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 659_1q-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bam --METRICS_FILE 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT 21:09:50.940 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 [Thu Jun 04 21:09:50 GMT 2026] MarkDuplicates --INPUT 659_1q-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_1q-T1-TRNA-1_B23MHV2LT4_1.md.bam --METRICS_FILE 659_1q-T1-TRNA-1_B23MHV2LT4_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 [Thu Jun 04 21:09:50 GMT 2026] Executing as ?@nf-4e52f0e74e859e1fa835638eeddd156d-d60c6-fmh5g 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 2026-06-04 21:09:50 MarkDuplicates Start of doWork freeMemory: 105828800; totalMemory: 134217728; maxMemory: 63585648640 INFO 2026-06-04 21:09:50 MarkDuplicates Reading input file and constructing read end information. INFO 2026-06-04 21:09:50 MarkDuplicates Will retain up to 230382784 data points before spilling to disk. INFO 2026-06-04 21:09:54 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:01s. Time for last 1,000,000: 1s. Last read position: chr1:1,049,665 INFO 2026-06-04 21:09:54 MarkDuplicates Tracking 4831 as yet unmatched pairs. 2102 records in RAM. INFO 2026-06-04 21:09:56 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: chr1:1,704,938 INFO 2026-06-04 21:09:56 MarkDuplicates Tracking 5786 as yet unmatched pairs. 147 records in RAM. INFO 2026-06-04 21:09:58 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: chr1:6,387,928 INFO 2026-06-04 21:09:58 MarkDuplicates Tracking 8361 as yet unmatched pairs. 16 records in RAM. INFO 2026-06-04 21:09:59 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: chr1:8,868,044 INFO 2026-06-04 21:09:59 MarkDuplicates Tracking 13648 as yet unmatched pairs. 2633 records in RAM. INFO 2026-06-04 21:10:01 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: chr1:11,240,376 INFO 2026-06-04 21:10:01 MarkDuplicates Tracking 13997 as yet unmatched pairs. 201 records in RAM. INFO 2026-06-04 21:10:03 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: chr1:15,567,964 INFO 2026-06-04 21:10:03 MarkDuplicates Tracking 16733 as yet unmatched pairs. 321 records in RAM. INFO 2026-06-04 21:10:05 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: chr1:16,588,873 INFO 2026-06-04 21:10:05 MarkDuplicates Tracking 18922 as yet unmatched pairs. 182 records in RAM. INFO 2026-06-04 21:10:07 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: chr1:19,106,576 INFO 2026-06-04 21:10:07 MarkDuplicates Tracking 21832 as yet unmatched pairs. 343 records in RAM. INFO 2026-06-04 21:10:08 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: chr1:20,776,652 INFO 2026-06-04 21:10:08 MarkDuplicates Tracking 24570 as yet unmatched pairs. 458 records in RAM. INFO 2026-06-04 21:10:10 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: chr1:21,865,326 INFO 2026-06-04 21:10:10 MarkDuplicates Tracking 27016 as yet unmatched pairs. 219 records in RAM. INFO 2026-06-04 21:10:13 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 2s. Last read position: chr1:23,337,764 INFO 2026-06-04 21:10:13 MarkDuplicates Tracking 30649 as yet unmatched pairs. 1316 records in RAM. INFO 2026-06-04 21:10:14 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: chr1:25,781,041 INFO 2026-06-04 21:10:14 MarkDuplicates Tracking 32402 as yet unmatched pairs. 651 records in RAM. INFO 2026-06-04 21:10:16 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: chr1:26,779,501 INFO 2026-06-04 21:10:16 MarkDuplicates Tracking 34638 as yet unmatched pairs. 314 records in RAM. INFO 2026-06-04 21:10:18 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 1s. Last read position: chr1:27,892,220 INFO 2026-06-04 21:10:18 MarkDuplicates Tracking 37461 as yet unmatched pairs. 360 records in RAM. INFO 2026-06-04 21:10:19 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 1s. Last read position: chr1:30,995,139 INFO 2026-06-04 21:10:19 MarkDuplicates Tracking 39917 as yet unmatched pairs. 255 records in RAM. INFO 2026-06-04 21:10:21 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 1s. Last read position: chr1:31,793,369 INFO 2026-06-04 21:10:21 MarkDuplicates Tracking 43178 as yet unmatched pairs. 606 records in RAM. INFO 2026-06-04 21:10:23 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 1s. Last read position: chr1:32,770,378 INFO 2026-06-04 21:10:23 MarkDuplicates Tracking 45716 as yet unmatched pairs. 436 records in RAM. INFO 2026-06-04 21:10:25 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 1s. Last read position: chr1:35,192,574 INFO 2026-06-04 21:10:25 MarkDuplicates Tracking 49472 as yet unmatched pairs. 1595 records in RAM. INFO 2026-06-04 21:10:26 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 1s. Last read position: chr1:37,566,987 INFO 2026-06-04 21:10:26 MarkDuplicates Tracking 50607 as yet unmatched pairs. 173 records in RAM. INFO 2026-06-04 21:10:27 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 1s. Last read position: chr1:39,850,239 INFO 2026-06-04 21:10:27 MarkDuplicates Tracking 53083 as yet unmatched pairs. 169 records in RAM. INFO 2026-06-04 21:10:30 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 2s. Last read position: chr1:42,927,019 INFO 2026-06-04 21:10:30 MarkDuplicates Tracking 57376 as yet unmatched pairs. 1958 records in RAM. INFO 2026-06-04 21:10:31 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 1s. Last read position: chr1:43,591,512 INFO 2026-06-04 21:10:31 MarkDuplicates Tracking 59595 as yet unmatched pairs. 1165 records in RAM. INFO 2026-06-04 21:10:33 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 1s. Last read position: chr1:45,010,603 INFO 2026-06-04 21:10:33 MarkDuplicates Tracking 61256 as yet unmatched pairs. 190 records in RAM. INFO 2026-06-04 21:10:35 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 1s. Last read position: chr1:46,718,076 INFO 2026-06-04 21:10:35 MarkDuplicates Tracking 64260 as yet unmatched pairs. 684 records in RAM. INFO 2026-06-04 21:10:37 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: chr1:52,337,836 INFO 2026-06-04 21:10:37 MarkDuplicates Tracking 66275 as yet unmatched pairs. 150 records in RAM. INFO 2026-06-04 21:10:39 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 2s. Last read position: chr1:58,576,197 INFO 2026-06-04 21:10:39 MarkDuplicates Tracking 71136 as yet unmatched pairs. 2436 records in RAM. INFO 2026-06-04 21:10:41 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 1s. Last read position: chr1:64,866,877 INFO 2026-06-04 21:10:41 MarkDuplicates Tracking 72726 as yet unmatched pairs. 1336 records in RAM. INFO 2026-06-04 21:10:42 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 1s. Last read position: chr1:81,942,969 INFO 2026-06-04 21:10:42 MarkDuplicates Tracking 73853 as yet unmatched pairs. 294 records in RAM. INFO 2026-06-04 21:10:44 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 1s. Last read position: chr1:89,584,525 INFO 2026-06-04 21:10:44 MarkDuplicates Tracking 76384 as yet unmatched pairs. 310 records in RAM. INFO 2026-06-04 21:10:46 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 2s. Last read position: chr1:94,926,899 INFO 2026-06-04 21:10:46 MarkDuplicates Tracking 78665 as yet unmatched pairs. 169 records in RAM. INFO 2026-06-04 21:10:47 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 1s. Last read position: chr1:109,269,168 INFO 2026-06-04 21:10:47 MarkDuplicates Tracking 80907 as yet unmatched pairs. 138 records in RAM. INFO 2026-06-04 21:10:49 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 1s. Last read position: chr1:109,693,212 INFO 2026-06-04 21:10:49 MarkDuplicates Tracking 91544 as yet unmatched pairs. 8493 records in RAM. INFO 2026-06-04 21:10:50 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 1s. Last read position: chr1:112,698,317 INFO 2026-06-04 21:10:50 MarkDuplicates Tracking 85831 as yet unmatched pairs. 237 records in RAM. INFO 2026-06-04 21:10:52 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 1s. Last read position: chr1:114,732,603 INFO 2026-06-04 21:10:52 MarkDuplicates Tracking 88960 as yet unmatched pairs. 881 records in RAM. INFO 2026-06-04 21:10:53 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 1s. Last read position: chr1:119,916,092 INFO 2026-06-04 21:10:53 MarkDuplicates Tracking 91080 as yet unmatched pairs. 526 records in RAM. INFO 2026-06-04 21:10:54 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 1s. Last read position: chr1:145,573,972 INFO 2026-06-04 21:10:54 MarkDuplicates Tracking 92468 as yet unmatched pairs. 252 records in RAM. INFO 2026-06-04 21:10:56 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 1s. Last read position: chr1:147,611,825 INFO 2026-06-04 21:10:56 MarkDuplicates Tracking 94021 as yet unmatched pairs. 338 records in RAM. INFO 2026-06-04 21:10:57 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 1s. Last read position: chr1:149,607,484 INFO 2026-06-04 21:10:57 MarkDuplicates Tracking 94859 as yet unmatched pairs. 81 records in RAM. INFO 2026-06-04 21:10:58 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 1s. Last read position: chr1:150,266,476 INFO 2026-06-04 21:10:58 MarkDuplicates Tracking 97947 as yet unmatched pairs. 1246 records in RAM. INFO 2026-06-04 21:11:00 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 1s. Last read position: chr1:151,266,332 INFO 2026-06-04 21:11:00 MarkDuplicates Tracking 99670 as yet unmatched pairs. 504 records in RAM. INFO 2026-06-04 21:11:01 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 1s. Last read position: chr1:152,910,185 INFO 2026-06-04 21:11:01 MarkDuplicates Tracking 103959 as yet unmatched pairs. 2369 records in RAM. INFO 2026-06-04 21:11:03 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 1s. Last read position: chr1:153,534,681 INFO 2026-06-04 21:11:03 MarkDuplicates Tracking 108101 as yet unmatched pairs. 3741 records in RAM. INFO 2026-06-04 21:11:04 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 1s. Last read position: chr1:154,170,428 INFO 2026-06-04 21:11:04 MarkDuplicates Tracking 119943 as yet unmatched pairs. 13123 records in RAM. INFO 2026-06-04 21:11:06 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 1s. Last read position: chr1:154,963,770 INFO 2026-06-04 21:11:06 MarkDuplicates Tracking 109704 as yet unmatched pairs. 589 records in RAM. INFO 2026-06-04 21:11:07 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 1s. Last read position: chr1:155,521,099 INFO 2026-06-04 21:11:07 MarkDuplicates Tracking 111943 as yet unmatched pairs. 256 records in RAM. INFO 2026-06-04 21:11:09 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 1s. Last read position: chr1:156,136,045 INFO 2026-06-04 21:11:09 MarkDuplicates Tracking 117155 as yet unmatched pairs. 2801 records in RAM. INFO 2026-06-04 21:11:10 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 1s. Last read position: chr1:156,745,080 INFO 2026-06-04 21:11:10 MarkDuplicates Tracking 117659 as yet unmatched pairs. 568 records in RAM. INFO 2026-06-04 21:11:12 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 1s. Last read position: chr1:161,001,050 INFO 2026-06-04 21:11:12 MarkDuplicates Tracking 121747 as yet unmatched pairs. 2253 records in RAM. INFO 2026-06-04 21:11:15 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 2s. Last read position: chr1:165,682,152 INFO 2026-06-04 21:11:15 MarkDuplicates Tracking 122380 as yet unmatched pairs. 306 records in RAM. INFO 2026-06-04 21:11:16 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 1s. Last read position: chr1:171,557,899 INFO 2026-06-04 21:11:16 MarkDuplicates Tracking 125325 as yet unmatched pairs. 865 records in RAM. INFO 2026-06-04 21:11:18 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 1s. Last read position: chr1:180,015,864 INFO 2026-06-04 21:11:18 MarkDuplicates Tracking 127290 as yet unmatched pairs. 426 records in RAM. INFO 2026-06-04 21:11:20 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 1s. Last read position: chr1:183,140,462 INFO 2026-06-04 21:11:20 MarkDuplicates Tracking 129842 as yet unmatched pairs. 344 records in RAM. INFO 2026-06-04 21:11:21 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 1s. Last read position: chr1:186,346,270 INFO 2026-06-04 21:11:21 MarkDuplicates Tracking 133162 as yet unmatched pairs. 1304 records in RAM. INFO 2026-06-04 21:11:23 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 1s. Last read position: chr1:200,857,787 INFO 2026-06-04 21:11:23 MarkDuplicates Tracking 134603 as yet unmatched pairs. 517 records in RAM. INFO 2026-06-04 21:11:24 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 1s. Last read position: chr1:202,729,015 INFO 2026-06-04 21:11:24 MarkDuplicates Tracking 138692 as yet unmatched pairs. 2079 records in RAM. INFO 2026-06-04 21:11:26 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 1s. Last read position: chr1:204,112,920 INFO 2026-06-04 21:11:26 MarkDuplicates Tracking 139352 as yet unmatched pairs. 351 records in RAM. INFO 2026-06-04 21:11:28 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 1s. Last read position: chr1:206,021,058 INFO 2026-06-04 21:11:28 MarkDuplicates Tracking 142612 as yet unmatched pairs. 1128 records in RAM. INFO 2026-06-04 21:11:30 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 2s. Last read position: chr1:209,622,656 INFO 2026-06-04 21:11:30 MarkDuplicates Tracking 144340 as yet unmatched pairs. 376 records in RAM. INFO 2026-06-04 21:11:31 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 1s. Last read position: chr1:220,010,974 INFO 2026-06-04 21:11:31 MarkDuplicates Tracking 146817 as yet unmatched pairs. 319 records in RAM. INFO 2026-06-04 21:11:33 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 1s. Last read position: chr1:225,511,811 INFO 2026-06-04 21:11:33 MarkDuplicates Tracking 149093 as yet unmatched pairs. 185 records in RAM. INFO 2026-06-04 21:11:35 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 1s. Last read position: chr1:228,316,827 INFO 2026-06-04 21:11:35 MarkDuplicates Tracking 151437 as yet unmatched pairs. 25 records in RAM. INFO 2026-06-04 21:11:36 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 1s. Last read position: chr1:235,450,320 INFO 2026-06-04 21:11:36 MarkDuplicates Tracking 154296 as yet unmatched pairs. 171 records in RAM. INFO 2026-06-04 21:11:38 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 2s. Last read position: chr1:244,859,301 INFO 2026-06-04 21:11:38 MarkDuplicates Tracking 157763 as yet unmatched pairs. 1273 records in RAM. INFO 2026-06-04 21:11:41 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 3s. Last read position: chr2:8,747,890 INFO 2026-06-04 21:11:41 MarkDuplicates Tracking 159378 as yet unmatched pairs. 156928 records in RAM. INFO 2026-06-04 21:11:43 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 1s. Last read position: chr2:15,536,467 INFO 2026-06-04 21:11:43 MarkDuplicates Tracking 162158 as yet unmatched pairs. 159664 records in RAM. INFO 2026-06-04 21:11:45 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 1s. Last read position: chr2:20,203,959 INFO 2026-06-04 21:11:45 MarkDuplicates Tracking 173837 as yet unmatched pairs. 171303 records in RAM. INFO 2026-06-04 21:11:46 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 1s. Last read position: chr2:20,645,363 INFO 2026-06-04 21:11:46 MarkDuplicates Tracking 166891 as yet unmatched pairs. 164323 records in RAM. INFO 2026-06-04 21:11:48 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 1s. Last read position: chr2:26,254,245 INFO 2026-06-04 21:11:48 MarkDuplicates Tracking 169951 as yet unmatched pairs. 167358 records in RAM. INFO 2026-06-04 21:11:49 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 1s. Last read position: chr2:28,539,107 INFO 2026-06-04 21:11:49 MarkDuplicates Tracking 171872 as yet unmatched pairs. 169255 records in RAM. INFO 2026-06-04 21:11:51 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 1s. Last read position: chr2:32,415,609 INFO 2026-06-04 21:11:51 MarkDuplicates Tracking 175269 as yet unmatched pairs. 172593 records in RAM. INFO 2026-06-04 21:11:52 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,264 INFO 2026-06-04 21:11:52 MarkDuplicates Tracking 334202 as yet unmatched pairs. 160683 records in RAM. INFO 2026-06-04 21:11:55 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,264 INFO 2026-06-04 21:11:55 MarkDuplicates Tracking 1002944 as yet unmatched pairs. 110880 records in RAM. INFO 2026-06-04 21:11:56 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,406 INFO 2026-06-04 21:11:56 MarkDuplicates Tracking 1312746 as yet unmatched pairs. 87203 records in RAM. INFO 2026-06-04 21:11:57 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 0s. Last read position: chr2:32,916,406 INFO 2026-06-04 21:11:57 MarkDuplicates Tracking 1317030 as yet unmatched pairs. 86909 records in RAM. INFO 2026-06-04 21:11:58 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 1s. Last read position: chr2:37,645,962 INFO 2026-06-04 21:11:58 MarkDuplicates Tracking 1369533 as yet unmatched pairs. 81555 records in RAM. INFO 2026-06-04 21:12:00 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 1s. Last read position: chr2:43,224,325 INFO 2026-06-04 21:12:00 MarkDuplicates Tracking 1367902 as yet unmatched pairs. 79884 records in RAM. INFO 2026-06-04 21:12:02 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 1s. Last read position: chr2:47,160,688 INFO 2026-06-04 21:12:02 MarkDuplicates Tracking 1365600 as yet unmatched pairs. 77532 records in RAM. INFO 2026-06-04 21:12:03 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 1s. Last read position: chr2:54,655,912 INFO 2026-06-04 21:12:03 MarkDuplicates Tracking 1362228 as yet unmatched pairs. 74133 records in RAM. INFO 2026-06-04 21:12:05 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 1s. Last read position: chr2:61,188,182 INFO 2026-06-04 21:12:05 MarkDuplicates Tracking 1360282 as yet unmatched pairs. 72155 records in RAM. INFO 2026-06-04 21:12:06 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 1s. Last read position: chr2:65,205,499 INFO 2026-06-04 21:12:06 MarkDuplicates Tracking 1357391 as yet unmatched pairs. 69221 records in RAM. INFO 2026-06-04 21:12:08 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 1s. Last read position: chr2:71,076,638 INFO 2026-06-04 21:12:08 MarkDuplicates Tracking 1355627 as yet unmatched pairs. 67397 records in RAM. INFO 2026-06-04 21:12:09 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 1s. Last read position: chr2:73,908,720 INFO 2026-06-04 21:12:09 MarkDuplicates Tracking 1354492 as yet unmatched pairs. 66212 records in RAM. INFO 2026-06-04 21:12:11 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 1s. Last read position: chr2:75,652,519 INFO 2026-06-04 21:12:11 MarkDuplicates Tracking 1350397 as yet unmatched pairs. 62078 records in RAM. INFO 2026-06-04 21:12:13 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 1s. Last read position: chr2:86,507,524 INFO 2026-06-04 21:12:13 MarkDuplicates Tracking 1348126 as yet unmatched pairs. 59763 records in RAM. INFO 2026-06-04 21:12:14 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr2:96,278,576 INFO 2026-06-04 21:12:14 MarkDuplicates Tracking 1346095 as yet unmatched pairs. 57694 records in RAM. INFO 2026-06-04 21:12:15 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 1s. Last read position: chr2:100,988,309 INFO 2026-06-04 21:12:15 MarkDuplicates Tracking 1343311 as yet unmatched pairs. 54863 records in RAM. INFO 2026-06-04 21:12:17 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 1s. Last read position: chr2:106,425,993 INFO 2026-06-04 21:12:17 MarkDuplicates Tracking 1340721 as yet unmatched pairs. 52226 records in RAM. INFO 2026-06-04 21:12:18 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 1s. Last read position: chr2:108,766,519 INFO 2026-06-04 21:12:18 MarkDuplicates Tracking 1339729 as yet unmatched pairs. 51214 records in RAM. INFO 2026-06-04 21:12:20 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 1s. Last read position: chr2:110,087,605 INFO 2026-06-04 21:12:20 MarkDuplicates Tracking 1341077 as yet unmatched pairs. 52530 records in RAM. INFO 2026-06-04 21:12:21 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 1s. Last read position: chr2:112,388,684 INFO 2026-06-04 21:12:21 MarkDuplicates Tracking 1336855 as yet unmatched pairs. 48280 records in RAM. INFO 2026-06-04 21:12:23 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 2s. Last read position: chr2:113,916,991 INFO 2026-06-04 21:12:23 MarkDuplicates Tracking 1336399 as yet unmatched pairs. 47789 records in RAM. INFO 2026-06-04 21:12:25 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 1s. Last read position: chr2:130,075,066 INFO 2026-06-04 21:12:25 MarkDuplicates Tracking 1332114 as yet unmatched pairs. 43463 records in RAM. INFO 2026-06-04 21:12:27 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 2s. Last read position: chr2:138,278,961 INFO 2026-06-04 21:12:27 MarkDuplicates Tracking 1329743 as yet unmatched pairs. 41023 records in RAM. INFO 2026-06-04 21:12:29 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 1s. Last read position: chr2:159,320,321 INFO 2026-06-04 21:12:29 MarkDuplicates Tracking 1327708 as yet unmatched pairs. 38902 records in RAM. INFO 2026-06-04 21:12:31 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 1s. Last read position: chr2:168,161,796 INFO 2026-06-04 21:12:31 MarkDuplicates Tracking 1326260 as yet unmatched pairs. 37406 records in RAM. INFO 2026-06-04 21:12:32 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 1s. Last read position: chr2:173,027,111 INFO 2026-06-04 21:12:32 MarkDuplicates Tracking 1323030 as yet unmatched pairs. 34130 records in RAM. INFO 2026-06-04 21:12:34 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 1s. Last read position: chr2:178,536,223 INFO 2026-06-04 21:12:34 MarkDuplicates Tracking 1320841 as yet unmatched pairs. 31901 records in RAM. INFO 2026-06-04 21:12:35 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 1s. Last read position: chr2:186,699,305 INFO 2026-06-04 21:12:35 MarkDuplicates Tracking 1318494 as yet unmatched pairs. 29487 records in RAM. INFO 2026-06-04 21:12:37 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 1s. Last read position: chr2:196,770,007 INFO 2026-06-04 21:12:37 MarkDuplicates Tracking 1316424 as yet unmatched pairs. 27368 records in RAM. INFO 2026-06-04 21:12:38 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 1s. Last read position: chr2:201,064,054 INFO 2026-06-04 21:12:38 MarkDuplicates Tracking 1313669 as yet unmatched pairs. 24583 records in RAM. INFO 2026-06-04 21:12:40 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 1s. Last read position: chr2:206,004,834 INFO 2026-06-04 21:12:40 MarkDuplicates Tracking 1311450 as yet unmatched pairs. 22334 records in RAM. INFO 2026-06-04 21:12:41 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 1s. Last read position: chr2:215,372,081 INFO 2026-06-04 21:12:41 MarkDuplicates Tracking 1310262 as yet unmatched pairs. 21113 records in RAM. INFO 2026-06-04 21:12:43 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 1s. Last read position: chr2:216,501,338 INFO 2026-06-04 21:12:43 MarkDuplicates Tracking 1306638 as yet unmatched pairs. 17462 records in RAM. INFO 2026-06-04 21:12:44 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 1s. Last read position: chr2:218,580,594 INFO 2026-06-04 21:12:44 MarkDuplicates Tracking 1304435 as yet unmatched pairs. 15223 records in RAM. INFO 2026-06-04 21:12:46 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 1s. Last read position: chr2:223,917,964 INFO 2026-06-04 21:12:46 MarkDuplicates Tracking 1301652 as yet unmatched pairs. 12372 records in RAM. INFO 2026-06-04 21:12:47 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 1s. Last read position: chr2:230,875,732 INFO 2026-06-04 21:12:47 MarkDuplicates Tracking 1299288 as yet unmatched pairs. 9960 records in RAM. INFO 2026-06-04 21:12:49 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 1s. Last read position: chr2:233,164,285 INFO 2026-06-04 21:12:49 MarkDuplicates Tracking 1296779 as yet unmatched pairs. 7413 records in RAM. INFO 2026-06-04 21:12:50 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 1s. Last read position: chr2:237,334,641 INFO 2026-06-04 21:12:50 MarkDuplicates Tracking 1294500 as yet unmatched pairs. 5084 records in RAM. INFO 2026-06-04 21:12:52 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 1s. Last read position: chr2:240,524,025 INFO 2026-06-04 21:12:52 MarkDuplicates Tracking 1291828 as yet unmatched pairs. 2366 records in RAM. INFO 2026-06-04 21:12:54 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 1s. Last read position: chr3:4,800,561 INFO 2026-06-04 21:12:54 MarkDuplicates Tracking 1289210 as yet unmatched pairs. 77173 records in RAM. INFO 2026-06-04 21:12:55 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 1s. Last read position: chr3:11,558,601 INFO 2026-06-04 21:12:55 MarkDuplicates Tracking 1286902 as yet unmatched pairs. 74790 records in RAM. INFO 2026-06-04 21:12:58 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 2s. Last read position: chr3:14,484,927 INFO 2026-06-04 21:12:58 MarkDuplicates Tracking 1284196 as yet unmatched pairs. 72038 records in RAM. INFO 2026-06-04 21:13:01 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 2s. Last read position: chr3:25,755,097 INFO 2026-06-04 21:13:01 MarkDuplicates Tracking 1282052 as yet unmatched pairs. 69826 records in RAM. INFO 2026-06-04 21:13:03 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 1s. Last read position: chr3:37,315,525 INFO 2026-06-04 21:13:03 MarkDuplicates Tracking 1279700 as yet unmatched pairs. 67421 records in RAM. INFO 2026-06-04 21:13:05 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 2s. Last read position: chr3:40,488,102 INFO 2026-06-04 21:13:05 MarkDuplicates Tracking 1277041 as yet unmatched pairs. 64738 records in RAM. INFO 2026-06-04 21:13:07 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 1s. Last read position: chr3:44,580,685 INFO 2026-06-04 21:13:07 MarkDuplicates Tracking 1274514 as yet unmatched pairs. 62171 records in RAM. INFO 2026-06-04 21:13:08 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 1s. Last read position: chr3:47,122,470 INFO 2026-06-04 21:13:08 MarkDuplicates Tracking 1273067 as yet unmatched pairs. 60687 records in RAM. INFO 2026-06-04 21:13:10 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 1s. Last read position: chr3:48,409,951 INFO 2026-06-04 21:13:10 MarkDuplicates Tracking 1270263 as yet unmatched pairs. 57853 records in RAM. INFO 2026-06-04 21:13:12 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 1s. Last read position: chr3:49,012,615 INFO 2026-06-04 21:13:12 MarkDuplicates Tracking 1267728 as yet unmatched pairs. 55297 records in RAM. INFO 2026-06-04 21:13:13 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 1s. Last read position: chr3:49,425,403 INFO 2026-06-04 21:13:13 MarkDuplicates Tracking 1264215 as yet unmatched pairs. 51747 records in RAM. INFO 2026-06-04 21:13:15 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: chr3:50,270,136 INFO 2026-06-04 21:13:15 MarkDuplicates Tracking 1261783 as yet unmatched pairs. 49278 records in RAM. INFO 2026-06-04 21:13:16 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 1s. Last read position: chr3:52,211,445 INFO 2026-06-04 21:13:16 MarkDuplicates Tracking 1260283 as yet unmatched pairs. 47755 records in RAM. INFO 2026-06-04 21:13:18 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 1s. Last read position: chr3:53,186,199 INFO 2026-06-04 21:13:18 MarkDuplicates Tracking 1256786 as yet unmatched pairs. 44215 records in RAM. INFO 2026-06-04 21:13:19 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 1s. Last read position: chr3:58,105,147 INFO 2026-06-04 21:13:19 MarkDuplicates Tracking 1256263 as yet unmatched pairs. 43642 records in RAM. INFO 2026-06-04 21:13:21 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 1s. Last read position: chr3:62,003,420 INFO 2026-06-04 21:13:21 MarkDuplicates Tracking 1251571 as yet unmatched pairs. 38895 records in RAM. INFO 2026-06-04 21:13:22 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 1s. Last read position: chr3:78,746,744 INFO 2026-06-04 21:13:22 MarkDuplicates Tracking 1249388 as yet unmatched pairs. 36642 records in RAM. INFO 2026-06-04 21:13:23 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 1s. Last read position: chr3:101,676,790 INFO 2026-06-04 21:13:23 MarkDuplicates Tracking 1246846 as yet unmatched pairs. 34065 records in RAM. INFO 2026-06-04 21:13:25 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 1s. Last read position: chr3:113,798,281 INFO 2026-06-04 21:13:25 MarkDuplicates Tracking 1244666 as yet unmatched pairs. 31826 records in RAM. INFO 2026-06-04 21:13:27 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 1s. Last read position: chr3:122,407,318 INFO 2026-06-04 21:13:27 MarkDuplicates Tracking 1244860 as yet unmatched pairs. 31976 records in RAM. INFO 2026-06-04 21:13:28 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 1s. Last read position: chr3:126,988,693 INFO 2026-06-04 21:13:28 MarkDuplicates Tracking 1239921 as yet unmatched pairs. 26992 records in RAM. INFO 2026-06-04 21:13:30 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 1s. Last read position: chr3:129,394,042 INFO 2026-06-04 21:13:30 MarkDuplicates Tracking 1237025 as yet unmatched pairs. 24068 records in RAM. INFO 2026-06-04 21:13:31 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 1s. Last read position: chr3:136,250,366 INFO 2026-06-04 21:13:31 MarkDuplicates Tracking 1234542 as yet unmatched pairs. 21553 records in RAM. INFO 2026-06-04 21:13:33 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 1s. Last read position: chr3:143,972,342 INFO 2026-06-04 21:13:33 MarkDuplicates Tracking 1232160 as yet unmatched pairs. 19114 records in RAM. INFO 2026-06-04 21:13:34 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 1s. Last read position: chr3:156,678,142 INFO 2026-06-04 21:13:34 MarkDuplicates Tracking 1229897 as yet unmatched pairs. 16799 records in RAM. INFO 2026-06-04 21:13:36 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 1s. Last read position: chr3:169,975,613 INFO 2026-06-04 21:13:36 MarkDuplicates Tracking 1228333 as yet unmatched pairs. 15179 records in RAM. INFO 2026-06-04 21:13:37 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 1s. Last read position: chr3:180,953,769 INFO 2026-06-04 21:13:37 MarkDuplicates Tracking 1226145 as yet unmatched pairs. 12954 records in RAM. INFO 2026-06-04 21:13:39 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 1s. Last read position: chr3:184,316,187 INFO 2026-06-04 21:13:39 MarkDuplicates Tracking 1225116 as yet unmatched pairs. 11898 records in RAM. INFO 2026-06-04 21:13:40 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 1s. Last read position: chr3:188,341,703 INFO 2026-06-04 21:13:40 MarkDuplicates Tracking 1222655 as yet unmatched pairs. 9399 records in RAM. INFO 2026-06-04 21:13:43 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 2s. Last read position: chr3:194,431,145 INFO 2026-06-04 21:13:43 MarkDuplicates Tracking 1218395 as yet unmatched pairs. 5094 records in RAM. INFO 2026-06-04 21:13:45 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 2s. Last read position: chr3:195,779,172 INFO 2026-06-04 21:13:45 MarkDuplicates Tracking 1217003 as yet unmatched pairs. 3687 records in RAM. INFO 2026-06-04 21:13:48 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 2s. Last read position: chr3:195,967,896 INFO 2026-06-04 21:13:48 MarkDuplicates Tracking 1215184 as yet unmatched pairs. 1854 records in RAM. INFO 2026-06-04 21:13:50 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 2s. Last read position: chr4:867,408 INFO 2026-06-04 21:13:50 MarkDuplicates Tracking 1212865 as yet unmatched pairs. 64627 records in RAM. INFO 2026-06-04 21:13:52 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 1s. Last read position: chr4:1,744,531 INFO 2026-06-04 21:13:52 MarkDuplicates Tracking 1226317 as yet unmatched pairs. 78052 records in RAM. INFO 2026-06-04 21:13:53 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 1s. Last read position: chr4:1,745,004 INFO 2026-06-04 21:13:53 MarkDuplicates Tracking 1210492 as yet unmatched pairs. 62212 records in RAM. INFO 2026-06-04 21:13:55 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 1s. Last read position: chr4:1,801,497 INFO 2026-06-04 21:13:55 MarkDuplicates Tracking 1223948 as yet unmatched pairs. 75643 records in RAM. INFO 2026-06-04 21:13:56 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 1s. Last read position: chr4:1,804,399 INFO 2026-06-04 21:13:56 MarkDuplicates Tracking 1221027 as yet unmatched pairs. 72692 records in RAM. INFO 2026-06-04 21:13:58 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 1s. Last read position: chr4:1,805,453 INFO 2026-06-04 21:13:58 MarkDuplicates Tracking 1216033 as yet unmatched pairs. 67668 records in RAM. INFO 2026-06-04 21:13:59 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 1s. Last read position: chr4:1,806,101 INFO 2026-06-04 21:13:59 MarkDuplicates Tracking 1208042 as yet unmatched pairs. 59661 records in RAM. INFO 2026-06-04 21:14:01 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 1s. Last read position: chr4:1,806,643 INFO 2026-06-04 21:14:01 MarkDuplicates Tracking 1208678 as yet unmatched pairs. 60290 records in RAM. INFO 2026-06-04 21:14:02 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 1s. Last read position: chr4:2,884,519 INFO 2026-06-04 21:14:02 MarkDuplicates Tracking 1191958 as yet unmatched pairs. 43559 records in RAM. INFO 2026-06-04 21:14:04 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 1s. Last read position: chr4:6,861,330 INFO 2026-06-04 21:14:04 MarkDuplicates Tracking 1188396 as yet unmatched pairs. 39962 records in RAM. INFO 2026-06-04 21:14:05 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 1s. Last read position: chr4:13,603,651 INFO 2026-06-04 21:14:05 MarkDuplicates Tracking 1185880 as yet unmatched pairs. 37395 records in RAM. INFO 2026-06-04 21:14:06 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 1s. Last read position: chr4:37,847,113 INFO 2026-06-04 21:14:06 MarkDuplicates Tracking 1183476 as yet unmatched pairs. 34933 records in RAM. INFO 2026-06-04 21:14:08 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 1s. Last read position: chr4:41,661,480 INFO 2026-06-04 21:14:08 MarkDuplicates Tracking 1181134 as yet unmatched pairs. 32545 records in RAM. INFO 2026-06-04 21:14:09 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 1s. Last read position: chr4:55,118,643 INFO 2026-06-04 21:14:09 MarkDuplicates Tracking 1178621 as yet unmatched pairs. 29995 records in RAM. INFO 2026-06-04 21:14:11 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 1s. Last read position: chr4:70,689,649 INFO 2026-06-04 21:14:11 MarkDuplicates Tracking 1176326 as yet unmatched pairs. 27667 records in RAM. INFO 2026-06-04 21:14:13 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 1s. Last read position: chr4:77,048,466 INFO 2026-06-04 21:14:13 MarkDuplicates Tracking 1174516 as yet unmatched pairs. 25822 records in RAM. INFO 2026-06-04 21:14:14 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 1s. Last read position: chr4:84,688,086 INFO 2026-06-04 21:14:14 MarkDuplicates Tracking 1171513 as yet unmatched pairs. 22790 records in RAM. INFO 2026-06-04 21:14:15 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 1s. Last read position: chr4:87,178,540 INFO 2026-06-04 21:14:15 MarkDuplicates Tracking 1169189 as yet unmatched pairs. 20429 records in RAM. INFO 2026-06-04 21:14:17 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 1s. Last read position: chr4:100,398,308 INFO 2026-06-04 21:14:17 MarkDuplicates Tracking 1166894 as yet unmatched pairs. 18087 records in RAM. INFO 2026-06-04 21:14:18 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr4:108,622,599 INFO 2026-06-04 21:14:18 MarkDuplicates Tracking 1164468 as yet unmatched pairs. 15617 records in RAM. INFO 2026-06-04 21:14:20 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr4:122,271,417 INFO 2026-06-04 21:14:20 MarkDuplicates Tracking 1162426 as yet unmatched pairs. 13543 records in RAM. INFO 2026-06-04 21:14:23 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 2s. Last read position: chr4:139,725,685 INFO 2026-06-04 21:14:23 MarkDuplicates Tracking 1160094 as yet unmatched pairs. 11165 records in RAM. INFO 2026-06-04 21:14:25 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 2s. Last read position: chr4:150,872,736 INFO 2026-06-04 21:14:25 MarkDuplicates Tracking 1158925 as yet unmatched pairs. 9924 records in RAM. INFO 2026-06-04 21:14:27 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 2s. Last read position: chr4:165,337,816 INFO 2026-06-04 21:14:27 MarkDuplicates Tracking 1156486 as yet unmatched pairs. 7435 records in RAM. INFO 2026-06-04 21:14:29 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 1s. Last read position: chr4:174,493,257 INFO 2026-06-04 21:14:29 MarkDuplicates Tracking 1161110 as yet unmatched pairs. 12026 records in RAM. INFO 2026-06-04 21:14:30 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 1s. Last read position: chr4:186,618,060 INFO 2026-06-04 21:14:30 MarkDuplicates Tracking 1152327 as yet unmatched pairs. 3202 records in RAM. INFO 2026-06-04 21:14:32 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 2s. Last read position: chr5:883,965 INFO 2026-06-04 21:14:32 MarkDuplicates Tracking 1148414 as yet unmatched pairs. 62451 records in RAM. INFO 2026-06-04 21:14:34 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 1s. Last read position: chr5:10,263,133 INFO 2026-06-04 21:14:34 MarkDuplicates Tracking 1146235 as yet unmatched pairs. 60232 records in RAM. INFO 2026-06-04 21:14:35 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 1s. Last read position: chr5:14,389,289 INFO 2026-06-04 21:14:35 MarkDuplicates Tracking 1145974 as yet unmatched pairs. 59936 records in RAM. INFO 2026-06-04 21:14:37 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 1s. Last read position: chr5:31,422,787 INFO 2026-06-04 21:14:37 MarkDuplicates Tracking 1141236 as yet unmatched pairs. 55152 records in RAM. INFO 2026-06-04 21:14:39 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 1s. Last read position: chr5:36,177,207 INFO 2026-06-04 21:14:39 MarkDuplicates Tracking 1138306 as yet unmatched pairs. 52187 records in RAM. INFO 2026-06-04 21:14:40 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 1s. Last read position: chr5:40,832,532 INFO 2026-06-04 21:14:40 MarkDuplicates Tracking 1136685 as yet unmatched pairs. 50549 records in RAM. INFO 2026-06-04 21:14:42 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 1s. Last read position: chr5:54,518,305 INFO 2026-06-04 21:14:42 MarkDuplicates Tracking 1133522 as yet unmatched pairs. 47336 records in RAM. INFO 2026-06-04 21:14:43 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 1s. Last read position: chr5:66,044,220 INFO 2026-06-04 21:14:43 MarkDuplicates Tracking 1131648 as yet unmatched pairs. 45404 records in RAM. INFO 2026-06-04 21:14:45 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 1s. Last read position: chr5:70,100,758 INFO 2026-06-04 21:14:45 MarkDuplicates Tracking 1129057 as yet unmatched pairs. 42785 records in RAM. INFO 2026-06-04 21:14:48 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 3s. Last read position: chr5:74,635,220 INFO 2026-06-04 21:14:48 MarkDuplicates Tracking 1127429 as yet unmatched pairs. 41125 records in RAM. INFO 2026-06-04 21:14:49 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 1s. Last read position: chr5:80,428,631 INFO 2026-06-04 21:14:49 MarkDuplicates Tracking 1125299 as yet unmatched pairs. 38950 records in RAM. INFO 2026-06-04 21:14:51 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 1s. Last read position: chr5:95,540,719 INFO 2026-06-04 21:14:51 MarkDuplicates Tracking 1122674 as yet unmatched pairs. 36261 records in RAM. INFO 2026-06-04 21:14:52 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 1s. Last read position: chr5:109,344,806 INFO 2026-06-04 21:14:52 MarkDuplicates Tracking 1120188 as yet unmatched pairs. 33715 records in RAM. INFO 2026-06-04 21:14:54 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 1s. Last read position: chr5:119,531,325 INFO 2026-06-04 21:14:54 MarkDuplicates Tracking 1117901 as yet unmatched pairs. 31361 records in RAM. INFO 2026-06-04 21:14:56 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 1s. Last read position: chr5:132,866,982 INFO 2026-06-04 21:14:56 MarkDuplicates Tracking 1116181 as yet unmatched pairs. 29614 records in RAM. INFO 2026-06-04 21:14:57 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 1s. Last read position: chr5:135,369,450 INFO 2026-06-04 21:14:57 MarkDuplicates Tracking 1113189 as yet unmatched pairs. 26599 records in RAM. INFO 2026-06-04 21:14:59 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 1s. Last read position: chr5:138,924,667 INFO 2026-06-04 21:14:59 MarkDuplicates Tracking 1111502 as yet unmatched pairs. 24894 records in RAM. INFO 2026-06-04 21:15:00 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 1s. Last read position: chr5:141,096,082 INFO 2026-06-04 21:15:00 MarkDuplicates Tracking 1108008 as yet unmatched pairs. 21347 records in RAM. INFO 2026-06-04 21:15:01 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr5:141,863,475 INFO 2026-06-04 21:15:01 MarkDuplicates Tracking 1107081 as yet unmatched pairs. 20396 records in RAM. INFO 2026-06-04 21:15:03 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 1s. Last read position: chr5:147,828,082 INFO 2026-06-04 21:15:03 MarkDuplicates Tracking 1108296 as yet unmatched pairs. 21572 records in RAM. INFO 2026-06-04 21:15:04 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 1s. Last read position: chr5:150,404,681 INFO 2026-06-04 21:15:04 MarkDuplicates Tracking 1104694 as yet unmatched pairs. 17933 records in RAM. INFO 2026-06-04 21:15:06 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 1s. Last read position: chr5:151,786,705 INFO 2026-06-04 21:15:06 MarkDuplicates Tracking 1099979 as yet unmatched pairs. 13181 records in RAM. INFO 2026-06-04 21:15:07 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 1s. Last read position: chr5:163,441,879 INFO 2026-06-04 21:15:07 MarkDuplicates Tracking 1097246 as yet unmatched pairs. 10391 records in RAM. INFO 2026-06-04 21:15:10 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 3s. Last read position: chr5:171,407,724 INFO 2026-06-04 21:15:10 MarkDuplicates Tracking 1103062 as yet unmatched pairs. 16175 records in RAM. INFO 2026-06-04 21:15:12 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:05:20s. Time for last 1,000,000: 2s. Last read position: chr5:177,536,532 INFO 2026-06-04 21:15:12 MarkDuplicates Tracking 1091386 as yet unmatched pairs. 4477 records in RAM. INFO 2026-06-04 21:15:14 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 2s. Last read position: chr5:179,836,488 INFO 2026-06-04 21:15:14 MarkDuplicates Tracking 1089187 as yet unmatched pairs. 2264 records in RAM. INFO 2026-06-04 21:15:17 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 2s. Last read position: chr6:3,154,190 INFO 2026-06-04 21:15:17 MarkDuplicates Tracking 1085849 as yet unmatched pairs. 73792 records in RAM. INFO 2026-06-04 21:15:18 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 1s. Last read position: chr6:7,580,126 INFO 2026-06-04 21:15:18 MarkDuplicates Tracking 1083951 as yet unmatched pairs. 71849 records in RAM. INFO 2026-06-04 21:15:20 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 1s. Last read position: chr6:17,799,953 INFO 2026-06-04 21:15:20 MarkDuplicates Tracking 1080980 as yet unmatched pairs. 68837 records in RAM. INFO 2026-06-04 21:15:21 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 1s. Last read position: chr6:26,156,559 INFO 2026-06-04 21:15:21 MarkDuplicates Tracking 1079757 as yet unmatched pairs. 67582 records in RAM. INFO 2026-06-04 21:15:22 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 1s. Last read position: chr6:27,808,316 INFO 2026-06-04 21:15:22 MarkDuplicates Tracking 1076280 as yet unmatched pairs. 64082 records in RAM. INFO 2026-06-04 21:15:24 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 1s. Last read position: chr6:30,346,711 INFO 2026-06-04 21:15:24 MarkDuplicates Tracking 1073441 as yet unmatched pairs. 61222 records in RAM. INFO 2026-06-04 21:15:25 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 1s. Last read position: chr6:31,269,017 INFO 2026-06-04 21:15:25 MarkDuplicates Tracking 1073103 as yet unmatched pairs. 60863 records in RAM. INFO 2026-06-04 21:15:27 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 1s. Last read position: chr6:31,647,774 INFO 2026-06-04 21:15:27 MarkDuplicates Tracking 1069148 as yet unmatched pairs. 56893 records in RAM. INFO 2026-06-04 21:15:28 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 1s. Last read position: chr6:31,828,979 INFO 2026-06-04 21:15:28 MarkDuplicates Tracking 1067061 as yet unmatched pairs. 54784 records in RAM. INFO 2026-06-04 21:15:29 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 1s. Last read position: chr6:32,853,514 INFO 2026-06-04 21:15:29 MarkDuplicates Tracking 1064284 as yet unmatched pairs. 51994 records in RAM. INFO 2026-06-04 21:15:31 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 1s. Last read position: chr6:33,443,221 INFO 2026-06-04 21:15:31 MarkDuplicates Tracking 1061627 as yet unmatched pairs. 49326 records in RAM. INFO 2026-06-04 21:15:32 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 1s. Last read position: chr6:35,869,804 INFO 2026-06-04 21:15:32 MarkDuplicates Tracking 1059555 as yet unmatched pairs. 47218 records in RAM. INFO 2026-06-04 21:15:34 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 2s. Last read position: chr6:41,930,754 INFO 2026-06-04 21:15:34 MarkDuplicates Tracking 1056428 as yet unmatched pairs. 44035 records in RAM. INFO 2026-06-04 21:15:36 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 1s. Last read position: chr6:43,355,067 INFO 2026-06-04 21:15:36 MarkDuplicates Tracking 1053945 as yet unmatched pairs. 41523 records in RAM. INFO 2026-06-04 21:15:38 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 1s. Last read position: chr6:44,253,045 INFO 2026-06-04 21:15:38 MarkDuplicates Tracking 1052838 as yet unmatched pairs. 40378 records in RAM. INFO 2026-06-04 21:15:40 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 1s. Last read position: chr6:47,309,466 INFO 2026-06-04 21:15:40 MarkDuplicates Tracking 1050543 as yet unmatched pairs. 38063 records in RAM. INFO 2026-06-04 21:15:41 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 1s. Last read position: chr6:56,530,021 INFO 2026-06-04 21:15:41 MarkDuplicates Tracking 1047215 as yet unmatched pairs. 34643 records in RAM. INFO 2026-06-04 21:15:43 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 1s. Last read position: chr6:56,636,557 INFO 2026-06-04 21:15:43 MarkDuplicates Tracking 1045026 as yet unmatched pairs. 32433 records in RAM. INFO 2026-06-04 21:15:44 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 1s. Last read position: chr6:75,205,784 INFO 2026-06-04 21:15:44 MarkDuplicates Tracking 1042053 as yet unmatched pairs. 29426 records in RAM. INFO 2026-06-04 21:15:46 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 1s. Last read position: chr6:85,533,759 INFO 2026-06-04 21:15:46 MarkDuplicates Tracking 1040287 as yet unmatched pairs. 27623 records in RAM. INFO 2026-06-04 21:15:47 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 1s. Last read position: chr6:99,401,606 INFO 2026-06-04 21:15:47 MarkDuplicates Tracking 1037664 as yet unmatched pairs. 24954 records in RAM. INFO 2026-06-04 21:15:49 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 1s. Last read position: chr6:109,368,844 INFO 2026-06-04 21:15:49 MarkDuplicates Tracking 1040255 as yet unmatched pairs. 27511 records in RAM. INFO 2026-06-04 21:15:51 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 1s. Last read position: chr6:115,972,499 INFO 2026-06-04 21:15:51 MarkDuplicates Tracking 1032497 as yet unmatched pairs. 19714 records in RAM. INFO 2026-06-04 21:15:52 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 1s. Last read position: chr6:130,083,671 INFO 2026-06-04 21:15:52 MarkDuplicates Tracking 1030242 as yet unmatched pairs. 17409 records in RAM. INFO 2026-06-04 21:15:54 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 1s. Last read position: chr6:138,092,012 INFO 2026-06-04 21:15:54 MarkDuplicates Tracking 1029317 as yet unmatched pairs. 16452 records in RAM. INFO 2026-06-04 21:15:55 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 1s. Last read position: chr6:143,860,432 INFO 2026-06-04 21:15:55 MarkDuplicates Tracking 1025367 as yet unmatched pairs. 12461 records in RAM. INFO 2026-06-04 21:15:57 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 1s. Last read position: chr6:151,352,272 INFO 2026-06-04 21:15:57 MarkDuplicates Tracking 1023033 as yet unmatched pairs. 10098 records in RAM. INFO 2026-06-04 21:15:58 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 1s. Last read position: chr6:158,766,680 INFO 2026-06-04 21:15:58 MarkDuplicates Tracking 1020754 as yet unmatched pairs. 7765 records in RAM. INFO 2026-06-04 21:16:00 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 2s. Last read position: chr6:158,784,699 INFO 2026-06-04 21:16:00 MarkDuplicates Tracking 1021528 as yet unmatched pairs. 8528 records in RAM. INFO 2026-06-04 21:16:02 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 1s. Last read position: chr6:160,639,300 INFO 2026-06-04 21:16:02 MarkDuplicates Tracking 1015802 as yet unmatched pairs. 2791 records in RAM. INFO 2026-06-04 21:16:04 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 2s. Last read position: chr6:170,546,114 INFO 2026-06-04 21:16:04 MarkDuplicates Tracking 1014202 as yet unmatched pairs. 1144 records in RAM. INFO 2026-06-04 21:16:07 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 2s. Last read position: chr7:2,919,544 INFO 2026-06-04 21:16:07 MarkDuplicates Tracking 1010780 as yet unmatched pairs. 68450 records in RAM. INFO 2026-06-04 21:16:08 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:06:16s. Time for last 1,000,000: 1s. Last read position: chr7:5,527,762 INFO 2026-06-04 21:16:08 MarkDuplicates Tracking 1022686 as yet unmatched pairs. 80308 records in RAM. INFO 2026-06-04 21:16:10 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 1s. Last read position: chr7:5,528,391 INFO 2026-06-04 21:16:10 MarkDuplicates Tracking 1012008 as yet unmatched pairs. 69614 records in RAM. INFO 2026-06-04 21:16:11 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 1s. Last read position: chr7:5,529,286 INFO 2026-06-04 21:16:11 MarkDuplicates Tracking 1026365 as yet unmatched pairs. 83952 records in RAM. INFO 2026-06-04 21:16:12 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 1s. Last read position: chr7:6,474,247 INFO 2026-06-04 21:16:12 MarkDuplicates Tracking 1000130 as yet unmatched pairs. 57690 records in RAM. INFO 2026-06-04 21:16:14 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 1s. Last read position: chr7:17,339,724 INFO 2026-06-04 21:16:14 MarkDuplicates Tracking 999773 as yet unmatched pairs. 57302 records in RAM. INFO 2026-06-04 21:16:16 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 1s. Last read position: chr7:27,095,717 INFO 2026-06-04 21:16:16 MarkDuplicates Tracking 995085 as yet unmatched pairs. 52552 records in RAM. INFO 2026-06-04 21:16:17 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 1s. Last read position: chr7:40,063,022 INFO 2026-06-04 21:16:17 MarkDuplicates Tracking 992822 as yet unmatched pairs. 50255 records in RAM. INFO 2026-06-04 21:16:19 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 1s. Last read position: chr7:44,884,501 INFO 2026-06-04 21:16:19 MarkDuplicates Tracking 990288 as yet unmatched pairs. 47701 records in RAM. INFO 2026-06-04 21:16:20 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 1s. Last read position: chr7:56,061,763 INFO 2026-06-04 21:16:20 MarkDuplicates Tracking 987783 as yet unmatched pairs. 45163 records in RAM. INFO 2026-06-04 21:16:21 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 1s. Last read position: chr7:73,022,283 INFO 2026-06-04 21:16:21 MarkDuplicates Tracking 985471 as yet unmatched pairs. 42826 records in RAM. INFO 2026-06-04 21:16:23 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:06:31s. Time for last 1,000,000: 1s. Last read position: chr7:74,317,547 INFO 2026-06-04 21:16:23 MarkDuplicates Tracking 983974 as yet unmatched pairs. 41307 records in RAM. INFO 2026-06-04 21:16:25 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 1s. Last read position: chr7:75,422,337 INFO 2026-06-04 21:16:25 MarkDuplicates Tracking 983093 as yet unmatched pairs. 40406 records in RAM. INFO 2026-06-04 21:16:26 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 1s. Last read position: chr7:76,303,065 INFO 2026-06-04 21:16:26 MarkDuplicates Tracking 988649 as yet unmatched pairs. 45948 records in RAM. INFO 2026-06-04 21:16:28 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 2s. Last read position: chr7:76,990,264 INFO 2026-06-04 21:16:28 MarkDuplicates Tracking 977705 as yet unmatched pairs. 34986 records in RAM. INFO 2026-06-04 21:16:30 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 2s. Last read position: chr7:91,973,910 INFO 2026-06-04 21:16:30 MarkDuplicates Tracking 977075 as yet unmatched pairs. 34311 records in RAM. INFO 2026-06-04 21:16:32 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 1s. Last read position: chr7:93,999,210 INFO 2026-06-04 21:16:32 MarkDuplicates Tracking 973317 as yet unmatched pairs. 30544 records in RAM. INFO 2026-06-04 21:16:34 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 1s. Last read position: chr7:99,049,573 INFO 2026-06-04 21:16:34 MarkDuplicates Tracking 970698 as yet unmatched pairs. 27886 records in RAM. INFO 2026-06-04 21:16:35 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 1s. Last read position: chr7:100,352,569 INFO 2026-06-04 21:16:35 MarkDuplicates Tracking 968656 as yet unmatched pairs. 25816 records in RAM. INFO 2026-06-04 21:16:37 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 1s. Last read position: chr7:102,170,454 INFO 2026-06-04 21:16:37 MarkDuplicates Tracking 965665 as yet unmatched pairs. 22790 records in RAM. INFO 2026-06-04 21:16:38 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:06:46s. Time for last 1,000,000: 1s. Last read position: chr7:102,660,078 INFO 2026-06-04 21:16:38 MarkDuplicates Tracking 964584 as yet unmatched pairs. 21698 records in RAM. INFO 2026-06-04 21:16:40 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:06:47s. Time for last 1,000,000: 1s. Last read position: chr7:107,924,226 INFO 2026-06-04 21:16:40 MarkDuplicates Tracking 962586 as yet unmatched pairs. 19667 records in RAM. INFO 2026-06-04 21:16:41 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 1s. Last read position: chr7:123,692,534 INFO 2026-06-04 21:16:41 MarkDuplicates Tracking 960163 as yet unmatched pairs. 17215 records in RAM. INFO 2026-06-04 21:17:37 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:07:45s. Time for last 1,000,000: 55s. Last read position: chr7:129,485,673 INFO 2026-06-04 21:17:37 MarkDuplicates Tracking 957178 as yet unmatched pairs. 14214 records in RAM. INFO 2026-06-04 21:17:39 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:07:47s. Time for last 1,000,000: 2s. Last read position: chr7:137,908,335 INFO 2026-06-04 21:17:39 MarkDuplicates Tracking 956078 as yet unmatched pairs. 13076 records in RAM. INFO 2026-06-04 21:17:41 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:07:49s. Time for last 1,000,000: 1s. Last read position: chr7:140,459,710 INFO 2026-06-04 21:17:41 MarkDuplicates Tracking 952914 as yet unmatched pairs. 9896 records in RAM. INFO 2026-06-04 21:17:43 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:07:50s. Time for last 1,000,000: 1s. Last read position: chr7:143,388,319 INFO 2026-06-04 21:17:43 MarkDuplicates Tracking 950564 as yet unmatched pairs. 7522 records in RAM. INFO 2026-06-04 21:17:44 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:07:52s. Time for last 1,000,000: 1s. Last read position: chr7:149,012,214 INFO 2026-06-04 21:17:44 MarkDuplicates Tracking 948687 as yet unmatched pairs. 5639 records in RAM. INFO 2026-06-04 21:17:45 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:07:53s. Time for last 1,000,000: 1s. Last read position: chr7:152,154,409 INFO 2026-06-04 21:17:45 MarkDuplicates Tracking 945645 as yet unmatched pairs. 2568 records in RAM. INFO 2026-06-04 21:17:47 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:07:54s. Time for last 1,000,000: 1s. Last read position: chr7:158,945,602 INFO 2026-06-04 21:17:47 MarkDuplicates Tracking 943231 as yet unmatched pairs. 110 records in RAM. INFO 2026-06-04 21:17:50 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:07:58s. Time for last 1,000,000: 3s. Last read position: chr8:13,100,541 INFO 2026-06-04 21:17:50 MarkDuplicates Tracking 940611 as yet unmatched pairs. 63078 records in RAM. INFO 2026-06-04 21:17:52 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:07:59s. Time for last 1,000,000: 1s. Last read position: chr8:21,999,097 INFO 2026-06-04 21:17:52 MarkDuplicates Tracking 938447 as yet unmatched pairs. 60882 records in RAM. INFO 2026-06-04 21:17:53 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:08:01s. Time for last 1,000,000: 1s. Last read position: chr8:25,506,535 INFO 2026-06-04 21:17:53 MarkDuplicates Tracking 935600 as yet unmatched pairs. 58009 records in RAM. INFO 2026-06-04 21:17:54 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:08:02s. Time for last 1,000,000: 1s. Last read position: chr8:30,504,334 INFO 2026-06-04 21:17:54 MarkDuplicates Tracking 935093 as yet unmatched pairs. 57448 records in RAM. INFO 2026-06-04 21:17:56 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:08:04s. Time for last 1,000,000: 1s. Last read position: chr8:38,326,833 INFO 2026-06-04 21:17:56 MarkDuplicates Tracking 933429 as yet unmatched pairs. 55739 records in RAM. INFO 2026-06-04 21:17:58 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 1s. Last read position: chr8:42,189,047 INFO 2026-06-04 21:17:58 MarkDuplicates Tracking 929450 as yet unmatched pairs. 51744 records in RAM. INFO 2026-06-04 21:17:59 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:08:07s. Time for last 1,000,000: 1s. Last read position: chr8:47,966,244 INFO 2026-06-04 21:17:59 MarkDuplicates Tracking 925932 as yet unmatched pairs. 48192 records in RAM. INFO 2026-06-04 21:18:01 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:08:08s. Time for last 1,000,000: 1s. Last read position: chr8:60,837,687 INFO 2026-06-04 21:18:01 MarkDuplicates Tracking 923374 as yet unmatched pairs. 45604 records in RAM. INFO 2026-06-04 21:18:02 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:08:10s. Time for last 1,000,000: 1s. Last read position: chr8:67,434,622 INFO 2026-06-04 21:18:02 MarkDuplicates Tracking 920996 as yet unmatched pairs. 43194 records in RAM. INFO 2026-06-04 21:18:04 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:08:12s. Time for last 1,000,000: 1s. Last read position: chr8:81,283,413 INFO 2026-06-04 21:18:04 MarkDuplicates Tracking 921639 as yet unmatched pairs. 43801 records in RAM. INFO 2026-06-04 21:18:06 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:08:14s. Time for last 1,000,000: 2s. Last read position: chr8:94,832,093 INFO 2026-06-04 21:18:06 MarkDuplicates Tracking 917142 as yet unmatched pairs. 39273 records in RAM. INFO 2026-06-04 21:18:08 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:08:15s. Time for last 1,000,000: 1s. Last read position: chr8:100,704,319 INFO 2026-06-04 21:18:08 MarkDuplicates Tracking 925375 as yet unmatched pairs. 47462 records in RAM. INFO 2026-06-04 21:18:09 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:08:17s. Time for last 1,000,000: 1s. Last read position: chr8:100,721,403 INFO 2026-06-04 21:18:09 MarkDuplicates Tracking 915063 as yet unmatched pairs. 37135 records in RAM. INFO 2026-06-04 21:18:10 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:08:18s. Time for last 1,000,000: 1s. Last read position: chr8:106,447,982 INFO 2026-06-04 21:18:10 MarkDuplicates Tracking 909205 as yet unmatched pairs. 31230 records in RAM. INFO 2026-06-04 21:18:12 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:08:20s. Time for last 1,000,000: 1s. Last read position: chr8:123,255,826 INFO 2026-06-04 21:18:12 MarkDuplicates Tracking 906960 as yet unmatched pairs. 28941 records in RAM. INFO 2026-06-04 21:18:13 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 1s. Last read position: chr8:130,124,027 INFO 2026-06-04 21:18:13 MarkDuplicates Tracking 904264 as yet unmatched pairs. 26213 records in RAM. INFO 2026-06-04 21:18:15 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 1s. Last read position: chr8:140,664,925 INFO 2026-06-04 21:18:15 MarkDuplicates Tracking 902325 as yet unmatched pairs. 24238 records in RAM. INFO 2026-06-04 21:18:16 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:08:24s. Time for last 1,000,000: 1s. Last read position: chr8:143,726,862 INFO 2026-06-04 21:18:16 MarkDuplicates Tracking 898831 as yet unmatched pairs. 20708 records in RAM. INFO 2026-06-04 21:18:17 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 1s. Last read position: chr8:143,858,702 INFO 2026-06-04 21:18:17 MarkDuplicates Tracking 897159 as yet unmatched pairs. 19032 records in RAM. INFO 2026-06-04 21:18:19 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:08:26s. Time for last 1,000,000: 1s. Last read position: chr8:143,860,874 INFO 2026-06-04 21:18:19 MarkDuplicates Tracking 896652 as yet unmatched pairs. 18524 records in RAM. INFO 2026-06-04 21:18:20 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:08:27s. Time for last 1,000,000: 1s. Last read position: chr8:143,862,550 INFO 2026-06-04 21:18:20 MarkDuplicates Tracking 896113 as yet unmatched pairs. 17981 records in RAM. INFO 2026-06-04 21:18:21 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 1s. Last read position: chr8:143,864,236 INFO 2026-06-04 21:18:21 MarkDuplicates Tracking 894090 as yet unmatched pairs. 15947 records in RAM. INFO 2026-06-04 21:18:22 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 0s. Last read position: chr8:143,866,114 INFO 2026-06-04 21:18:22 MarkDuplicates Tracking 893111 as yet unmatched pairs. 14964 records in RAM. INFO 2026-06-04 21:18:23 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:08:31s. Time for last 1,000,000: 1s. Last read position: chr8:143,871,877 INFO 2026-06-04 21:18:23 MarkDuplicates Tracking 892529 as yet unmatched pairs. 14369 records in RAM. INFO 2026-06-04 21:18:25 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:08:33s. Time for last 1,000,000: 2s. Last read position: chr8:143,920,700 INFO 2026-06-04 21:18:25 MarkDuplicates Tracking 889388 as yet unmatched pairs. 11214 records in RAM. INFO 2026-06-04 21:18:27 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 1s. Last read position: chr8:143,926,723 INFO 2026-06-04 21:18:27 MarkDuplicates Tracking 885161 as yet unmatched pairs. 6966 records in RAM. INFO 2026-06-04 21:18:28 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:08:36s. Time for last 1,000,000: 1s. Last read position: chr8:144,097,240 INFO 2026-06-04 21:18:28 MarkDuplicates Tracking 881823 as yet unmatched pairs. 3598 records in RAM. INFO 2026-06-04 21:18:29 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 1s. Last read position: chr8:144,841,684 INFO 2026-06-04 21:18:29 MarkDuplicates Tracking 878780 as yet unmatched pairs. 533 records in RAM. INFO 2026-06-04 21:18:31 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:08:39s. Time for last 1,000,000: 1s. Last read position: chr9:5,810,056 INFO 2026-06-04 21:18:31 MarkDuplicates Tracking 878934 as yet unmatched pairs. 55548 records in RAM. INFO 2026-06-04 21:18:33 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:08:41s. Time for last 1,000,000: 1s. Last read position: chr9:19,290,703 INFO 2026-06-04 21:18:33 MarkDuplicates Tracking 874445 as yet unmatched pairs. 51027 records in RAM. INFO 2026-06-04 21:18:35 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:08:43s. Time for last 1,000,000: 1s. Last read position: chr9:33,264,253 INFO 2026-06-04 21:18:35 MarkDuplicates Tracking 872302 as yet unmatched pairs. 48846 records in RAM. INFO 2026-06-04 21:18:37 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:08:44s. Time for last 1,000,000: 1s. Last read position: chr9:33,944,372 INFO 2026-06-04 21:18:37 MarkDuplicates Tracking 868770 as yet unmatched pairs. 45286 records in RAM. INFO 2026-06-04 21:18:38 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:08:46s. Time for last 1,000,000: 1s. Last read position: chr9:35,706,878 INFO 2026-06-04 21:18:38 MarkDuplicates Tracking 866265 as yet unmatched pairs. 42755 records in RAM. INFO 2026-06-04 21:18:40 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:08:47s. Time for last 1,000,000: 1s. Last read position: chr9:65,676,000 INFO 2026-06-04 21:18:40 MarkDuplicates Tracking 864014 as yet unmatched pairs. 40452 records in RAM. INFO 2026-06-04 21:18:41 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 1s. Last read position: chr9:72,223,210 INFO 2026-06-04 21:18:41 MarkDuplicates Tracking 861818 as yet unmatched pairs. 38230 records in RAM. INFO 2026-06-04 21:18:42 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:08:50s. Time for last 1,000,000: 1s. Last read position: chr9:86,035,452 INFO 2026-06-04 21:18:42 MarkDuplicates Tracking 859572 as yet unmatched pairs. 35949 records in RAM. INFO 2026-06-04 21:18:44 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:08:52s. Time for last 1,000,000: 1s. Last read position: chr9:93,317,874 INFO 2026-06-04 21:18:44 MarkDuplicates Tracking 856903 as yet unmatched pairs. 33249 records in RAM. INFO 2026-06-04 21:18:46 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:08:53s. Time for last 1,000,000: 1s. Last read position: chr9:98,808,001 INFO 2026-06-04 21:18:46 MarkDuplicates Tracking 854476 as yet unmatched pairs. 30799 records in RAM. INFO 2026-06-04 21:18:47 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:08:55s. Time for last 1,000,000: 1s. Last read position: chr9:108,917,624 INFO 2026-06-04 21:18:47 MarkDuplicates Tracking 851951 as yet unmatched pairs. 28256 records in RAM. INFO 2026-06-04 21:18:49 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:08:56s. Time for last 1,000,000: 1s. Last read position: chr9:112,262,490 INFO 2026-06-04 21:18:49 MarkDuplicates Tracking 851004 as yet unmatched pairs. 27281 records in RAM. INFO 2026-06-04 21:18:50 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:08:58s. Time for last 1,000,000: 1s. Last read position: chr9:120,787,864 INFO 2026-06-04 21:18:50 MarkDuplicates Tracking 847440 as yet unmatched pairs. 23701 records in RAM. INFO 2026-06-04 21:18:52 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:08:59s. Time for last 1,000,000: 1s. Last read position: chr9:124,860,262 INFO 2026-06-04 21:18:52 MarkDuplicates Tracking 846058 as yet unmatched pairs. 22301 records in RAM. INFO 2026-06-04 21:18:53 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:09:01s. Time for last 1,000,000: 1s. Last read position: chr9:127,818,283 INFO 2026-06-04 21:18:53 MarkDuplicates Tracking 842298 as yet unmatched pairs. 18515 records in RAM. INFO 2026-06-04 21:18:55 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:09:02s. Time for last 1,000,000: 1s. Last read position: chr9:128,632,234 INFO 2026-06-04 21:18:55 MarkDuplicates Tracking 839428 as yet unmatched pairs. 15615 records in RAM. INFO 2026-06-04 21:18:57 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 2s. Last read position: chr9:130,100,665 INFO 2026-06-04 21:18:57 MarkDuplicates Tracking 836630 as yet unmatched pairs. 12809 records in RAM. INFO 2026-06-04 21:18:58 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:09:06s. Time for last 1,000,000: 1s. Last read position: chr9:132,281,538 INFO 2026-06-04 21:18:58 MarkDuplicates Tracking 834055 as yet unmatched pairs. 10216 records in RAM. INFO 2026-06-04 21:19:00 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 1s. Last read position: chr9:134,050,453 INFO 2026-06-04 21:19:00 MarkDuplicates Tracking 831794 as yet unmatched pairs. 7934 records in RAM. INFO 2026-06-04 21:19:01 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:09:09s. Time for last 1,000,000: 1s. Last read position: chr9:136,496,169 INFO 2026-06-04 21:19:01 MarkDuplicates Tracking 828787 as yet unmatched pairs. 4905 records in RAM. INFO 2026-06-04 21:19:03 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:09:10s. Time for last 1,000,000: 1s. Last read position: chr9:137,241,813 INFO 2026-06-04 21:19:03 MarkDuplicates Tracking 827151 as yet unmatched pairs. 3257 records in RAM. INFO 2026-06-04 21:19:05 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:09:12s. Time for last 1,000,000: 1s. Last read position: chr10:3,113,447 INFO 2026-06-04 21:19:05 MarkDuplicates Tracking 823227 as yet unmatched pairs. 54510 records in RAM. INFO 2026-06-04 21:19:06 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 1s. Last read position: chr10:6,242,283 INFO 2026-06-04 21:19:06 MarkDuplicates Tracking 820641 as yet unmatched pairs. 51903 records in RAM. INFO 2026-06-04 21:19:07 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:09:15s. Time for last 1,000,000: 1s. Last read position: chr10:15,684,055 INFO 2026-06-04 21:19:07 MarkDuplicates Tracking 818239 as yet unmatched pairs. 49477 records in RAM. INFO 2026-06-04 21:19:09 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:09:17s. Time for last 1,000,000: 2s. Last read position: chr10:27,131,918 INFO 2026-06-04 21:19:09 MarkDuplicates Tracking 816165 as yet unmatched pairs. 47370 records in RAM. INFO 2026-06-04 21:19:11 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:09:19s. Time for last 1,000,000: 1s. Last read position: chr10:32,028,505 INFO 2026-06-04 21:19:11 MarkDuplicates Tracking 818202 as yet unmatched pairs. 49391 records in RAM. INFO 2026-06-04 21:19:12 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 1s. Last read position: chr10:32,923,635 INFO 2026-06-04 21:19:12 MarkDuplicates Tracking 815129 as yet unmatched pairs. 46305 records in RAM. INFO 2026-06-04 21:19:14 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 1s. Last read position: chr10:43,387,222 INFO 2026-06-04 21:19:14 MarkDuplicates Tracking 809518 as yet unmatched pairs. 40651 records in RAM. INFO 2026-06-04 21:19:15 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:09:23s. Time for last 1,000,000: 1s. Last read position: chr10:46,388,448 INFO 2026-06-04 21:19:15 MarkDuplicates Tracking 807195 as yet unmatched pairs. 38322 records in RAM. INFO 2026-06-04 21:19:17 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:09:24s. Time for last 1,000,000: 1s. Last read position: chr10:59,794,516 INFO 2026-06-04 21:19:17 MarkDuplicates Tracking 807154 as yet unmatched pairs. 38264 records in RAM. INFO 2026-06-04 21:19:18 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:09:26s. Time for last 1,000,000: 1s. Last read position: chr10:68,747,372 INFO 2026-06-04 21:19:18 MarkDuplicates Tracking 803761 as yet unmatched pairs. 34834 records in RAM. INFO 2026-06-04 21:19:19 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:09:27s. Time for last 1,000,000: 1s. Last read position: chr10:71,510,116 INFO 2026-06-04 21:19:19 MarkDuplicates Tracking 800268 as yet unmatched pairs. 31324 records in RAM. INFO 2026-06-04 21:19:21 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:09:29s. Time for last 1,000,000: 1s. Last read position: chr10:73,837,468 INFO 2026-06-04 21:19:21 MarkDuplicates Tracking 798693 as yet unmatched pairs. 29721 records in RAM. INFO 2026-06-04 21:19:23 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:09:30s. Time for last 1,000,000: 1s. Last read position: chr10:78,037,243 INFO 2026-06-04 21:19:23 MarkDuplicates Tracking 795885 as yet unmatched pairs. 26868 records in RAM. INFO 2026-06-04 21:19:24 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:09:32s. Time for last 1,000,000: 1s. Last read position: chr10:86,943,489 INFO 2026-06-04 21:19:24 MarkDuplicates Tracking 792695 as yet unmatched pairs. 23656 records in RAM. INFO 2026-06-04 21:19:26 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:09:33s. Time for last 1,000,000: 1s. Last read position: chr10:91,630,154 INFO 2026-06-04 21:19:26 MarkDuplicates Tracking 790687 as yet unmatched pairs. 21623 records in RAM. INFO 2026-06-04 21:19:28 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 1s. Last read position: chr10:94,334,643 INFO 2026-06-04 21:19:28 MarkDuplicates Tracking 788043 as yet unmatched pairs. 18963 records in RAM. INFO 2026-06-04 21:19:29 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 1s. Last read position: chr10:97,426,288 INFO 2026-06-04 21:19:29 MarkDuplicates Tracking 785666 as yet unmatched pairs. 16572 records in RAM. INFO 2026-06-04 21:19:31 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:09:39s. Time for last 1,000,000: 1s. Last read position: chr10:101,003,519 INFO 2026-06-04 21:19:31 MarkDuplicates Tracking 783491 as yet unmatched pairs. 14378 records in RAM. INFO 2026-06-04 21:19:32 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:09:40s. Time for last 1,000,000: 1s. Last read position: chr10:102,689,924 INFO 2026-06-04 21:19:32 MarkDuplicates Tracking 780680 as yet unmatched pairs. 11553 records in RAM. INFO 2026-06-04 21:19:34 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:09:42s. Time for last 1,000,000: 1s. Last read position: chr10:110,130,406 INFO 2026-06-04 21:19:34 MarkDuplicates Tracking 778443 as yet unmatched pairs. 9293 records in RAM. INFO 2026-06-04 21:19:35 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:09:43s. Time for last 1,000,000: 1s. Last read position: chr10:118,039,301 INFO 2026-06-04 21:19:35 MarkDuplicates Tracking 775850 as yet unmatched pairs. 6666 records in RAM. INFO 2026-06-04 21:19:37 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:09:45s. Time for last 1,000,000: 1s. Last read position: chr10:122,211,365 INFO 2026-06-04 21:19:37 MarkDuplicates Tracking 773954 as yet unmatched pairs. 4756 records in RAM. INFO 2026-06-04 21:19:38 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:09:46s. Time for last 1,000,000: 1s. Last read position: chr10:128,105,411 INFO 2026-06-04 21:19:38 MarkDuplicates Tracking 771539 as yet unmatched pairs. 2298 records in RAM. INFO 2026-06-04 21:19:40 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:09:48s. Time for last 1,000,000: 2s. Last read position: chr11:396,618 INFO 2026-06-04 21:19:40 MarkDuplicates Tracking 768842 as yet unmatched pairs. 94604 records in RAM. INFO 2026-06-04 21:19:42 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:09:50s. Time for last 1,000,000: 1s. Last read position: chr11:838,006 INFO 2026-06-04 21:19:42 MarkDuplicates Tracking 766160 as yet unmatched pairs. 91910 records in RAM. INFO 2026-06-04 21:19:44 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:09:51s. Time for last 1,000,000: 1s. Last read position: chr11:1,757,518 INFO 2026-06-04 21:19:44 MarkDuplicates Tracking 764977 as yet unmatched pairs. 90711 records in RAM. INFO 2026-06-04 21:19:45 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:09:53s. Time for last 1,000,000: 1s. Last read position: chr11:2,135,440 INFO 2026-06-04 21:19:45 MarkDuplicates Tracking 763592 as yet unmatched pairs. 89302 records in RAM. INFO 2026-06-04 21:19:46 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:09:54s. Time for last 1,000,000: 1s. Last read position: chr11:5,664,834 INFO 2026-06-04 21:19:46 MarkDuplicates Tracking 757795 as yet unmatched pairs. 83485 records in RAM. INFO 2026-06-04 21:19:48 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:09:56s. Time for last 1,000,000: 1s. Last read position: chr11:9,021,178 INFO 2026-06-04 21:19:48 MarkDuplicates Tracking 754768 as yet unmatched pairs. 80442 records in RAM. INFO 2026-06-04 21:19:50 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:09:58s. Time for last 1,000,000: 2s. Last read position: chr11:10,800,975 INFO 2026-06-04 21:19:50 MarkDuplicates Tracking 753134 as yet unmatched pairs. 78793 records in RAM. INFO 2026-06-04 21:19:52 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:10:00s. Time for last 1,000,000: 1s. Last read position: chr11:14,475,785 INFO 2026-06-04 21:19:52 MarkDuplicates Tracking 750319 as yet unmatched pairs. 75962 records in RAM. INFO 2026-06-04 21:19:53 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:10:01s. Time for last 1,000,000: 1s. Last read position: chr11:18,481,858 INFO 2026-06-04 21:19:53 MarkDuplicates Tracking 747670 as yet unmatched pairs. 73294 records in RAM. INFO 2026-06-04 21:19:55 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:10:03s. Time for last 1,000,000: 1s. Last read position: chr11:33,347,336 INFO 2026-06-04 21:19:55 MarkDuplicates Tracking 745088 as yet unmatched pairs. 70693 records in RAM. INFO 2026-06-04 21:19:56 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:10:04s. Time for last 1,000,000: 1s. Last read position: chr11:43,330,008 INFO 2026-06-04 21:19:56 MarkDuplicates Tracking 742758 as yet unmatched pairs. 68327 records in RAM. INFO 2026-06-04 21:19:58 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 1s. Last read position: chr11:46,858,905 INFO 2026-06-04 21:19:58 MarkDuplicates Tracking 739976 as yet unmatched pairs. 65524 records in RAM. INFO 2026-06-04 21:19:59 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:10:07s. Time for last 1,000,000: 1s. Last read position: chr11:57,313,748 INFO 2026-06-04 21:19:59 MarkDuplicates Tracking 737944 as yet unmatched pairs. 63481 records in RAM. INFO 2026-06-04 21:20:01 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 1s. Last read position: chr11:59,172,592 INFO 2026-06-04 21:20:01 MarkDuplicates Tracking 735445 as yet unmatched pairs. 60969 records in RAM. INFO 2026-06-04 21:20:02 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:10:10s. Time for last 1,000,000: 1s. Last read position: chr11:61,393,205 INFO 2026-06-04 21:20:02 MarkDuplicates Tracking 732627 as yet unmatched pairs. 58130 records in RAM. INFO 2026-06-04 21:20:04 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 1s. Last read position: chr11:62,522,931 INFO 2026-06-04 21:20:04 MarkDuplicates Tracking 731836 as yet unmatched pairs. 57326 records in RAM. INFO 2026-06-04 21:20:05 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:10:13s. Time for last 1,000,000: 1s. Last read position: chr11:62,567,470 INFO 2026-06-04 21:20:05 MarkDuplicates Tracking 729053 as yet unmatched pairs. 54525 records in RAM. INFO 2026-06-04 21:20:07 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:10:14s. Time for last 1,000,000: 1s. Last read position: chr11:63,903,118 INFO 2026-06-04 21:20:07 MarkDuplicates Tracking 725637 as yet unmatched pairs. 51100 records in RAM. INFO 2026-06-04 21:20:08 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:10:16s. Time for last 1,000,000: 1s. Last read position: chr11:64,768,106 INFO 2026-06-04 21:20:08 MarkDuplicates Tracking 723716 as yet unmatched pairs. 49170 records in RAM. INFO 2026-06-04 21:20:10 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:10:18s. Time for last 1,000,000: 1s. Last read position: chr11:65,376,412 INFO 2026-06-04 21:20:10 MarkDuplicates Tracking 719699 as yet unmatched pairs. 45140 records in RAM. INFO 2026-06-04 21:20:11 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:10:19s. Time for last 1,000,000: 1s. Last read position: chr11:65,660,195 INFO 2026-06-04 21:20:11 MarkDuplicates Tracking 717805 as yet unmatched pairs. 43183 records in RAM. INFO 2026-06-04 21:20:13 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:10:21s. Time for last 1,000,000: 1s. Last read position: chr11:66,287,820 INFO 2026-06-04 21:20:13 MarkDuplicates Tracking 714570 as yet unmatched pairs. 39937 records in RAM. INFO 2026-06-04 21:20:15 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:10:22s. Time for last 1,000,000: 1s. Last read position: chr11:67,311,767 INFO 2026-06-04 21:20:15 MarkDuplicates Tracking 712119 as yet unmatched pairs. 37465 records in RAM. INFO 2026-06-04 21:20:17 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:10:24s. Time for last 1,000,000: 2s. Last read position: chr11:68,049,698 INFO 2026-06-04 21:20:17 MarkDuplicates Tracking 708733 as yet unmatched pairs. 34070 records in RAM. INFO 2026-06-04 21:20:18 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 1s. Last read position: chr11:70,348,242 INFO 2026-06-04 21:20:18 MarkDuplicates Tracking 705775 as yet unmatched pairs. 31093 records in RAM. INFO 2026-06-04 21:20:20 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:10:27s. Time for last 1,000,000: 1s. Last read position: chr11:72,696,995 INFO 2026-06-04 21:20:20 MarkDuplicates Tracking 703320 as yet unmatched pairs. 28620 records in RAM. INFO 2026-06-04 21:20:21 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:10:29s. Time for last 1,000,000: 1s. Last read position: chr11:75,784,649 INFO 2026-06-04 21:20:21 MarkDuplicates Tracking 701052 as yet unmatched pairs. 26322 records in RAM. INFO 2026-06-04 21:20:22 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:10:30s. Time for last 1,000,000: 1s. Last read position: chr11:85,654,244 INFO 2026-06-04 21:20:22 MarkDuplicates Tracking 698282 as yet unmatched pairs. 23533 records in RAM. INFO 2026-06-04 21:20:24 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:10:32s. Time for last 1,000,000: 1s. Last read position: chr11:94,972,064 INFO 2026-06-04 21:20:24 MarkDuplicates Tracking 696107 as yet unmatched pairs. 21335 records in RAM. INFO 2026-06-04 21:20:25 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:10:33s. Time for last 1,000,000: 1s. Last read position: chr11:102,402,034 INFO 2026-06-04 21:20:25 MarkDuplicates Tracking 697292 as yet unmatched pairs. 22483 records in RAM. INFO 2026-06-04 21:20:27 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:10:35s. Time for last 1,000,000: 1s. Last read position: chr11:113,760,348 INFO 2026-06-04 21:20:27 MarkDuplicates Tracking 690900 as yet unmatched pairs. 16072 records in RAM. INFO 2026-06-04 21:20:28 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:10:36s. Time for last 1,000,000: 1s. Last read position: chr11:118,407,069 INFO 2026-06-04 21:20:28 MarkDuplicates Tracking 690574 as yet unmatched pairs. 15722 records in RAM. INFO 2026-06-04 21:20:30 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:10:38s. Time for last 1,000,000: 1s. Last read position: chr11:119,049,777 INFO 2026-06-04 21:20:30 MarkDuplicates Tracking 686038 as yet unmatched pairs. 11160 records in RAM. INFO 2026-06-04 21:20:31 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:10:39s. Time for last 1,000,000: 1s. Last read position: chr11:120,424,308 INFO 2026-06-04 21:20:31 MarkDuplicates Tracking 683521 as yet unmatched pairs. 8632 records in RAM. INFO 2026-06-04 21:20:33 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:10:40s. Time for last 1,000,000: 1s. Last read position: chr11:124,669,415 INFO 2026-06-04 21:20:33 MarkDuplicates Tracking 680585 as yet unmatched pairs. 5676 records in RAM. INFO 2026-06-04 21:20:34 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:10:42s. Time for last 1,000,000: 1s. Last read position: chr11:128,970,521 INFO 2026-06-04 21:20:34 MarkDuplicates Tracking 678791 as yet unmatched pairs. 3866 records in RAM. INFO 2026-06-04 21:20:36 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:10:43s. Time for last 1,000,000: 1s. Last read position: chr11:134,177,412 INFO 2026-06-04 21:20:36 MarkDuplicates Tracking 675335 as yet unmatched pairs. 384 records in RAM. INFO 2026-06-04 21:20:38 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 2s. Last read position: chr12:4,654,406 INFO 2026-06-04 21:20:38 MarkDuplicates Tracking 673317 as yet unmatched pairs. 81705 records in RAM. INFO 2026-06-04 21:20:40 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:10:48s. Time for last 1,000,000: 1s. Last read position: chr12:6,578,048 INFO 2026-06-04 21:20:40 MarkDuplicates Tracking 670844 as yet unmatched pairs. 79216 records in RAM. INFO 2026-06-04 21:20:42 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:10:50s. Time for last 1,000,000: 1s. Last read position: chr12:6,945,844 INFO 2026-06-04 21:20:42 MarkDuplicates Tracking 667847 as yet unmatched pairs. 76208 records in RAM. INFO 2026-06-04 21:20:43 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:10:51s. Time for last 1,000,000: 1s. Last read position: chr12:10,699,639 INFO 2026-06-04 21:20:43 MarkDuplicates Tracking 666155 as yet unmatched pairs. 74500 records in RAM. INFO 2026-06-04 21:20:45 MarkDuplicates Read 368,000,000 records. Elapsed time: 00:10:53s. Time for last 1,000,000: 1s. Last read position: chr12:14,503,846 INFO 2026-06-04 21:20:45 MarkDuplicates Tracking 663637 as yet unmatched pairs. 71966 records in RAM. INFO 2026-06-04 21:20:46 MarkDuplicates Read 369,000,000 records. Elapsed time: 00:10:54s. Time for last 1,000,000: 1s. Last read position: chr12:25,744,582 INFO 2026-06-04 21:20:46 MarkDuplicates Tracking 660658 as yet unmatched pairs. 68973 records in RAM. INFO 2026-06-04 21:20:48 MarkDuplicates Read 370,000,000 records. Elapsed time: 00:10:56s. Time for last 1,000,000: 1s. Last read position: chr12:32,581,994 INFO 2026-06-04 21:20:48 MarkDuplicates Tracking 658215 as yet unmatched pairs. 66508 records in RAM. INFO 2026-06-04 21:20:49 MarkDuplicates Read 371,000,000 records. Elapsed time: 00:10:57s. Time for last 1,000,000: 1s. Last read position: chr12:46,363,750 INFO 2026-06-04 21:20:49 MarkDuplicates Tracking 658184 as yet unmatched pairs. 66453 records in RAM. INFO 2026-06-04 21:20:51 MarkDuplicates Read 372,000,000 records. Elapsed time: 00:10:59s. Time for last 1,000,000: 1s. Last read position: chr12:48,923,009 INFO 2026-06-04 21:20:51 MarkDuplicates Tracking 653236 as yet unmatched pairs. 61486 records in RAM. INFO 2026-06-04 21:20:52 MarkDuplicates Read 373,000,000 records. Elapsed time: 00:11:00s. Time for last 1,000,000: 1s. Last read position: chr12:49,128,649 INFO 2026-06-04 21:20:52 MarkDuplicates Tracking 653104 as yet unmatched pairs. 61338 records in RAM. INFO 2026-06-04 21:20:54 MarkDuplicates Read 374,000,000 records. Elapsed time: 00:11:01s. Time for last 1,000,000: 1s. Last read position: chr12:49,762,894 INFO 2026-06-04 21:20:54 MarkDuplicates Tracking 650167 as yet unmatched pairs. 58391 records in RAM. INFO 2026-06-04 21:20:55 MarkDuplicates Read 375,000,000 records. Elapsed time: 00:11:03s. Time for last 1,000,000: 1s. Last read position: chr12:52,172,227 INFO 2026-06-04 21:20:55 MarkDuplicates Tracking 646394 as yet unmatched pairs. 54593 records in RAM. INFO 2026-06-04 21:20:57 MarkDuplicates Read 376,000,000 records. Elapsed time: 00:11:05s. Time for last 1,000,000: 1s. Last read position: chr12:52,901,949 INFO 2026-06-04 21:20:57 MarkDuplicates Tracking 644390 as yet unmatched pairs. 52573 records in RAM. INFO 2026-06-04 21:20:58 MarkDuplicates Read 377,000,000 records. Elapsed time: 00:11:06s. Time for last 1,000,000: 1s. Last read position: chr12:53,314,329 INFO 2026-06-04 21:20:58 MarkDuplicates Tracking 641168 as yet unmatched pairs. 49340 records in RAM. INFO 2026-06-04 21:21:00 MarkDuplicates Read 378,000,000 records. Elapsed time: 00:11:08s. Time for last 1,000,000: 1s. Last read position: chr12:54,281,859 INFO 2026-06-04 21:21:00 MarkDuplicates Tracking 643797 as yet unmatched pairs. 51954 records in RAM. INFO 2026-06-04 21:21:02 MarkDuplicates Read 379,000,000 records. Elapsed time: 00:11:10s. Time for last 1,000,000: 1s. Last read position: chr12:55,819,122 INFO 2026-06-04 21:21:02 MarkDuplicates Tracking 636784 as yet unmatched pairs. 44932 records in RAM. INFO 2026-06-04 21:21:04 MarkDuplicates Read 380,000,000 records. Elapsed time: 00:11:11s. Time for last 1,000,000: 1s. Last read position: chr12:56,160,126 INFO 2026-06-04 21:21:04 MarkDuplicates Tracking 639879 as yet unmatched pairs. 48017 records in RAM. INFO 2026-06-04 21:21:05 MarkDuplicates Read 381,000,000 records. Elapsed time: 00:11:13s. Time for last 1,000,000: 1s. Last read position: chr12:56,639,979 INFO 2026-06-04 21:21:05 MarkDuplicates Tracking 632428 as yet unmatched pairs. 40563 records in RAM. INFO 2026-06-04 21:21:07 MarkDuplicates Read 382,000,000 records. Elapsed time: 00:11:14s. Time for last 1,000,000: 1s. Last read position: chr12:57,098,580 INFO 2026-06-04 21:21:07 MarkDuplicates Tracking 633588 as yet unmatched pairs. 41711 records in RAM. INFO 2026-06-04 21:21:08 MarkDuplicates Read 383,000,000 records. Elapsed time: 00:11:16s. Time for last 1,000,000: 1s. Last read position: chr12:57,268,312 INFO 2026-06-04 21:21:08 MarkDuplicates Tracking 626533 as yet unmatched pairs. 34647 records in RAM. INFO 2026-06-04 21:21:09 MarkDuplicates Read 384,000,000 records. Elapsed time: 00:11:17s. Time for last 1,000,000: 1s. Last read position: chr12:64,414,970 INFO 2026-06-04 21:21:09 MarkDuplicates Tracking 624913 as yet unmatched pairs. 33021 records in RAM. INFO 2026-06-04 21:21:11 MarkDuplicates Read 385,000,000 records. Elapsed time: 00:11:19s. Time for last 1,000,000: 1s. Last read position: chr12:69,586,763 INFO 2026-06-04 21:21:11 MarkDuplicates Tracking 622167 as yet unmatched pairs. 30257 records in RAM. INFO 2026-06-04 21:21:12 MarkDuplicates Read 386,000,000 records. Elapsed time: 00:11:20s. Time for last 1,000,000: 1s. Last read position: chr12:79,594,417 INFO 2026-06-04 21:21:12 MarkDuplicates Tracking 619164 as yet unmatched pairs. 27244 records in RAM. INFO 2026-06-04 21:21:14 MarkDuplicates Read 387,000,000 records. Elapsed time: 00:11:22s. Time for last 1,000,000: 1s. Last read position: chr12:93,641,172 INFO 2026-06-04 21:21:14 MarkDuplicates Tracking 616579 as yet unmatched pairs. 24633 records in RAM. INFO 2026-06-04 21:21:16 MarkDuplicates Read 388,000,000 records. Elapsed time: 00:11:23s. Time for last 1,000,000: 1s. Last read position: chr12:101,363,617 INFO 2026-06-04 21:21:16 MarkDuplicates Tracking 614347 as yet unmatched pairs. 22376 records in RAM. INFO 2026-06-04 21:21:17 MarkDuplicates Read 389,000,000 records. Elapsed time: 00:11:25s. Time for last 1,000,000: 1s. Last read position: chr12:107,693,087 INFO 2026-06-04 21:21:17 MarkDuplicates Tracking 612269 as yet unmatched pairs. 20266 records in RAM. INFO 2026-06-04 21:21:19 MarkDuplicates Read 390,000,000 records. Elapsed time: 00:11:26s. Time for last 1,000,000: 1s. Last read position: chr12:110,440,341 INFO 2026-06-04 21:21:19 MarkDuplicates Tracking 610291 as yet unmatched pairs. 18277 records in RAM. INFO 2026-06-04 21:21:21 MarkDuplicates Read 391,000,000 records. Elapsed time: 00:11:28s. Time for last 1,000,000: 2s. Last read position: chr12:112,486,472 INFO 2026-06-04 21:21:21 MarkDuplicates Tracking 607090 as yet unmatched pairs. 15061 records in RAM. INFO 2026-06-04 21:21:22 MarkDuplicates Read 392,000,000 records. Elapsed time: 00:11:30s. Time for last 1,000,000: 1s. Last read position: chr12:118,082,188 INFO 2026-06-04 21:21:22 MarkDuplicates Tracking 604209 as yet unmatched pairs. 12162 records in RAM. INFO 2026-06-04 21:21:24 MarkDuplicates Read 393,000,000 records. Elapsed time: 00:11:32s. Time for last 1,000,000: 1s. Last read position: chr12:120,464,082 INFO 2026-06-04 21:21:24 MarkDuplicates Tracking 602258 as yet unmatched pairs. 10194 records in RAM. INFO 2026-06-04 21:21:26 MarkDuplicates Read 394,000,000 records. Elapsed time: 00:11:33s. Time for last 1,000,000: 1s. Last read position: chr12:122,341,300 INFO 2026-06-04 21:21:26 MarkDuplicates Tracking 599648 as yet unmatched pairs. 7566 records in RAM. INFO 2026-06-04 21:21:28 MarkDuplicates Read 395,000,000 records. Elapsed time: 00:11:35s. Time for last 1,000,000: 1s. Last read position: chr12:124,336,648 INFO 2026-06-04 21:21:28 MarkDuplicates Tracking 596865 as yet unmatched pairs. 4763 records in RAM. INFO 2026-06-04 21:21:29 MarkDuplicates Read 396,000,000 records. Elapsed time: 00:11:37s. Time for last 1,000,000: 1s. Last read position: chr12:132,021,261 INFO 2026-06-04 21:21:29 MarkDuplicates Tracking 594422 as yet unmatched pairs. 2304 records in RAM. INFO 2026-06-04 21:21:31 MarkDuplicates Read 397,000,000 records. Elapsed time: 00:11:39s. Time for last 1,000,000: 1s. Last read position: chr13:19,993,357 INFO 2026-06-04 21:21:31 MarkDuplicates Tracking 594096 as yet unmatched pairs. 28479 records in RAM. INFO 2026-06-04 21:21:32 MarkDuplicates Read 398,000,000 records. Elapsed time: 00:11:40s. Time for last 1,000,000: 1s. Last read position: chr13:20,192,813 INFO 2026-06-04 21:21:32 MarkDuplicates Tracking 589367 as yet unmatched pairs. 23738 records in RAM. INFO 2026-06-04 21:21:34 MarkDuplicates Read 399,000,000 records. Elapsed time: 00:11:42s. Time for last 1,000,000: 1s. Last read position: chr13:27,254,244 INFO 2026-06-04 21:21:34 MarkDuplicates Tracking 588263 as yet unmatched pairs. 22618 records in RAM. INFO 2026-06-04 21:21:35 MarkDuplicates Read 400,000,000 records. Elapsed time: 00:11:43s. Time for last 1,000,000: 1s. Last read position: chr13:32,517,702 INFO 2026-06-04 21:21:35 MarkDuplicates Tracking 585403 as yet unmatched pairs. 19740 records in RAM. INFO 2026-06-04 21:21:37 MarkDuplicates Read 401,000,000 records. Elapsed time: 00:11:44s. Time for last 1,000,000: 1s. Last read position: chr13:41,865,736 INFO 2026-06-04 21:21:37 MarkDuplicates Tracking 582556 as yet unmatched pairs. 16870 records in RAM. INFO 2026-06-04 21:21:38 MarkDuplicates Read 402,000,000 records. Elapsed time: 00:11:46s. Time for last 1,000,000: 1s. Last read position: chr13:46,146,964 INFO 2026-06-04 21:21:38 MarkDuplicates Tracking 580791 as yet unmatched pairs. 15075 records in RAM. INFO 2026-06-04 21:21:40 MarkDuplicates Read 403,000,000 records. Elapsed time: 00:11:47s. Time for last 1,000,000: 1s. Last read position: chr13:52,652,872 INFO 2026-06-04 21:21:40 MarkDuplicates Tracking 577567 as yet unmatched pairs. 11804 records in RAM. INFO 2026-06-04 21:21:41 MarkDuplicates Read 404,000,000 records. Elapsed time: 00:11:49s. Time for last 1,000,000: 1s. Last read position: chr13:77,217,886 INFO 2026-06-04 21:21:41 MarkDuplicates Tracking 575279 as yet unmatched pairs. 9504 records in RAM. INFO 2026-06-04 21:21:42 MarkDuplicates Read 405,000,000 records. Elapsed time: 00:11:50s. Time for last 1,000,000: 1s. Last read position: chr13:98,439,147 INFO 2026-06-04 21:21:42 MarkDuplicates Tracking 573117 as yet unmatched pairs. 7299 records in RAM. INFO 2026-06-04 21:21:44 MarkDuplicates Read 406,000,000 records. Elapsed time: 00:11:51s. Time for last 1,000,000: 1s. Last read position: chr13:109,785,052 INFO 2026-06-04 21:21:44 MarkDuplicates Tracking 570244 as yet unmatched pairs. 4403 records in RAM. INFO 2026-06-04 21:21:45 MarkDuplicates Read 407,000,000 records. Elapsed time: 00:11:53s. Time for last 1,000,000: 1s. Last read position: chr13:111,283,033 INFO 2026-06-04 21:21:45 MarkDuplicates Tracking 567631 as yet unmatched pairs. 1767 records in RAM. INFO 2026-06-04 21:21:47 MarkDuplicates Read 408,000,000 records. Elapsed time: 00:11:55s. Time for last 1,000,000: 1s. Last read position: chr14:20,457,080 INFO 2026-06-04 21:21:47 MarkDuplicates Tracking 566213 as yet unmatched pairs. 46896 records in RAM. INFO 2026-06-04 21:21:48 MarkDuplicates Read 409,000,000 records. Elapsed time: 00:11:56s. Time for last 1,000,000: 1s. Last read position: chr14:22,836,782 INFO 2026-06-04 21:21:48 MarkDuplicates Tracking 562878 as yet unmatched pairs. 43551 records in RAM. INFO 2026-06-04 21:21:50 MarkDuplicates Read 410,000,000 records. Elapsed time: 00:11:57s. Time for last 1,000,000: 1s. Last read position: chr14:23,563,400 INFO 2026-06-04 21:21:50 MarkDuplicates Tracking 560341 as yet unmatched pairs. 41004 records in RAM. INFO 2026-06-04 21:21:52 MarkDuplicates Read 411,000,000 records. Elapsed time: 00:12:00s. Time for last 1,000,000: 2s. Last read position: chr14:24,145,422 INFO 2026-06-04 21:21:52 MarkDuplicates Tracking 558822 as yet unmatched pairs. 39469 records in RAM. INFO 2026-06-04 21:21:55 MarkDuplicates Read 412,000,000 records. Elapsed time: 00:12:03s. Time for last 1,000,000: 2s. Last read position: chr14:31,109,480 INFO 2026-06-04 21:21:55 MarkDuplicates Tracking 555220 as yet unmatched pairs. 35856 records in RAM. INFO 2026-06-04 21:21:56 MarkDuplicates Read 413,000,000 records. Elapsed time: 00:12:04s. Time for last 1,000,000: 1s. Last read position: chr14:35,881,111 INFO 2026-06-04 21:21:56 MarkDuplicates Tracking 552420 as yet unmatched pairs. 33038 records in RAM. INFO 2026-06-04 21:21:58 MarkDuplicates Read 414,000,000 records. Elapsed time: 00:12:06s. Time for last 1,000,000: 1s. Last read position: chr14:49,894,105 INFO 2026-06-04 21:21:58 MarkDuplicates Tracking 551592 as yet unmatched pairs. 32144 records in RAM. INFO 2026-06-04 21:21:59 MarkDuplicates Read 415,000,000 records. Elapsed time: 00:12:07s. Time for last 1,000,000: 1s. Last read position: chr14:55,140,349 INFO 2026-06-04 21:21:59 MarkDuplicates Tracking 548060 as yet unmatched pairs. 28594 records in RAM. INFO 2026-06-04 21:22:01 MarkDuplicates Read 416,000,000 records. Elapsed time: 00:12:09s. Time for last 1,000,000: 1s. Last read position: chr14:61,280,519 INFO 2026-06-04 21:22:01 MarkDuplicates Tracking 545483 as yet unmatched pairs. 26006 records in RAM. INFO 2026-06-04 21:22:02 MarkDuplicates Read 417,000,000 records. Elapsed time: 00:12:10s. Time for last 1,000,000: 1s. Last read position: chr14:64,750,069 INFO 2026-06-04 21:22:02 MarkDuplicates Tracking 542873 as yet unmatched pairs. 23383 records in RAM. INFO 2026-06-04 21:22:04 MarkDuplicates Read 418,000,000 records. Elapsed time: 00:12:11s. Time for last 1,000,000: 1s. Last read position: chr14:69,234,845 INFO 2026-06-04 21:22:04 MarkDuplicates Tracking 540220 as yet unmatched pairs. 20709 records in RAM. INFO 2026-06-04 21:22:05 MarkDuplicates Read 419,000,000 records. Elapsed time: 00:12:13s. Time for last 1,000,000: 1s. Last read position: chr14:73,739,642 INFO 2026-06-04 21:22:05 MarkDuplicates Tracking 538021 as yet unmatched pairs. 18487 records in RAM. INFO 2026-06-04 21:22:06 MarkDuplicates Read 420,000,000 records. Elapsed time: 00:12:14s. Time for last 1,000,000: 1s. Last read position: chr14:75,764,634 INFO 2026-06-04 21:22:06 MarkDuplicates Tracking 535181 as yet unmatched pairs. 15634 records in RAM. INFO 2026-06-04 21:22:08 MarkDuplicates Read 421,000,000 records. Elapsed time: 00:12:16s. Time for last 1,000,000: 2s. Last read position: chr14:90,403,883 INFO 2026-06-04 21:22:08 MarkDuplicates Tracking 534402 as yet unmatched pairs. 14838 records in RAM. INFO 2026-06-04 21:22:10 MarkDuplicates Read 422,000,000 records. Elapsed time: 00:12:18s. Time for last 1,000,000: 1s. Last read position: chr14:95,095,984 INFO 2026-06-04 21:22:10 MarkDuplicates Tracking 531316 as yet unmatched pairs. 11734 records in RAM. INFO 2026-06-04 21:22:11 MarkDuplicates Read 423,000,000 records. Elapsed time: 00:12:19s. Time for last 1,000,000: 1s. Last read position: chr14:102,004,788 INFO 2026-06-04 21:22:11 MarkDuplicates Tracking 528240 as yet unmatched pairs. 8621 records in RAM. INFO 2026-06-04 21:22:13 MarkDuplicates Read 424,000,000 records. Elapsed time: 00:12:21s. Time for last 1,000,000: 1s. Last read position: chr14:102,952,433 INFO 2026-06-04 21:22:13 MarkDuplicates Tracking 525517 as yet unmatched pairs. 5879 records in RAM. INFO 2026-06-04 21:22:15 MarkDuplicates Read 425,000,000 records. Elapsed time: 00:12:23s. Time for last 1,000,000: 1s. Last read position: chr14:104,712,956 INFO 2026-06-04 21:22:15 MarkDuplicates Tracking 522413 as yet unmatched pairs. 2759 records in RAM. INFO 2026-06-04 21:22:17 MarkDuplicates Read 426,000,000 records. Elapsed time: 00:12:25s. Time for last 1,000,000: 2s. Last read position: chr15:21,294,683 INFO 2026-06-04 21:22:17 MarkDuplicates Tracking 519581 as yet unmatched pairs. 43635 records in RAM. INFO 2026-06-04 21:22:19 MarkDuplicates Read 427,000,000 records. Elapsed time: 00:12:26s. Time for last 1,000,000: 1s. Last read position: chr15:30,630,695 INFO 2026-06-04 21:22:19 MarkDuplicates Tracking 517610 as yet unmatched pairs. 41648 records in RAM. INFO 2026-06-04 21:22:20 MarkDuplicates Read 428,000,000 records. Elapsed time: 00:12:28s. Time for last 1,000,000: 1s. Last read position: chr15:39,967,767 INFO 2026-06-04 21:22:20 MarkDuplicates Tracking 515707 as yet unmatched pairs. 39730 records in RAM. INFO 2026-06-04 21:22:21 MarkDuplicates Read 429,000,000 records. Elapsed time: 00:12:29s. Time for last 1,000,000: 1s. Last read position: chr15:41,713,264 INFO 2026-06-04 21:22:21 MarkDuplicates Tracking 513386 as yet unmatched pairs. 37402 records in RAM. INFO 2026-06-04 21:22:23 MarkDuplicates Read 430,000,000 records. Elapsed time: 00:12:31s. Time for last 1,000,000: 1s. Last read position: chr15:43,428,146 INFO 2026-06-04 21:22:23 MarkDuplicates Tracking 510578 as yet unmatched pairs. 34588 records in RAM. INFO 2026-06-04 21:22:24 MarkDuplicates Read 431,000,000 records. Elapsed time: 00:12:32s. Time for last 1,000,000: 1s. Last read position: chr15:44,402,933 INFO 2026-06-04 21:22:24 MarkDuplicates Tracking 508558 as yet unmatched pairs. 32564 records in RAM. INFO 2026-06-04 21:22:26 MarkDuplicates Read 432,000,000 records. Elapsed time: 00:12:33s. Time for last 1,000,000: 1s. Last read position: chr15:50,569,946 INFO 2026-06-04 21:22:26 MarkDuplicates Tracking 505989 as yet unmatched pairs. 29981 records in RAM. INFO 2026-06-04 21:22:27 MarkDuplicates Read 433,000,000 records. Elapsed time: 00:12:35s. Time for last 1,000,000: 1s. Last read position: chr15:57,166,420 INFO 2026-06-04 21:22:27 MarkDuplicates Tracking 505694 as yet unmatched pairs. 29671 records in RAM. INFO 2026-06-04 21:22:29 MarkDuplicates Read 434,000,000 records. Elapsed time: 00:12:36s. Time for last 1,000,000: 1s. Last read position: chr15:60,347,623 INFO 2026-06-04 21:22:29 MarkDuplicates Tracking 502060 as yet unmatched pairs. 26024 records in RAM. INFO 2026-06-04 21:22:30 MarkDuplicates Read 435,000,000 records. Elapsed time: 00:12:38s. Time for last 1,000,000: 1s. Last read position: chr15:64,118,161 INFO 2026-06-04 21:22:30 MarkDuplicates Tracking 499348 as yet unmatched pairs. 23292 records in RAM. INFO 2026-06-04 21:22:31 MarkDuplicates Read 436,000,000 records. Elapsed time: 00:12:39s. Time for last 1,000,000: 1s. Last read position: chr15:66,499,453 INFO 2026-06-04 21:22:31 MarkDuplicates Tracking 497130 as yet unmatched pairs. 21052 records in RAM. INFO 2026-06-04 21:22:33 MarkDuplicates Read 437,000,000 records. Elapsed time: 00:12:41s. Time for last 1,000,000: 1s. Last read position: chr15:71,341,216 INFO 2026-06-04 21:22:33 MarkDuplicates Tracking 493842 as yet unmatched pairs. 17741 records in RAM. INFO 2026-06-04 21:22:34 MarkDuplicates Read 438,000,000 records. Elapsed time: 00:12:42s. Time for last 1,000,000: 1s. Last read position: chr15:73,998,031 INFO 2026-06-04 21:22:34 MarkDuplicates Tracking 492321 as yet unmatched pairs. 16206 records in RAM. INFO 2026-06-04 21:22:36 MarkDuplicates Read 439,000,000 records. Elapsed time: 00:12:43s. Time for last 1,000,000: 1s. Last read position: chr15:75,517,279 INFO 2026-06-04 21:22:36 MarkDuplicates Tracking 488702 as yet unmatched pairs. 12582 records in RAM. INFO 2026-06-04 21:22:37 MarkDuplicates Read 440,000,000 records. Elapsed time: 00:12:45s. Time for last 1,000,000: 1s. Last read position: chr15:78,921,994 INFO 2026-06-04 21:22:37 MarkDuplicates Tracking 486920 as yet unmatched pairs. 10789 records in RAM. INFO 2026-06-04 21:22:38 MarkDuplicates Read 441,000,000 records. Elapsed time: 00:12:46s. Time for last 1,000,000: 1s. Last read position: chr15:84,433,329 INFO 2026-06-04 21:22:38 MarkDuplicates Tracking 483516 as yet unmatched pairs. 7369 records in RAM. INFO 2026-06-04 21:22:40 MarkDuplicates Read 442,000,000 records. Elapsed time: 00:12:47s. Time for last 1,000,000: 1s. Last read position: chr15:89,867,311 INFO 2026-06-04 21:22:40 MarkDuplicates Tracking 481533 as yet unmatched pairs. 5377 records in RAM. INFO 2026-06-04 21:22:41 MarkDuplicates Read 443,000,000 records. Elapsed time: 00:12:49s. Time for last 1,000,000: 1s. Last read position: chr15:90,918,728 INFO 2026-06-04 21:22:41 MarkDuplicates Tracking 478745 as yet unmatched pairs. 2577 records in RAM. INFO 2026-06-04 21:22:43 MarkDuplicates Read 444,000,000 records. Elapsed time: 00:12:51s. Time for last 1,000,000: 2s. Last read position: chr16:14,484 INFO 2026-06-04 21:22:43 MarkDuplicates Tracking 476194 as yet unmatched pairs. 69703 records in RAM. INFO 2026-06-04 21:22:45 MarkDuplicates Read 445,000,000 records. Elapsed time: 00:12:52s. Time for last 1,000,000: 1s. Last read position: chr16:1,228,663 INFO 2026-06-04 21:22:45 MarkDuplicates Tracking 473186 as yet unmatched pairs. 66686 records in RAM. INFO 2026-06-04 21:22:46 MarkDuplicates Read 446,000,000 records. Elapsed time: 00:12:54s. Time for last 1,000,000: 1s. Last read position: chr16:2,090,982 INFO 2026-06-04 21:22:46 MarkDuplicates Tracking 470247 as yet unmatched pairs. 63737 records in RAM. INFO 2026-06-04 21:22:47 MarkDuplicates Read 447,000,000 records. Elapsed time: 00:12:55s. Time for last 1,000,000: 1s. Last read position: chr16:2,763,319 INFO 2026-06-04 21:22:47 MarkDuplicates Tracking 469612 as yet unmatched pairs. 63089 records in RAM. INFO 2026-06-04 21:22:49 MarkDuplicates Read 448,000,000 records. Elapsed time: 00:12:57s. Time for last 1,000,000: 1s. Last read position: chr16:3,285,153 INFO 2026-06-04 21:22:49 MarkDuplicates Tracking 464953 as yet unmatched pairs. 58428 records in RAM. INFO 2026-06-04 21:22:50 MarkDuplicates Read 449,000,000 records. Elapsed time: 00:12:58s. Time for last 1,000,000: 1s. Last read position: chr16:4,883,872 INFO 2026-06-04 21:22:50 MarkDuplicates Tracking 462391 as yet unmatched pairs. 55854 records in RAM. INFO 2026-06-04 21:22:52 MarkDuplicates Read 450,000,000 records. Elapsed time: 00:12:59s. Time for last 1,000,000: 1s. Last read position: chr16:11,927,739 INFO 2026-06-04 21:22:52 MarkDuplicates Tracking 460521 as yet unmatched pairs. 53976 records in RAM. INFO 2026-06-04 21:22:53 MarkDuplicates Read 451,000,000 records. Elapsed time: 00:13:01s. Time for last 1,000,000: 1s. Last read position: chr16:14,951,884 INFO 2026-06-04 21:22:53 MarkDuplicates Tracking 458317 as yet unmatched pairs. 51771 records in RAM. INFO 2026-06-04 21:22:54 MarkDuplicates Read 452,000,000 records. Elapsed time: 00:13:02s. Time for last 1,000,000: 1s. Last read position: chr16:16,321,189 INFO 2026-06-04 21:22:54 MarkDuplicates Tracking 456703 as yet unmatched pairs. 50151 records in RAM. INFO 2026-06-04 21:22:56 MarkDuplicates Read 453,000,000 records. Elapsed time: 00:13:04s. Time for last 1,000,000: 1s. Last read position: chr16:18,517,228 INFO 2026-06-04 21:22:56 MarkDuplicates Tracking 456430 as yet unmatched pairs. 49877 records in RAM. INFO 2026-06-04 21:22:58 MarkDuplicates Read 454,000,000 records. Elapsed time: 00:13:05s. Time for last 1,000,000: 1s. Last read position: chr16:21,170,444 INFO 2026-06-04 21:22:58 MarkDuplicates Tracking 453856 as yet unmatched pairs. 47286 records in RAM. INFO 2026-06-04 21:22:59 MarkDuplicates Read 455,000,000 records. Elapsed time: 00:13:07s. Time for last 1,000,000: 1s. Last read position: chr16:21,519,894 INFO 2026-06-04 21:22:59 MarkDuplicates Tracking 453249 as yet unmatched pairs. 46674 records in RAM. INFO 2026-06-04 21:23:00 MarkDuplicates Read 456,000,000 records. Elapsed time: 00:13:08s. Time for last 1,000,000: 1s. Last read position: chr16:21,971,976 INFO 2026-06-04 21:23:00 MarkDuplicates Tracking 452182 as yet unmatched pairs. 45603 records in RAM. INFO 2026-06-04 21:23:02 MarkDuplicates Read 457,000,000 records. Elapsed time: 00:13:10s. Time for last 1,000,000: 1s. Last read position: chr16:22,534,984 INFO 2026-06-04 21:23:02 MarkDuplicates Tracking 452933 as yet unmatched pairs. 46347 records in RAM. INFO 2026-06-04 21:23:03 MarkDuplicates Read 458,000,000 records. Elapsed time: 00:13:11s. Time for last 1,000,000: 1s. Last read position: chr16:27,340,200 INFO 2026-06-04 21:23:03 MarkDuplicates Tracking 450540 as yet unmatched pairs. 43946 records in RAM. INFO 2026-06-04 21:23:05 MarkDuplicates Read 459,000,000 records. Elapsed time: 00:13:13s. Time for last 1,000,000: 1s. Last read position: chr16:28,724,387 INFO 2026-06-04 21:23:05 MarkDuplicates Tracking 447444 as yet unmatched pairs. 40841 records in RAM. INFO 2026-06-04 21:23:06 MarkDuplicates Read 460,000,000 records. Elapsed time: 00:13:14s. Time for last 1,000,000: 1s. Last read position: chr16:29,383,917 INFO 2026-06-04 21:23:06 MarkDuplicates Tracking 446238 as yet unmatched pairs. 39632 records in RAM. INFO 2026-06-04 21:23:07 MarkDuplicates Read 461,000,000 records. Elapsed time: 00:13:15s. Time for last 1,000,000: 1s. Last read position: chr16:29,799,063 INFO 2026-06-04 21:23:07 MarkDuplicates Tracking 444764 as yet unmatched pairs. 38157 records in RAM. INFO 2026-06-04 21:23:09 MarkDuplicates Read 462,000,000 records. Elapsed time: 00:13:16s. Time for last 1,000,000: 1s. Last read position: chr16:30,069,965 INFO 2026-06-04 21:23:09 MarkDuplicates Tracking 450965 as yet unmatched pairs. 44355 records in RAM. INFO 2026-06-04 21:23:10 MarkDuplicates Read 463,000,000 records. Elapsed time: 00:13:18s. Time for last 1,000,000: 1s. Last read position: chr16:30,231,395 INFO 2026-06-04 21:23:10 MarkDuplicates Tracking 440241 as yet unmatched pairs. 33628 records in RAM. INFO 2026-06-04 21:23:11 MarkDuplicates Read 464,000,000 records. Elapsed time: 00:13:19s. Time for last 1,000,000: 1s. Last read position: chr16:30,835,027 INFO 2026-06-04 21:23:11 MarkDuplicates Tracking 437909 as yet unmatched pairs. 31286 records in RAM. INFO 2026-06-04 21:23:13 MarkDuplicates Read 465,000,000 records. Elapsed time: 00:13:20s. Time for last 1,000,000: 1s. Last read position: chr16:31,191,067 INFO 2026-06-04 21:23:13 MarkDuplicates Tracking 440396 as yet unmatched pairs. 33771 records in RAM. INFO 2026-06-04 21:23:14 MarkDuplicates Read 466,000,000 records. Elapsed time: 00:13:22s. Time for last 1,000,000: 1s. Last read position: chr16:50,794,362 INFO 2026-06-04 21:23:14 MarkDuplicates Tracking 432913 as yet unmatched pairs. 26284 records in RAM. INFO 2026-06-04 21:23:15 MarkDuplicates Read 467,000,000 records. Elapsed time: 00:13:23s. Time for last 1,000,000: 1s. Last read position: chr16:57,434,027 INFO 2026-06-04 21:23:15 MarkDuplicates Tracking 430645 as yet unmatched pairs. 24008 records in RAM. INFO 2026-06-04 21:23:17 MarkDuplicates Read 468,000,000 records. Elapsed time: 00:13:25s. Time for last 1,000,000: 1s. Last read position: chr16:61,817,591 INFO 2026-06-04 21:23:17 MarkDuplicates Tracking 427918 as yet unmatched pairs. 21267 records in RAM. INFO 2026-06-04 21:23:18 MarkDuplicates Read 469,000,000 records. Elapsed time: 00:13:26s. Time for last 1,000,000: 1s. Last read position: chr16:67,876,007 INFO 2026-06-04 21:23:18 MarkDuplicates Tracking 425342 as yet unmatched pairs. 18686 records in RAM. INFO 2026-06-04 21:23:20 MarkDuplicates Read 470,000,000 records. Elapsed time: 00:13:27s. Time for last 1,000,000: 1s. Last read position: chr16:69,109,710 INFO 2026-06-04 21:23:20 MarkDuplicates Tracking 424236 as yet unmatched pairs. 17575 records in RAM. INFO 2026-06-04 21:23:21 MarkDuplicates Read 471,000,000 records. Elapsed time: 00:13:29s. Time for last 1,000,000: 1s. Last read position: chr16:70,220,847 INFO 2026-06-04 21:23:21 MarkDuplicates Tracking 420204 as yet unmatched pairs. 13539 records in RAM. INFO 2026-06-04 21:23:23 MarkDuplicates Read 472,000,000 records. Elapsed time: 00:13:31s. Time for last 1,000,000: 1s. Last read position: chr16:72,787,206 INFO 2026-06-04 21:23:23 MarkDuplicates Tracking 417810 as yet unmatched pairs. 11125 records in RAM. INFO 2026-06-04 21:23:25 MarkDuplicates Read 473,000,000 records. Elapsed time: 00:13:33s. Time for last 1,000,000: 2s. Last read position: chr16:75,630,422 INFO 2026-06-04 21:23:25 MarkDuplicates Tracking 415354 as yet unmatched pairs. 8655 records in RAM. INFO 2026-06-04 21:23:27 MarkDuplicates Read 474,000,000 records. Elapsed time: 00:13:35s. Time for last 1,000,000: 1s. Last read position: chr16:84,745,125 INFO 2026-06-04 21:23:27 MarkDuplicates Tracking 412499 as yet unmatched pairs. 5785 records in RAM. INFO 2026-06-04 21:23:29 MarkDuplicates Read 475,000,000 records. Elapsed time: 00:13:37s. Time for last 1,000,000: 1s. Last read position: chr16:89,145,280 INFO 2026-06-04 21:23:29 MarkDuplicates Tracking 409673 as yet unmatched pairs. 2940 records in RAM. INFO 2026-06-04 21:23:30 MarkDuplicates Read 476,000,000 records. Elapsed time: 00:13:38s. Time for last 1,000,000: 1s. Last read position: chr16:90,031,403 INFO 2026-06-04 21:23:30 MarkDuplicates Tracking 406984 as yet unmatched pairs. 221 records in RAM. INFO 2026-06-04 21:23:33 MarkDuplicates Read 477,000,000 records. Elapsed time: 00:13:40s. Time for last 1,000,000: 2s. Last read position: chr17:1,365,010 INFO 2026-06-04 21:23:33 MarkDuplicates Tracking 409010 as yet unmatched pairs. 125223 records in RAM. INFO 2026-06-04 21:23:34 MarkDuplicates Read 478,000,000 records. Elapsed time: 00:13:42s. Time for last 1,000,000: 1s. Last read position: chr17:2,300,101 INFO 2026-06-04 21:23:34 MarkDuplicates Tracking 401801 as yet unmatched pairs. 118012 records in RAM. INFO 2026-06-04 21:23:36 MarkDuplicates Read 479,000,000 records. Elapsed time: 00:13:43s. Time for last 1,000,000: 1s. Last read position: chr17:4,558,044 INFO 2026-06-04 21:23:36 MarkDuplicates Tracking 399201 as yet unmatched pairs. 115406 records in RAM. INFO 2026-06-04 21:23:37 MarkDuplicates Read 480,000,000 records. Elapsed time: 00:13:45s. Time for last 1,000,000: 1s. Last read position: chr17:5,410,788 INFO 2026-06-04 21:23:37 MarkDuplicates Tracking 396805 as yet unmatched pairs. 113003 records in RAM. INFO 2026-06-04 21:23:39 MarkDuplicates Read 481,000,000 records. Elapsed time: 00:13:46s. Time for last 1,000,000: 1s. Last read position: chr17:7,311,923 INFO 2026-06-04 21:23:39 MarkDuplicates Tracking 394223 as yet unmatched pairs. 110419 records in RAM. INFO 2026-06-04 21:23:40 MarkDuplicates Read 482,000,000 records. Elapsed time: 00:13:48s. Time for last 1,000,000: 1s. Last read position: chr17:7,513,668 INFO 2026-06-04 21:23:40 MarkDuplicates Tracking 392960 as yet unmatched pairs. 109152 records in RAM. INFO 2026-06-04 21:23:42 MarkDuplicates Read 483,000,000 records. Elapsed time: 00:13:49s. Time for last 1,000,000: 1s. Last read position: chr17:7,887,037 INFO 2026-06-04 21:23:42 MarkDuplicates Tracking 389187 as yet unmatched pairs. 105373 records in RAM. INFO 2026-06-04 21:23:43 MarkDuplicates Read 484,000,000 records. Elapsed time: 00:13:51s. Time for last 1,000,000: 1s. Last read position: chr17:13,003,521 INFO 2026-06-04 21:23:43 MarkDuplicates Tracking 386543 as yet unmatched pairs. 102723 records in RAM. INFO 2026-06-04 21:23:44 MarkDuplicates Read 485,000,000 records. Elapsed time: 00:13:52s. Time for last 1,000,000: 1s. Last read position: chr17:16,382,610 INFO 2026-06-04 21:23:44 MarkDuplicates Tracking 384063 as yet unmatched pairs. 100241 records in RAM. INFO 2026-06-04 21:23:46 MarkDuplicates Read 486,000,000 records. Elapsed time: 00:13:54s. Time for last 1,000,000: 1s. Last read position: chr17:17,813,687 INFO 2026-06-04 21:23:46 MarkDuplicates Tracking 381755 as yet unmatched pairs. 97925 records in RAM. INFO 2026-06-04 21:23:47 MarkDuplicates Read 487,000,000 records. Elapsed time: 00:13:55s. Time for last 1,000,000: 1s. Last read position: chr17:19,958,132 INFO 2026-06-04 21:23:47 MarkDuplicates Tracking 379428 as yet unmatched pairs. 95593 records in RAM. INFO 2026-06-04 21:23:49 MarkDuplicates Read 488,000,000 records. Elapsed time: 00:13:56s. Time for last 1,000,000: 1s. Last read position: chr17:28,634,859 INFO 2026-06-04 21:23:49 MarkDuplicates Tracking 377412 as yet unmatched pairs. 93568 records in RAM. INFO 2026-06-04 21:23:50 MarkDuplicates Read 489,000,000 records. Elapsed time: 00:13:58s. Time for last 1,000,000: 1s. Last read position: chr17:29,491,783 INFO 2026-06-04 21:23:50 MarkDuplicates Tracking 374794 as yet unmatched pairs. 90946 records in RAM. INFO 2026-06-04 21:23:52 MarkDuplicates Read 490,000,000 records. Elapsed time: 00:14:00s. Time for last 1,000,000: 2s. Last read position: chr17:31,937,495 INFO 2026-06-04 21:23:52 MarkDuplicates Tracking 372773 as yet unmatched pairs. 88921 records in RAM. INFO 2026-06-04 21:23:54 MarkDuplicates Read 491,000,000 records. Elapsed time: 00:14:01s. Time for last 1,000,000: 1s. Last read position: chr17:35,820,181 INFO 2026-06-04 21:23:54 MarkDuplicates Tracking 375211 as yet unmatched pairs. 91354 records in RAM. INFO 2026-06-04 21:23:55 MarkDuplicates Read 492,000,000 records. Elapsed time: 00:14:03s. Time for last 1,000,000: 1s. Last read position: chr17:37,561,496 INFO 2026-06-04 21:23:55 MarkDuplicates Tracking 367620 as yet unmatched pairs. 83762 records in RAM. INFO 2026-06-04 21:23:56 MarkDuplicates Read 493,000,000 records. Elapsed time: 00:14:04s. Time for last 1,000,000: 1s. Last read position: chr17:38,721,930 INFO 2026-06-04 21:23:56 MarkDuplicates Tracking 365539 as yet unmatched pairs. 81674 records in RAM. INFO 2026-06-04 21:23:59 MarkDuplicates Read 494,000,000 records. Elapsed time: 00:14:06s. Time for last 1,000,000: 2s. Last read position: chr17:39,509,727 INFO 2026-06-04 21:23:59 MarkDuplicates Tracking 363269 as yet unmatched pairs. 79403 records in RAM. INFO 2026-06-04 21:24:00 MarkDuplicates Read 495,000,000 records. Elapsed time: 00:14:08s. Time for last 1,000,000: 1s. Last read position: chr17:39,723,910 INFO 2026-06-04 21:24:00 MarkDuplicates Tracking 361494 as yet unmatched pairs. 77626 records in RAM. INFO 2026-06-04 21:24:02 MarkDuplicates Read 496,000,000 records. Elapsed time: 00:14:10s. Time for last 1,000,000: 2s. Last read position: chr17:40,363,178 INFO 2026-06-04 21:24:02 MarkDuplicates Tracking 357633 as yet unmatched pairs. 73760 records in RAM. INFO 2026-06-04 21:24:04 MarkDuplicates Read 497,000,000 records. Elapsed time: 00:14:12s. Time for last 1,000,000: 1s. Last read position: chr17:41,502,403 INFO 2026-06-04 21:24:04 MarkDuplicates Tracking 359739 as yet unmatched pairs. 75851 records in RAM. INFO 2026-06-04 21:24:06 MarkDuplicates Read 498,000,000 records. Elapsed time: 00:14:14s. Time for last 1,000,000: 1s. Last read position: chr17:41,527,833 INFO 2026-06-04 21:24:06 MarkDuplicates Tracking 353211 as yet unmatched pairs. 69319 records in RAM. INFO 2026-06-04 21:26:12 MarkDuplicates Read 499,000,000 records. Elapsed time: 00:16:19s. Time for last 1,000,000: 125s. Last read position: chr17:41,619,609 INFO 2026-06-04 21:26:12 MarkDuplicates Tracking 365154 as yet unmatched pairs. 81258 records in RAM. INFO 2026-06-04 21:26:13 MarkDuplicates Read 500,000,000 records. Elapsed time: 00:16:21s. Time for last 1,000,000: 1s. Last read position: chr17:41,621,626 INFO 2026-06-04 21:26:13 MarkDuplicates Tracking 368825 as yet unmatched pairs. 84923 records in RAM. INFO 2026-06-04 21:26:15 MarkDuplicates Read 501,000,000 records. Elapsed time: 00:16:23s. Time for last 1,000,000: 1s. Last read position: chr17:41,624,100 INFO 2026-06-04 21:26:15 MarkDuplicates Tracking 357007 as yet unmatched pairs. 73099 records in RAM. INFO 2026-06-04 21:26:16 MarkDuplicates Read 502,000,000 records. Elapsed time: 00:16:24s. Time for last 1,000,000: 1s. Last read position: chr17:41,763,084 INFO 2026-06-04 21:26:16 MarkDuplicates Tracking 342965 as yet unmatched pairs. 59052 records in RAM. INFO 2026-06-04 21:26:18 MarkDuplicates Read 503,000,000 records. Elapsed time: 00:16:26s. Time for last 1,000,000: 1s. Last read position: chr17:42,563,250 INFO 2026-06-04 21:26:18 MarkDuplicates Tracking 338372 as yet unmatched pairs. 54452 records in RAM. INFO 2026-06-04 21:26:19 MarkDuplicates Read 504,000,000 records. Elapsed time: 00:16:27s. Time for last 1,000,000: 1s. Last read position: chr17:44,075,845 INFO 2026-06-04 21:26:19 MarkDuplicates Tracking 335510 as yet unmatched pairs. 51574 records in RAM. INFO 2026-06-04 21:26:21 MarkDuplicates Read 505,000,000 records. Elapsed time: 00:16:29s. Time for last 1,000,000: 1s. Last read position: chr17:45,150,101 INFO 2026-06-04 21:26:21 MarkDuplicates Tracking 333129 as yet unmatched pairs. 49186 records in RAM. INFO 2026-06-04 21:26:22 MarkDuplicates Read 506,000,000 records. Elapsed time: 00:16:30s. Time for last 1,000,000: 1s. Last read position: chr17:47,658,613 INFO 2026-06-04 21:26:22 MarkDuplicates Tracking 331636 as yet unmatched pairs. 47690 records in RAM. INFO 2026-06-04 21:26:24 MarkDuplicates Read 507,000,000 records. Elapsed time: 00:16:31s. Time for last 1,000,000: 1s. Last read position: chr17:50,076,664 INFO 2026-06-04 21:26:24 MarkDuplicates Tracking 328799 as yet unmatched pairs. 44847 records in RAM. INFO 2026-06-04 21:26:25 MarkDuplicates Read 508,000,000 records. Elapsed time: 00:16:33s. Time for last 1,000,000: 1s. Last read position: chr17:50,195,453 INFO 2026-06-04 21:26:25 MarkDuplicates Tracking 326589 as yet unmatched pairs. 42626 records in RAM. INFO 2026-06-04 21:26:27 MarkDuplicates Read 509,000,000 records. Elapsed time: 00:16:35s. Time for last 1,000,000: 1s. Last read position: chr17:50,745,818 INFO 2026-06-04 21:26:27 MarkDuplicates Tracking 322619 as yet unmatched pairs. 38650 records in RAM. INFO 2026-06-04 21:26:29 MarkDuplicates Read 510,000,000 records. Elapsed time: 00:16:36s. Time for last 1,000,000: 1s. Last read position: chr17:58,495,089 INFO 2026-06-04 21:26:29 MarkDuplicates Tracking 320364 as yet unmatched pairs. 36372 records in RAM. INFO 2026-06-04 21:26:30 MarkDuplicates Read 511,000,000 records. Elapsed time: 00:16:38s. Time for last 1,000,000: 1s. Last read position: chr17:59,682,686 INFO 2026-06-04 21:26:30 MarkDuplicates Tracking 319655 as yet unmatched pairs. 35661 records in RAM. INFO 2026-06-04 21:26:32 MarkDuplicates Read 512,000,000 records. Elapsed time: 00:16:40s. Time for last 1,000,000: 1s. Last read position: chr17:62,627,734 INFO 2026-06-04 21:26:32 MarkDuplicates Tracking 315231 as yet unmatched pairs. 31221 records in RAM. INFO 2026-06-04 21:26:34 MarkDuplicates Read 513,000,000 records. Elapsed time: 00:16:42s. Time for last 1,000,000: 2s. Last read position: chr17:64,503,454 INFO 2026-06-04 21:26:34 MarkDuplicates Tracking 314458 as yet unmatched pairs. 30439 records in RAM. INFO 2026-06-04 21:26:36 MarkDuplicates Read 514,000,000 records. Elapsed time: 00:16:44s. Time for last 1,000,000: 1s. Last read position: chr17:67,948,285 INFO 2026-06-04 21:26:36 MarkDuplicates Tracking 310525 as yet unmatched pairs. 26483 records in RAM. INFO 2026-06-04 21:26:38 MarkDuplicates Read 515,000,000 records. Elapsed time: 00:16:46s. Time for last 1,000,000: 2s. Last read position: chr17:73,233,227 INFO 2026-06-04 21:26:38 MarkDuplicates Tracking 307762 as yet unmatched pairs. 23712 records in RAM. INFO 2026-06-04 21:26:40 MarkDuplicates Read 516,000,000 records. Elapsed time: 00:16:48s. Time for last 1,000,000: 1s. Last read position: chr17:75,495,324 INFO 2026-06-04 21:26:40 MarkDuplicates Tracking 305257 as yet unmatched pairs. 21200 records in RAM. INFO 2026-06-04 21:26:41 MarkDuplicates Read 517,000,000 records. Elapsed time: 00:16:49s. Time for last 1,000,000: 1s. Last read position: chr17:75,757,428 INFO 2026-06-04 21:26:41 MarkDuplicates Tracking 303134 as yet unmatched pairs. 19074 records in RAM. INFO 2026-06-04 21:26:42 MarkDuplicates Read 518,000,000 records. Elapsed time: 00:16:50s. Time for last 1,000,000: 1s. Last read position: chr17:76,270,242 INFO 2026-06-04 21:26:42 MarkDuplicates Tracking 300487 as yet unmatched pairs. 16409 records in RAM. INFO 2026-06-04 21:26:44 MarkDuplicates Read 519,000,000 records. Elapsed time: 00:16:52s. Time for last 1,000,000: 1s. Last read position: chr17:78,701,677 INFO 2026-06-04 21:26:44 MarkDuplicates Tracking 296669 as yet unmatched pairs. 12583 records in RAM. INFO 2026-06-04 21:26:45 MarkDuplicates Read 520,000,000 records. Elapsed time: 00:16:53s. Time for last 1,000,000: 1s. Last read position: chr17:81,192,314 INFO 2026-06-04 21:26:45 MarkDuplicates Tracking 293752 as yet unmatched pairs. 9655 records in RAM. INFO 2026-06-04 21:26:47 MarkDuplicates Read 521,000,000 records. Elapsed time: 00:16:54s. Time for last 1,000,000: 1s. Last read position: chr17:81,511,987 INFO 2026-06-04 21:26:47 MarkDuplicates Tracking 298178 as yet unmatched pairs. 14074 records in RAM. INFO 2026-06-04 21:26:48 MarkDuplicates Read 522,000,000 records. Elapsed time: 00:16:56s. Time for last 1,000,000: 1s. Last read position: chr17:81,890,795 INFO 2026-06-04 21:26:48 MarkDuplicates Tracking 288190 as yet unmatched pairs. 4076 records in RAM. INFO 2026-06-04 21:26:50 MarkDuplicates Read 523,000,000 records. Elapsed time: 00:16:57s. Time for last 1,000,000: 1s. Last read position: chr17:82,439,645 INFO 2026-06-04 21:26:50 MarkDuplicates Tracking 285309 as yet unmatched pairs. 1187 records in RAM. INFO 2026-06-04 21:26:51 MarkDuplicates Read 524,000,000 records. Elapsed time: 00:16:59s. Time for last 1,000,000: 1s. Last read position: chr18:6,462,116 INFO 2026-06-04 21:26:51 MarkDuplicates Tracking 282881 as yet unmatched pairs. 17643 records in RAM. INFO 2026-06-04 21:26:53 MarkDuplicates Read 525,000,000 records. Elapsed time: 00:17:01s. Time for last 1,000,000: 2s. Last read position: chr18:12,325,220 INFO 2026-06-04 21:26:53 MarkDuplicates Tracking 280481 as yet unmatched pairs. 15233 records in RAM. INFO 2026-06-04 21:26:56 MarkDuplicates Read 526,000,000 records. Elapsed time: 00:17:03s. Time for last 1,000,000: 2s. Last read position: chr18:26,038,570 INFO 2026-06-04 21:26:56 MarkDuplicates Tracking 278931 as yet unmatched pairs. 13668 records in RAM. INFO 2026-06-04 21:26:58 MarkDuplicates Read 527,000,000 records. Elapsed time: 00:17:06s. Time for last 1,000,000: 2s. Last read position: chr18:36,126,737 INFO 2026-06-04 21:26:58 MarkDuplicates Tracking 276450 as yet unmatched pairs. 11183 records in RAM. INFO 2026-06-04 21:27:00 MarkDuplicates Read 528,000,000 records. Elapsed time: 00:17:07s. Time for last 1,000,000: 1s. Last read position: chr18:49,482,324 INFO 2026-06-04 21:27:00 MarkDuplicates Tracking 273851 as yet unmatched pairs. 8569 records in RAM. INFO 2026-06-04 21:27:01 MarkDuplicates Read 529,000,000 records. Elapsed time: 00:17:09s. Time for last 1,000,000: 1s. Last read position: chr18:57,607,487 INFO 2026-06-04 21:27:01 MarkDuplicates Tracking 270976 as yet unmatched pairs. 5689 records in RAM. INFO 2026-06-04 21:27:02 MarkDuplicates Read 530,000,000 records. Elapsed time: 00:17:10s. Time for last 1,000,000: 1s. Last read position: chr18:62,574,655 INFO 2026-06-04 21:27:02 MarkDuplicates Tracking 268068 as yet unmatched pairs. 2778 records in RAM. INFO 2026-06-04 21:27:04 MarkDuplicates Read 531,000,000 records. Elapsed time: 00:17:12s. Time for last 1,000,000: 2s. Last read position: chr19:307,108 INFO 2026-06-04 21:27:04 MarkDuplicates Tracking 265304 as yet unmatched pairs. 104479 records in RAM. INFO 2026-06-04 21:27:06 MarkDuplicates Read 532,000,000 records. Elapsed time: 00:17:14s. Time for last 1,000,000: 1s. Last read position: chr19:1,032,676 INFO 2026-06-04 21:27:06 MarkDuplicates Tracking 263004 as yet unmatched pairs. 102173 records in RAM. INFO 2026-06-04 21:27:08 MarkDuplicates Read 533,000,000 records. Elapsed time: 00:17:15s. Time for last 1,000,000: 1s. Last read position: chr19:1,440,177 INFO 2026-06-04 21:27:08 MarkDuplicates Tracking 262367 as yet unmatched pairs. 101533 records in RAM. INFO 2026-06-04 21:27:09 MarkDuplicates Read 534,000,000 records. Elapsed time: 00:17:17s. Time for last 1,000,000: 1s. Last read position: chr19:2,235,762 INFO 2026-06-04 21:27:09 MarkDuplicates Tracking 256939 as yet unmatched pairs. 96096 records in RAM. INFO 2026-06-04 21:27:10 MarkDuplicates Read 535,000,000 records. Elapsed time: 00:17:18s. Time for last 1,000,000: 1s. Last read position: chr19:3,983,264 INFO 2026-06-04 21:27:10 MarkDuplicates Tracking 254850 as yet unmatched pairs. 94000 records in RAM. INFO 2026-06-04 21:27:12 MarkDuplicates Read 536,000,000 records. Elapsed time: 00:17:20s. Time for last 1,000,000: 1s. Last read position: chr19:5,214,664 INFO 2026-06-04 21:27:12 MarkDuplicates Tracking 250703 as yet unmatched pairs. 89848 records in RAM. INFO 2026-06-04 21:27:13 MarkDuplicates Read 537,000,000 records. Elapsed time: 00:17:21s. Time for last 1,000,000: 1s. Last read position: chr19:6,422,340 INFO 2026-06-04 21:27:13 MarkDuplicates Tracking 248640 as yet unmatched pairs. 87783 records in RAM. INFO 2026-06-04 21:27:15 MarkDuplicates Read 538,000,000 records. Elapsed time: 00:17:23s. Time for last 1,000,000: 1s. Last read position: chr19:8,333,746 INFO 2026-06-04 21:27:15 MarkDuplicates Tracking 244920 as yet unmatched pairs. 84062 records in RAM. INFO 2026-06-04 21:27:16 MarkDuplicates Read 539,000,000 records. Elapsed time: 00:17:24s. Time for last 1,000,000: 1s. Last read position: chr19:10,258,504 INFO 2026-06-04 21:27:16 MarkDuplicates Tracking 242883 as yet unmatched pairs. 82020 records in RAM. INFO 2026-06-04 21:27:18 MarkDuplicates Read 540,000,000 records. Elapsed time: 00:17:26s. Time for last 1,000,000: 1s. Last read position: chr19:10,830,236 INFO 2026-06-04 21:27:18 MarkDuplicates Tracking 239929 as yet unmatched pairs. 79058 records in RAM. INFO 2026-06-04 21:27:20 MarkDuplicates Read 541,000,000 records. Elapsed time: 00:17:27s. Time for last 1,000,000: 1s. Last read position: chr19:11,447,129 INFO 2026-06-04 21:27:20 MarkDuplicates Tracking 236973 as yet unmatched pairs. 76102 records in RAM. INFO 2026-06-04 21:27:22 MarkDuplicates Read 542,000,000 records. Elapsed time: 00:17:29s. Time for last 1,000,000: 2s. Last read position: chr19:12,792,696 INFO 2026-06-04 21:27:22 MarkDuplicates Tracking 235461 as yet unmatched pairs. 74583 records in RAM. INFO 2026-06-04 21:27:24 MarkDuplicates Read 543,000,000 records. Elapsed time: 00:17:31s. Time for last 1,000,000: 1s. Last read position: chr19:14,097,780 INFO 2026-06-04 21:27:24 MarkDuplicates Tracking 232321 as yet unmatched pairs. 71439 records in RAM. INFO 2026-06-04 21:27:25 MarkDuplicates Read 544,000,000 records. Elapsed time: 00:17:33s. Time for last 1,000,000: 1s. Last read position: chr19:15,174,118 INFO 2026-06-04 21:27:25 MarkDuplicates Tracking 229371 as yet unmatched pairs. 68483 records in RAM. INFO 2026-06-04 21:27:27 MarkDuplicates Read 545,000,000 records. Elapsed time: 00:17:35s. Time for last 1,000,000: 1s. Last read position: chr19:15,265,365 INFO 2026-06-04 21:27:27 MarkDuplicates Tracking 227049 as yet unmatched pairs. 66159 records in RAM. INFO 2026-06-04 21:27:28 MarkDuplicates Read 546,000,000 records. Elapsed time: 00:17:36s. Time for last 1,000,000: 1s. Last read position: chr19:16,385,103 INFO 2026-06-04 21:27:28 MarkDuplicates Tracking 223385 as yet unmatched pairs. 62488 records in RAM. INFO 2026-06-04 21:27:29 MarkDuplicates Read 547,000,000 records. Elapsed time: 00:17:37s. Time for last 1,000,000: 1s. Last read position: chr19:17,808,008 INFO 2026-06-04 21:27:29 MarkDuplicates Tracking 220544 as yet unmatched pairs. 59642 records in RAM. INFO 2026-06-04 21:27:31 MarkDuplicates Read 548,000,000 records. Elapsed time: 00:17:39s. Time for last 1,000,000: 1s. Last read position: chr19:18,759,922 INFO 2026-06-04 21:27:31 MarkDuplicates Tracking 217699 as yet unmatched pairs. 56795 records in RAM. INFO 2026-06-04 21:27:33 MarkDuplicates Read 549,000,000 records. Elapsed time: 00:17:40s. Time for last 1,000,000: 1s. Last read position: chr19:20,196,981 INFO 2026-06-04 21:27:33 MarkDuplicates Tracking 214985 as yet unmatched pairs. 54077 records in RAM. INFO 2026-06-04 21:27:34 MarkDuplicates Read 550,000,000 records. Elapsed time: 00:17:42s. Time for last 1,000,000: 1s. Last read position: chr19:34,352,796 INFO 2026-06-04 21:27:34 MarkDuplicates Tracking 212450 as yet unmatched pairs. 51533 records in RAM. INFO 2026-06-04 21:27:35 MarkDuplicates Read 551,000,000 records. Elapsed time: 00:17:43s. Time for last 1,000,000: 1s. Last read position: chr19:35,267,698 INFO 2026-06-04 21:27:35 MarkDuplicates Tracking 210885 as yet unmatched pairs. 49968 records in RAM. INFO 2026-06-04 21:27:37 MarkDuplicates Read 552,000,000 records. Elapsed time: 00:17:45s. Time for last 1,000,000: 1s. Last read position: chr19:37,153,460 INFO 2026-06-04 21:27:37 MarkDuplicates Tracking 207016 as yet unmatched pairs. 46095 records in RAM. INFO 2026-06-04 21:27:38 MarkDuplicates Read 553,000,000 records. Elapsed time: 00:17:46s. Time for last 1,000,000: 1s. Last read position: chr19:38,721,562 INFO 2026-06-04 21:27:38 MarkDuplicates Tracking 205342 as yet unmatched pairs. 44416 records in RAM. INFO 2026-06-04 21:27:40 MarkDuplicates Read 554,000,000 records. Elapsed time: 00:17:47s. Time for last 1,000,000: 1s. Last read position: chr19:39,415,030 INFO 2026-06-04 21:27:40 MarkDuplicates Tracking 201822 as yet unmatched pairs. 40894 records in RAM. INFO 2026-06-04 21:27:41 MarkDuplicates Read 555,000,000 records. Elapsed time: 00:17:49s. Time for last 1,000,000: 1s. Last read position: chr19:40,240,094 INFO 2026-06-04 21:27:41 MarkDuplicates Tracking 200933 as yet unmatched pairs. 39999 records in RAM. INFO 2026-06-04 21:27:43 MarkDuplicates Read 556,000,000 records. Elapsed time: 00:17:50s. Time for last 1,000,000: 1s. Last read position: chr19:41,506,453 INFO 2026-06-04 21:27:43 MarkDuplicates Tracking 196520 as yet unmatched pairs. 35586 records in RAM. INFO 2026-06-04 21:27:44 MarkDuplicates Read 557,000,000 records. Elapsed time: 00:17:52s. Time for last 1,000,000: 1s. Last read position: chr19:42,273,969 INFO 2026-06-04 21:27:44 MarkDuplicates Tracking 194150 as yet unmatched pairs. 33215 records in RAM. INFO 2026-06-04 21:27:46 MarkDuplicates Read 558,000,000 records. Elapsed time: 00:17:54s. Time for last 1,000,000: 2s. Last read position: chr19:43,627,686 INFO 2026-06-04 21:27:46 MarkDuplicates Tracking 191323 as yet unmatched pairs. 30379 records in RAM. INFO 2026-06-04 21:27:48 MarkDuplicates Read 559,000,000 records. Elapsed time: 00:17:56s. Time for last 1,000,000: 1s. Last read position: chr19:45,396,180 INFO 2026-06-04 21:27:48 MarkDuplicates Tracking 189221 as yet unmatched pairs. 28276 records in RAM. INFO 2026-06-04 21:27:49 MarkDuplicates Read 560,000,000 records. Elapsed time: 00:17:57s. Time for last 1,000,000: 1s. Last read position: chr19:46,608,873 INFO 2026-06-04 21:27:49 MarkDuplicates Tracking 186375 as yet unmatched pairs. 25426 records in RAM. INFO 2026-06-04 21:27:51 MarkDuplicates Read 561,000,000 records. Elapsed time: 00:17:59s. Time for last 1,000,000: 1s. Last read position: chr19:48,383,148 INFO 2026-06-04 21:27:51 MarkDuplicates Tracking 183152 as yet unmatched pairs. 22200 records in RAM. INFO 2026-06-04 21:27:52 MarkDuplicates Read 562,000,000 records. Elapsed time: 00:18:00s. Time for last 1,000,000: 1s. Last read position: chr19:49,181,424 INFO 2026-06-04 21:27:52 MarkDuplicates Tracking 180534 as yet unmatched pairs. 19581 records in RAM. INFO 2026-06-04 21:27:54 MarkDuplicates Read 563,000,000 records. Elapsed time: 00:18:01s. Time for last 1,000,000: 1s. Last read position: chr19:49,669,091 INFO 2026-06-04 21:27:54 MarkDuplicates Tracking 177355 as yet unmatched pairs. 16397 records in RAM. INFO 2026-06-04 21:27:55 MarkDuplicates Read 564,000,000 records. Elapsed time: 00:18:03s. Time for last 1,000,000: 1s. Last read position: chr19:50,280,273 INFO 2026-06-04 21:27:55 MarkDuplicates Tracking 174749 as yet unmatched pairs. 13781 records in RAM. INFO 2026-06-04 21:27:57 MarkDuplicates Read 565,000,000 records. Elapsed time: 00:18:05s. Time for last 1,000,000: 1s. Last read position: chr19:52,222,158 INFO 2026-06-04 21:27:57 MarkDuplicates Tracking 172490 as yet unmatched pairs. 11518 records in RAM. INFO 2026-06-04 21:27:58 MarkDuplicates Read 566,000,000 records. Elapsed time: 00:18:06s. Time for last 1,000,000: 1s. Last read position: chr19:54,171,870 INFO 2026-06-04 21:27:58 MarkDuplicates Tracking 169726 as yet unmatched pairs. 8753 records in RAM. INFO 2026-06-04 21:27:59 MarkDuplicates Read 567,000,000 records. Elapsed time: 00:18:07s. Time for last 1,000,000: 1s. Last read position: chr19:55,305,560 INFO 2026-06-04 21:27:59 MarkDuplicates Tracking 166363 as yet unmatched pairs. 5381 records in RAM. INFO 2026-06-04 21:28:01 MarkDuplicates Read 568,000,000 records. Elapsed time: 00:18:09s. Time for last 1,000,000: 1s. Last read position: chr19:57,682,072 INFO 2026-06-04 21:28:01 MarkDuplicates Tracking 163695 as yet unmatched pairs. 2711 records in RAM. INFO 2026-06-04 21:28:02 MarkDuplicates Read 569,000,000 records. Elapsed time: 00:18:10s. Time for last 1,000,000: 1s. Last read position: chr19:58,551,908 INFO 2026-06-04 21:28:02 MarkDuplicates Tracking 161923 as yet unmatched pairs. 934 records in RAM. INFO 2026-06-04 21:28:04 MarkDuplicates Read 570,000,000 records. Elapsed time: 00:18:12s. Time for last 1,000,000: 1s. Last read position: chr20:3,148,630 INFO 2026-06-04 21:28:04 MarkDuplicates Tracking 158724 as yet unmatched pairs. 35683 records in RAM. INFO 2026-06-04 21:28:05 MarkDuplicates Read 571,000,000 records. Elapsed time: 00:18:13s. Time for last 1,000,000: 1s. Last read position: chr20:10,639,565 INFO 2026-06-04 21:28:05 MarkDuplicates Tracking 156514 as yet unmatched pairs. 33467 records in RAM. INFO 2026-06-04 21:28:07 MarkDuplicates Read 572,000,000 records. Elapsed time: 00:18:15s. Time for last 1,000,000: 1s. Last read position: chr20:20,000,617 INFO 2026-06-04 21:28:07 MarkDuplicates Tracking 153788 as yet unmatched pairs. 30739 records in RAM. INFO 2026-06-04 21:28:08 MarkDuplicates Read 573,000,000 records. Elapsed time: 00:18:16s. Time for last 1,000,000: 1s. Last read position: chr20:31,514,647 INFO 2026-06-04 21:28:08 MarkDuplicates Tracking 151452 as yet unmatched pairs. 28400 records in RAM. INFO 2026-06-04 21:28:10 MarkDuplicates Read 574,000,000 records. Elapsed time: 00:18:18s. Time for last 1,000,000: 1s. Last read position: chr20:34,393,825 INFO 2026-06-04 21:28:10 MarkDuplicates Tracking 152062 as yet unmatched pairs. 29009 records in RAM. INFO 2026-06-04 21:28:12 MarkDuplicates Read 575,000,000 records. Elapsed time: 00:18:20s. Time for last 1,000,000: 1s. Last read position: chr20:35,653,241 INFO 2026-06-04 21:28:12 MarkDuplicates Tracking 146004 as yet unmatched pairs. 22949 records in RAM. INFO 2026-06-04 21:28:14 MarkDuplicates Read 576,000,000 records. Elapsed time: 00:18:21s. Time for last 1,000,000: 1s. Last read position: chr20:37,210,052 INFO 2026-06-04 21:28:14 MarkDuplicates Tracking 143771 as yet unmatched pairs. 20714 records in RAM. INFO 2026-06-04 21:28:15 MarkDuplicates Read 577,000,000 records. Elapsed time: 00:18:23s. Time for last 1,000,000: 1s. Last read position: chr20:43,460,136 INFO 2026-06-04 21:28:15 MarkDuplicates Tracking 142037 as yet unmatched pairs. 18975 records in RAM. INFO 2026-06-04 21:28:17 MarkDuplicates Read 578,000,000 records. Elapsed time: 00:18:24s. Time for last 1,000,000: 1s. Last read position: chr20:45,894,731 INFO 2026-06-04 21:28:17 MarkDuplicates Tracking 139104 as yet unmatched pairs. 16040 records in RAM. INFO 2026-06-04 21:28:18 MarkDuplicates Read 579,000,000 records. Elapsed time: 00:18:26s. Time for last 1,000,000: 1s. Last read position: chr20:49,270,573 INFO 2026-06-04 21:28:18 MarkDuplicates Tracking 136096 as yet unmatched pairs. 13029 records in RAM. INFO 2026-06-04 21:28:19 MarkDuplicates Read 580,000,000 records. Elapsed time: 00:18:27s. Time for last 1,000,000: 1s. Last read position: chr20:54,162,746 INFO 2026-06-04 21:28:19 MarkDuplicates Tracking 133453 as yet unmatched pairs. 10382 records in RAM. INFO 2026-06-04 21:28:21 MarkDuplicates Read 581,000,000 records. Elapsed time: 00:18:29s. Time for last 1,000,000: 1s. Last read position: chr20:59,030,351 INFO 2026-06-04 21:28:21 MarkDuplicates Tracking 132933 as yet unmatched pairs. 9857 records in RAM. INFO 2026-06-04 21:28:22 MarkDuplicates Read 582,000,000 records. Elapsed time: 00:18:30s. Time for last 1,000,000: 1s. Last read position: chr20:62,387,632 INFO 2026-06-04 21:28:22 MarkDuplicates Tracking 129241 as yet unmatched pairs. 6159 records in RAM. INFO 2026-06-04 21:28:24 MarkDuplicates Read 583,000,000 records. Elapsed time: 00:18:31s. Time for last 1,000,000: 1s. Last read position: chr20:63,733,334 INFO 2026-06-04 21:28:24 MarkDuplicates Tracking 124300 as yet unmatched pairs. 1218 records in RAM. INFO 2026-06-04 21:28:25 MarkDuplicates Read 584,000,000 records. Elapsed time: 00:18:33s. Time for last 1,000,000: 1s. Last read position: chr21:8,216,855 INFO 2026-06-04 21:28:25 MarkDuplicates Tracking 122178 as yet unmatched pairs. 18684 records in RAM. INFO 2026-06-04 21:28:26 MarkDuplicates Read 585,000,000 records. Elapsed time: 00:18:34s. Time for last 1,000,000: 1s. Last read position: chr21:8,442,005 INFO 2026-06-04 21:28:26 MarkDuplicates Tracking 121564 as yet unmatched pairs. 18062 records in RAM. INFO 2026-06-04 21:28:27 MarkDuplicates Read 586,000,000 records. Elapsed time: 00:18:35s. Time for last 1,000,000: 1s. Last read position: chr21:26,089,956 INFO 2026-06-04 21:28:27 MarkDuplicates Tracking 120396 as yet unmatched pairs. 16888 records in RAM. INFO 2026-06-04 21:28:29 MarkDuplicates Read 587,000,000 records. Elapsed time: 00:18:37s. Time for last 1,000,000: 1s. Last read position: chr21:33,426,897 INFO 2026-06-04 21:28:29 MarkDuplicates Tracking 117702 as yet unmatched pairs. 14191 records in RAM. INFO 2026-06-04 21:28:30 MarkDuplicates Read 588,000,000 records. Elapsed time: 00:18:38s. Time for last 1,000,000: 1s. Last read position: chr21:36,338,804 INFO 2026-06-04 21:28:30 MarkDuplicates Tracking 114866 as yet unmatched pairs. 11352 records in RAM. INFO 2026-06-04 21:28:31 MarkDuplicates Read 589,000,000 records. Elapsed time: 00:18:39s. Time for last 1,000,000: 1s. Last read position: chr21:39,345,213 INFO 2026-06-04 21:28:31 MarkDuplicates Tracking 112644 as yet unmatched pairs. 9126 records in RAM. INFO 2026-06-04 21:28:33 MarkDuplicates Read 590,000,000 records. Elapsed time: 00:18:41s. Time for last 1,000,000: 1s. Last read position: chr21:43,421,607 INFO 2026-06-04 21:28:33 MarkDuplicates Tracking 109659 as yet unmatched pairs. 6135 records in RAM. INFO 2026-06-04 21:28:35 MarkDuplicates Read 591,000,000 records. Elapsed time: 00:18:42s. Time for last 1,000,000: 1s. Last read position: chr21:45,986,969 INFO 2026-06-04 21:28:35 MarkDuplicates Tracking 107447 as yet unmatched pairs. 3923 records in RAM. INFO 2026-06-04 21:28:37 MarkDuplicates Read 592,000,000 records. Elapsed time: 00:18:44s. Time for last 1,000,000: 2s. Last read position: chr21:46,459,134 INFO 2026-06-04 21:28:37 MarkDuplicates Tracking 104119 as yet unmatched pairs. 591 records in RAM. INFO 2026-06-04 21:28:38 MarkDuplicates Read 593,000,000 records. Elapsed time: 00:18:46s. Time for last 1,000,000: 1s. Last read position: chr22:20,086,080 INFO 2026-06-04 21:28:38 MarkDuplicates Tracking 101789 as yet unmatched pairs. 36912 records in RAM. INFO 2026-06-04 21:28:40 MarkDuplicates Read 594,000,000 records. Elapsed time: 00:18:48s. Time for last 1,000,000: 1s. Last read position: chr22:23,181,666 INFO 2026-06-04 21:28:40 MarkDuplicates Tracking 99347 as yet unmatched pairs. 34465 records in RAM. INFO 2026-06-04 21:28:41 MarkDuplicates Read 595,000,000 records. Elapsed time: 00:18:49s. Time for last 1,000,000: 1s. Last read position: chr22:24,263,541 INFO 2026-06-04 21:28:41 MarkDuplicates Tracking 95861 as yet unmatched pairs. 30976 records in RAM. INFO 2026-06-04 21:28:43 MarkDuplicates Read 596,000,000 records. Elapsed time: 00:18:50s. Time for last 1,000,000: 1s. Last read position: chr22:29,286,903 INFO 2026-06-04 21:28:43 MarkDuplicates Tracking 95759 as yet unmatched pairs. 30872 records in RAM. INFO 2026-06-04 21:28:44 MarkDuplicates Read 597,000,000 records. Elapsed time: 00:18:52s. Time for last 1,000,000: 1s. Last read position: chr22:29,806,190 INFO 2026-06-04 21:28:44 MarkDuplicates Tracking 91331 as yet unmatched pairs. 26443 records in RAM. INFO 2026-06-04 21:28:46 MarkDuplicates Read 598,000,000 records. Elapsed time: 00:18:53s. Time for last 1,000,000: 1s. Last read position: chr22:31,806,118 INFO 2026-06-04 21:28:46 MarkDuplicates Tracking 88534 as yet unmatched pairs. 23639 records in RAM. INFO 2026-06-04 21:28:47 MarkDuplicates Read 599,000,000 records. Elapsed time: 00:18:55s. Time for last 1,000,000: 1s. Last read position: chr22:36,285,763 INFO 2026-06-04 21:28:47 MarkDuplicates Tracking 86905 as yet unmatched pairs. 22009 records in RAM. INFO 2026-06-04 21:28:48 MarkDuplicates Read 600,000,000 records. Elapsed time: 00:18:56s. Time for last 1,000,000: 1s. Last read position: chr22:36,324,638 INFO 2026-06-04 21:28:48 MarkDuplicates Tracking 85822 as yet unmatched pairs. 20926 records in RAM. INFO 2026-06-04 21:28:50 MarkDuplicates Read 601,000,000 records. Elapsed time: 00:18:58s. Time for last 1,000,000: 1s. Last read position: chr22:37,877,778 INFO 2026-06-04 21:28:50 MarkDuplicates Tracking 81051 as yet unmatched pairs. 16154 records in RAM. INFO 2026-06-04 21:28:51 MarkDuplicates Read 602,000,000 records. Elapsed time: 00:18:59s. Time for last 1,000,000: 1s. Last read position: chr22:38,866,535 INFO 2026-06-04 21:28:51 MarkDuplicates Tracking 77989 as yet unmatched pairs. 13087 records in RAM. INFO 2026-06-04 21:28:53 MarkDuplicates Read 603,000,000 records. Elapsed time: 00:19:01s. Time for last 1,000,000: 1s. Last read position: chr22:41,177,142 INFO 2026-06-04 21:28:53 MarkDuplicates Tracking 76004 as yet unmatched pairs. 11101 records in RAM. INFO 2026-06-04 21:28:54 MarkDuplicates Read 604,000,000 records. Elapsed time: 00:19:02s. Time for last 1,000,000: 1s. Last read position: chr22:42,213,342 INFO 2026-06-04 21:28:54 MarkDuplicates Tracking 73164 as yet unmatched pairs. 8259 records in RAM. INFO 2026-06-04 21:28:55 MarkDuplicates Read 605,000,000 records. Elapsed time: 00:19:03s. Time for last 1,000,000: 1s. Last read position: chr22:45,922,618 INFO 2026-06-04 21:28:55 MarkDuplicates Tracking 70775 as yet unmatched pairs. 5870 records in RAM. INFO 2026-06-04 21:28:57 MarkDuplicates Read 606,000,000 records. Elapsed time: 00:19:05s. Time for last 1,000,000: 1s. Last read position: chr22:50,284,597 INFO 2026-06-04 21:28:57 MarkDuplicates Tracking 69858 as yet unmatched pairs. 4948 records in RAM. INFO 2026-06-04 21:28:59 MarkDuplicates Read 607,000,000 records. Elapsed time: 00:19:07s. Time for last 1,000,000: 2s. Last read position: chrX:1,389,588 INFO 2026-06-04 21:28:59 MarkDuplicates Tracking 66732 as yet unmatched pairs. 63083 records in RAM. INFO 2026-06-04 21:29:01 MarkDuplicates Read 608,000,000 records. Elapsed time: 00:19:09s. Time for last 1,000,000: 1s. Last read position: chrX:10,567,163 INFO 2026-06-04 21:29:01 MarkDuplicates Tracking 63040 as yet unmatched pairs. 59389 records in RAM. INFO 2026-06-04 21:29:02 MarkDuplicates Read 609,000,000 records. Elapsed time: 00:19:10s. Time for last 1,000,000: 1s. Last read position: chrX:16,719,741 INFO 2026-06-04 21:29:02 MarkDuplicates Tracking 59504 as yet unmatched pairs. 55853 records in RAM. INFO 2026-06-04 21:29:04 MarkDuplicates Read 610,000,000 records. Elapsed time: 00:19:12s. Time for last 1,000,000: 1s. Last read position: chrX:21,967,279 INFO 2026-06-04 21:29:04 MarkDuplicates Tracking 57392 as yet unmatched pairs. 53734 records in RAM. INFO 2026-06-04 21:29:05 MarkDuplicates Read 611,000,000 records. Elapsed time: 00:19:13s. Time for last 1,000,000: 1s. Last read position: chrX:34,630,364 INFO 2026-06-04 21:29:05 MarkDuplicates Tracking 56517 as yet unmatched pairs. 52859 records in RAM. INFO 2026-06-04 21:29:07 MarkDuplicates Read 612,000,000 records. Elapsed time: 00:19:15s. Time for last 1,000,000: 1s. Last read position: chrX:41,168,080 INFO 2026-06-04 21:29:07 MarkDuplicates Tracking 53879 as yet unmatched pairs. 50220 records in RAM. INFO 2026-06-04 21:29:08 MarkDuplicates Read 613,000,000 records. Elapsed time: 00:19:16s. Time for last 1,000,000: 1s. Last read position: chrX:43,656,299 INFO 2026-06-04 21:29:08 MarkDuplicates Tracking 50151 as yet unmatched pairs. 46492 records in RAM. INFO 2026-06-04 21:29:10 MarkDuplicates Read 614,000,000 records. Elapsed time: 00:19:18s. Time for last 1,000,000: 1s. Last read position: chrX:47,059,011 INFO 2026-06-04 21:29:10 MarkDuplicates Tracking 47199 as yet unmatched pairs. 43539 records in RAM. INFO 2026-06-04 21:29:11 MarkDuplicates Read 615,000,000 records. Elapsed time: 00:19:19s. Time for last 1,000,000: 1s. Last read position: chrX:47,563,028 INFO 2026-06-04 21:29:11 MarkDuplicates Tracking 44792 as yet unmatched pairs. 41128 records in RAM. INFO 2026-06-04 21:29:13 MarkDuplicates Read 616,000,000 records. Elapsed time: 00:19:20s. Time for last 1,000,000: 1s. Last read position: chrX:48,901,991 INFO 2026-06-04 21:29:13 MarkDuplicates Tracking 42520 as yet unmatched pairs. 38856 records in RAM. INFO 2026-06-04 21:29:14 MarkDuplicates Read 617,000,000 records. Elapsed time: 00:19:22s. Time for last 1,000,000: 1s. Last read position: chrX:49,174,674 INFO 2026-06-04 21:29:14 MarkDuplicates Tracking 39860 as yet unmatched pairs. 36196 records in RAM. INFO 2026-06-04 21:29:15 MarkDuplicates Read 618,000,000 records. Elapsed time: 00:19:23s. Time for last 1,000,000: 1s. Last read position: chrX:53,216,185 INFO 2026-06-04 21:29:15 MarkDuplicates Tracking 37430 as yet unmatched pairs. 33765 records in RAM. INFO 2026-06-04 21:29:17 MarkDuplicates Read 619,000,000 records. Elapsed time: 00:19:25s. Time for last 1,000,000: 1s. Last read position: chrX:53,560,289 INFO 2026-06-04 21:29:17 MarkDuplicates Tracking 35057 as yet unmatched pairs. 31392 records in RAM. INFO 2026-06-04 21:29:18 MarkDuplicates Read 620,000,000 records. Elapsed time: 00:19:26s. Time for last 1,000,000: 1s. Last read position: chrX:54,470,124 INFO 2026-06-04 21:29:18 MarkDuplicates Tracking 31847 as yet unmatched pairs. 28182 records in RAM. INFO 2026-06-04 21:29:20 MarkDuplicates Read 621,000,000 records. Elapsed time: 00:19:28s. Time for last 1,000,000: 1s. Last read position: chrX:68,234,486 INFO 2026-06-04 21:29:20 MarkDuplicates Tracking 29451 as yet unmatched pairs. 25786 records in RAM. INFO 2026-06-04 21:29:21 MarkDuplicates Read 622,000,000 records. Elapsed time: 00:19:29s. Time for last 1,000,000: 1s. Last read position: chrX:72,130,893 INFO 2026-06-04 21:29:21 MarkDuplicates Tracking 27217 as yet unmatched pairs. 23552 records in RAM. INFO 2026-06-04 21:29:23 MarkDuplicates Read 623,000,000 records. Elapsed time: 00:19:31s. Time for last 1,000,000: 1s. Last read position: chrX:77,899,585 INFO 2026-06-04 21:29:23 MarkDuplicates Tracking 27182 as yet unmatched pairs. 23517 records in RAM. INFO 2026-06-04 21:29:25 MarkDuplicates Read 624,000,000 records. Elapsed time: 00:19:32s. Time for last 1,000,000: 1s. Last read position: chrX:101,625,355 INFO 2026-06-04 21:29:25 MarkDuplicates Tracking 22665 as yet unmatched pairs. 18999 records in RAM. INFO 2026-06-04 21:29:26 MarkDuplicates Read 625,000,000 records. Elapsed time: 00:19:34s. Time for last 1,000,000: 1s. Last read position: chrX:111,620,965 INFO 2026-06-04 21:29:26 MarkDuplicates Tracking 19919 as yet unmatched pairs. 16253 records in RAM. INFO 2026-06-04 21:29:27 MarkDuplicates Read 626,000,000 records. Elapsed time: 00:19:35s. Time for last 1,000,000: 1s. Last read position: chrX:124,071,249 INFO 2026-06-04 21:29:27 MarkDuplicates Tracking 17770 as yet unmatched pairs. 14104 records in RAM. INFO 2026-06-04 21:29:29 MarkDuplicates Read 627,000,000 records. Elapsed time: 00:19:37s. Time for last 1,000,000: 1s. Last read position: chrX:139,785,258 INFO 2026-06-04 21:29:29 MarkDuplicates Tracking 15356 as yet unmatched pairs. 11689 records in RAM. INFO 2026-06-04 21:29:30 MarkDuplicates Read 628,000,000 records. Elapsed time: 00:19:38s. Time for last 1,000,000: 1s. Last read position: chrX:153,700,564 INFO 2026-06-04 21:29:30 MarkDuplicates Tracking 12537 as yet unmatched pairs. 8868 records in RAM. INFO 2026-06-04 21:29:32 MarkDuplicates Read 629,000,000 records. Elapsed time: 00:19:39s. Time for last 1,000,000: 1s. Last read position: chrX:154,351,646 INFO 2026-06-04 21:29:32 MarkDuplicates Tracking 11735 as yet unmatched pairs. 8066 records in RAM. INFO 2026-06-04 21:29:33 MarkDuplicates Read 630,000,000 records. Elapsed time: 00:19:41s. Time for last 1,000,000: 1s. Last read position: chrX:154,364,924 INFO 2026-06-04 21:29:33 MarkDuplicates Tracking 8791 as yet unmatched pairs. 5120 records in RAM. INFO 2026-06-04 21:29:35 MarkDuplicates Read 631,000,000 records. Elapsed time: 00:19:42s. Time for last 1,000,000: 1s. Last read position: chrX:155,071,504 INFO 2026-06-04 21:29:35 MarkDuplicates Tracking 4020 as yet unmatched pairs. 349 records in RAM. INFO 2026-06-04 21:29:36 MarkDuplicates Read 632,000,000 records. Elapsed time: 00:19:44s. Time for last 1,000,000: 1s. Last read position: GL000220.1:116,836 INFO 2026-06-04 21:29:36 MarkDuplicates Tracking 1646 as yet unmatched pairs. 64 records in RAM. INFO 2026-06-04 21:29:37 MarkDuplicates Read 633,000,000 records. Elapsed time: 00:19:45s. Time for last 1,000,000: 0s. Last read position: KI270733.1:133,429 INFO 2026-06-04 21:29:37 MarkDuplicates Tracking 284 as yet unmatched pairs. 274 records in RAM. INFO 2026-06-04 21:29:37 MarkDuplicates Read 633527483 records. 0 pairs never matched. INFO 2026-06-04 21:30:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 204141128; totalMemory: 234881024; maxMemory: 63585648640 INFO 2026-06-04 21:30:28 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk. INFO 2026-06-04 21:30:30 MarkDuplicates Traversing read pair information and detecting duplicates. WARNING 2026-06-04 21:30:30 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered. INFO 2026-06-04 21:30:45 OpticalDuplicateFinder Large duplicate set. size = 1366 INFO 2026-06-04 21:30:45 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:21,848 INFO 2026-06-04 21:30:45 OpticalDuplicateFinder Large duplicate set. size = 1967 INFO 2026-06-04 21:30:45 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-18,196 INFO 2026-06-04 21:30:45 OpticalDuplicateFinder Large duplicate set. size = 1190 INFO 2026-06-04 21:30:45 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,333 INFO 2026-06-04 21:30:45 OpticalDuplicateFinder Large duplicate set. size = 1400 INFO 2026-06-04 21:30:45 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:21,015 INFO 2026-06-04 21:30:45 OpticalDuplicateFinder Large duplicate set. size = 1497 INFO 2026-06-04 21:30:45 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-22,047 INFO 2026-06-04 21:30:45 OpticalDuplicateFinder Large duplicate set. size = 1084 INFO 2026-06-04 21:30:45 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-14,685 INFO 2026-06-04 21:30:45 OpticalDuplicateFinder Large duplicate set. size = 1162 INFO 2026-06-04 21:30:45 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 2026-06-04 21:30:45 OpticalDuplicateFinder Large duplicate set. size = 1210 INFO 2026-06-04 21:30:45 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-13,941 INFO 2026-06-04 21:30:45 OpticalDuplicateFinder Large duplicate set. size = 1285 INFO 2026-06-04 21:30:45 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,334 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder Large duplicate set. size = 1241 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,137 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder Large duplicate set. size = 1468 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:26,556 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder Large duplicate set. size = 1168 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,122 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder Large duplicate set. size = 1283 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,615 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder Large duplicate set. size = 2034 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,194 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:23,474 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder Large duplicate set. size = 1408 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:2,545 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder Large duplicate set. size = 1282 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-13,957 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder Large duplicate set. size = 1224 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,911 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder Large duplicate set. size = 1051 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,927 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder Large duplicate set. size = 1036 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,145 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder Large duplicate set. size = 1058 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,531 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder Large duplicate set. size = 1127 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,947 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder Large duplicate set. size = 1242 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,526 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder Large duplicate set. size = 1082 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,274 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder Large duplicate set. size = 1105 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,267 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder Large duplicate set. size = 1014 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,482 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder Large duplicate set. size = 1099 INFO 2026-06-04 21:30:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-27,104 INFO 2026-06-04 21:30:54 OpticalDuplicateFinder Large duplicate set. size = 1442 INFO 2026-06-04 21:30:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:17,520 INFO 2026-06-04 21:30:54 OpticalDuplicateFinder Large duplicate set. size = 1068 INFO 2026-06-04 21:30:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,916 INFO 2026-06-04 21:30:54 OpticalDuplicateFinder Large duplicate set. size = 1109 INFO 2026-06-04 21:30:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,414 INFO 2026-06-04 21:30:54 OpticalDuplicateFinder Large duplicate set. size = 1148 INFO 2026-06-04 21:30:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,996 INFO 2026-06-04 21:30:54 OpticalDuplicateFinder Large duplicate set. size = 2076 INFO 2026-06-04 21:30:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:6,259 INFO 2026-06-04 21:30:54 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:21,079 INFO 2026-06-04 21:30:54 OpticalDuplicateFinder Large duplicate set. size = 1950 INFO 2026-06-04 21:30:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,699 INFO 2026-06-04 21:30:54 OpticalDuplicateFinder Large duplicate set. size = 1023 INFO 2026-06-04 21:30:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,692 INFO 2026-06-04 21:30:54 OpticalDuplicateFinder Large duplicate set. size = 1054 INFO 2026-06-04 21:30:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,889 INFO 2026-06-04 21:30:57 OpticalDuplicateFinder Large duplicate set. size = 1207 INFO 2026-06-04 21:30:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,962 INFO 2026-06-04 21:31:03 OpticalDuplicateFinder Large duplicate set. size = 1218 INFO 2026-06-04 21:31:03 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,664 INFO 2026-06-04 21:31:03 OpticalDuplicateFinder Large duplicate set. size = 1220 INFO 2026-06-04 21:31:03 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,844 INFO 2026-06-04 21:31:11 OpticalDuplicateFinder Large duplicate set. size = 1164 INFO 2026-06-04 21:31:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,148 INFO 2026-06-04 21:31:11 OpticalDuplicateFinder Large duplicate set. size = 1108 INFO 2026-06-04 21:31:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:2,893 INFO 2026-06-04 21:31:11 OpticalDuplicateFinder Large duplicate set. size = 1066 INFO 2026-06-04 21:31:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,233 INFO 2026-06-04 21:31:17 OpticalDuplicateFinder Large duplicate set. size = 1156 INFO 2026-06-04 21:31:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,664 INFO 2026-06-04 21:31:17 OpticalDuplicateFinder Large duplicate set. size = 1350 INFO 2026-06-04 21:31:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,536 INFO 2026-06-04 21:31:17 OpticalDuplicateFinder Large duplicate set. size = 1251 INFO 2026-06-04 21:31:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,630 INFO 2026-06-04 21:31:18 OpticalDuplicateFinder Large duplicate set. size = 1055 INFO 2026-06-04 21:31:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,638 INFO 2026-06-04 21:31:18 OpticalDuplicateFinder Large duplicate set. size = 1173 INFO 2026-06-04 21:31:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:8,095 INFO 2026-06-04 21:31:18 OpticalDuplicateFinder Large duplicate set. size = 1024 INFO 2026-06-04 21:31:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,694 INFO 2026-06-04 21:31:18 OpticalDuplicateFinder Large duplicate set. size = 1167 INFO 2026-06-04 21:31:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,034 INFO 2026-06-04 21:31:18 OpticalDuplicateFinder Large duplicate set. size = 1126 INFO 2026-06-04 21:31:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,009 INFO 2026-06-04 21:31:18 OpticalDuplicateFinder Large duplicate set. size = 1375 INFO 2026-06-04 21:31:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:31,823 INFO 2026-06-04 21:31:18 OpticalDuplicateFinder Large duplicate set. size = 1406 INFO 2026-06-04 21:31:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,926 INFO 2026-06-04 21:31:18 OpticalDuplicateFinder Large duplicate set. size = 1099 INFO 2026-06-04 21:31:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:10,020 INFO 2026-06-04 21:31:18 OpticalDuplicateFinder Large duplicate set. size = 1523 INFO 2026-06-04 21:31:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,810 INFO 2026-06-04 21:31:18 OpticalDuplicateFinder Large duplicate set. size = 1057 INFO 2026-06-04 21:31:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:23,474 INFO 2026-06-04 21:31:18 OpticalDuplicateFinder Large duplicate set. size = 1625 INFO 2026-06-04 21:31:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,405 INFO 2026-06-04 21:31:18 OpticalDuplicateFinder Large duplicate set. size = 1523 INFO 2026-06-04 21:31:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:31,637 INFO 2026-06-04 21:31:19 OpticalDuplicateFinder Large duplicate set. size = 2368 INFO 2026-06-04 21:31:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,845 INFO 2026-06-04 21:31:19 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,366 INFO 2026-06-04 21:31:19 OpticalDuplicateFinder Large duplicate set. size = 1194 INFO 2026-06-04 21:31:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,709 INFO 2026-06-04 21:31:46 MarkDuplicates Traversing fragment information and detecting duplicates. WARNING 2026-06-04 21:31:46 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered. INFO 2026-06-04 21:32:47 MarkDuplicates Sorting list of duplicate records. INFO 2026-06-04 21:32:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 203929968; totalMemory: 234881024; maxMemory: 63585648640 INFO 2026-06-04 21:32:47 MarkDuplicates Marking 269465034 records as duplicates. INFO 2026-06-04 21:32:47 MarkDuplicates Found 12933638 optical duplicate clusters. INFO 2026-06-04 21:32:47 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2026-06-04 21:33:04 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:16s. Time for last 10,000,000: 16s. Last read position: chr1:21,865,326 INFO 2026-06-04 21:33:19 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:32s. Time for last 10,000,000: 15s. Last read position: chr1:39,850,239 INFO 2026-06-04 21:33:35 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:47s. Time for last 10,000,000: 15s. Last read position: chr1:94,926,899 INFO 2026-06-04 21:33:50 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:02s. Time for last 10,000,000: 15s. Last read position: chr1:151,266,332 INFO 2026-06-04 21:34:05 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:17s. Time for last 10,000,000: 15s. Last read position: chr1:171,557,899 INFO 2026-06-04 21:34:20 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:33s. Time for last 10,000,000: 15s. Last read position: chr1:225,511,811 INFO 2026-06-04 21:34:36 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:01:48s. Time for last 10,000,000: 15s. Last read position: chr2:32,415,609 INFO 2026-06-04 21:34:51 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:03s. Time for last 10,000,000: 15s. Last read position: chr2:65,205,499 INFO 2026-06-04 21:35:06 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:19s. Time for last 10,000,000: 15s. Last read position: chr2:112,388,684 INFO 2026-06-04 21:35:22 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:34s. Time for last 10,000,000: 15s. Last read position: chr2:201,064,054 INFO 2026-06-04 21:35:37 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:02:49s. Time for last 10,000,000: 15s. Last read position: chr3:4,800,561 INFO 2026-06-04 21:35:52 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:05s. Time for last 10,000,000: 15s. Last read position: chr3:49,425,403 INFO 2026-06-04 21:36:08 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:20s. Time for last 10,000,000: 15s. Last read position: chr3:126,988,693 INFO 2026-06-04 21:36:23 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:03:36s. Time for last 10,000,000: 15s. Last read position: chr3:195,779,172 INFO 2026-06-04 21:36:38 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:03:51s. Time for last 10,000,000: 15s. Last read position: chr4:2,884,519 INFO 2026-06-04 21:36:54 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:07s. Time for last 10,000,000: 15s. Last read position: chr4:100,398,308 INFO 2026-06-04 21:37:10 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:04:22s. Time for last 10,000,000: 15s. Last read position: chr5:14,389,289 INFO 2026-06-04 21:37:25 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:04:38s. Time for last 10,000,000: 15s. Last read position: chr5:109,344,806 INFO 2026-06-04 21:37:41 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:04:53s. Time for last 10,000,000: 15s. Last read position: chr5:163,441,879 INFO 2026-06-04 21:37:56 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:05:09s. Time for last 10,000,000: 15s. Last read position: chr6:31,269,017 INFO 2026-06-04 21:38:11 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:05:24s. Time for last 10,000,000: 15s. Last read position: chr6:56,530,021 INFO 2026-06-04 21:38:27 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:05:39s. Time for last 10,000,000: 15s. Last read position: chr6:151,352,272 INFO 2026-06-04 21:38:42 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:05:55s. Time for last 10,000,000: 15s. Last read position: chr7:17,339,724 INFO 2026-06-04 21:38:57 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:06:10s. Time for last 10,000,000: 15s. Last read position: chr7:91,973,910 INFO 2026-06-04 21:39:13 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:06:26s. Time for last 10,000,000: 15s. Last read position: chr7:140,459,710 INFO 2026-06-04 21:39:28 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:06:41s. Time for last 10,000,000: 15s. Last read position: chr8:42,189,047 INFO 2026-06-04 21:39:44 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:06:57s. Time for last 10,000,000: 15s. Last read position: chr8:130,124,027 INFO 2026-06-04 21:39:59 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:07:11s. Time for last 10,000,000: 14s. Last read position: chr8:143,926,723 INFO 2026-06-04 21:40:14 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:07:27s. Time for last 10,000,000: 15s. Last read position: chr9:86,035,452 INFO 2026-06-04 21:40:30 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:07:43s. Time for last 10,000,000: 15s. Last read position: chr9:132,281,538 INFO 2026-06-04 21:40:45 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:07:58s. Time for last 10,000,000: 15s. Last read position: chr10:43,387,222 INFO 2026-06-04 21:41:01 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:08:14s. Time for last 10,000,000: 15s. Last read position: chr10:97,426,288 INFO 2026-06-04 21:41:17 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:08:29s. Time for last 10,000,000: 15s. Last read position: chr11:2,135,440 INFO 2026-06-04 21:41:32 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:08:45s. Time for last 10,000,000: 15s. Last read position: chr11:59,172,592 INFO 2026-06-04 21:41:48 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:09:00s. Time for last 10,000,000: 15s. Last read position: chr11:68,049,698 INFO 2026-06-04 21:42:03 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:09:16s. Time for last 10,000,000: 15s. Last read position: chr11:120,424,308 INFO 2026-06-04 21:42:19 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:09:31s. Time for last 10,000,000: 15s. Last read position: chr12:32,581,994 INFO 2026-06-04 21:42:34 MarkDuplicates Written 380,000,000 records. Elapsed time: 00:09:47s. Time for last 10,000,000: 15s. Last read position: chr12:56,160,126 INFO 2026-06-04 21:42:50 MarkDuplicates Written 390,000,000 records. Elapsed time: 00:10:02s. Time for last 10,000,000: 15s. Last read position: chr12:110,440,341 INFO 2026-06-04 21:43:05 MarkDuplicates Written 400,000,000 records. Elapsed time: 00:10:18s. Time for last 10,000,000: 15s. Last read position: chr13:32,517,702 INFO 2026-06-04 21:43:21 MarkDuplicates Written 410,000,000 records. Elapsed time: 00:10:34s. Time for last 10,000,000: 15s. Last read position: chr14:23,563,400 INFO 2026-06-04 21:43:36 MarkDuplicates Written 420,000,000 records. Elapsed time: 00:10:49s. Time for last 10,000,000: 15s. Last read position: chr14:75,764,634 INFO 2026-06-04 21:43:52 MarkDuplicates Written 430,000,000 records. Elapsed time: 00:11:05s. Time for last 10,000,000: 15s. Last read position: chr15:43,428,146 INFO 2026-06-04 21:44:07 MarkDuplicates Written 440,000,000 records. Elapsed time: 00:11:20s. Time for last 10,000,000: 15s. Last read position: chr15:78,921,994 INFO 2026-06-04 21:44:23 MarkDuplicates Written 450,000,000 records. Elapsed time: 00:11:35s. Time for last 10,000,000: 15s. Last read position: chr16:11,927,739 INFO 2026-06-04 21:44:38 MarkDuplicates Written 460,000,000 records. Elapsed time: 00:11:51s. Time for last 10,000,000: 15s. Last read position: chr16:29,383,917 INFO 2026-06-04 21:44:53 MarkDuplicates Written 470,000,000 records. Elapsed time: 00:12:06s. Time for last 10,000,000: 15s. Last read position: chr16:69,109,710 INFO 2026-06-04 21:45:09 MarkDuplicates Written 480,000,000 records. Elapsed time: 00:12:21s. Time for last 10,000,000: 15s. Last read position: chr17:5,410,788 INFO 2026-06-04 21:45:24 MarkDuplicates Written 490,000,000 records. Elapsed time: 00:12:36s. Time for last 10,000,000: 15s. Last read position: chr17:31,937,495 INFO 2026-06-04 21:45:39 MarkDuplicates Written 500,000,000 records. Elapsed time: 00:12:51s. Time for last 10,000,000: 15s. Last read position: chr17:41,621,626 INFO 2026-06-04 21:45:54 MarkDuplicates Written 510,000,000 records. Elapsed time: 00:13:07s. Time for last 10,000,000: 15s. Last read position: chr17:58,495,089 INFO 2026-06-04 21:46:11 MarkDuplicates Written 520,000,000 records. Elapsed time: 00:13:23s. Time for last 10,000,000: 16s. Last read position: chr17:81,192,314 INFO 2026-06-04 21:46:27 MarkDuplicates Written 530,000,000 records. Elapsed time: 00:13:39s. Time for last 10,000,000: 16s. Last read position: chr18:62,574,655 INFO 2026-06-04 21:46:42 MarkDuplicates Written 540,000,000 records. Elapsed time: 00:13:55s. Time for last 10,000,000: 15s. Last read position: chr19:10,830,236 INFO 2026-06-04 21:46:57 MarkDuplicates Written 550,000,000 records. Elapsed time: 00:14:10s. Time for last 10,000,000: 15s. Last read position: chr19:34,352,796 INFO 2026-06-04 21:47:13 MarkDuplicates Written 560,000,000 records. Elapsed time: 00:14:25s. Time for last 10,000,000: 15s. Last read position: chr19:46,608,873 INFO 2026-06-04 21:47:28 MarkDuplicates Written 570,000,000 records. Elapsed time: 00:14:40s. Time for last 10,000,000: 15s. Last read position: chr20:3,148,630 INFO 2026-06-04 21:47:43 MarkDuplicates Written 580,000,000 records. Elapsed time: 00:14:56s. Time for last 10,000,000: 15s. Last read position: chr20:54,162,746 INFO 2026-06-04 21:47:58 MarkDuplicates Written 590,000,000 records. Elapsed time: 00:15:11s. Time for last 10,000,000: 14s. Last read position: chr21:43,421,607 INFO 2026-06-04 21:48:13 MarkDuplicates Written 600,000,000 records. Elapsed time: 00:15:26s. Time for last 10,000,000: 15s. Last read position: chr22:36,324,638 INFO 2026-06-04 21:48:28 MarkDuplicates Written 610,000,000 records. Elapsed time: 00:15:41s. Time for last 10,000,000: 15s. Last read position: chrX:21,967,279 INFO 2026-06-04 21:48:44 MarkDuplicates Written 620,000,000 records. Elapsed time: 00:15:56s. Time for last 10,000,000: 15s. Last read position: chrX:54,470,124 INFO 2026-06-04 21:48:59 MarkDuplicates Written 630,000,000 records. Elapsed time: 00:16:12s. Time for last 10,000,000: 15s. Last read position: chrX:154,364,924 INFO 2026-06-04 21:49:11 MarkDuplicates Writing complete. Closing input iterator. INFO 2026-06-04 21:49:11 MarkDuplicates Duplicate Index cleanup. INFO 2026-06-04 21:49:11 MarkDuplicates Getting Memory Stats. INFO 2026-06-04 21:49:11 MarkDuplicates Before output close freeMemory: 203879576; totalMemory: 234881024; maxMemory: 63585648640 INFO 2026-06-04 21:49:11 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2026-06-04 21:49:11 MarkDuplicates After output close freeMemory: 104131864; totalMemory: 134217728; maxMemory: 63585648640 [Thu Jun 04 21:49:11 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 39.34 minutes. Runtime.totalMemory()=134217728 ls: *cram: No such file or directory ls: *.crai: No such file or directory