2026-06-03 20:28:59 MarkDuplicates Tracking 569104 as yet unmatched pairs. 40220 records in RAM. INFO 2026-06-03 20:29:01 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 1s. Last read position: chr7:98,293,398 INFO 2026-06-03 20:29:01 MarkDuplicates Tracking 567620 as yet unmatched pairs. 38723 records in RAM. INFO 2026-06-03 20:29:02 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 1s. Last read position: chr7:100,096,032 INFO 2026-06-03 20:29:02 MarkDuplicates Tracking 566411 as yet unmatched pairs. 37506 records in RAM. INFO 2026-06-03 20:29:04 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 1s. Last read position: chr7:100,884,537 INFO 2026-06-03 20:29:04 MarkDuplicates Tracking 564496 as yet unmatched pairs. 35579 records in RAM. INFO 2026-06-03 20:29:05 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 1s. Last read position: chr7:100,959,619 INFO 2026-06-03 20:29:05 MarkDuplicates Tracking 564259 as yet unmatched pairs. 35332 records in RAM. INFO 2026-06-03 20:29:07 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 1s. Last read position: chr7:100,991,736 INFO 2026-06-03 20:29:07 MarkDuplicates Tracking 565256 as yet unmatched pairs. 36327 records in RAM. INFO 2026-06-03 20:29:08 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 1s. Last read position: chr7:100,992,601 INFO 2026-06-03 20:29:08 MarkDuplicates Tracking 564328 as yet unmatched pairs. 35399 records in RAM. INFO 2026-06-03 20:29:09 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 1s. Last read position: chr7:100,992,978 INFO 2026-06-03 20:29:09 MarkDuplicates Tracking 565690 as yet unmatched pairs. 36759 records in RAM. INFO 2026-06-03 20:29:10 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 1s. Last read position: chr7:100,993,321 INFO 2026-06-03 20:29:10 MarkDuplicates Tracking 566877 as yet unmatched pairs. 37946 records in RAM. INFO 2026-06-03 20:29:12 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 1s. Last read position: chr7:100,993,641 INFO 2026-06-03 20:29:12 MarkDuplicates Tracking 565887 as yet unmatched pairs. 36956 records in RAM. INFO 2026-06-03 20:29:12 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 0s. Last read position: chr7:100,993,800 INFO 2026-06-03 20:29:12 MarkDuplicates Tracking 567763 as yet unmatched pairs. 38830 records in RAM. INFO 2026-06-03 20:29:13 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 1s. Last read position: chr7:100,994,145 INFO 2026-06-03 20:29:13 MarkDuplicates Tracking 562827 as yet unmatched pairs. 33894 records in RAM. INFO 2026-06-03 20:29:15 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 1s. Last read position: chr7:100,994,645 INFO 2026-06-03 20:29:15 MarkDuplicates Tracking 565009 as yet unmatched pairs. 36076 records in RAM. INFO 2026-06-03 20:29:16 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 0s. Last read position: chr7:100,994,915 INFO 2026-06-03 20:29:16 MarkDuplicates Tracking 564612 as yet unmatched pairs. 35679 records in RAM. INFO 2026-06-03 20:29:16 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:06:16s. Time for last 1,000,000: 0s. Last read position: chr7:100,995,142 INFO 2026-06-03 20:29:16 MarkDuplicates Tracking 564678 as yet unmatched pairs. 35745 records in RAM. INFO 2026-06-03 20:29:17 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 0s. Last read position: chr7:100,995,499 INFO 2026-06-03 20:29:17 MarkDuplicates Tracking 566817 as yet unmatched pairs. 37884 records in RAM. INFO 2026-06-03 20:29:18 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 1s. Last read position: chr7:100,996,035 INFO 2026-06-03 20:29:18 MarkDuplicates Tracking 565070 as yet unmatched pairs. 36136 records in RAM. INFO 2026-06-03 20:29:19 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 0s. Last read position: chr7:100,996,225 INFO 2026-06-03 20:29:19 MarkDuplicates Tracking 565015 as yet unmatched pairs. 36081 records in RAM. INFO 2026-06-03 20:29:20 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 0s. Last read position: chr7:100,996,388 INFO 2026-06-03 20:29:20 MarkDuplicates Tracking 583011 as yet unmatched pairs. 54077 records in RAM. INFO 2026-06-03 20:29:22 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 1s. Last read position: chr7:100,996,535 INFO 2026-06-03 20:29:22 MarkDuplicates Tracking 564311 as yet unmatched pairs. 35374 records in RAM. INFO 2026-06-03 20:29:23 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 1s. Last read position: chr7:100,996,807 INFO 2026-06-03 20:29:23 MarkDuplicates Tracking 573260 as yet unmatched pairs. 44320 records in RAM. INFO 2026-06-03 20:29:25 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 1s. Last read position: chr7:100,996,928 INFO 2026-06-03 20:29:25 MarkDuplicates Tracking 599826 as yet unmatched pairs. 70883 records in RAM. INFO 2026-06-03 20:29:27 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 1s. Last read position: chr7:100,997,137 INFO 2026-06-03 20:29:27 MarkDuplicates Tracking 577490 as yet unmatched pairs. 48538 records in RAM. INFO 2026-06-03 20:29:28 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 1s. Last read position: chr7:100,997,386 INFO 2026-06-03 20:29:28 MarkDuplicates Tracking 568406 as yet unmatched pairs. 39452 records in RAM. INFO 2026-06-03 20:29:30 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 1s. Last read position: chr7:100,997,552 INFO 2026-06-03 20:29:30 MarkDuplicates Tracking 572565 as yet unmatched pairs. 43609 records in RAM. INFO 2026-06-03 20:29:31 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:06:31s. Time for last 1,000,000: 1s. Last read position: chr7:100,997,849 INFO 2026-06-03 20:29:31 MarkDuplicates Tracking 564900 as yet unmatched pairs. 35939 records in RAM. INFO 2026-06-03 20:29:33 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 1s. Last read position: chr7:100,998,007 INFO 2026-06-03 20:29:33 MarkDuplicates Tracking 575859 as yet unmatched pairs. 46897 records in RAM. INFO 2026-06-03 20:29:34 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:06:33s. Time for last 1,000,000: 0s. Last read position: chr7:100,998,226 INFO 2026-06-03 20:29:34 MarkDuplicates Tracking 561379 as yet unmatched pairs. 32415 records in RAM. INFO 2026-06-03 20:29:35 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 0s. Last read position: chr7:100,998,350 INFO 2026-06-03 20:29:35 MarkDuplicates Tracking 559922 as yet unmatched pairs. 30958 records in RAM. INFO 2026-06-03 20:29:35 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:06:35s. Time for last 1,000,000: 0s. Last read position: chr7:100,998,563 INFO 2026-06-03 20:29:35 MarkDuplicates Tracking 563266 as yet unmatched pairs. 34302 records in RAM. INFO 2026-06-03 20:29:36 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 1s. Last read position: chr7:100,998,689 INFO 2026-06-03 20:29:36 MarkDuplicates Tracking 581590 as yet unmatched pairs. 52626 records in RAM. INFO 2026-06-03 20:29:38 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 1s. Last read position: chr7:100,998,893 INFO 2026-06-03 20:29:38 MarkDuplicates Tracking 558884 as yet unmatched pairs. 29920 records in RAM. INFO 2026-06-03 20:29:39 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 0s. Last read position: chr7:100,999,060 INFO 2026-06-03 20:29:39 MarkDuplicates Tracking 560767 as yet unmatched pairs. 31803 records in RAM. INFO 2026-06-03 20:29:40 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 1s. Last read position: chr7:100,999,495 INFO 2026-06-03 20:29:40 MarkDuplicates Tracking 571036 as yet unmatched pairs. 42062 records in RAM. INFO 2026-06-03 20:29:41 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 1s. Last read position: chr7:100,999,722 INFO 2026-06-03 20:29:41 MarkDuplicates Tracking 566955 as yet unmatched pairs. 37979 records in RAM. INFO 2026-06-03 20:29:42 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 1s. Last read position: chr7:100,999,957 INFO 2026-06-03 20:29:42 MarkDuplicates Tracking 566028 as yet unmatched pairs. 37049 records in RAM. INFO 2026-06-03 20:29:44 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 1s. Last read position: chr7:101,000,243 INFO 2026-06-03 20:29:44 MarkDuplicates Tracking 561682 as yet unmatched pairs. 32701 records in RAM. INFO 2026-06-03 20:29:45 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 1s. Last read position: chr7:101,000,499 INFO 2026-06-03 20:29:45 MarkDuplicates Tracking 562306 as yet unmatched pairs. 33323 records in RAM. INFO 2026-06-03 20:29:47 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:06:46s. Time for last 1,000,000: 1s. Last read position: chr7:101,000,757 INFO 2026-06-03 20:29:47 MarkDuplicates Tracking 582770 as yet unmatched pairs. 53784 records in RAM. INFO 2026-06-03 20:29:48 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:06:47s. Time for last 1,000,000: 1s. Last read position: chr7:101,000,969 INFO 2026-06-03 20:29:48 MarkDuplicates Tracking 570386 as yet unmatched pairs. 41398 records in RAM. INFO 2026-06-03 20:30:53 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:07:52s. Time for last 1,000,000: 64s. Last read position: chr7:101,001,209 INFO 2026-06-03 20:30:53 MarkDuplicates Tracking 565992 as yet unmatched pairs. 36999 records in RAM. INFO 2026-06-03 20:30:54 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:07:53s. Time for last 1,000,000: 1s. Last read position: chr7:101,001,362 INFO 2026-06-03 20:30:54 MarkDuplicates Tracking 561329 as yet unmatched pairs. 32334 records in RAM. INFO 2026-06-03 20:30:55 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:07:54s. Time for last 1,000,000: 0s. Last read position: chr7:101,001,540 INFO 2026-06-03 20:30:55 MarkDuplicates Tracking 554655 as yet unmatched pairs. 25660 records in RAM. INFO 2026-06-03 20:30:56 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:07:55s. Time for last 1,000,000: 0s. Last read position: chr7:101,001,689 INFO 2026-06-03 20:30:56 MarkDuplicates Tracking 554602 as yet unmatched pairs. 25607 records in RAM. INFO 2026-06-03 20:30:57 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:07:56s. Time for last 1,000,000: 0s. Last read position: chr7:101,001,870 INFO 2026-06-03 20:30:57 MarkDuplicates Tracking 556130 as yet unmatched pairs. 27135 records in RAM. INFO 2026-06-03 20:30:58 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:07:57s. Time for last 1,000,000: 0s. Last read position: chr7:101,002,289 INFO 2026-06-03 20:30:58 MarkDuplicates Tracking 561858 as yet unmatched pairs. 32862 records in RAM. INFO 2026-06-03 20:30:59 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:07:58s. Time for last 1,000,000: 1s. Last read position: chr7:101,002,536 INFO 2026-06-03 20:30:59 MarkDuplicates Tracking 567673 as yet unmatched pairs. 38670 records in RAM. INFO 2026-06-03 20:31:00 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:07:59s. Time for last 1,000,000: 1s. Last read position: chr7:101,002,946 INFO 2026-06-03 20:31:00 MarkDuplicates Tracking 571647 as yet unmatched pairs. 42642 records in RAM. INFO 2026-06-03 20:31:01 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:08:00s. Time for last 1,000,000: 1s. Last read position: chr7:101,003,545 INFO 2026-06-03 20:31:01 MarkDuplicates Tracking 547147 as yet unmatched pairs. 18132 records in RAM. INFO 2026-06-03 20:31:02 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:08:01s. Time for last 1,000,000: 0s. Last read position: chr7:101,003,969 INFO 2026-06-03 20:31:02 MarkDuplicates Tracking 545481 as yet unmatched pairs. 16466 records in RAM. INFO 2026-06-03 20:31:03 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:08:02s. Time for last 1,000,000: 1s. Last read position: chr7:101,004,338 INFO 2026-06-03 20:31:03 MarkDuplicates Tracking 545444 as yet unmatched pairs. 16429 records in RAM. INFO 2026-06-03 20:31:05 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:08:04s. Time for last 1,000,000: 1s. Last read position: chr7:101,031,636 INFO 2026-06-03 20:31:05 MarkDuplicates Tracking 544697 as yet unmatched pairs. 15677 records in RAM. INFO 2026-06-03 20:31:06 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 1s. Last read position: chr7:101,088,620 INFO 2026-06-03 20:31:06 MarkDuplicates Tracking 543109 as yet unmatched pairs. 14086 records in RAM. INFO 2026-06-03 20:31:07 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:08:07s. Time for last 1,000,000: 1s. Last read position: chr7:102,655,121 INFO 2026-06-03 20:31:07 MarkDuplicates Tracking 542488 as yet unmatched pairs. 13456 records in RAM. INFO 2026-06-03 20:31:09 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:08:08s. Time for last 1,000,000: 1s. Last read position: chr7:107,787,378 INFO 2026-06-03 20:31:09 MarkDuplicates Tracking 543882 as yet unmatched pairs. 14831 records in RAM. INFO 2026-06-03 20:31:10 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:08:09s. Time for last 1,000,000: 1s. Last read position: chr7:116,906,288 INFO 2026-06-03 20:31:10 MarkDuplicates Tracking 540413 as yet unmatched pairs. 11352 records in RAM. INFO 2026-06-03 20:31:12 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:08:11s. Time for last 1,000,000: 1s. Last read position: chr7:127,698,884 INFO 2026-06-03 20:31:12 MarkDuplicates Tracking 539094 as yet unmatched pairs. 10015 records in RAM. INFO 2026-06-03 20:31:14 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:08:13s. Time for last 1,000,000: 1s. Last read position: chr7:128,858,134 INFO 2026-06-03 20:31:14 MarkDuplicates Tracking 537174 as yet unmatched pairs. 8089 records in RAM. INFO 2026-06-03 20:31:16 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:08:15s. Time for last 1,000,000: 2s. Last read position: chr7:135,929,846 INFO 2026-06-03 20:31:16 MarkDuplicates Tracking 536234 as yet unmatched pairs. 7129 records in RAM. INFO 2026-06-03 20:31:17 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 1s. Last read position: chr7:140,702,881 INFO 2026-06-03 20:31:17 MarkDuplicates Tracking 536634 as yet unmatched pairs. 7524 records in RAM. INFO 2026-06-03 20:31:19 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:08:18s. Time for last 1,000,000: 1s. Last read position: chr7:144,299,431 INFO 2026-06-03 20:31:19 MarkDuplicates Tracking 533279 as yet unmatched pairs. 4158 records in RAM. INFO 2026-06-03 20:31:20 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 1s. Last read position: chr7:150,803,418 INFO 2026-06-03 20:31:20 MarkDuplicates Tracking 532368 as yet unmatched pairs. 3234 records in RAM. INFO 2026-06-03 20:31:21 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:08:20s. Time for last 1,000,000: 1s. Last read position: chr7:152,177,269 INFO 2026-06-03 20:31:21 MarkDuplicates Tracking 530450 as yet unmatched pairs. 1309 records in RAM. INFO 2026-06-03 20:31:23 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:08:22s. Time for last 1,000,000: 1s. Last read position: chr8:8,319,025 INFO 2026-06-03 20:31:23 MarkDuplicates Tracking 528982 as yet unmatched pairs. 28982 records in RAM. INFO 2026-06-03 20:31:24 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:08:24s. Time for last 1,000,000: 1s. Last read position: chr8:17,754,678 INFO 2026-06-03 20:31:24 MarkDuplicates Tracking 527745 as yet unmatched pairs. 27716 records in RAM. INFO 2026-06-03 20:31:26 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 1s. Last read position: chr8:22,606,105 INFO 2026-06-03 20:31:26 MarkDuplicates Tracking 526881 as yet unmatched pairs. 26842 records in RAM. INFO 2026-06-03 20:31:27 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:08:26s. Time for last 1,000,000: 1s. Last read position: chr8:26,653,339 INFO 2026-06-03 20:31:27 MarkDuplicates Tracking 524947 as yet unmatched pairs. 24890 records in RAM. INFO 2026-06-03 20:31:29 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:08:28s. Time for last 1,000,000: 1s. Last read position: chr8:30,799,693 INFO 2026-06-03 20:31:29 MarkDuplicates Tracking 524372 as yet unmatched pairs. 24303 records in RAM. INFO 2026-06-03 20:31:30 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 1s. Last read position: chr8:38,267,361 INFO 2026-06-03 20:31:30 MarkDuplicates Tracking 521789 as yet unmatched pairs. 21712 records in RAM. INFO 2026-06-03 20:31:32 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:08:31s. Time for last 1,000,000: 1s. Last read position: chr8:39,055,635 INFO 2026-06-03 20:31:32 MarkDuplicates Tracking 521180 as yet unmatched pairs. 21090 records in RAM. INFO 2026-06-03 20:31:33 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 1s. Last read position: chr8:47,737,631 INFO 2026-06-03 20:31:33 MarkDuplicates Tracking 519292 as yet unmatched pairs. 19182 records in RAM. INFO 2026-06-03 20:31:35 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 1s. Last read position: chr8:61,578,196 INFO 2026-06-03 20:31:35 MarkDuplicates Tracking 517828 as yet unmatched pairs. 17712 records in RAM. INFO 2026-06-03 20:31:36 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 1s. Last read position: chr8:73,291,171 INFO 2026-06-03 20:31:36 MarkDuplicates Tracking 517025 as yet unmatched pairs. 16900 records in RAM. INFO 2026-06-03 20:31:38 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 1s. Last read position: chr8:86,547,711 INFO 2026-06-03 20:31:38 MarkDuplicates Tracking 515371 as yet unmatched pairs. 15232 records in RAM. INFO 2026-06-03 20:31:39 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:08:38s. Time for last 1,000,000: 1s. Last read position: chr8:98,027,514 INFO 2026-06-03 20:31:39 MarkDuplicates Tracking 514127 as yet unmatched pairs. 13978 records in RAM. INFO 2026-06-03 20:31:41 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 1s. Last read position: chr8:102,651,588 INFO 2026-06-03 20:31:41 MarkDuplicates Tracking 512917 as yet unmatched pairs. 12764 records in RAM. INFO 2026-06-03 20:31:43 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:08:42s. Time for last 1,000,000: 1s. Last read position: chr8:120,515,930 INFO 2026-06-03 20:31:43 MarkDuplicates Tracking 511352 as yet unmatched pairs. 11174 records in RAM. INFO 2026-06-03 20:31:45 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:08:44s. Time for last 1,000,000: 1s. Last read position: chr8:140,275,777 INFO 2026-06-03 20:31:45 MarkDuplicates Tracking 510324 as yet unmatched pairs. 10122 records in RAM. INFO 2026-06-03 20:31:46 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:08:45s. Time for last 1,000,000: 1s. Last read position: chr8:143,730,536 INFO 2026-06-03 20:31:46 MarkDuplicates Tracking 508384 as yet unmatched pairs. 8150 records in RAM. INFO 2026-06-03 20:31:47 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:08:47s. Time for last 1,000,000: 1s. Last read position: chr8:143,861,478 INFO 2026-06-03 20:31:47 MarkDuplicates Tracking 507496 as yet unmatched pairs. 7261 records in RAM. INFO 2026-06-03 20:31:49 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 1s. Last read position: chr8:143,866,084 INFO 2026-06-03 20:31:49 MarkDuplicates Tracking 506867 as yet unmatched pairs. 6630 records in RAM. INFO 2026-06-03 20:31:50 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 1s. Last read position: chr8:143,920,932 INFO 2026-06-03 20:31:50 MarkDuplicates Tracking 506086 as yet unmatched pairs. 5848 records in RAM. INFO 2026-06-03 20:31:51 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:08:50s. Time for last 1,000,000: 1s. Last read position: chr8:143,934,397 INFO 2026-06-03 20:31:51 MarkDuplicates Tracking 503639 as yet unmatched pairs. 3394 records in RAM. INFO 2026-06-03 20:31:53 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:08:52s. Time for last 1,000,000: 1s. Last read position: chr8:144,409,512 INFO 2026-06-03 20:31:53 MarkDuplicates Tracking 501236 as yet unmatched pairs. 979 records in RAM. INFO 2026-06-03 20:31:54 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:08:53s. Time for last 1,000,000: 1s. Last read position: chr9:5,086,109 INFO 2026-06-03 20:31:54 MarkDuplicates Tracking 499659 as yet unmatched pairs. 34081 records in RAM. INFO 2026-06-03 20:31:56 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:08:55s. Time for last 1,000,000: 1s. Last read position: chr9:19,050,122 INFO 2026-06-03 20:31:56 MarkDuplicates Tracking 498632 as yet unmatched pairs. 33026 records in RAM. INFO 2026-06-03 20:31:57 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:08:56s. Time for last 1,000,000: 1s. Last read position: chr9:33,278,171 INFO 2026-06-03 20:31:57 MarkDuplicates Tracking 497251 as yet unmatched pairs. 31634 records in RAM. INFO 2026-06-03 20:31:59 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:08:58s. Time for last 1,000,000: 1s. Last read position: chr9:35,403,210 INFO 2026-06-03 20:31:59 MarkDuplicates Tracking 495818 as yet unmatched pairs. 30195 records in RAM. INFO 2026-06-03 20:32:00 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:08:59s. Time for last 1,000,000: 1s. Last read position: chr9:35,725,241 INFO 2026-06-03 20:32:00 MarkDuplicates Tracking 495081 as yet unmatched pairs. 29438 records in RAM. INFO 2026-06-03 20:32:01 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:09:01s. Time for last 1,000,000: 1s. Last read position: chr9:63,372,793 INFO 2026-06-03 20:32:01 MarkDuplicates Tracking 492862 as yet unmatched pairs. 27197 records in RAM. INFO 2026-06-03 20:32:03 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:09:02s. Time for last 1,000,000: 1s. Last read position: chr9:76,107,276 INFO 2026-06-03 20:32:03 MarkDuplicates Tracking 491880 as yet unmatched pairs. 26199 records in RAM. INFO 2026-06-03 20:32:04 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:09:03s. Time for last 1,000,000: 1s. Last read position: chr9:86,033,321 INFO 2026-06-03 20:32:04 MarkDuplicates Tracking 490786 as yet unmatched pairs. 25088 records in RAM. INFO 2026-06-03 20:32:06 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 1s. Last read position: chr9:93,268,692 INFO 2026-06-03 20:32:06 MarkDuplicates Tracking 489274 as yet unmatched pairs. 23571 records in RAM. INFO 2026-06-03 20:32:07 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:09:07s. Time for last 1,000,000: 1s. Last read position: chr9:98,131,015 INFO 2026-06-03 20:32:07 MarkDuplicates Tracking 487827 as yet unmatched pairs. 22097 records in RAM. INFO 2026-06-03 20:32:09 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 1s. Last read position: chr9:106,926,605 INFO 2026-06-03 20:32:09 MarkDuplicates Tracking 486452 as yet unmatched pairs. 20713 records in RAM. INFO 2026-06-03 20:32:10 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:09:09s. Time for last 1,000,000: 1s. Last read position: chr9:112,080,102 INFO 2026-06-03 20:32:10 MarkDuplicates Tracking 485022 as yet unmatched pairs. 19269 records in RAM. INFO 2026-06-03 20:32:11 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:09:11s. Time for last 1,000,000: 1s. Last read position: chr9:116,302,723 INFO 2026-06-03 20:32:11 MarkDuplicates Tracking 483541 as yet unmatched pairs. 17784 records in RAM. INFO 2026-06-03 20:32:13 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:09:12s. Time for last 1,000,000: 1s. Last read position: chr9:121,356,091 INFO 2026-06-03 20:32:13 MarkDuplicates Tracking 482314 as yet unmatched pairs. 16541 records in RAM. INFO 2026-06-03 20:32:14 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 1s. Last read position: chr9:125,239,156 INFO 2026-06-03 20:32:14 MarkDuplicates Tracking 480699 as yet unmatched pairs. 14914 records in RAM. INFO 2026-06-03 20:32:16 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:09:15s. Time for last 1,000,000: 1s. Last read position: chr9:127,890,720 INFO 2026-06-03 20:32:16 MarkDuplicates Tracking 483110 as yet unmatched pairs. 17319 records in RAM. INFO 2026-06-03 20:32:17 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 1s. Last read position: chr9:128,579,655 INFO 2026-06-03 20:32:17 MarkDuplicates Tracking 478279 as yet unmatched pairs. 12481 records in RAM. INFO 2026-06-03 20:32:19 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:09:18s. Time for last 1,000,000: 1s. Last read position: chr9:129,147,398 INFO 2026-06-03 20:32:19 MarkDuplicates Tracking 476608 as yet unmatched pairs. 10804 records in RAM. INFO 2026-06-03 20:32:21 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 1s. Last read position: chr9:130,884,898 INFO 2026-06-03 20:32:21 MarkDuplicates Tracking 475097 as yet unmatched pairs. 9285 records in RAM. INFO 2026-06-03 20:32:22 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:09:21s. Time for last 1,000,000: 1s. Last read position: chr9:133,108,010 INFO 2026-06-03 20:32:22 MarkDuplicates Tracking 473287 as yet unmatched pairs. 7468 records in RAM. INFO 2026-06-03 20:32:23 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 1s. Last read position: chr9:134,785,051 INFO 2026-06-03 20:32:23 MarkDuplicates Tracking 472229 as yet unmatched pairs. 6394 records in RAM. INFO 2026-06-03 20:32:25 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:09:24s. Time for last 1,000,000: 1s. Last read position: chr9:136,476,589 INFO 2026-06-03 20:32:25 MarkDuplicates Tracking 470661 as yet unmatched pairs. 4807 records in RAM. INFO 2026-06-03 20:32:27 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:09:26s. Time for last 1,000,000: 1s. Last read position: chr9:136,993,387 INFO 2026-06-03 20:32:27 MarkDuplicates Tracking 468332 as yet unmatched pairs. 2475 records in RAM. INFO 2026-06-03 20:32:28 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:09:27s. Time for last 1,000,000: 1s. Last read position: chr9:137,453,790 INFO 2026-06-03 20:32:28 MarkDuplicates Tracking 466537 as yet unmatched pairs. 652 records in RAM. INFO 2026-06-03 20:32:30 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:09:29s. Time for last 1,000,000: 2s. Last read position: chr10:5,909,018 INFO 2026-06-03 20:32:30 MarkDuplicates Tracking 465306 as yet unmatched pairs. 23382 records in RAM. INFO 2026-06-03 20:32:32 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:09:31s. Time for last 1,000,000: 1s. Last read position: chr10:17,235,333 INFO 2026-06-03 20:32:32 MarkDuplicates Tracking 465005 as yet unmatched pairs. 23068 records in RAM. INFO 2026-06-03 20:32:33 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:09:32s. Time for last 1,000,000: 1s. Last read position: chr10:29,463,522 INFO 2026-06-03 20:32:33 MarkDuplicates Tracking 462617 as yet unmatched pairs. 20672 records in RAM. INFO 2026-06-03 20:32:35 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:09:34s. Time for last 1,000,000: 1s. Last read position: chr10:32,292,498 INFO 2026-06-03 20:32:35 MarkDuplicates Tracking 461351 as yet unmatched pairs. 19401 records in RAM. INFO 2026-06-03 20:32:36 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 1s. Last read position: chr10:45,727,461 INFO 2026-06-03 20:32:36 MarkDuplicates Tracking 460497 as yet unmatched pairs. 18538 records in RAM. INFO 2026-06-03 20:32:38 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 1s. Last read position: chr10:50,093,858 INFO 2026-06-03 20:32:38 MarkDuplicates Tracking 459337 as yet unmatched pairs. 17371 records in RAM. INFO 2026-06-03 20:32:39 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:09:38s. Time for last 1,000,000: 1s. Last read position: chr10:68,901,379 INFO 2026-06-03 20:32:39 MarkDuplicates Tracking 457711 as yet unmatched pairs. 15733 records in RAM. INFO 2026-06-03 20:32:41 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:09:40s. Time for last 1,000,000: 1s. Last read position: chr10:73,517,067 INFO 2026-06-03 20:32:41 MarkDuplicates Tracking 456520 as yet unmatched pairs. 14527 records in RAM. INFO 2026-06-03 20:32:42 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:09:41s. Time for last 1,000,000: 1s. Last read position: chr10:77,084,651 INFO 2026-06-03 20:32:42 MarkDuplicates Tracking 455235 as yet unmatched pairs. 13233 records in RAM. INFO 2026-06-03 20:32:43 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:09:42s. Time for last 1,000,000: 1s. Last read position: chr10:86,717,926 INFO 2026-06-03 20:32:43 MarkDuplicates Tracking 453624 as yet unmatched pairs. 11607 records in RAM. INFO 2026-06-03 20:32:45 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 1s. Last read position: chr10:91,807,381 INFO 2026-06-03 20:32:45 MarkDuplicates Tracking 452390 as yet unmatched pairs. 10358 records in RAM. INFO 2026-06-03 20:32:46 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:09:45s. Time for last 1,000,000: 1s. Last read position: chr10:95,682,705 INFO 2026-06-03 20:32:46 MarkDuplicates Tracking 451046 as yet unmatched pairs. 9005 records in RAM. INFO 2026-06-03 20:32:48 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:09:47s. Time for last 1,000,000: 1s. Last read position: chr10:100,193,352 INFO 2026-06-03 20:32:48 MarkDuplicates Tracking 449524 as yet unmatched pairs. 7479 records in RAM. INFO 2026-06-03 20:32:49 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:09:48s. Time for last 1,000,000: 1s. Last read position: chr10:102,484,283 INFO 2026-06-03 20:32:49 MarkDuplicates Tracking 448193 as yet unmatched pairs. 6141 records in RAM. INFO 2026-06-03 20:32:50 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:09:49s. Time for last 1,000,000: 1s. Last read position: chr10:109,865,200 INFO 2026-06-03 20:32:50 MarkDuplicates Tracking 446748 as yet unmatched pairs. 4678 records in RAM. INFO 2026-06-03 20:32:52 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:09:51s. Time for last 1,000,000: 1s. Last read position: chr10:116,915,483 INFO 2026-06-03 20:32:52 MarkDuplicates Tracking 445678 as yet unmatched pairs. 3590 records in RAM. INFO 2026-06-03 20:32:53 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:09:52s. Time for last 1,000,000: 1s. Last read position: chr10:122,237,469 INFO 2026-06-03 20:32:53 MarkDuplicates Tracking 444205 as yet unmatched pairs. 2107 records in RAM. INFO 2026-06-03 20:32:55 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:09:54s. Time for last 1,000,000: 1s. Last read position: chr10:128,108,602 INFO 2026-06-03 20:32:55 MarkDuplicates Tracking 442810 as yet unmatched pairs. 698 records in RAM. INFO 2026-06-03 20:32:56 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:09:56s. Time for last 1,000,000: 1s. Last read position: chr11:394,328 INFO 2026-06-03 20:32:56 MarkDuplicates Tracking 441576 as yet unmatched pairs. 64495 records in RAM. INFO 2026-06-03 20:32:58 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:09:57s. Time for last 1,000,000: 1s. Last read position: chr11:709,348 INFO 2026-06-03 20:32:58 MarkDuplicates Tracking 440464 as yet unmatched pairs. 63375 records in RAM. INFO 2026-06-03 20:33:00 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 1s. Last read position: chr11:1,075,734 INFO 2026-06-03 20:33:00 MarkDuplicates Tracking 446176 as yet unmatched pairs. 69080 records in RAM. INFO 2026-06-03 20:33:01 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:10:00s. Time for last 1,000,000: 1s. Last read position: chr11:1,078,475 INFO 2026-06-03 20:33:01 MarkDuplicates Tracking 452243 as yet unmatched pairs. 75136 records in RAM. INFO 2026-06-03 20:33:02 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:10:01s. Time for last 1,000,000: 1s. Last read position: chr11:1,084,655 INFO 2026-06-03 20:33:02 MarkDuplicates Tracking 441129 as yet unmatched pairs. 64018 records in RAM. INFO 2026-06-03 20:33:04 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:10:03s. Time for last 1,000,000: 1s. Last read position: chr11:1,088,090 INFO 2026-06-03 20:33:04 MarkDuplicates Tracking 444064 as yet unmatched pairs. 66946 records in RAM. INFO 2026-06-03 20:33:05 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:10:05s. Time for last 1,000,000: 1s. Last read position: chr11:1,094,177 INFO 2026-06-03 20:33:05 MarkDuplicates Tracking 438933 as yet unmatched pairs. 61807 records in RAM. INFO 2026-06-03 20:33:07 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 1s. Last read position: chr11:1,182,309 INFO 2026-06-03 20:33:07 MarkDuplicates Tracking 431587 as yet unmatched pairs. 54433 records in RAM. INFO 2026-06-03 20:33:08 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:10:07s. Time for last 1,000,000: 1s. Last read position: chr11:1,186,337 INFO 2026-06-03 20:33:08 MarkDuplicates Tracking 429984 as yet unmatched pairs. 52824 records in RAM. INFO 2026-06-03 20:33:09 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:10:08s. Time for last 1,000,000: 1s. Last read position: chr11:1,191,361 INFO 2026-06-03 20:33:09 MarkDuplicates Tracking 429976 as yet unmatched pairs. 52813 records in RAM. INFO 2026-06-03 20:33:11 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:10:10s. Time for last 1,000,000: 1s. Last read position: chr11:1,242,542 INFO 2026-06-03 20:33:11 MarkDuplicates Tracking 427858 as yet unmatched pairs. 50687 records in RAM. INFO 2026-06-03 20:33:12 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:10:11s. Time for last 1,000,000: 1s. Last read position: chr11:1,245,062 INFO 2026-06-03 20:33:12 MarkDuplicates Tracking 427180 as yet unmatched pairs. 50007 records in RAM. INFO 2026-06-03 20:33:13 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 1s. Last read position: chr11:1,248,036 INFO 2026-06-03 20:33:13 MarkDuplicates Tracking 426981 as yet unmatched pairs. 49807 records in RAM. INFO 2026-06-03 20:33:14 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:10:13s. Time for last 1,000,000: 1s. Last read position: chr11:1,250,873 INFO 2026-06-03 20:33:14 MarkDuplicates Tracking 425923 as yet unmatched pairs. 48738 records in RAM. INFO 2026-06-03 20:33:15 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:10:15s. Time for last 1,000,000: 1s. Last read position: chr11:2,133,189 INFO 2026-06-03 20:33:15 MarkDuplicates Tracking 423933 as yet unmatched pairs. 46743 records in RAM. INFO 2026-06-03 20:33:17 MarkDuplicates Read 368,000,000 records. Elapsed time: 00:10:16s. Time for last 1,000,000: 1s. Last read position: chr11:6,390,845 INFO 2026-06-03 20:33:17 MarkDuplicates Tracking 422448 as yet unmatched pairs. 45252 records in RAM. INFO 2026-06-03 20:33:18 MarkDuplicates Read 369,000,000 records. Elapsed time: 00:10:18s. Time for last 1,000,000: 1s. Last read position: chr11:8,730,653 INFO 2026-06-03 20:33:18 MarkDuplicates Tracking 421089 as yet unmatched pairs. 43882 records in RAM. INFO 2026-06-03 20:33:20 MarkDuplicates Read 370,000,000 records. Elapsed time: 00:10:19s. Time for last 1,000,000: 1s. Last read position: chr11:11,967,065 INFO 2026-06-03 20:33:20 MarkDuplicates Tracking 420074 as yet unmatched pairs. 42864 records in RAM. INFO 2026-06-03 20:33:22 MarkDuplicates Read 371,000,000 records. Elapsed time: 00:10:21s. Time for last 1,000,000: 1s. Last read position: chr11:17,501,119 INFO 2026-06-03 20:33:22 MarkDuplicates Tracking 418521 as yet unmatched pairs. 41292 records in RAM. INFO 2026-06-03 20:33:23 MarkDuplicates Read 372,000,000 records. Elapsed time: 00:10:22s. Time for last 1,000,000: 1s. Last read position: chr11:33,574,808 INFO 2026-06-03 20:33:23 MarkDuplicates Tracking 416802 as yet unmatched pairs. 39564 records in RAM. INFO 2026-06-03 20:33:25 MarkDuplicates Read 373,000,000 records. Elapsed time: 00:10:25s. Time for last 1,000,000: 2s. Last read position: chr11:45,806,073 INFO 2026-06-03 20:33:25 MarkDuplicates Tracking 415828 as yet unmatched pairs. 38583 records in RAM. INFO 2026-06-03 20:33:27 MarkDuplicates Read 374,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 1s. Last read position: chr11:46,681,068 INFO 2026-06-03 20:33:27 MarkDuplicates Tracking 414390 as yet unmatched pairs. 37137 records in RAM. INFO 2026-06-03 20:33:29 MarkDuplicates Read 375,000,000 records. Elapsed time: 00:10:28s. Time for last 1,000,000: 1s. Last read position: chr11:57,309,866 INFO 2026-06-03 20:33:29 MarkDuplicates Tracking 412651 as yet unmatched pairs. 35395 records in RAM. INFO 2026-06-03 20:33:31 MarkDuplicates Read 376,000,000 records. Elapsed time: 00:10:30s. Time for last 1,000,000: 1s. Last read position: chr11:59,181,857 INFO 2026-06-03 20:33:31 MarkDuplicates Tracking 411591 as yet unmatched pairs. 34332 records in RAM. INFO 2026-06-03 20:33:32 MarkDuplicates Read 377,000,000 records. Elapsed time: 00:10:32s. Time for last 1,000,000: 1s. Last read position: chr11:61,771,682 INFO 2026-06-03 20:33:32 MarkDuplicates Tracking 409941 as yet unmatched pairs. 32674 records in RAM. INFO 2026-06-03 20:33:34 MarkDuplicates Read 378,000,000 records. Elapsed time: 00:10:33s. Time for last 1,000,000: 1s. Last read position: chr11:62,521,451 INFO 2026-06-03 20:33:34 MarkDuplicates Tracking 410135 as yet unmatched pairs. 32863 records in RAM. INFO 2026-06-03 20:33:35 MarkDuplicates Read 379,000,000 records. Elapsed time: 00:10:35s. Time for last 1,000,000: 1s. Last read position: chr11:62,528,741 INFO 2026-06-03 20:33:35 MarkDuplicates Tracking 408885 as yet unmatched pairs. 31611 records in RAM. INFO 2026-06-03 20:33:37 MarkDuplicates Read 380,000,000 records. Elapsed time: 00:10:36s. Time for last 1,000,000: 1s. Last read position: chr11:62,616,981 INFO 2026-06-03 20:33:37 MarkDuplicates Tracking 406181 as yet unmatched pairs. 28903 records in RAM. INFO 2026-06-03 20:33:38 MarkDuplicates Read 381,000,000 records. Elapsed time: 00:10:38s. Time for last 1,000,000: 1s. Last read position: chr11:64,117,148 INFO 2026-06-03 20:33:38 MarkDuplicates Tracking 404790 as yet unmatched pairs. 27508 records in RAM. INFO 2026-06-03 20:33:40 MarkDuplicates Read 382,000,000 records. Elapsed time: 00:10:39s. Time for last 1,000,000: 1s. Last read position: chr11:64,829,520 INFO 2026-06-03 20:33:40 MarkDuplicates Tracking 403046 as yet unmatched pairs. 25756 records in RAM. INFO 2026-06-03 20:33:41 MarkDuplicates Read 383,000,000 records. Elapsed time: 00:10:40s. Time for last 1,000,000: 1s. Last read position: chr11:65,537,838 INFO 2026-06-03 20:33:41 MarkDuplicates Tracking 401497 as yet unmatched pairs. 24192 records in RAM. INFO 2026-06-03 20:33:43 MarkDuplicates Read 384,000,000 records. Elapsed time: 00:10:42s. Time for last 1,000,000: 1s. Last read position: chr11:65,655,733 INFO 2026-06-03 20:33:43 MarkDuplicates Tracking 400176 as yet unmatched pairs. 22860 records in RAM. INFO 2026-06-03 20:33:44 MarkDuplicates Read 385,000,000 records. Elapsed time: 00:10:43s. Time for last 1,000,000: 1s. Last read position: chr11:66,316,489 INFO 2026-06-03 20:33:44 MarkDuplicates Tracking 398112 as yet unmatched pairs. 20783 records in RAM. INFO 2026-06-03 20:33:46 MarkDuplicates Read 386,000,000 records. Elapsed time: 00:10:45s. Time for last 1,000,000: 1s. Last read position: chr11:67,433,365 INFO 2026-06-03 20:33:46 MarkDuplicates Tracking 396343 as yet unmatched pairs. 19011 records in RAM. INFO 2026-06-03 20:33:47 MarkDuplicates Read 387,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 1s. Last read position: chr11:68,548,141 INFO 2026-06-03 20:33:47 MarkDuplicates Tracking 394817 as yet unmatched pairs. 17478 records in RAM. INFO 2026-06-03 20:33:49 MarkDuplicates Read 388,000,000 records. Elapsed time: 00:10:48s. Time for last 1,000,000: 1s. Last read position: chr11:71,438,888 INFO 2026-06-03 20:33:49 MarkDuplicates Tracking 393067 as yet unmatched pairs. 15716 records in RAM. INFO 2026-06-03 20:33:50 MarkDuplicates Read 389,000,000 records. Elapsed time: 00:10:49s. Time for last 1,000,000: 1s. Last read position: chr11:73,309,492 INFO 2026-06-03 20:33:50 MarkDuplicates Tracking 391495 as yet unmatched pairs. 14136 records in RAM. INFO 2026-06-03 20:33:51 MarkDuplicates Read 390,000,000 records. Elapsed time: 00:10:51s. Time for last 1,000,000: 1s. Last read position: chr11:76,544,335 INFO 2026-06-03 20:33:51 MarkDuplicates Tracking 390105 as yet unmatched pairs. 12740 records in RAM. INFO 2026-06-03 20:33:53 MarkDuplicates Read 391,000,000 records. Elapsed time: 00:10:52s. Time for last 1,000,000: 1s. Last read position: chr11:85,726,072 INFO 2026-06-03 20:33:53 MarkDuplicates Tracking 389011 as yet unmatched pairs. 11634 records in RAM. INFO 2026-06-03 20:33:54 MarkDuplicates Read 392,000,000 records. Elapsed time: 00:10:53s. Time for last 1,000,000: 1s. Last read position: chr11:95,173,049 INFO 2026-06-03 20:33:54 MarkDuplicates Tracking 387446 as yet unmatched pairs. 10062 records in RAM. INFO 2026-06-03 20:33:56 MarkDuplicates Read 393,000,000 records. Elapsed time: 00:10:55s. Time for last 1,000,000: 1s. Last read position: chr11:108,491,044 INFO 2026-06-03 20:33:56 MarkDuplicates Tracking 386439 as yet unmatched pairs. 9051 records in RAM. INFO 2026-06-03 20:33:57 MarkDuplicates Read 394,000,000 records. Elapsed time: 00:10:56s. Time for last 1,000,000: 1s. Last read position: chr11:116,859,422 INFO 2026-06-03 20:33:57 MarkDuplicates Tracking 384976 as yet unmatched pairs. 7583 records in RAM. INFO 2026-06-03 20:33:59 MarkDuplicates Read 395,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 1s. Last read position: chr11:118,503,104 INFO 2026-06-03 20:33:59 MarkDuplicates Tracking 383721 as yet unmatched pairs. 6320 records in RAM. INFO 2026-06-03 20:34:00 MarkDuplicates Read 396,000,000 records. Elapsed time: 00:10:59s. Time for last 1,000,000: 1s. Last read position: chr11:119,186,226 INFO 2026-06-03 20:34:00 MarkDuplicates Tracking 382654 as yet unmatched pairs. 5243 records in RAM. INFO 2026-06-03 20:34:01 MarkDuplicates Read 397,000,000 records. Elapsed time: 00:11:01s. Time for last 1,000,000: 1s. Last read position: chr11:123,059,617 INFO 2026-06-03 20:34:01 MarkDuplicates Tracking 381733 as yet unmatched pairs. 4319 records in RAM. INFO 2026-06-03 20:34:03 MarkDuplicates Read 398,000,000 records. Elapsed time: 00:11:02s. Time for last 1,000,000: 1s. Last read position: chr11:128,490,540 INFO 2026-06-03 20:34:03 MarkDuplicates Tracking 379516 as yet unmatched pairs. 2088 records in RAM. INFO 2026-06-03 20:34:04 MarkDuplicates Read 399,000,000 records. Elapsed time: 00:11:03s. Time for last 1,000,000: 1s. Last read position: chr11:133,922,569 INFO 2026-06-03 20:34:04 MarkDuplicates Tracking 377740 as yet unmatched pairs. 295 records in RAM. INFO 2026-06-03 20:34:06 MarkDuplicates Read 400,000,000 records. Elapsed time: 00:11:05s. Time for last 1,000,000: 1s. Last read position: chr12:3,696,976 INFO 2026-06-03 20:34:06 MarkDuplicates Tracking 376306 as yet unmatched pairs. 41781 records in RAM. INFO 2026-06-03 20:34:08 MarkDuplicates Read 401,000,000 records. Elapsed time: 00:11:07s. Time for last 1,000,000: 1s. Last read position: chr12:6,526,551 INFO 2026-06-03 20:34:08 MarkDuplicates Tracking 374905 as yet unmatched pairs. 40376 records in RAM. INFO 2026-06-03 20:34:09 MarkDuplicates Read 402,000,000 records. Elapsed time: 00:11:08s. Time for last 1,000,000: 1s. Last read position: chr12:6,941,536 INFO 2026-06-03 20:34:09 MarkDuplicates Tracking 373510 as yet unmatched pairs. 38976 records in RAM. INFO 2026-06-03 20:34:10 MarkDuplicates Read 403,000,000 records. Elapsed time: 00:11:09s. Time for last 1,000,000: 1s. Last read position: chr12:8,945,474 INFO 2026-06-03 20:34:10 MarkDuplicates Tracking 372158 as yet unmatched pairs. 37621 records in RAM. INFO 2026-06-03 20:34:12 MarkDuplicates Read 404,000,000 records. Elapsed time: 00:11:11s. Time for last 1,000,000: 1s. Last read position: chr12:11,680,714 INFO 2026-06-03 20:34:12 MarkDuplicates Tracking 371082 as yet unmatched pairs. 36543 records in RAM. INFO 2026-06-03 20:34:13 MarkDuplicates Read 405,000,000 records. Elapsed time: 00:11:12s. Time for last 1,000,000: 1s. Last read position: chr12:15,911,401 INFO 2026-06-03 20:34:13 MarkDuplicates Tracking 369676 as yet unmatched pairs. 35132 records in RAM. INFO 2026-06-03 20:34:15 MarkDuplicates Read 406,000,000 records. Elapsed time: 00:11:14s. Time for last 1,000,000: 1s. Last read position: chr12:30,669,164 INFO 2026-06-03 20:34:15 MarkDuplicates Tracking 368394 as yet unmatched pairs. 33842 records in RAM. INFO 2026-06-03 20:34:16 MarkDuplicates Read 407,000,000 records. Elapsed time: 00:11:15s. Time for last 1,000,000: 1s. Last read position: chr12:46,361,185 INFO 2026-06-03 20:34:16 MarkDuplicates Tracking 367601 as yet unmatched pairs. 33039 records in RAM. INFO 2026-06-03 20:34:18 MarkDuplicates Read 408,000,000 records. Elapsed time: 00:11:17s. Time for last 1,000,000: 1s. Last read position: chr12:49,040,028 INFO 2026-06-03 20:34:18 MarkDuplicates Tracking 365554 as yet unmatched pairs. 30991 records in RAM. INFO 2026-06-03 20:34:19 MarkDuplicates Read 409,000,000 records. Elapsed time: 00:11:18s. Time for last 1,000,000: 1s. Last read position: chr12:49,272,449 INFO 2026-06-03 20:34:19 MarkDuplicates Tracking 365371 as yet unmatched pairs. 30807 records in RAM. INFO 2026-06-03 20:34:20 MarkDuplicates Read 410,000,000 records. Elapsed time: 00:11:20s. Time for last 1,000,000: 1s. Last read position: chr12:51,064,457 INFO 2026-06-03 20:34:20 MarkDuplicates Tracking 363215 as yet unmatched pairs. 28636 records in RAM. INFO 2026-06-03 20:34:22 MarkDuplicates Read 411,000,000 records. Elapsed time: 00:11:21s. Time for last 1,000,000: 1s. Last read position: chr12:52,949,477 INFO 2026-06-03 20:34:22 MarkDuplicates Tracking 362314 as yet unmatched pairs. 27727 records in RAM. INFO 2026-06-03 20:34:23 MarkDuplicates Read 412,000,000 records. Elapsed time: 00:11:22s. Time for last 1,000,000: 1s. Last read position: chr12:53,454,794 INFO 2026-06-03 20:34:23 MarkDuplicates Tracking 361406 as yet unmatched pairs. 26817 records in RAM. INFO 2026-06-03 20:34:25 MarkDuplicates Read 413,000,000 records. Elapsed time: 00:11:24s. Time for last 1,000,000: 1s. Last read position: chr12:55,702,899 INFO 2026-06-03 20:34:25 MarkDuplicates Tracking 359187 as yet unmatched pairs. 24592 records in RAM. INFO 2026-06-03 20:34:26 MarkDuplicates Read 414,000,000 records. Elapsed time: 00:11:25s. Time for last 1,000,000: 1s. Last read position: chr12:56,101,624 INFO 2026-06-03 20:34:26 MarkDuplicates Tracking 358128 as yet unmatched pairs. 23525 records in RAM. INFO 2026-06-03 20:34:28 MarkDuplicates Read 415,000,000 records. Elapsed time: 00:11:27s. Time for last 1,000,000: 1s. Last read position: chr12:56,349,598 INFO 2026-06-03 20:34:28 MarkDuplicates Tracking 356844 as yet unmatched pairs. 22235 records in RAM. INFO 2026-06-03 20:34:29 MarkDuplicates Read 416,000,000 records. Elapsed time: 00:11:29s. Time for last 1,000,000: 1s. Last read position: chr12:57,096,893 INFO 2026-06-03 20:34:29 MarkDuplicates Tracking 358860 as yet unmatched pairs. 24245 records in RAM. INFO 2026-06-03 20:34:31 MarkDuplicates Read 417,000,000 records. Elapsed time: 00:11:30s. Time for last 1,000,000: 1s. Last read position: chr12:57,173,306 INFO 2026-06-03 20:34:31 MarkDuplicates Tracking 354610 as yet unmatched pairs. 19989 records in RAM. INFO 2026-06-03 20:34:33 MarkDuplicates Read 418,000,000 records. Elapsed time: 00:11:32s. Time for last 1,000,000: 2s. Last read position: chr12:57,516,922 INFO 2026-06-03 20:34:33 MarkDuplicates Tracking 352399 as yet unmatched pairs. 17771 records in RAM. INFO 2026-06-03 20:34:34 MarkDuplicates Read 419,000,000 records. Elapsed time: 00:11:33s. Time for last 1,000,000: 1s. Last read position: chr12:64,430,055 INFO 2026-06-03 20:34:34 MarkDuplicates Tracking 350950 as yet unmatched pairs. 16318 records in RAM. INFO 2026-06-03 20:34:36 MarkDuplicates Read 420,000,000 records. Elapsed time: 00:11:35s. Time for last 1,000,000: 1s. Last read position: chr12:71,138,031 INFO 2026-06-03 20:34:36 MarkDuplicates Tracking 352954 as yet unmatched pairs. 18317 records in RAM. INFO 2026-06-03 20:34:38 MarkDuplicates Read 421,000,000 records. Elapsed time: 00:11:37s. Time for last 1,000,000: 1s. Last read position: chr12:90,090,459 INFO 2026-06-03 20:34:38 MarkDuplicates Tracking 348363 as yet unmatched pairs. 13715 records in RAM. INFO 2026-06-03 20:34:39 MarkDuplicates Read 422,000,000 records. Elapsed time: 00:11:39s. Time for last 1,000,000: 1s. Last read position: chr12:98,597,922 INFO 2026-06-03 20:34:39 MarkDuplicates Tracking 348414 as yet unmatched pairs. 13759 records in RAM. INFO 2026-06-03 20:34:41 MarkDuplicates Read 423,000,000 records. Elapsed time: 00:11:40s. Time for last 1,000,000: 1s. Last read position: chr12:105,177,006 INFO 2026-06-03 20:34:41 MarkDuplicates Tracking 346177 as yet unmatched pairs. 11517 records in RAM. INFO 2026-06-03 20:34:42 MarkDuplicates Read 424,000,000 records. Elapsed time: 00:11:41s. Time for last 1,000,000: 1s. Last read position: chr12:110,147,023 INFO 2026-06-03 20:34:42 MarkDuplicates Tracking 344495 as yet unmatched pairs. 9834 records in RAM. INFO 2026-06-03 20:34:44 MarkDuplicates Read 425,000,000 records. Elapsed time: 00:11:43s. Time for last 1,000,000: 1s. Last read position: chr12:112,265,842 INFO 2026-06-03 20:34:44 MarkDuplicates Tracking 343138 as yet unmatched pairs. 8472 records in RAM. INFO 2026-06-03 20:34:45 MarkDuplicates Read 426,000,000 records. Elapsed time: 00:11:44s. Time for last 1,000,000: 1s. Last read position: chr12:118,035,085 INFO 2026-06-03 20:34:45 MarkDuplicates Tracking 341635 as yet unmatched pairs. 6967 records in RAM. INFO 2026-06-03 20:34:46 MarkDuplicates Read 427,000,000 records. Elapsed time: 00:11:46s. Time for last 1,000,000: 1s. Last read position: chr12:120,581,115 INFO 2026-06-03 20:34:46 MarkDuplicates Tracking 340132 as yet unmatched pairs. 5460 records in RAM. INFO 2026-06-03 20:34:48 MarkDuplicates Read 428,000,000 records. Elapsed time: 00:11:47s. Time for last 1,000,000: 1s. Last read position: chr12:122,365,542 INFO 2026-06-03 20:34:48 MarkDuplicates Tracking 338723 as yet unmatched pairs. 4044 records in RAM. INFO 2026-06-03 20:34:49 MarkDuplicates Read 429,000,000 records. Elapsed time: 00:11:48s. Time for last 1,000,000: 1s. Last read position: chr12:124,348,103 INFO 2026-06-03 20:34:49 MarkDuplicates Tracking 337253 as yet unmatched pairs. 2572 records in RAM. INFO 2026-06-03 20:34:51 MarkDuplicates Read 430,000,000 records. Elapsed time: 00:11:50s. Time for last 1,000,000: 1s. Last read position: chr12:132,490,817 INFO 2026-06-03 20:34:51 MarkDuplicates Tracking 335745 as yet unmatched pairs. 1060 records in RAM. INFO 2026-06-03 20:34:52 MarkDuplicates Read 431,000,000 records. Elapsed time: 00:11:51s. Time for last 1,000,000: 1s. Last read position: chr13:20,512,404 INFO 2026-06-03 20:34:52 MarkDuplicates Tracking 334432 as yet unmatched pairs. 12314 records in RAM. INFO 2026-06-03 20:34:54 MarkDuplicates Read 432,000,000 records. Elapsed time: 00:11:53s. Time for last 1,000,000: 1s. Last read position: chr13:30,461,464 INFO 2026-06-03 20:34:54 MarkDuplicates Tracking 332972 as yet unmatched pairs. 10842 records in RAM. INFO 2026-06-03 20:34:55 MarkDuplicates Read 433,000,000 records. Elapsed time: 00:11:54s. Time for last 1,000,000: 1s. Last read position: chr13:40,993,031 INFO 2026-06-03 20:34:55 MarkDuplicates Tracking 331680 as yet unmatched pairs. 9545 records in RAM. INFO 2026-06-03 20:34:57 MarkDuplicates Read 434,000,000 records. Elapsed time: 00:11:56s. Time for last 1,000,000: 1s. Last read position: chr13:48,258,167 INFO 2026-06-03 20:34:57 MarkDuplicates Tracking 331638 as yet unmatched pairs. 9501 records in RAM. INFO 2026-06-03 20:34:58 MarkDuplicates Read 435,000,000 records. Elapsed time: 00:11:57s. Time for last 1,000,000: 1s. Last read position: chr13:72,771,080 INFO 2026-06-03 20:34:58 MarkDuplicates Tracking 329356 as yet unmatched pairs. 7204 records in RAM. INFO 2026-06-03 20:34:59 MarkDuplicates Read 436,000,000 records. Elapsed time: 00:11:58s. Time for last 1,000,000: 1s. Last read position: chr13:94,443,605 INFO 2026-06-03 20:34:59 MarkDuplicates Tracking 329694 as yet unmatched pairs. 7525 records in RAM. INFO 2026-06-03 20:35:01 MarkDuplicates Read 437,000,000 records. Elapsed time: 00:12:00s. Time for last 1,000,000: 1s. Last read position: chr13:102,866,744 INFO 2026-06-03 20:35:01 MarkDuplicates Tracking 326578 as yet unmatched pairs. 4403 records in RAM. INFO 2026-06-03 20:35:03 MarkDuplicates Read 438,000,000 records. Elapsed time: 00:12:02s. Time for last 1,000,000: 1s. Last read position: chr13:110,428,494 INFO 2026-06-03 20:35:03 MarkDuplicates Tracking 326105 as yet unmatched pairs. 3928 records in RAM. INFO 2026-06-03 20:35:05 MarkDuplicates Read 439,000,000 records. Elapsed time: 00:12:04s. Time for last 1,000,000: 2s. Last read position: chr13:113,066,086 INFO 2026-06-03 20:35:05 MarkDuplicates Tracking 323375 as yet unmatched pairs. 1185 records in RAM. INFO 2026-06-03 20:35:06 MarkDuplicates Read 440,000,000 records. Elapsed time: 00:12:06s. Time for last 1,000,000: 1s. Last read position: chr14:20,801,646 INFO 2026-06-03 20:35:06 MarkDuplicates Tracking 323597 as yet unmatched pairs. 29719 records in RAM. INFO 2026-06-03 20:35:08 MarkDuplicates Read 441,000,000 records. Elapsed time: 00:12:07s. Time for last 1,000,000: 1s. Last read position: chr14:22,845,782 INFO 2026-06-03 20:35:08 MarkDuplicates Tracking 320418 as yet unmatched pairs. 26538 records in RAM. INFO 2026-06-03 20:35:10 MarkDuplicates Read 442,000,000 records. Elapsed time: 00:12:09s. Time for last 1,000,000: 2s. Last read position: chr14:24,098,474 INFO 2026-06-03 20:35:10 MarkDuplicates Tracking 318912 as yet unmatched pairs. 25021 records in RAM. INFO 2026-06-03 20:35:12 MarkDuplicates Read 443,000,000 records. Elapsed time: 00:12:11s. Time for last 1,000,000: 1s. Last read position: chr14:26,472,376 INFO 2026-06-03 20:35:12 MarkDuplicates Tracking 317186 as yet unmatched pairs. 23292 records in RAM. INFO 2026-06-03 20:35:13 MarkDuplicates Read 444,000,000 records. Elapsed time: 00:12:12s. Time for last 1,000,000: 1s. Last read position: chr14:39,055,268 INFO 2026-06-03 20:35:13 MarkDuplicates Tracking 316179 as yet unmatched pairs. 22274 records in RAM. INFO 2026-06-03 20:35:15 MarkDuplicates Read 445,000,000 records. Elapsed time: 00:12:14s. Time for last 1,000,000: 1s. Last read position: chr14:50,729,532 INFO 2026-06-03 20:35:15 MarkDuplicates Tracking 314922 as yet unmatched pairs. 20997 records in RAM. INFO 2026-06-03 20:35:16 MarkDuplicates Read 446,000,000 records. Elapsed time: 00:12:15s. Time for last 1,000,000: 1s. Last read position: chr14:55,382,119 INFO 2026-06-03 20:35:16 MarkDuplicates Tracking 313440 as yet unmatched pairs. 19511 records in RAM. INFO 2026-06-03 20:35:18 MarkDuplicates Read 447,000,000 records. Elapsed time: 00:12:17s. Time for last 1,000,000: 1s. Last read position: chr14:64,132,296 INFO 2026-06-03 20:35:18 MarkDuplicates Tracking 312169 as yet unmatched pairs. 18238 records in RAM. INFO 2026-06-03 20:35:19 MarkDuplicates Read 448,000,000 records. Elapsed time: 00:12:18s. Time for last 1,000,000: 1s. Last read position: chr14:68,879,009 INFO 2026-06-03 20:35:19 MarkDuplicates Tracking 311670 as yet unmatched pairs. 17732 records in RAM. INFO 2026-06-03 20:35:21 MarkDuplicates Read 449,000,000 records. Elapsed time: 00:12:20s. Time for last 1,000,000: 1s. Last read position: chr14:73,277,119 INFO 2026-06-03 20:35:21 MarkDuplicates Tracking 310057 as yet unmatched pairs. 16114 records in RAM. INFO 2026-06-03 20:35:22 MarkDuplicates Read 450,000,000 records. Elapsed time: 00:12:21s. Time for last 1,000,000: 1s. Last read position: chr14:75,176,384 INFO 2026-06-03 20:35:22 MarkDuplicates Tracking 308588 as yet unmatched pairs. 14636 records in RAM. INFO 2026-06-03 20:35:23 MarkDuplicates Read 451,000,000 records. Elapsed time: 00:12:23s. Time for last 1,000,000: 1s. Last read position: chr14:88,574,765 INFO 2026-06-03 20:35:23 MarkDuplicates Tracking 306675 as yet unmatched pairs. 12716 records in RAM. INFO 2026-06-03 20:35:25 MarkDuplicates Read 452,000,000 records. Elapsed time: 00:12:24s. Time for last 1,000,000: 1s. Last read position: chr14:93,242,304 INFO 2026-06-03 20:35:25 MarkDuplicates Tracking 305290 as yet unmatched pairs. 11320 records in RAM. INFO 2026-06-03 20:35:26 MarkDuplicates Read 453,000,000 records. Elapsed time: 00:12:25s. Time for last 1,000,000: 1s. Last read position: chr14:100,276,621 INFO 2026-06-03 20:35:26 MarkDuplicates Tracking 303831 as yet unmatched pairs. 9849 records in RAM. INFO 2026-06-03 20:35:28 MarkDuplicates Read 454,000,000 records. Elapsed time: 00:12:27s. Time for last 1,000,000: 1s. Last read position: chr14:102,326,008 INFO 2026-06-03 20:35:28 MarkDuplicates Tracking 302329 as yet unmatched pairs. 8335 records in RAM. INFO 2026-06-03 20:35:29 MarkDuplicates Read 455,000,000 records. Elapsed time: 00:12:28s. Time for last 1,000,000: 1s. Last read position: chr14:103,560,648 INFO 2026-06-03 20:35:29 MarkDuplicates Tracking 300494 as yet unmatched pairs. 6500 records in RAM. INFO 2026-06-03 20:35:31 MarkDuplicates Read 456,000,000 records. Elapsed time: 00:12:30s. Time for last 1,000,000: 1s. Last read position: chr14:104,894,294 INFO 2026-06-03 20:35:31 MarkDuplicates Tracking 299019 as yet unmatched pairs. 5019 records in RAM. INFO 2026-06-03 20:35:32 MarkDuplicates Read 457,000,000 records. Elapsed time: 00:12:31s. Time for last 1,000,000: 1s. Last read position: chr14:105,587,146 INFO 2026-06-03 20:35:32 MarkDuplicates Tracking 302429 as yet unmatched pairs. 8425 records in RAM. INFO 2026-06-03 20:35:34 MarkDuplicates Read 458,000,000 records. Elapsed time: 00:12:33s. Time for last 1,000,000: 1s. Last read position: chr14:105,707,269 INFO 2026-06-03 20:35:34 MarkDuplicates Tracking 313356 as yet unmatched pairs. 19350 records in RAM. INFO 2026-06-03 20:35:35 MarkDuplicates Read 459,000,000 records. Elapsed time: 00:12:34s. Time for last 1,000,000: 1s. Last read position: chr14:105,741,674 INFO 2026-06-03 20:35:35 MarkDuplicates Tracking 297261 as yet unmatched pairs. 3251 records in RAM. INFO 2026-06-03 20:35:37 MarkDuplicates Read 460,000,000 records. Elapsed time: 00:12:36s. Time for last 1,000,000: 1s. Last read position: chr15:24,975,450 INFO 2026-06-03 20:35:37 MarkDuplicates Tracking 293712 as yet unmatched pairs. 26853 records in RAM. INFO 2026-06-03 20:35:39 MarkDuplicates Read 461,000,000 records. Elapsed time: 00:12:38s. Time for last 1,000,000: 1s. Last read position: chr15:32,718,144 INFO 2026-06-03 20:35:39 MarkDuplicates Tracking 293631 as yet unmatched pairs. 26763 records in RAM. INFO 2026-06-03 20:35:40 MarkDuplicates Read 462,000,000 records. Elapsed time: 00:12:39s. Time for last 1,000,000: 1s. Last read position: chr15:34,386,643 INFO 2026-06-03 20:35:40 MarkDuplicates Tracking 291348 as yet unmatched pairs. 24477 records in RAM. INFO 2026-06-03 20:35:42 MarkDuplicates Read 463,000,000 records. Elapsed time: 00:12:41s. Time for last 1,000,000: 1s. Last read position: chr15:40,471,883 INFO 2026-06-03 20:35:42 MarkDuplicates Tracking 289958 as yet unmatched pairs. 23083 records in RAM. INFO 2026-06-03 20:35:44 MarkDuplicates Read 464,000,000 records. Elapsed time: 00:12:43s. Time for last 1,000,000: 1s. Last read position: chr15:42,237,358 INFO 2026-06-03 20:35:44 MarkDuplicates Tracking 288429 as yet unmatched pairs. 21552 records in RAM. INFO 2026-06-03 20:35:45 MarkDuplicates Read 465,000,000 records. Elapsed time: 00:12:44s. Time for last 1,000,000: 1s. Last read position: chr15:43,756,739 INFO 2026-06-03 20:35:45 MarkDuplicates Tracking 288257 as yet unmatched pairs. 21376 records in RAM. INFO 2026-06-03 20:35:47 MarkDuplicates Read 466,000,000 records. Elapsed time: 00:12:46s. Time for last 1,000,000: 1s. Last read position: chr15:45,095,022 INFO 2026-06-03 20:35:47 MarkDuplicates Tracking 288146 as yet unmatched pairs. 21262 records in RAM. INFO 2026-06-03 20:35:48 MarkDuplicates Read 467,000,000 records. Elapsed time: 00:12:47s. Time for last 1,000,000: 1s. Last read position: chr15:48,136,843 INFO 2026-06-03 20:35:48 MarkDuplicates Tracking 284303 as yet unmatched pairs. 17416 records in RAM. INFO 2026-06-03 20:35:50 MarkDuplicates Read 468,000,000 records. Elapsed time: 00:12:49s. Time for last 1,000,000: 1s. Last read position: chr15:51,869,254 INFO 2026-06-03 20:35:50 MarkDuplicates Tracking 282950 as yet unmatched pairs. 16059 records in RAM. INFO 2026-06-03 20:35:51 MarkDuplicates Read 469,000,000 records. Elapsed time: 00:12:50s. Time for last 1,000,000: 1s. Last read position: chr15:58,646,191 INFO 2026-06-03 20:35:51 MarkDuplicates Tracking 281705 as yet unmatched pairs. 14809 records in RAM. INFO 2026-06-03 20:35:52 MarkDuplicates Read 470,000,000 records. Elapsed time: 00:12:51s. Time for last 1,000,000: 1s. Last read position: chr15:62,739,360 INFO 2026-06-03 20:35:52 MarkDuplicates Tracking 280365 as yet unmatched pairs. 13459 records in RAM. INFO 2026-06-03 20:35:54 MarkDuplicates Read 471,000,000 records. Elapsed time: 00:12:53s. Time for last 1,000,000: 1s. Last read position: chr15:64,680,311 INFO 2026-06-03 20:35:54 MarkDuplicates Tracking 278842 as yet unmatched pairs. 11930 records in RAM. INFO 2026-06-03 20:35:55 MarkDuplicates Read 472,000,000 records. Elapsed time: 00:12:54s. Time for last 1,000,000: 1s. Last read position: chr15:69,446,899 INFO 2026-06-03 20:35:55 MarkDuplicates Tracking 277400 as yet unmatched pairs. 10477 records in RAM. INFO 2026-06-03 20:35:57 MarkDuplicates Read 473,000,000 records. Elapsed time: 00:12:56s. Time for last 1,000,000: 1s. Last read position: chr15:73,708,373 INFO 2026-06-03 20:35:57 MarkDuplicates Tracking 276400 as yet unmatched pairs. 9474 records in RAM. INFO 2026-06-03 20:35:58 MarkDuplicates Read 474,000,000 records. Elapsed time: 00:12:57s. Time for last 1,000,000: 1s. Last read position: chr15:75,412,786 INFO 2026-06-03 20:35:58 MarkDuplicates Tracking 274702 as yet unmatched pairs. 7772 records in RAM. INFO 2026-06-03 20:35:59 MarkDuplicates Read 475,000,000 records. Elapsed time: 00:12:59s. Time for last 1,000,000: 1s. Last read position: chr15:78,490,470 INFO 2026-06-03 20:35:59 MarkDuplicates Tracking 273007 as yet unmatched pairs. 6072 records in RAM. INFO 2026-06-03 20:36:01 MarkDuplicates Read 476,000,000 records. Elapsed time: 00:13:00s. Time for last 1,000,000: 1s. Last read position: chr15:84,512,405 INFO 2026-06-03 20:36:01 MarkDuplicates Tracking 271855 as yet unmatched pairs. 4917 records in RAM. INFO 2026-06-03 20:36:02 MarkDuplicates Read 477,000,000 records. Elapsed time: 00:13:01s. Time for last 1,000,000: 1s. Last read position: chr15:88,907,337 INFO 2026-06-03 20:36:02 MarkDuplicates Tracking 271568 as yet unmatched pairs. 4620 records in RAM. INFO 2026-06-03 20:36:04 MarkDuplicates Read 478,000,000 records. Elapsed time: 00:13:03s. Time for last 1,000,000: 1s. Last read position: chr15:90,877,535 INFO 2026-06-03 20:36:04 MarkDuplicates Tracking 269556 as yet unmatched pairs. 2596 records in RAM. INFO 2026-06-03 20:36:05 MarkDuplicates Read 479,000,000 records. Elapsed time: 00:13:04s. Time for last 1,000,000: 1s. Last read position: chr15:99,131,463 INFO 2026-06-03 20:36:05 MarkDuplicates Tracking 269499 as yet unmatched pairs. 2532 records in RAM. INFO 2026-06-03 20:36:07 MarkDuplicates Read 480,000,000 records. Elapsed time: 00:13:06s. Time for last 1,000,000: 1s. Last read position: chr16:404,979 INFO 2026-06-03 20:36:07 MarkDuplicates Tracking 266410 as yet unmatched pairs. 40170 records in RAM. INFO 2026-06-03 20:36:08 MarkDuplicates Read 481,000,000 records. Elapsed time: 00:13:07s. Time for last 1,000,000: 1s. Last read position: chr16:1,446,289 INFO 2026-06-03 20:36:08 MarkDuplicates Tracking 264819 as yet unmatched pairs. 38574 records in RAM. INFO 2026-06-03 20:36:10 MarkDuplicates Read 482,000,000 records. Elapsed time: 00:13:09s. Time for last 1,000,000: 1s. Last read position: chr16:2,100,475 INFO 2026-06-03 20:36:10 MarkDuplicates Tracking 262726 as yet unmatched pairs. 36471 records in RAM. INFO 2026-06-03 20:36:12 MarkDuplicates Read 483,000,000 records. Elapsed time: 00:13:11s. Time for last 1,000,000: 1s. Last read position: chr16:2,762,331 INFO 2026-06-03 20:36:12 MarkDuplicates Tracking 261444 as yet unmatched pairs. 35183 records in RAM. INFO 2026-06-03 20:36:13 MarkDuplicates Read 484,000,000 records. Elapsed time: 00:13:12s. Time for last 1,000,000: 1s. Last read position: chr16:3,067,455 INFO 2026-06-03 20:36:13 MarkDuplicates Tracking 260330 as yet unmatched pairs. 34068 records in RAM. INFO 2026-06-03 20:36:15 MarkDuplicates Read 485,000,000 records. Elapsed time: 00:13:14s. Time for last 1,000,000: 1s. Last read position: chr16:4,799,762 INFO 2026-06-03 20:36:15 MarkDuplicates Tracking 258183 as yet unmatched pairs. 31916 records in RAM. INFO 2026-06-03 20:36:17 MarkDuplicates Read 486,000,000 records. Elapsed time: 00:13:16s. Time for last 1,000,000: 2s. Last read position: chr16:13,935,464 INFO 2026-06-03 20:36:17 MarkDuplicates Tracking 256682 as yet unmatched pairs. 30411 records in RAM. INFO 2026-06-03 20:36:18 MarkDuplicates Read 487,000,000 records. Elapsed time: 00:13:18s. Time for last 1,000,000: 1s. Last read position: chr16:15,031,875 INFO 2026-06-03 20:36:18 MarkDuplicates Tracking 256077 as yet unmatched pairs. 29796 records in RAM. INFO 2026-06-03 20:36:20 MarkDuplicates Read 488,000,000 records. Elapsed time: 00:13:19s. Time for last 1,000,000: 1s. Last read position: chr16:15,720,898 INFO 2026-06-03 20:36:20 MarkDuplicates Tracking 258134 as yet unmatched pairs. 31852 records in RAM. INFO 2026-06-03 20:36:21 MarkDuplicates Read 489,000,000 records. Elapsed time: 00:13:20s. Time for last 1,000,000: 1s. Last read position: chr16:15,753,414 INFO 2026-06-03 20:36:21 MarkDuplicates Tracking 255454 as yet unmatched pairs. 29168 records in RAM. INFO 2026-06-03 20:36:23 MarkDuplicates Read 490,000,000 records. Elapsed time: 00:13:22s. Time for last 1,000,000: 1s. Last read position: chr16:16,310,526 INFO 2026-06-03 20:36:23 MarkDuplicates Tracking 251936 as yet unmatched pairs. 25647 records in RAM. INFO 2026-06-03 20:36:24 MarkDuplicates Read 491,000,000 records. Elapsed time: 00:13:23s. Time for last 1,000,000: 1s. Last read position: chr16:18,358,329 INFO 2026-06-03 20:36:24 MarkDuplicates Tracking 251970 as yet unmatched pairs. 25681 records in RAM. INFO 2026-06-03 20:36:25 MarkDuplicates Read 492,000,000 records. Elapsed time: 00:13:24s. Time for last 1,000,000: 1s. Last read position: chr16:19,472,096 INFO 2026-06-03 20:36:25 MarkDuplicates Tracking 250789 as yet unmatched pairs. 24498 records in RAM. INFO 2026-06-03 20:36:26 MarkDuplicates Read 493,000,000 records. Elapsed time: 00:13:25s. Time for last 1,000,000: 1s. Last read position: chr16:21,812,599 INFO 2026-06-03 20:36:26 MarkDuplicates Tracking 249802 as yet unmatched pairs. 23509 records in RAM. INFO 2026-06-03 20:36:28 MarkDuplicates Read 494,000,000 records. Elapsed time: 00:13:27s. Time for last 1,000,000: 1s. Last read position: chr16:22,527,952 INFO 2026-06-03 20:36:28 MarkDuplicates Tracking 249337 as yet unmatched pairs. 23041 records in RAM. INFO 2026-06-03 20:36:29 MarkDuplicates Read 495,000,000 records. Elapsed time: 00:13:28s. Time for last 1,000,000: 1s. Last read position: chr16:24,930,912 INFO 2026-06-03 20:36:29 MarkDuplicates Tracking 248588 as yet unmatched pairs. 22292 records in RAM. INFO 2026-06-03 20:36:30 MarkDuplicates Read 496,000,000 records. Elapsed time: 00:13:29s. Time for last 1,000,000: 1s. Last read position: chr16:28,723,229 INFO 2026-06-03 20:36:30 MarkDuplicates Tracking 247271 as yet unmatched pairs. 20974 records in RAM. INFO 2026-06-03 20:36:31 MarkDuplicates Read 497,000,000 records. Elapsed time: 00:13:30s. Time for last 1,000,000: 1s. Last read position: chr16:29,461,896 INFO 2026-06-03 20:36:31 MarkDuplicates Tracking 246959 as yet unmatched pairs. 20656 records in RAM. INFO 2026-06-03 20:36:33 MarkDuplicates Read 498,000,000 records. Elapsed time: 00:13:32s. Time for last 1,000,000: 1s. Last read position: chr16:29,835,712 INFO 2026-06-03 20:36:33 MarkDuplicates Tracking 245998 as yet unmatched pairs. 19695 records in RAM. INFO 2026-06-03 20:36:34 MarkDuplicates Read 499,000,000 records. Elapsed time: 00:13:33s. Time for last 1,000,000: 1s. Last read position: chr16:30,195,116 INFO 2026-06-03 20:36:34 MarkDuplicates Tracking 244100 as yet unmatched pairs. 17790 records in RAM. INFO 2026-06-03 20:36:35 MarkDuplicates Read 500,000,000 records. Elapsed time: 00:13:34s. Time for last 1,000,000: 1s. Last read position: chr16:30,712,096 INFO 2026-06-03 20:36:35 MarkDuplicates Tracking 242597 as yet unmatched pairs. 16282 records in RAM. INFO 2026-06-03 20:36:37 MarkDuplicates Read 501,000,000 records. Elapsed time: 00:13:36s. Time for last 1,000,000: 2s. Last read position: chr16:31,185,143 INFO 2026-06-03 20:36:37 MarkDuplicates Tracking 242573 as yet unmatched pairs. 16251 records in RAM. INFO 2026-06-03 20:36:39 MarkDuplicates Read 502,000,000 records. Elapsed time: 00:13:38s. Time for last 1,000,000: 1s. Last read position: chr16:50,750,098 INFO 2026-06-03 20:36:39 MarkDuplicates Tracking 239777 as yet unmatched pairs. 13455 records in RAM. INFO 2026-06-03 20:36:40 MarkDuplicates Read 503,000,000 records. Elapsed time: 00:13:39s. Time for last 1,000,000: 1s. Last read position: chr16:56,940,182 INFO 2026-06-03 20:36:40 MarkDuplicates Tracking 238694 as yet unmatched pairs. 12366 records in RAM. INFO 2026-06-03 20:36:42 MarkDuplicates Read 504,000,000 records. Elapsed time: 00:13:41s. Time for last 1,000,000: 1s. Last read position: chr16:66,563,121 INFO 2026-06-03 20:36:42 MarkDuplicates Tracking 237184 as yet unmatched pairs. 10849 records in RAM. INFO 2026-06-03 20:36:44 MarkDuplicates Read 505,000,000 records. Elapsed time: 00:13:43s. Time for last 1,000,000: 1s. Last read position: chr16:67,878,201 INFO 2026-06-03 20:36:44 MarkDuplicates Tracking 235344 as yet unmatched pairs. 9007 records in RAM. INFO 2026-06-03 20:36:46 MarkDuplicates Read 506,000,000 records. Elapsed time: 00:13:45s. Time for last 1,000,000: 1s. Last read position: chr16:69,659,728 INFO 2026-06-03 20:36:46 MarkDuplicates Tracking 234007 as yet unmatched pairs. 7665 records in RAM. INFO 2026-06-03 20:36:47 MarkDuplicates Read 507,000,000 records. Elapsed time: 00:13:46s. Time for last 1,000,000: 1s. Last read position: chr16:71,921,436 INFO 2026-06-03 20:36:47 MarkDuplicates Tracking 233245 as yet unmatched pairs. 6901 records in RAM. INFO 2026-06-03 20:36:48 MarkDuplicates Read 508,000,000 records. Elapsed time: 00:13:48s. Time for last 1,000,000: 1s. Last read position: chr16:75,640,285 INFO 2026-06-03 20:36:48 MarkDuplicates Tracking 231073 as yet unmatched pairs. 4724 records in RAM. INFO 2026-06-03 20:36:50 MarkDuplicates Read 509,000,000 records. Elapsed time: 00:13:49s. Time for last 1,000,000: 1s. Last read position: chr16:85,663,599 INFO 2026-06-03 20:36:50 MarkDuplicates Tracking 229618 as yet unmatched pairs. 3259 records in RAM. INFO 2026-06-03 20:36:51 MarkDuplicates Read 510,000,000 records. Elapsed time: 00:13:50s. Time for last 1,000,000: 1s. Last read position: chr16:88,810,530 INFO 2026-06-03 20:36:51 MarkDuplicates Tracking 227984 as yet unmatched pairs. 1617 records in RAM. INFO 2026-06-03 20:36:53 MarkDuplicates Read 511,000,000 records. Elapsed time: 00:13:52s. Time for last 1,000,000: 1s. Last read position: chr17:745,696 INFO 2026-06-03 20:36:53 MarkDuplicates Tracking 226235 as yet unmatched pairs. 58656 records in RAM. INFO 2026-06-03 20:36:55 MarkDuplicates Read 512,000,000 records. Elapsed time: 00:13:54s. Time for last 1,000,000: 1s. Last read position: chr17:1,656,536 INFO 2026-06-03 20:36:55 MarkDuplicates Tracking 224914 as yet unmatched pairs. 57331 records in RAM. INFO 2026-06-03 20:36:56 MarkDuplicates Read 513,000,000 records. Elapsed time: 00:13:55s. Time for last 1,000,000: 1s. Last read position: chr17:3,652,306 INFO 2026-06-03 20:36:56 MarkDuplicates Tracking 223149 as yet unmatched pairs. 55566 records in RAM. INFO 2026-06-03 20:36:58 MarkDuplicates Read 514,000,000 records. Elapsed time: 00:13:57s. Time for last 1,000,000: 1s. Last read position: chr17:4,738,862 INFO 2026-06-03 20:36:58 MarkDuplicates Tracking 222093 as yet unmatched pairs. 54506 records in RAM. INFO 2026-06-03 20:36:59 MarkDuplicates Read 515,000,000 records. Elapsed time: 00:13:58s. Time for last 1,000,000: 1s. Last read position: chr17:5,541,896 INFO 2026-06-03 20:36:59 MarkDuplicates Tracking 220127 as yet unmatched pairs. 52535 records in RAM. INFO 2026-06-03 20:37:00 MarkDuplicates Read 516,000,000 records. Elapsed time: 00:14:00s. Time for last 1,000,000: 1s. Last read position: chr17:7,393,826 INFO 2026-06-03 20:37:00 MarkDuplicates Tracking 218793 as yet unmatched pairs. 51201 records in RAM. INFO 2026-06-03 20:37:02 MarkDuplicates Read 517,000,000 records. Elapsed time: 00:14:01s. Time for last 1,000,000: 1s. Last read position: chr17:7,676,102 INFO 2026-06-03 20:37:02 MarkDuplicates Tracking 217931 as yet unmatched pairs. 50338 records in RAM. INFO 2026-06-03 20:37:04 MarkDuplicates Read 518,000,000 records. Elapsed time: 00:14:03s. Time for last 1,000,000: 1s. Last read position: chr17:9,946,964 INFO 2026-06-03 20:37:04 MarkDuplicates Tracking 217586 as yet unmatched pairs. 49988 records in RAM. INFO 2026-06-03 20:37:05 MarkDuplicates Read 519,000,000 records. Elapsed time: 00:14:04s. Time for last 1,000,000: 1s. Last read position: chr17:16,382,421 INFO 2026-06-03 20:37:05 MarkDuplicates Tracking 215852 as yet unmatched pairs. 48253 records in RAM. INFO 2026-06-03 20:37:07 MarkDuplicates Read 520,000,000 records. Elapsed time: 00:14:06s. Time for last 1,000,000: 1s. Last read position: chr17:18,252,078 INFO 2026-06-03 20:37:07 MarkDuplicates Tracking 213269 as yet unmatched pairs. 45667 records in RAM. INFO 2026-06-03 20:37:09 MarkDuplicates Read 521,000,000 records. Elapsed time: 00:14:08s. Time for last 1,000,000: 1s. Last read position: chr17:22,204,379 INFO 2026-06-03 20:37:09 MarkDuplicates Tracking 211665 as yet unmatched pairs. 44056 records in RAM. INFO 2026-06-03 20:37:11 MarkDuplicates Read 522,000,000 records. Elapsed time: 00:14:10s. Time for last 1,000,000: 2s. Last read position: chr17:28,749,239 INFO 2026-06-03 20:37:11 MarkDuplicates Tracking 210839 as yet unmatched pairs. 43229 records in RAM. INFO 2026-06-03 20:38:16 MarkDuplicates Read 523,000,000 records. Elapsed time: 00:15:15s. Time for last 1,000,000: 65s. Last read position: chr17:31,229,059 INFO 2026-06-03 20:38:16 MarkDuplicates Tracking 208979 as yet unmatched pairs. 41368 records in RAM. INFO 2026-06-03 20:39:25 MarkDuplicates Read 524,000,000 records. Elapsed time: 00:16:24s. Time for last 1,000,000: 68s. Last read position: chr17:35,820,374 INFO 2026-06-03 20:39:25 MarkDuplicates Tracking 208406 as yet unmatched pairs. 40794 records in RAM. INFO 2026-06-03 20:39:26 MarkDuplicates Read 525,000,000 records. Elapsed time: 00:16:25s. Time for last 1,000,000: 1s. Last read position: chr17:38,466,527 INFO 2026-06-03 20:39:26 MarkDuplicates Tracking 206890 as yet unmatched pairs. 39274 records in RAM. INFO 2026-06-03 20:39:27 MarkDuplicates Read 526,000,000 records. Elapsed time: 00:16:27s. Time for last 1,000,000: 1s. Last read position: chr17:39,709,375 INFO 2026-06-03 20:39:27 MarkDuplicates Tracking 206052 as yet unmatched pairs. 38435 records in RAM. INFO 2026-06-03 20:39:29 MarkDuplicates Read 527,000,000 records. Elapsed time: 00:16:28s. Time for last 1,000,000: 1s. Last read position: chr17:40,189,312 INFO 2026-06-03 20:39:29 MarkDuplicates Tracking 203635 as yet unmatched pairs. 36018 records in RAM. INFO 2026-06-03 20:39:30 MarkDuplicates Read 528,000,000 records. Elapsed time: 00:16:30s. Time for last 1,000,000: 1s. Last read position: chr17:41,688,937 INFO 2026-06-03 20:39:30 MarkDuplicates Tracking 201984 as yet unmatched pairs. 34364 records in RAM. INFO 2026-06-03 20:39:32 MarkDuplicates Read 529,000,000 records. Elapsed time: 00:16:31s. Time for last 1,000,000: 1s. Last read position: chr17:42,404,631 INFO 2026-06-03 20:39:32 MarkDuplicates Tracking 201057 as yet unmatched pairs. 33434 records in RAM. INFO 2026-06-03 20:39:33 MarkDuplicates Read 530,000,000 records. Elapsed time: 00:16:32s. Time for last 1,000,000: 1s. Last read position: chr17:43,400,052 INFO 2026-06-03 20:39:33 MarkDuplicates Tracking 199062 as yet unmatched pairs. 31433 records in RAM. INFO 2026-06-03 20:39:35 MarkDuplicates Read 531,000,000 records. Elapsed time: 00:16:34s. Time for last 1,000,000: 1s. Last read position: chr17:45,115,093 INFO 2026-06-03 20:39:35 MarkDuplicates Tracking 197859 as yet unmatched pairs. 30226 records in RAM. INFO 2026-06-03 20:39:37 MarkDuplicates Read 532,000,000 records. Elapsed time: 00:16:36s. Time for last 1,000,000: 1s. Last read position: chr17:46,570,780 INFO 2026-06-03 20:39:37 MarkDuplicates Tracking 196478 as yet unmatched pairs. 28845 records in RAM. INFO 2026-06-03 20:39:38 MarkDuplicates Read 533,000,000 records. Elapsed time: 00:16:37s. Time for last 1,000,000: 1s. Last read position: chr17:48,705,208 INFO 2026-06-03 20:39:38 MarkDuplicates Tracking 194977 as yet unmatched pairs. 27344 records in RAM. INFO 2026-06-03 20:39:40 MarkDuplicates Read 534,000,000 records. Elapsed time: 00:16:39s. Time for last 1,000,000: 1s. Last read position: chr17:50,149,188 INFO 2026-06-03 20:39:40 MarkDuplicates Tracking 193595 as yet unmatched pairs. 25957 records in RAM. INFO 2026-06-03 20:39:42 MarkDuplicates Read 535,000,000 records. Elapsed time: 00:16:41s. Time for last 1,000,000: 1s. Last read position: chr17:50,189,521 INFO 2026-06-03 20:39:42 MarkDuplicates Tracking 199184 as yet unmatched pairs. 31540 records in RAM. INFO 2026-06-03 20:39:44 MarkDuplicates Read 536,000,000 records. Elapsed time: 00:16:43s. Time for last 1,000,000: 2s. Last read position: chr17:50,194,398 INFO 2026-06-03 20:39:44 MarkDuplicates Tracking 196994 as yet unmatched pairs. 29349 records in RAM. INFO 2026-06-03 20:39:45 MarkDuplicates Read 537,000,000 records. Elapsed time: 00:16:45s. Time for last 1,000,000: 1s. Last read position: chr17:50,198,469 INFO 2026-06-03 20:39:45 MarkDuplicates Tracking 194778 as yet unmatched pairs. 27132 records in RAM. INFO 2026-06-03 20:39:47 MarkDuplicates Read 538,000,000 records. Elapsed time: 00:16:46s. Time for last 1,000,000: 1s. Last read position: chr17:51,203,864 INFO 2026-06-03 20:39:47 MarkDuplicates Tracking 187032 as yet unmatched pairs. 19386 records in RAM. INFO 2026-06-03 20:39:48 MarkDuplicates Read 539,000,000 records. Elapsed time: 00:16:47s. Time for last 1,000,000: 1s. Last read position: chr17:59,660,544 INFO 2026-06-03 20:39:48 MarkDuplicates Tracking 188135 as yet unmatched pairs. 20484 records in RAM. INFO 2026-06-03 20:39:50 MarkDuplicates Read 540,000,000 records. Elapsed time: 00:16:49s. Time for last 1,000,000: 1s. Last read position: chr17:60,158,375 INFO 2026-06-03 20:39:50 MarkDuplicates Tracking 184817 as yet unmatched pairs. 17166 records in RAM. INFO 2026-06-03 20:39:51 MarkDuplicates Read 541,000,000 records. Elapsed time: 00:16:50s. Time for last 1,000,000: 1s. Last read position: chr17:63,833,112 INFO 2026-06-03 20:39:51 MarkDuplicates Tracking 182987 as yet unmatched pairs. 15336 records in RAM. INFO 2026-06-03 20:39:52 MarkDuplicates Read 542,000,000 records. Elapsed time: 00:16:52s. Time for last 1,000,000: 1s. Last read position: chr17:67,826,074 INFO 2026-06-03 20:39:52 MarkDuplicates Tracking 181485 as yet unmatched pairs. 13830 records in RAM. INFO 2026-06-03 20:39:54 MarkDuplicates Read 543,000,000 records. Elapsed time: 00:16:53s. Time for last 1,000,000: 1s. Last read position: chr17:73,286,217 INFO 2026-06-03 20:39:54 MarkDuplicates Tracking 180257 as yet unmatched pairs. 12600 records in RAM. INFO 2026-06-03 20:39:55 MarkDuplicates Read 544,000,000 records. Elapsed time: 00:16:54s. Time for last 1,000,000: 1s. Last read position: chr17:75,573,595 INFO 2026-06-03 20:39:55 MarkDuplicates Tracking 179113 as yet unmatched pairs. 11455 records in RAM. INFO 2026-06-03 20:39:57 MarkDuplicates Read 545,000,000 records. Elapsed time: 00:16:56s. Time for last 1,000,000: 1s. Last read position: chr17:75,753,802 INFO 2026-06-03 20:39:57 MarkDuplicates Tracking 177687 as yet unmatched pairs. 10027 records in RAM. INFO 2026-06-03 20:39:58 MarkDuplicates Read 546,000,000 records. Elapsed time: 00:16:57s. Time for last 1,000,000: 1s. Last read position: chr17:76,629,448 INFO 2026-06-03 20:39:58 MarkDuplicates Tracking 175869 as yet unmatched pairs. 8206 records in RAM. INFO 2026-06-03 20:39:59 MarkDuplicates Read 547,000,000 records. Elapsed time: 00:16:59s. Time for last 1,000,000: 1s. Last read position: chr17:78,857,569 INFO 2026-06-03 20:39:59 MarkDuplicates Tracking 174975 as yet unmatched pairs. 7309 records in RAM. INFO 2026-06-03 20:40:01 MarkDuplicates Read 548,000,000 records. Elapsed time: 00:17:00s. Time for last 1,000,000: 1s. Last read position: chr17:80,340,039 INFO 2026-06-03 20:40:01 MarkDuplicates Tracking 172879 as yet unmatched pairs. 5208 records in RAM. INFO 2026-06-03 20:40:03 MarkDuplicates Read 549,000,000 records. Elapsed time: 00:17:02s. Time for last 1,000,000: 1s. Last read position: chr17:81,589,076 INFO 2026-06-03 20:40:03 MarkDuplicates Tracking 170838 as yet unmatched pairs. 3166 records in RAM. INFO 2026-06-03 20:40:04 MarkDuplicates Read 550,000,000 records. Elapsed time: 00:17:03s. Time for last 1,000,000: 1s. Last read position: chr17:82,036,234 INFO 2026-06-03 20:40:04 MarkDuplicates Tracking 169251 as yet unmatched pairs. 1579 records in RAM. INFO 2026-06-03 20:40:05 MarkDuplicates Read 551,000,000 records. Elapsed time: 00:17:04s. Time for last 1,000,000: 1s. Last read position: chr18:756,699 INFO 2026-06-03 20:40:05 MarkDuplicates Tracking 167589 as yet unmatched pairs. 8635 records in RAM. INFO 2026-06-03 20:40:07 MarkDuplicates Read 552,000,000 records. Elapsed time: 00:17:06s. Time for last 1,000,000: 1s. Last read position: chr18:9,936,177 INFO 2026-06-03 20:40:07 MarkDuplicates Tracking 167087 as yet unmatched pairs. 8132 records in RAM. INFO 2026-06-03 20:40:08 MarkDuplicates Read 553,000,000 records. Elapsed time: 00:17:07s. Time for last 1,000,000: 1s. Last read position: chr18:24,178,010 INFO 2026-06-03 20:40:08 MarkDuplicates Tracking 164682 as yet unmatched pairs. 5723 records in RAM. INFO 2026-06-03 20:40:10 MarkDuplicates Read 554,000,000 records. Elapsed time: 00:17:09s. Time for last 1,000,000: 1s. Last read position: chr18:41,799,190 INFO 2026-06-03 20:40:10 MarkDuplicates Tracking 163318 as yet unmatched pairs. 4358 records in RAM. INFO 2026-06-03 20:40:12 MarkDuplicates Read 555,000,000 records. Elapsed time: 00:17:11s. Time for last 1,000,000: 2s. Last read position: chr18:54,188,906 INFO 2026-06-03 20:40:12 MarkDuplicates Tracking 162071 as yet unmatched pairs. 3110 records in RAM. INFO 2026-06-03 20:40:14 MarkDuplicates Read 556,000,000 records. Elapsed time: 00:17:13s. Time for last 1,000,000: 2s. Last read position: chr18:62,368,861 INFO 2026-06-03 20:40:14 MarkDuplicates Tracking 160576 as yet unmatched pairs. 1612 records in RAM. INFO 2026-06-03 20:40:17 MarkDuplicates Read 557,000,000 records. Elapsed time: 00:17:16s. Time for last 1,000,000: 2s. Last read position: chr19:307,064 INFO 2026-06-03 20:40:17 MarkDuplicates Tracking 159042 as yet unmatched pairs. 76544 records in RAM. INFO 2026-06-03 20:40:19 MarkDuplicates Read 558,000,000 records. Elapsed time: 00:17:18s. Time for last 1,000,000: 2s. Last read position: chr19:929,628 INFO 2026-06-03 20:40:19 MarkDuplicates Tracking 157260 as yet unmatched pairs. 74762 records in RAM. INFO 2026-06-03 20:40:20 MarkDuplicates Read 559,000,000 records. Elapsed time: 00:17:19s. Time for last 1,000,000: 1s. Last read position: chr19:1,300,504 INFO 2026-06-03 20:40:20 MarkDuplicates Tracking 156049 as yet unmatched pairs. 73549 records in RAM. INFO 2026-06-03 20:40:22 MarkDuplicates Read 560,000,000 records. Elapsed time: 00:17:21s. Time for last 1,000,000: 1s. Last read position: chr19:2,137,727 INFO 2026-06-03 20:40:22 MarkDuplicates Tracking 153844 as yet unmatched pairs. 71344 records in RAM. INFO 2026-06-03 20:40:23 MarkDuplicates Read 561,000,000 records. Elapsed time: 00:17:22s. Time for last 1,000,000: 1s. Last read position: chr19:3,544,662 INFO 2026-06-03 20:40:23 MarkDuplicates Tracking 152288 as yet unmatched pairs. 69788 records in RAM. INFO 2026-06-03 20:40:25 MarkDuplicates Read 562,000,000 records. Elapsed time: 00:17:24s. Time for last 1,000,000: 1s. Last read position: chr19:4,488,816 INFO 2026-06-03 20:40:25 MarkDuplicates Tracking 150302 as yet unmatched pairs. 67802 records in RAM. INFO 2026-06-03 20:40:26 MarkDuplicates Read 563,000,000 records. Elapsed time: 00:17:25s. Time for last 1,000,000: 1s. Last read position: chr19:5,789,255 INFO 2026-06-03 20:40:26 MarkDuplicates Tracking 148656 as yet unmatched pairs. 66152 records in RAM. INFO 2026-06-03 20:40:27 MarkDuplicates Read 564,000,000 records. Elapsed time: 00:17:27s. Time for last 1,000,000: 1s. Last read position: chr19:6,759,657 INFO 2026-06-03 20:40:27 MarkDuplicates Tracking 147272 as yet unmatched pairs. 64767 records in RAM. INFO 2026-06-03 20:40:29 MarkDuplicates Read 565,000,000 records. Elapsed time: 00:17:28s. Time for last 1,000,000: 1s. Last read position: chr19:8,390,402 INFO 2026-06-03 20:40:29 MarkDuplicates Tracking 145720 as yet unmatched pairs. 63214 records in RAM. INFO 2026-06-03 20:40:30 MarkDuplicates Read 566,000,000 records. Elapsed time: 00:17:30s. Time for last 1,000,000: 1s. Last read position: chr19:10,224,146 INFO 2026-06-03 20:40:30 MarkDuplicates Tracking 143834 as yet unmatched pairs. 61325 records in RAM. INFO 2026-06-03 20:40:32 MarkDuplicates Read 567,000,000 records. Elapsed time: 00:17:31s. Time for last 1,000,000: 1s. Last read position: chr19:10,986,961 INFO 2026-06-03 20:40:32 MarkDuplicates Tracking 142441 as yet unmatched pairs. 59932 records in RAM. INFO 2026-06-03 20:40:33 MarkDuplicates Read 568,000,000 records. Elapsed time: 00:17:32s. Time for last 1,000,000: 1s. Last read position: chr19:11,666,754 INFO 2026-06-03 20:40:33 MarkDuplicates Tracking 140727 as yet unmatched pairs. 58218 records in RAM. INFO 2026-06-03 20:40:35 MarkDuplicates Read 569,000,000 records. Elapsed time: 00:17:34s. Time for last 1,000,000: 1s. Last read position: chr19:13,025,136 INFO 2026-06-03 20:40:35 MarkDuplicates Tracking 139641 as yet unmatched pairs. 57131 records in RAM. INFO 2026-06-03 20:40:36 MarkDuplicates Read 570,000,000 records. Elapsed time: 00:17:35s. Time for last 1,000,000: 1s. Last read position: chr19:14,452,012 INFO 2026-06-03 20:40:36 MarkDuplicates Tracking 137564 as yet unmatched pairs. 55050 records in RAM. INFO 2026-06-03 20:40:38 MarkDuplicates Read 571,000,000 records. Elapsed time: 00:17:37s. Time for last 1,000,000: 1s. Last read position: chr19:15,244,742 INFO 2026-06-03 20:40:38 MarkDuplicates Tracking 137539 as yet unmatched pairs. 55022 records in RAM. INFO 2026-06-03 20:40:40 MarkDuplicates Read 572,000,000 records. Elapsed time: 00:17:39s. Time for last 1,000,000: 2s. Last read position: chr19:16,869,675 INFO 2026-06-03 20:40:40 MarkDuplicates Tracking 134455 as yet unmatched pairs. 51932 records in RAM. INFO 2026-06-03 20:40:42 MarkDuplicates Read 573,000,000 records. Elapsed time: 00:17:41s. Time for last 1,000,000: 1s. Last read position: chr19:17,862,110 INFO 2026-06-03 20:40:42 MarkDuplicates Tracking 133349 as yet unmatched pairs. 50826 records in RAM. INFO 2026-06-03 20:40:43 MarkDuplicates Read 574,000,000 records. Elapsed time: 00:17:43s. Time for last 1,000,000: 1s. Last read position: chr19:18,777,236 INFO 2026-06-03 20:40:43 MarkDuplicates Tracking 131195 as yet unmatched pairs. 48671 records in RAM. INFO 2026-06-03 20:40:45 MarkDuplicates Read 575,000,000 records. Elapsed time: 00:17:44s. Time for last 1,000,000: 1s. Last read position: chr19:30,007,494 INFO 2026-06-03 20:40:45 MarkDuplicates Tracking 129305 as yet unmatched pairs. 46775 records in RAM. INFO 2026-06-03 20:40:46 MarkDuplicates Read 576,000,000 records. Elapsed time: 00:17:45s. Time for last 1,000,000: 1s. Last read position: chr19:35,123,278 INFO 2026-06-03 20:40:46 MarkDuplicates Tracking 129912 as yet unmatched pairs. 47381 records in RAM. INFO 2026-06-03 20:40:48 MarkDuplicates Read 577,000,000 records. Elapsed time: 00:17:47s. Time for last 1,000,000: 1s. Last read position: chr19:36,039,424 INFO 2026-06-03 20:40:48 MarkDuplicates Tracking 125554 as yet unmatched pairs. 43021 records in RAM. INFO 2026-06-03 20:40:49 MarkDuplicates Read 578,000,000 records. Elapsed time: 00:17:48s. Time for last 1,000,000: 1s. Last read position: chr19:38,647,807 INFO 2026-06-03 20:40:49 MarkDuplicates Tracking 125757 as yet unmatched pairs. 43224 records in RAM. INFO 2026-06-03 20:40:51 MarkDuplicates Read 579,000,000 records. Elapsed time: 00:17:50s. Time for last 1,000,000: 1s. Last read position: chr19:38,849,845 INFO 2026-06-03 20:40:51 MarkDuplicates Tracking 122512 as yet unmatched pairs. 39979 records in RAM. INFO 2026-06-03 20:40:52 MarkDuplicates Read 580,000,000 records. Elapsed time: 00:17:51s. Time for last 1,000,000: 1s. Last read position: chr19:39,863,860 INFO 2026-06-03 20:40:52 MarkDuplicates Tracking 122579 as yet unmatched pairs. 40044 records in RAM. INFO 2026-06-03 20:40:53 MarkDuplicates Read 581,000,000 records. Elapsed time: 00:17:53s. Time for last 1,000,000: 1s. Last read position: chr19:39,875,417 INFO 2026-06-03 20:40:53 MarkDuplicates Tracking 125107 as yet unmatched pairs. 42568 records in RAM. INFO 2026-06-03 20:40:54 MarkDuplicates Read 582,000,000 records. Elapsed time: 00:17:54s. Time for last 1,000,000: 1s. Last read position: chr19:39,877,259 INFO 2026-06-03 20:40:54 MarkDuplicates Tracking 124968 as yet unmatched pairs. 42428 records in RAM. INFO 2026-06-03 20:40:56 MarkDuplicates Read 583,000,000 records. Elapsed time: 00:17:55s. Time for last 1,000,000: 1s. Last read position: chr19:39,883,353 INFO 2026-06-03 20:40:56 MarkDuplicates Tracking 127647 as yet unmatched pairs. 45107 records in RAM. INFO 2026-06-03 20:40:57 MarkDuplicates Read 584,000,000 records. Elapsed time: 00:17:56s. Time for last 1,000,000: 1s. Last read position: chr19:39,889,595 INFO 2026-06-03 20:40:57 MarkDuplicates Tracking 120593 as yet unmatched pairs. 38051 records in RAM. INFO 2026-06-03 20:40:58 MarkDuplicates Read 585,000,000 records. Elapsed time: 00:17:58s. Time for last 1,000,000: 1s. Last read position: chr19:39,891,859 INFO 2026-06-03 20:40:58 MarkDuplicates Tracking 130990 as yet unmatched pairs. 48448 records in RAM. INFO 2026-06-03 20:41:00 MarkDuplicates Read 586,000,000 records. Elapsed time: 00:17:59s. Time for last 1,000,000: 1s. Last read position: chr19:39,893,425 INFO 2026-06-03 20:41:00 MarkDuplicates Tracking 120595 as yet unmatched pairs. 38053 records in RAM. INFO 2026-06-03 20:41:01 MarkDuplicates Read 587,000,000 records. Elapsed time: 00:18:00s. Time for last 1,000,000: 1s. Last read position: chr19:39,899,634 INFO 2026-06-03 20:41:01 MarkDuplicates Tracking 116839 as yet unmatched pairs. 34297 records in RAM. INFO 2026-06-03 20:41:02 MarkDuplicates Read 588,000,000 records. Elapsed time: 00:18:02s. Time for last 1,000,000: 1s. Last read position: chr19:39,913,690 INFO 2026-06-03 20:41:02 MarkDuplicates Tracking 118129 as yet unmatched pairs. 35587 records in RAM. INFO 2026-06-03 20:41:04 MarkDuplicates Read 589,000,000 records. Elapsed time: 00:18:03s. Time for last 1,000,000: 1s. Last read position: chr19:39,918,430 INFO 2026-06-03 20:41:04 MarkDuplicates Tracking 115224 as yet unmatched pairs. 32681 records in RAM. INFO 2026-06-03 20:41:05 MarkDuplicates Read 590,000,000 records. Elapsed time: 00:18:05s. Time for last 1,000,000: 1s. Last read position: chr19:39,943,397 INFO 2026-06-03 20:41:05 MarkDuplicates Tracking 108893 as yet unmatched pairs. 26350 records in RAM. INFO 2026-06-03 20:41:08 MarkDuplicates Read 591,000,000 records. Elapsed time: 00:18:07s. Time for last 1,000,000: 2s. Last read position: chr19:40,622,405 INFO 2026-06-03 20:41:08 MarkDuplicates Tracking 107397 as yet unmatched pairs. 24847 records in RAM. INFO 2026-06-03 20:41:09 MarkDuplicates Read 592,000,000 records. Elapsed time: 00:18:08s. Time for last 1,000,000: 1s. Last read position: chr19:41,686,921 INFO 2026-06-03 20:41:09 MarkDuplicates Tracking 105190 as yet unmatched pairs. 22640 records in RAM. INFO 2026-06-03 20:41:11 MarkDuplicates Read 593,000,000 records. Elapsed time: 00:18:10s. Time for last 1,000,000: 1s. Last read position: chr19:41,715,877 INFO 2026-06-03 20:41:11 MarkDuplicates Tracking 110229 as yet unmatched pairs. 27677 records in RAM. INFO 2026-06-03 20:41:12 MarkDuplicates Read 594,000,000 records. Elapsed time: 00:18:11s. Time for last 1,000,000: 1s. Last read position: chr19:41,755,571 INFO 2026-06-03 20:41:12 MarkDuplicates Tracking 105878 as yet unmatched pairs. 23326 records in RAM. INFO 2026-06-03 20:41:13 MarkDuplicates Read 595,000,000 records. Elapsed time: 00:18:12s. Time for last 1,000,000: 1s. Last read position: chr19:42,272,778 INFO 2026-06-03 20:41:13 MarkDuplicates Tracking 101424 as yet unmatched pairs. 18868 records in RAM. INFO 2026-06-03 20:41:15 MarkDuplicates Read 596,000,000 records. Elapsed time: 00:18:14s. Time for last 1,000,000: 1s. Last read position: chr19:43,511,451 INFO 2026-06-03 20:41:15 MarkDuplicates Tracking 99972 as yet unmatched pairs. 17413 records in RAM. INFO 2026-06-03 20:41:16 MarkDuplicates Read 597,000,000 records. Elapsed time: 00:18:15s. Time for last 1,000,000: 1s. Last read position: chr19:45,271,545 INFO 2026-06-03 20:41:16 MarkDuplicates Tracking 97685 as yet unmatched pairs. 15119 records in RAM. INFO 2026-06-03 20:41:18 MarkDuplicates Read 598,000,000 records. Elapsed time: 00:18:17s. Time for last 1,000,000: 1s. Last read position: chr19:46,608,238 INFO 2026-06-03 20:41:18 MarkDuplicates Tracking 97072 as yet unmatched pairs. 14502 records in RAM. INFO 2026-06-03 20:41:19 MarkDuplicates Read 599,000,000 records. Elapsed time: 00:18:18s. Time for last 1,000,000: 1s. Last read position: chr19:48,150,198 INFO 2026-06-03 20:41:19 MarkDuplicates Tracking 94311 as yet unmatched pairs. 11740 records in RAM. INFO 2026-06-03 20:41:20 MarkDuplicates Read 600,000,000 records. Elapsed time: 00:18:19s. Time for last 1,000,000: 1s. Last read position: chr19:49,104,687 INFO 2026-06-03 20:41:20 MarkDuplicates Tracking 93077 as yet unmatched pairs. 10506 records in RAM. INFO 2026-06-03 20:41:22 MarkDuplicates Read 601,000,000 records. Elapsed time: 00:18:21s. Time for last 1,000,000: 1s. Last read position: chr19:49,636,676 INFO 2026-06-03 20:41:22 MarkDuplicates Tracking 91632 as yet unmatched pairs. 9061 records in RAM. INFO 2026-06-03 20:41:23 MarkDuplicates Read 602,000,000 records. Elapsed time: 00:18:23s. Time for last 1,000,000: 1s. Last read position: chr19:50,276,014 INFO 2026-06-03 20:41:23 MarkDuplicates Tracking 89703 as yet unmatched pairs. 7125 records in RAM. INFO 2026-06-03 20:41:25 MarkDuplicates Read 603,000,000 records. Elapsed time: 00:18:24s. Time for last 1,000,000: 1s. Last read position: chr19:52,915,265 INFO 2026-06-03 20:41:25 MarkDuplicates Tracking 87929 as yet unmatched pairs. 5348 records in RAM. INFO 2026-06-03 20:41:26 MarkDuplicates Read 604,000,000 records. Elapsed time: 00:18:25s. Time for last 1,000,000: 1s. Last read position: chr19:54,462,784 INFO 2026-06-03 20:41:26 MarkDuplicates Tracking 86462 as yet unmatched pairs. 3880 records in RAM. INFO 2026-06-03 20:41:27 MarkDuplicates Read 605,000,000 records. Elapsed time: 00:18:26s. Time for last 1,000,000: 1s. Last read position: chr19:55,602,115 INFO 2026-06-03 20:41:27 MarkDuplicates Tracking 84744 as yet unmatched pairs. 2162 records in RAM. INFO 2026-06-03 20:41:29 MarkDuplicates Read 606,000,000 records. Elapsed time: 00:18:28s. Time for last 1,000,000: 1s. Last read position: chr19:58,294,593 INFO 2026-06-03 20:41:29 MarkDuplicates Tracking 83245 as yet unmatched pairs. 663 records in RAM. INFO 2026-06-03 20:41:30 MarkDuplicates Read 607,000,000 records. Elapsed time: 00:18:30s. Time for last 1,000,000: 1s. Last read position: chr20:2,655,463 INFO 2026-06-03 20:41:30 MarkDuplicates Tracking 81772 as yet unmatched pairs. 19537 records in RAM. INFO 2026-06-03 20:41:32 MarkDuplicates Read 608,000,000 records. Elapsed time: 00:18:31s. Time for last 1,000,000: 1s. Last read position: chr20:5,165,814 INFO 2026-06-03 20:41:32 MarkDuplicates Tracking 80281 as yet unmatched pairs. 18042 records in RAM. INFO 2026-06-03 20:41:34 MarkDuplicates Read 609,000,000 records. Elapsed time: 00:18:33s. Time for last 1,000,000: 1s. Last read position: chr20:17,658,633 INFO 2026-06-03 20:41:34 MarkDuplicates Tracking 78926 as yet unmatched pairs. 16687 records in RAM. INFO 2026-06-03 20:41:35 MarkDuplicates Read 610,000,000 records. Elapsed time: 00:18:35s. Time for last 1,000,000: 1s. Last read position: chr20:24,983,690 INFO 2026-06-03 20:41:35 MarkDuplicates Tracking 77437 as yet unmatched pairs. 15195 records in RAM. INFO 2026-06-03 20:41:37 MarkDuplicates Read 611,000,000 records. Elapsed time: 00:18:36s. Time for last 1,000,000: 1s. Last read position: chr20:32,704,036 INFO 2026-06-03 20:41:37 MarkDuplicates Tracking 75935 as yet unmatched pairs. 13681 records in RAM. INFO 2026-06-03 20:41:38 MarkDuplicates Read 612,000,000 records. Elapsed time: 00:18:38s. Time for last 1,000,000: 1s. Last read position: chr20:35,547,434 INFO 2026-06-03 20:41:38 MarkDuplicates Tracking 74683 as yet unmatched pairs. 12428 records in RAM. INFO 2026-06-03 20:41:40 MarkDuplicates Read 613,000,000 records. Elapsed time: 00:18:39s. Time for last 1,000,000: 1s. Last read position: chr20:37,179,351 INFO 2026-06-03 20:41:40 MarkDuplicates Tracking 73320 as yet unmatched pairs. 11061 records in RAM. INFO 2026-06-03 20:41:41 MarkDuplicates Read 614,000,000 records. Elapsed time: 00:18:40s. Time for last 1,000,000: 1s. Last read position: chr20:43,460,968 INFO 2026-06-03 20:41:41 MarkDuplicates Tracking 72086 as yet unmatched pairs. 9821 records in RAM. INFO 2026-06-03 20:41:42 MarkDuplicates Read 615,000,000 records. Elapsed time: 00:18:42s. Time for last 1,000,000: 1s. Last read position: chr20:45,892,845 INFO 2026-06-03 20:41:42 MarkDuplicates Tracking 71053 as yet unmatched pairs. 8788 records in RAM. INFO 2026-06-03 20:41:44 MarkDuplicates Read 616,000,000 records. Elapsed time: 00:18:43s. Time for last 1,000,000: 1s. Last read position: chr20:49,254,617 INFO 2026-06-03 20:41:44 MarkDuplicates Tracking 68671 as yet unmatched pairs. 6404 records in RAM. INFO 2026-06-03 20:41:46 MarkDuplicates Read 617,000,000 records. Elapsed time: 00:18:45s. Time for last 1,000,000: 1s. Last read position: chr20:56,359,012 INFO 2026-06-03 20:41:46 MarkDuplicates Tracking 67530 as yet unmatched pairs. 5259 records in RAM. INFO 2026-06-03 20:41:47 MarkDuplicates Read 618,000,000 records. Elapsed time: 00:18:46s. Time for last 1,000,000: 1s. Last read position: chr20:62,139,144 INFO 2026-06-03 20:41:47 MarkDuplicates Tracking 65774 as yet unmatched pairs. 3502 records in RAM. INFO 2026-06-03 20:41:48 MarkDuplicates Read 619,000,000 records. Elapsed time: 00:18:47s. Time for last 1,000,000: 1s. Last read position: chr20:63,272,826 INFO 2026-06-03 20:41:48 MarkDuplicates Tracking 63893 as yet unmatched pairs. 1620 records in RAM. INFO 2026-06-03 20:41:50 MarkDuplicates Read 620,000,000 records. Elapsed time: 00:18:49s. Time for last 1,000,000: 1s. Last read position: chr21:5,141,355 INFO 2026-06-03 20:41:50 MarkDuplicates Tracking 62193 as yet unmatched pairs. 13571 records in RAM. INFO 2026-06-03 20:41:51 MarkDuplicates Read 621,000,000 records. Elapsed time: 00:18:50s. Time for last 1,000,000: 1s. Last read position: chr21:8,397,705 INFO 2026-06-03 20:41:51 MarkDuplicates Tracking 61299 as yet unmatched pairs. 12672 records in RAM. INFO 2026-06-03 20:41:52 MarkDuplicates Read 622,000,000 records. Elapsed time: 00:18:51s. Time for last 1,000,000: 0s. Last read position: chr21:8,460,119 INFO 2026-06-03 20:41:52 MarkDuplicates Tracking 60303 as yet unmatched pairs. 11673 records in RAM. INFO 2026-06-03 20:41:53 MarkDuplicates Read 623,000,000 records. Elapsed time: 00:18:52s. Time for last 1,000,000: 1s. Last read position: chr21:29,038,367 INFO 2026-06-03 20:41:53 MarkDuplicates Tracking 59117 as yet unmatched pairs. 10486 records in RAM. INFO 2026-06-03 20:41:55 MarkDuplicates Read 624,000,000 records. Elapsed time: 00:18:54s. Time for last 1,000,000: 1s. Last read position: chr21:33,907,425 INFO 2026-06-03 20:41:55 MarkDuplicates Tracking 58005 as yet unmatched pairs. 9370 records in RAM. INFO 2026-06-03 20:41:56 MarkDuplicates Read 625,000,000 records. Elapsed time: 00:18:55s. Time for last 1,000,000: 1s. Last read position: chr21:39,660,987 INFO 2026-06-03 20:41:56 MarkDuplicates Tracking 56810 as yet unmatched pairs. 8172 records in RAM. INFO 2026-06-03 20:41:58 MarkDuplicates Read 626,000,000 records. Elapsed time: 00:18:57s. Time for last 1,000,000: 1s. Last read position: chr21:41,992,617 INFO 2026-06-03 20:41:58 MarkDuplicates Tracking 54688 as yet unmatched pairs. 6046 records in RAM. INFO 2026-06-03 20:41:59 MarkDuplicates Read 627,000,000 records. Elapsed time: 00:18:59s. Time for last 1,000,000: 1s. Last read position: chr21:44,323,904 INFO 2026-06-03 20:41:59 MarkDuplicates Tracking 53390 as yet unmatched pairs. 4748 records in RAM. INFO 2026-06-03 20:42:02 MarkDuplicates Read 628,000,000 records. Elapsed time: 00:19:01s. Time for last 1,000,000: 2s. Last read position: chr21:45,515,780 INFO 2026-06-03 20:42:02 MarkDuplicates Tracking 51272 as yet unmatched pairs. 2628 records in RAM. INFO 2026-06-03 20:42:03 MarkDuplicates Read 629,000,000 records. Elapsed time: 00:19:02s. Time for last 1,000,000: 1s. Last read position: chr21:46,126,094 INFO 2026-06-03 20:42:03 MarkDuplicates Tracking 51051 as yet unmatched pairs. 2406 records in RAM. INFO 2026-06-03 20:42:05 MarkDuplicates Read 630,000,000 records. Elapsed time: 00:19:04s. Time for last 1,000,000: 1s. Last read position: chr22:17,841,827 INFO 2026-06-03 20:42:05 MarkDuplicates Tracking 48512 as yet unmatched pairs. 21867 records in RAM. INFO 2026-06-03 20:42:06 MarkDuplicates Read 631,000,000 records. Elapsed time: 00:19:05s. Time for last 1,000,000: 1s. Last read position: chr22:20,734,435 INFO 2026-06-03 20:42:06 MarkDuplicates Tracking 46675 as yet unmatched pairs. 20030 records in RAM. INFO 2026-06-03 20:42:07 MarkDuplicates Read 632,000,000 records. Elapsed time: 00:19:06s. Time for last 1,000,000: 1s. Last read position: chr22:23,312,999 INFO 2026-06-03 20:42:07 MarkDuplicates Tracking 45530 as yet unmatched pairs. 18882 records in RAM. INFO 2026-06-03 20:42:09 MarkDuplicates Read 633,000,000 records. Elapsed time: 00:19:08s. Time for last 1,000,000: 1s. Last read position: chr22:26,541,359 INFO 2026-06-03 20:42:09 MarkDuplicates Tracking 43613 as yet unmatched pairs. 16965 records in RAM. INFO 2026-06-03 20:42:11 MarkDuplicates Read 634,000,000 records. Elapsed time: 00:19:10s. Time for last 1,000,000: 1s. Last read position: chr22:29,311,558 INFO 2026-06-03 20:42:11 MarkDuplicates Tracking 42124 as yet unmatched pairs. 15475 records in RAM. INFO 2026-06-03 20:42:12 MarkDuplicates Read 635,000,000 records. Elapsed time: 00:19:11s. Time for last 1,000,000: 1s. Last read position: chr22:31,262,741 INFO 2026-06-03 20:42:12 MarkDuplicates Tracking 40604 as yet unmatched pairs. 13955 records in RAM. INFO 2026-06-03 20:42:13 MarkDuplicates Read 636,000,000 records. Elapsed time: 00:19:13s. Time for last 1,000,000: 1s. Last read position: chr22:36,282,634 INFO 2026-06-03 20:42:13 MarkDuplicates Tracking 39623 as yet unmatched pairs. 12974 records in RAM. INFO 2026-06-03 20:42:15 MarkDuplicates Read 637,000,000 records. Elapsed time: 00:19:14s. Time for last 1,000,000: 1s. Last read position: chr22:37,061,542 INFO 2026-06-03 20:42:15 MarkDuplicates Tracking 37527 as yet unmatched pairs. 10875 records in RAM. INFO 2026-06-03 20:42:17 MarkDuplicates Read 638,000,000 records. Elapsed time: 00:19:16s. Time for last 1,000,000: 1s. Last read position: chr22:38,085,689 INFO 2026-06-03 20:42:17 MarkDuplicates Tracking 36208 as yet unmatched pairs. 9554 records in RAM. INFO 2026-06-03 20:42:18 MarkDuplicates Read 639,000,000 records. Elapsed time: 00:19:17s. Time for last 1,000,000: 1s. Last read position: chr22:39,488,827 INFO 2026-06-03 20:42:18 MarkDuplicates Tracking 34141 as yet unmatched pairs. 7487 records in RAM. INFO 2026-06-03 20:42:20 MarkDuplicates Read 640,000,000 records. Elapsed time: 00:19:19s. Time for last 1,000,000: 1s. Last read position: chr22:41,499,730 INFO 2026-06-03 20:42:20 MarkDuplicates Tracking 33059 as yet unmatched pairs. 6395 records in RAM. INFO 2026-06-03 20:42:21 MarkDuplicates Read 641,000,000 records. Elapsed time: 00:19:20s. Time for last 1,000,000: 1s. Last read position: chr22:43,159,392 INFO 2026-06-03 20:42:21 MarkDuplicates Tracking 31917 as yet unmatched pairs. 5253 records in RAM. INFO 2026-06-03 20:42:23 MarkDuplicates Read 642,000,000 records. Elapsed time: 00:19:22s. Time for last 1,000,000: 1s. Last read position: chr22:49,886,507 INFO 2026-06-03 20:42:23 MarkDuplicates Tracking 29868 as yet unmatched pairs. 3204 records in RAM. INFO 2026-06-03 20:42:24 MarkDuplicates Read 643,000,000 records. Elapsed time: 00:19:23s. Time for last 1,000,000: 1s. Last read position: chr22:50,464,587 INFO 2026-06-03 20:42:24 MarkDuplicates Tracking 28183 as yet unmatched pairs. 1519 records in RAM. INFO 2026-06-03 20:42:26 MarkDuplicates Read 644,000,000 records. Elapsed time: 00:19:25s. Time for last 1,000,000: 2s. Last read position: chrX:3,310,679 INFO 2026-06-03 20:42:26 MarkDuplicates Tracking 26035 as yet unmatched pairs. 22280 records in RAM. INFO 2026-06-03 20:42:28 MarkDuplicates Read 645,000,000 records. Elapsed time: 00:19:27s. Time for last 1,000,000: 1s. Last read position: chrX:17,047,413 INFO 2026-06-03 20:42:28 MarkDuplicates Tracking 24643 as yet unmatched pairs. 20887 records in RAM. INFO 2026-06-03 20:42:29 MarkDuplicates Read 646,000,000 records. Elapsed time: 00:19:28s. Time for last 1,000,000: 1s. Last read position: chrX:40,052,108 INFO 2026-06-03 20:42:29 MarkDuplicates Tracking 23800 as yet unmatched pairs. 20040 records in RAM. INFO 2026-06-03 20:42:31 MarkDuplicates Read 647,000,000 records. Elapsed time: 00:19:30s. Time for last 1,000,000: 1s. Last read position: chrX:46,575,344 INFO 2026-06-03 20:42:31 MarkDuplicates Tracking 22005 as yet unmatched pairs. 18245 records in RAM. INFO 2026-06-03 20:42:32 MarkDuplicates Read 648,000,000 records. Elapsed time: 00:19:31s. Time for last 1,000,000: 1s. Last read position: chrX:48,909,811 INFO 2026-06-03 20:42:32 MarkDuplicates Tracking 20766 as yet unmatched pairs. 17006 records in RAM. INFO 2026-06-03 20:42:34 MarkDuplicates Read 649,000,000 records. Elapsed time: 00:19:33s. Time for last 1,000,000: 1s. Last read position: chrX:53,405,872 INFO 2026-06-03 20:42:34 MarkDuplicates Tracking 19260 as yet unmatched pairs. 15500 records in RAM. INFO 2026-06-03 20:42:35 MarkDuplicates Read 650,000,000 records. Elapsed time: 00:19:34s. Time for last 1,000,000: 1s. Last read position: chrX:65,731,117 INFO 2026-06-03 20:42:35 MarkDuplicates Tracking 18413 as yet unmatched pairs. 14653 records in RAM. INFO 2026-06-03 20:42:36 MarkDuplicates Read 651,000,000 records. Elapsed time: 00:19:36s. Time for last 1,000,000: 1s. Last read position: chrX:71,383,035 INFO 2026-06-03 20:42:36 MarkDuplicates Tracking 16572 as yet unmatched pairs. 12812 records in RAM. INFO 2026-06-03 20:42:38 MarkDuplicates Read 652,000,000 records. Elapsed time: 00:19:37s. Time for last 1,000,000: 1s. Last read position: chrX:80,699,965 INFO 2026-06-03 20:42:38 MarkDuplicates Tracking 15238 as yet unmatched pairs. 11478 records in RAM. INFO 2026-06-03 20:42:39 MarkDuplicates Read 653,000,000 records. Elapsed time: 00:19:38s. Time for last 1,000,000: 1s. Last read position: chrX:106,840,738 INFO 2026-06-03 20:42:39 MarkDuplicates Tracking 13967 as yet unmatched pairs. 10206 records in RAM. INFO 2026-06-03 20:42:41 MarkDuplicates Read 654,000,000 records. Elapsed time: 00:19:40s. Time for last 1,000,000: 1s. Last read position: chrX:119,936,343 INFO 2026-06-03 20:42:41 MarkDuplicates Tracking 12608 as yet unmatched pairs. 8847 records in RAM. INFO 2026-06-03 20:42:42 MarkDuplicates Read 655,000,000 records. Elapsed time: 00:19:41s. Time for last 1,000,000: 1s. Last read position: chrX:136,208,599 INFO 2026-06-03 20:42:42 MarkDuplicates Tracking 13873 as yet unmatched pairs. 10112 records in RAM. INFO 2026-06-03 20:42:43 MarkDuplicates Read 656,000,000 records. Elapsed time: 00:19:43s. Time for last 1,000,000: 1s. Last read position: chrX:153,770,197 INFO 2026-06-03 20:42:43 MarkDuplicates Tracking 10193 as yet unmatched pairs. 6431 records in RAM. INFO 2026-06-03 20:42:45 MarkDuplicates Read 657,000,000 records. Elapsed time: 00:19:44s. Time for last 1,000,000: 1s. Last read position: chrX:154,349,778 INFO 2026-06-03 20:42:45 MarkDuplicates Tracking 10509 as yet unmatched pairs. 6747 records in RAM. INFO 2026-06-03 20:42:46 MarkDuplicates Read 658,000,000 records. Elapsed time: 00:19:45s. Time for last 1,000,000: 1s. Last read position: chrX:154,360,228 INFO 2026-06-03 20:42:46 MarkDuplicates Tracking 9735 as yet unmatched pairs. 5973 records in RAM. INFO 2026-06-03 20:42:48 MarkDuplicates Read 659,000,000 records. Elapsed time: 00:19:47s. Time for last 1,000,000: 1s. Last read position: chrX:154,367,907 INFO 2026-06-03 20:42:48 MarkDuplicates Tracking 8150 as yet unmatched pairs. 4388 records in RAM. INFO 2026-06-03 20:42:49 MarkDuplicates Read 660,000,000 records. Elapsed time: 00:19:48s. Time for last 1,000,000: 1s. Last read position: chrY:11,116,664 INFO 2026-06-03 20:42:49 MarkDuplicates Tracking 3760 as yet unmatched pairs. 23 records in RAM. INFO 2026-06-03 20:42:50 MarkDuplicates Read 661,000,000 records. Elapsed time: 00:19:50s. Time for last 1,000,000: 1s. Last read position: GL000220.1:158,158 INFO 2026-06-03 20:42:50 MarkDuplicates Tracking 2251 as yet unmatched pairs. 67 records in RAM. INFO 2026-06-03 20:42:51 MarkDuplicates Read 662,000,000 records. Elapsed time: 00:19:51s. Time for last 1,000,000: 1s. Last read position: KI270733.1:133,628 INFO 2026-06-03 20:42:51 MarkDuplicates Tracking 3190 as yet unmatched pairs. 3179 records in RAM. INFO 2026-06-03 20:42:52 MarkDuplicates Read 662725267 records. 0 pairs never matched. INFO 2026-06-03 20:43:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 204138448; totalMemory: 234881024; maxMemory: 63585648640 INFO 2026-06-03 20:43:40 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk. INFO 2026-06-03 20:43:43 MarkDuplicates Traversing read pair information and detecting duplicates. WARNING 2026-06-03 20:43:44 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered. INFO 2026-06-03 20:44:02 OpticalDuplicateFinder Large duplicate set. size = 1386 INFO 2026-06-03 20:44:02 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-25,761 INFO 2026-06-03 20:44:06 OpticalDuplicateFinder Large duplicate set. size = 1244 INFO 2026-06-03 20:44:06 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,831 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder Large duplicate set. size = 1086 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:14,235 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder Large duplicate set. size = 1822 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:8,750 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder Large duplicate set. size = 1028 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,366 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder Large duplicate set. size = 1739 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:14,429 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder Large duplicate set. size = 1215 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,263 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder Large duplicate set. size = 1342 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,075 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder Large duplicate set. size = 2065 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-14,160 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,850 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder Large duplicate set. size = 1767 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:4,786 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder Large duplicate set. size = 1037 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,059 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder Large duplicate set. size = 1305 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:4,357 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder Large duplicate set. size = 1518 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:25,068 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder Large duplicate set. size = 1076 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:23,280 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder Large duplicate set. size = 1118 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,715 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder Large duplicate set. size = 1397 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,703 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder Large duplicate set. size = 1060 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,400 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder Large duplicate set. size = 1076 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,140 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder Large duplicate set. size = 1005 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,689 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder Large duplicate set. size = 1447 INFO 2026-06-03 20:44:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:17,795 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder Large duplicate set. size = 1079 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:15,263 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder Large duplicate set. size = 1198 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,213 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder Large duplicate set. size = 1222 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:21,007 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder Large duplicate set. size = 1368 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,186 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder Large duplicate set. size = 1117 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:4,632 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder Large duplicate set. size = 1089 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,057 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder Large duplicate set. size = 1832 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:21,274 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder Large duplicate set. size = 2522 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,341 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,600 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder Large duplicate set. size = 1436 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,864 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder Large duplicate set. size = 1037 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,732 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder Large duplicate set. size = 1132 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,964 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder Large duplicate set. size = 1003 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:4,705 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder Large duplicate set. size = 1056 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,150 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder Large duplicate set. size = 1445 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,565 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder Large duplicate set. size = 1402 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,493 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder Large duplicate set. size = 1060 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,238 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder Large duplicate set. size = 2049 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,138 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:2,076 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder Large duplicate set. size = 1115 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,025 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder Large duplicate set. size = 1132 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-27,031 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder Large duplicate set. size = 1147 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:1,526 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder Large duplicate set. size = 1012 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:4,560 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder Large duplicate set. size = 2021 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:25,529 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,040 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder Large duplicate set. size = 1024 INFO 2026-06-03 20:44:09 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-21,335 INFO 2026-06-03 20:44:10 OpticalDuplicateFinder Large duplicate set. size = 1069 INFO 2026-06-03 20:44:10 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,891 INFO 2026-06-03 20:44:10 OpticalDuplicateFinder Large duplicate set. size = 1851 INFO 2026-06-03 20:44:10 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,029 INFO 2026-06-03 20:44:10 OpticalDuplicateFinder Large duplicate set. size = 1162 INFO 2026-06-03 20:44:10 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,213 INFO 2026-06-03 20:44:10 OpticalDuplicateFinder Large duplicate set. size = 1122 INFO 2026-06-03 20:44:10 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:7,116 INFO 2026-06-03 20:44:10 OpticalDuplicateFinder Large duplicate set. size = 1030 INFO 2026-06-03 20:44:10 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,763 INFO 2026-06-03 20:44:10 OpticalDuplicateFinder Large duplicate set. size = 1001 INFO 2026-06-03 20:44:10 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,277 INFO 2026-06-03 20:44:10 OpticalDuplicateFinder Large duplicate set. size = 2136 INFO 2026-06-03 20:44:10 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,414 INFO 2026-06-03 20:44:10 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-25,235 INFO 2026-06-03 20:44:10 OpticalDuplicateFinder Large duplicate set. size = 1044 INFO 2026-06-03 20:44:10 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:31,540 INFO 2026-06-03 20:44:10 OpticalDuplicateFinder Large duplicate set. size = 4201 INFO 2026-06-03 20:44:10 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:24,825 INFO 2026-06-03 20:44:10 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,576 INFO 2026-06-03 20:44:10 OpticalDuplicateFinder compared 3,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:8,427 INFO 2026-06-03 20:44:10 OpticalDuplicateFinder compared 4,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:2,756 INFO 2026-06-03 20:44:10 OpticalDuplicateFinder Large duplicate set. size = 1216 INFO 2026-06-03 20:44:10 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,092 INFO 2026-06-03 20:44:10 OpticalDuplicateFinder Large duplicate set. size = 1259 INFO 2026-06-03 20:44:10 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-18,285 INFO 2026-06-03 20:44:11 OpticalDuplicateFinder Large duplicate set. size = 1357 INFO 2026-06-03 20:44:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,917 INFO 2026-06-03 20:44:11 OpticalDuplicateFinder Large duplicate set. size = 1025 INFO 2026-06-03 20:44:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,231 INFO 2026-06-03 20:44:11 OpticalDuplicateFinder Large duplicate set. size = 1106 INFO 2026-06-03 20:44:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,905 INFO 2026-06-03 20:44:11 OpticalDuplicateFinder Large duplicate set. size = 2523 INFO 2026-06-03 20:44:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,479 INFO 2026-06-03 20:44:11 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,518 INFO 2026-06-03 20:44:11 OpticalDuplicateFinder Large duplicate set. size = 1013 INFO 2026-06-03 20:44:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:31,354 INFO 2026-06-03 20:44:11 OpticalDuplicateFinder Large duplicate set. size = 1398 INFO 2026-06-03 20:44:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,282 INFO 2026-06-03 20:44:11 OpticalDuplicateFinder Large duplicate set. size = 1005 INFO 2026-06-03 20:44:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:6,307 INFO 2026-06-03 20:44:11 OpticalDuplicateFinder Large duplicate set. size = 1003 INFO 2026-06-03 20:44:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:17,504 INFO 2026-06-03 20:45:04 MarkDuplicates Traversing fragment information and detecting duplicates. WARNING 2026-06-03 20:45:04 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered. INFO 2026-06-03 20:46:08 MarkDuplicates Sorting list of duplicate records. INFO 2026-06-03 20:46:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 203928424; totalMemory: 234881024; maxMemory: 63585648640 INFO 2026-06-03 20:46:09 MarkDuplicates Marking 289718011 records as duplicates. INFO 2026-06-03 20:46:09 MarkDuplicates Found 17623361 optical duplicate clusters. INFO 2026-06-03 20:46:09 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2026-06-03 20:46:25 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:16s. Time for last 10,000,000: 16s. Last read position: chr1:22,120,038 INFO 2026-06-03 20:46:41 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:32s. Time for last 10,000,000: 15s. Last read position: chr1:43,984,948 INFO 2026-06-03 20:46:57 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:48s. Time for last 10,000,000: 15s. Last read position: chr1:114,739,769 INFO 2026-06-03 20:47:13 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:03s. Time for last 10,000,000: 15s. Last read position: chr1:155,187,290 INFO 2026-06-03 20:47:29 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:19s. Time for last 10,000,000: 15s. Last read position: chr1:186,679,170 INFO 2026-06-03 20:47:45 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:35s. Time for last 10,000,000: 15s. Last read position: chr1:235,335,283 INFO 2026-06-03 20:48:00 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:01:50s. Time for last 10,000,000: 15s. Last read position: chr2:37,671,620 INFO 2026-06-03 20:48:15 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:06s. Time for last 10,000,000: 15s. Last read position: chr2:97,557,111 INFO 2026-06-03 20:48:31 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:21s. Time for last 10,000,000: 15s. Last read position: chr2:186,659,046 INFO 2026-06-03 20:48:47 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:37s. Time for last 10,000,000: 15s. Last read position: chr2:223,975,772 INFO 2026-06-03 20:49:02 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:02:53s. Time for last 10,000,000: 15s. Last read position: chr3:41,225,079 INFO 2026-06-03 20:49:18 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:09s. Time for last 10,000,000: 15s. Last read position: chr3:87,227,496 INFO 2026-06-03 20:49:34 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:24s. Time for last 10,000,000: 15s. Last read position: chr3:179,221,018 INFO 2026-06-03 20:49:49 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:03:39s. Time for last 10,000,000: 15s. Last read position: chr3:197,913,779 INFO 2026-06-03 20:50:05 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:03:55s. Time for last 10,000,000: 15s. Last read position: chr4:86,359,649 INFO 2026-06-03 20:50:20 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:11s. Time for last 10,000,000: 15s. Last read position: chr5:16,465,434 INFO 2026-06-03 20:50:36 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:04:26s. Time for last 10,000,000: 15s. Last read position: chr5:135,571,383 INFO 2026-06-03 20:50:52 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:04:42s. Time for last 10,000,000: 15s. Last read position: chr5:177,332,117 INFO 2026-06-03 20:51:07 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:04:57s. Time for last 10,000,000: 15s. Last read position: chr6:31,627,987 INFO 2026-06-03 20:51:23 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:05:13s. Time for last 10,000,000: 15s. Last read position: chr6:52,509,528 INFO 2026-06-03 20:51:38 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:05:29s. Time for last 10,000,000: 15s. Last read position: chr6:154,450,133 INFO 2026-06-03 20:51:54 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:05:44s. Time for last 10,000,000: 15s. Last read position: chr7:44,112,182 INFO 2026-06-03 20:52:09 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:05:59s. Time for last 10,000,000: 15s. Last read position: chr7:100,884,537 INFO 2026-06-03 20:52:23 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:06:14s. Time for last 10,000,000: 14s. Last read position: chr7:100,994,915 INFO 2026-06-03 20:52:38 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:06:29s. Time for last 10,000,000: 14s. Last read position: chr7:100,997,386 INFO 2026-06-03 20:52:53 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:06:44s. Time for last 10,000,000: 15s. Last read position: chr7:100,999,495 INFO 2026-06-03 20:53:08 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:06:58s. Time for last 10,000,000: 14s. Last read position: chr7:101,001,689 INFO 2026-06-03 20:53:23 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:07:13s. Time for last 10,000,000: 14s. Last read position: chr7:102,655,121 INFO 2026-06-03 20:53:38 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:07:28s. Time for last 10,000,000: 15s. Last read position: chr8:8,319,025 INFO 2026-06-03 20:53:54 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:07:44s. Time for last 10,000,000: 15s. Last read position: chr8:86,547,711 INFO 2026-06-03 20:54:09 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:08:00s. Time for last 10,000,000: 15s. Last read position: chr8:144,409,512 INFO 2026-06-03 20:54:25 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:08:15s. Time for last 10,000,000: 15s. Last read position: chr9:98,131,015 INFO 2026-06-03 20:54:41 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:08:31s. Time for last 10,000,000: 15s. Last read position: chr9:133,108,010 INFO 2026-06-03 20:54:57 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:08:47s. Time for last 10,000,000: 15s. Last read position: chr10:50,093,858 INFO 2026-06-03 20:55:13 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:09:03s. Time for last 10,000,000: 15s. Last read position: chr10:116,915,483 INFO 2026-06-03 20:55:28 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:09:18s. Time for last 10,000,000: 15s. Last read position: chr11:1,182,309 INFO 2026-06-03 20:55:43 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:09:34s. Time for last 10,000,000: 15s. Last read position: chr11:11,967,065 INFO 2026-06-03 20:55:59 MarkDuplicates Written 380,000,000 records. Elapsed time: 00:09:49s. Time for last 10,000,000: 15s. Last read position: chr11:62,616,981 INFO 2026-06-03 20:56:15 MarkDuplicates Written 390,000,000 records. Elapsed time: 00:10:05s. Time for last 10,000,000: 15s. Last read position: chr11:76,544,335 INFO 2026-06-03 20:56:31 MarkDuplicates Written 400,000,000 records. Elapsed time: 00:10:21s. Time for last 10,000,000: 15s. Last read position: chr12:3,696,976 INFO 2026-06-03 20:56:47 MarkDuplicates Written 410,000,000 records. Elapsed time: 00:10:37s. Time for last 10,000,000: 15s. Last read position: chr12:51,064,457 INFO 2026-06-03 20:57:02 MarkDuplicates Written 420,000,000 records. Elapsed time: 00:10:53s. Time for last 10,000,000: 15s. Last read position: chr12:71,138,031 INFO 2026-06-03 20:57:18 MarkDuplicates Written 430,000,000 records. Elapsed time: 00:11:09s. Time for last 10,000,000: 15s. Last read position: chr12:132,490,817 INFO 2026-06-03 20:57:34 MarkDuplicates Written 440,000,000 records. Elapsed time: 00:11:24s. Time for last 10,000,000: 15s. Last read position: chr14:20,801,646 INFO 2026-06-03 20:57:50 MarkDuplicates Written 450,000,000 records. Elapsed time: 00:11:40s. Time for last 10,000,000: 15s. Last read position: chr14:75,176,384 INFO 2026-06-03 20:58:05 MarkDuplicates Written 460,000,000 records. Elapsed time: 00:11:56s. Time for last 10,000,000: 15s. Last read position: chr15:24,975,450 INFO 2026-06-03 20:58:21 MarkDuplicates Written 470,000,000 records. Elapsed time: 00:12:11s. Time for last 10,000,000: 15s. Last read position: chr15:62,739,360 INFO 2026-06-03 20:58:37 MarkDuplicates Written 480,000,000 records. Elapsed time: 00:12:28s. Time for last 10,000,000: 16s. Last read position: chr16:404,979 INFO 2026-06-03 20:58:53 MarkDuplicates Written 490,000,000 records. Elapsed time: 00:12:43s. Time for last 10,000,000: 15s. Last read position: chr16:16,310,526 INFO 2026-06-03 20:59:09 MarkDuplicates Written 500,000,000 records. Elapsed time: 00:12:59s. Time for last 10,000,000: 15s. Last read position: chr16:30,712,096 INFO 2026-06-03 20:59:25 MarkDuplicates Written 510,000,000 records. Elapsed time: 00:13:15s. Time for last 10,000,000: 15s. Last read position: chr16:88,810,530 INFO 2026-06-03 20:59:40 MarkDuplicates Written 520,000,000 records. Elapsed time: 00:13:31s. Time for last 10,000,000: 15s. Last read position: chr17:18,252,078 INFO 2026-06-03 20:59:56 MarkDuplicates Written 530,000,000 records. Elapsed time: 00:13:46s. Time for last 10,000,000: 15s. Last read position: chr17:43,400,052 INFO 2026-06-03 21:00:12 MarkDuplicates Written 540,000,000 records. Elapsed time: 00:14:02s. Time for last 10,000,000: 15s. Last read position: chr17:60,158,375 INFO 2026-06-03 21:00:27 MarkDuplicates Written 550,000,000 records. Elapsed time: 00:14:18s. Time for last 10,000,000: 15s. Last read position: chr17:82,036,234 INFO 2026-06-03 21:00:43 MarkDuplicates Written 560,000,000 records. Elapsed time: 00:14:34s. Time for last 10,000,000: 16s. Last read position: chr19:2,137,727 INFO 2026-06-03 21:00:59 MarkDuplicates Written 570,000,000 records. Elapsed time: 00:14:50s. Time for last 10,000,000: 15s. Last read position: chr19:14,452,012 INFO 2026-06-03 21:01:15 MarkDuplicates Written 580,000,000 records. Elapsed time: 00:15:06s. Time for last 10,000,000: 16s. Last read position: chr19:39,863,860 INFO 2026-06-03 21:01:31 MarkDuplicates Written 590,000,000 records. Elapsed time: 00:15:21s. Time for last 10,000,000: 15s. Last read position: chr19:39,943,397 INFO 2026-06-03 21:01:47 MarkDuplicates Written 600,000,000 records. Elapsed time: 00:15:37s. Time for last 10,000,000: 16s. Last read position: chr19:49,104,687 INFO 2026-06-03 21:02:03 MarkDuplicates Written 610,000,000 records. Elapsed time: 00:15:53s. Time for last 10,000,000: 15s. Last read position: chr20:24,983,690 INFO 2026-06-03 21:02:19 MarkDuplicates Written 620,000,000 records. Elapsed time: 00:16:09s. Time for last 10,000,000: 15s. Last read position: chr21:5,141,355 INFO 2026-06-03 21:02:34 MarkDuplicates Written 630,000,000 records. Elapsed time: 00:16:25s. Time for last 10,000,000: 15s. Last read position: chr22:17,841,827 INFO 2026-06-03 21:02:50 MarkDuplicates Written 640,000,000 records. Elapsed time: 00:16:41s. Time for last 10,000,000: 16s. Last read position: chr22:41,499,730 INFO 2026-06-03 21:03:06 MarkDuplicates Written 650,000,000 records. Elapsed time: 00:16:57s. Time for last 10,000,000: 16s. Last read position: chrX:65,731,117 INFO 2026-06-03 21:03:23 MarkDuplicates Written 660,000,000 records. Elapsed time: 00:17:13s. Time for last 10,000,000: 16s. Last read position: chrY:11,116,664 INFO 2026-06-03 21:03:35 MarkDuplicates Writing complete. Closing input iterator. INFO 2026-06-03 21:03:35 MarkDuplicates Duplicate Index cleanup. INFO 2026-06-03 21:03:35 MarkDuplicates Getting Memory Stats. INFO 2026-06-03 21:03:35 MarkDuplicates Before output close freeMemory: 203903608; totalMemory: 234881024; maxMemory: 63585648640 INFO 2026-06-03 21:03:35 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2026-06-03 21:03:35 MarkDuplicates After output close freeMemory: 104138664; totalMemory: 134217728; maxMemory: 63585648640 [Wed Jun 03 21:03:35 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 40.60 minutes. Runtime.totalMemory()=134217728 Tool returned: 0 ls: *cram: No such file or directory ls: *.crai: No such file or directory