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 tih_rna_sample_00111_23H5VFLT4_s30.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00111_23H5VFLT4_s30.md.bam --METRICS_FILE tih_rna_sample_00111_23H5VFLT4_s30.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT 07:56:17.904 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Mon Jun 08 07:56:17 GMT 2026] MarkDuplicates --INPUT tih_rna_sample_00111_23H5VFLT4_s30.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00111_23H5VFLT4_s30.md.bam --METRICS_FILE tih_rna_sample_00111_23H5VFLT4_s30.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Mon Jun 08 07:56:17 GMT 2026] Executing as ?@nf-c2d1dc963a7109c4d64230e721a97b2e-ac621-8m4fd on Linux 6.12.88 amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0 INFO 2026-06-08 07:56:17 MarkDuplicates Start of doWork freeMemory: 105829288; totalMemory: 134217728; maxMemory: 63585648640 INFO 2026-06-08 07:56:17 MarkDuplicates Reading input file and constructing read end information. INFO 2026-06-08 07:56:17 MarkDuplicates Will retain up to 230382784 data points before spilling to disk. INFO 2026-06-08 07:56:22 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:1,627,140 INFO 2026-06-08 07:56:22 MarkDuplicates Tracking 1108 as yet unmatched pairs. 110 records in RAM. INFO 2026-06-08 07:56:26 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 3s. Last read position: chr1:6,589,079 INFO 2026-06-08 07:56:26 MarkDuplicates Tracking 2242 as yet unmatched pairs. 79 records in RAM. INFO 2026-06-08 07:56:29 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 2s. Last read position: chr1:10,659,839 INFO 2026-06-08 07:56:29 MarkDuplicates Tracking 3156 as yet unmatched pairs. 116 records in RAM. INFO 2026-06-08 07:56:33 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 3s. Last read position: chr1:15,727,459 INFO 2026-06-08 07:56:33 MarkDuplicates Tracking 3766 as yet unmatched pairs. 22 records in RAM. INFO 2026-06-08 07:56:36 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 3s. Last read position: chr1:17,696,993 INFO 2026-06-08 07:56:36 MarkDuplicates Tracking 4418 as yet unmatched pairs. 124 records in RAM. INFO 2026-06-08 07:56:39 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 3s. Last read position: chr1:21,864,119 INFO 2026-06-08 07:56:39 MarkDuplicates Tracking 5195 as yet unmatched pairs. 110 records in RAM. INFO 2026-06-08 07:56:43 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 3s. Last read position: chr1:26,183,737 INFO 2026-06-08 07:56:43 MarkDuplicates Tracking 5862 as yet unmatched pairs. 94 records in RAM. INFO 2026-06-08 07:56:47 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 4s. Last read position: chr1:28,095,740 INFO 2026-06-08 07:56:47 MarkDuplicates Tracking 6690 as yet unmatched pairs. 94 records in RAM. INFO 2026-06-08 07:56:50 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 2s. Last read position: chr1:32,335,071 INFO 2026-06-08 07:56:50 MarkDuplicates Tracking 7374 as yet unmatched pairs. 71 records in RAM. INFO 2026-06-08 07:56:53 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 3s. Last read position: chr1:36,172,576 INFO 2026-06-08 07:56:53 MarkDuplicates Tracking 8094 as yet unmatched pairs. 14 records in RAM. INFO 2026-06-08 07:56:56 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 3s. Last read position: chr1:39,480,947 INFO 2026-06-08 07:56:56 MarkDuplicates Tracking 8875 as yet unmatched pairs. 131 records in RAM. INFO 2026-06-08 07:56:59 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 3s. Last read position: chr1:43,441,311 INFO 2026-06-08 07:56:59 MarkDuplicates Tracking 9477 as yet unmatched pairs. 36 records in RAM. INFO 2026-06-08 07:57:02 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 3s. Last read position: chr1:46,303,784 INFO 2026-06-08 07:57:02 MarkDuplicates Tracking 10180 as yet unmatched pairs. 20 records in RAM. INFO 2026-06-08 07:57:05 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: chr1:55,141,705 INFO 2026-06-08 07:57:05 MarkDuplicates Tracking 11000 as yet unmatched pairs. 111 records in RAM. INFO 2026-06-08 07:57:08 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 3s. Last read position: chr1:66,984,742 INFO 2026-06-08 07:57:08 MarkDuplicates Tracking 11628 as yet unmatched pairs. 114 records in RAM. INFO 2026-06-08 07:57:11 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 2s. Last read position: chr1:89,702,509 INFO 2026-06-08 07:57:11 MarkDuplicates Tracking 12069 as yet unmatched pairs. 12 records in RAM. INFO 2026-06-08 07:57:14 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 2s. Last read position: chr1:108,782,309 INFO 2026-06-08 07:57:14 MarkDuplicates Tracking 12687 as yet unmatched pairs. 66 records in RAM. INFO 2026-06-08 07:57:17 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 3s. Last read position: chr1:113,622,812 INFO 2026-06-08 07:57:17 MarkDuplicates Tracking 13543 as yet unmatched pairs. 279 records in RAM. INFO 2026-06-08 07:57:19 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 2s. Last read position: chr1:119,916,631 INFO 2026-06-08 07:57:19 MarkDuplicates Tracking 14373 as yet unmatched pairs. 516 records in RAM. INFO 2026-06-08 07:57:22 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 2s. Last read position: chr1:143,729,502 INFO 2026-06-08 07:57:22 MarkDuplicates Tracking 14291 as yet unmatched pairs. 4 records in RAM. INFO 2026-06-08 07:57:25 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 2s. Last read position: chr1:146,228,699 INFO 2026-06-08 07:57:25 MarkDuplicates Tracking 14730 as yet unmatched pairs. 28 records in RAM. INFO 2026-06-08 07:57:27 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 2s. Last read position: chr1:148,961,872 INFO 2026-06-08 07:57:27 MarkDuplicates Tracking 15104 as yet unmatched pairs. 97 records in RAM. INFO 2026-06-08 07:57:30 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 2s. Last read position: chr1:150,557,464 INFO 2026-06-08 07:57:30 MarkDuplicates Tracking 15858 as yet unmatched pairs. 381 records in RAM. INFO 2026-06-08 07:57:33 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 2s. Last read position: chr1:151,428,191 INFO 2026-06-08 07:57:33 MarkDuplicates Tracking 16612 as yet unmatched pairs. 327 records in RAM. INFO 2026-06-08 07:57:36 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 2s. Last read position: chr1:154,170,685 INFO 2026-06-08 07:57:36 MarkDuplicates Tracking 17961 as yet unmatched pairs. 995 records in RAM. INFO 2026-06-08 07:57:39 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 3s. Last read position: chr1:155,186,094 INFO 2026-06-08 07:57:39 MarkDuplicates Tracking 19038 as yet unmatched pairs. 1376 records in RAM. INFO 2026-06-08 07:57:42 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 2s. Last read position: chr1:155,192,005 INFO 2026-06-08 07:57:42 MarkDuplicates Tracking 21272 as yet unmatched pairs. 3135 records in RAM. INFO 2026-06-08 07:57:45 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 2s. Last read position: chr1:155,805,009 INFO 2026-06-08 07:57:45 MarkDuplicates Tracking 18867 as yet unmatched pairs. 15 records in RAM. INFO 2026-06-08 07:57:48 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 3s. Last read position: chr1:156,732,245 INFO 2026-06-08 07:57:48 MarkDuplicates Tracking 19808 as yet unmatched pairs. 104 records in RAM. INFO 2026-06-08 07:57:51 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 3s. Last read position: chr1:161,048,060 INFO 2026-06-08 07:57:51 MarkDuplicates Tracking 20708 as yet unmatched pairs. 338 records in RAM. INFO 2026-06-08 07:57:54 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 3s. Last read position: chr1:168,104,679 INFO 2026-06-08 07:57:54 MarkDuplicates Tracking 20962 as yet unmatched pairs. 2 records in RAM. INFO 2026-06-08 07:57:58 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 3s. Last read position: chr1:176,868,990 INFO 2026-06-08 07:57:58 MarkDuplicates Tracking 21512 as yet unmatched pairs. 3 records in RAM. INFO 2026-06-08 07:58:01 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 2s. Last read position: chr1:184,795,691 INFO 2026-06-08 07:58:01 MarkDuplicates Tracking 22286 as yet unmatched pairs. 88 records in RAM. INFO 2026-06-08 07:58:03 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 2s. Last read position: chr1:200,408,400 INFO 2026-06-08 07:58:03 MarkDuplicates Tracking 22805 as yet unmatched pairs. 114 records in RAM. INFO 2026-06-08 07:58:06 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 2s. Last read position: chr1:203,818,601 INFO 2026-06-08 07:58:06 MarkDuplicates Tracking 23747 as yet unmatched pairs. 360 records in RAM. INFO 2026-06-08 07:58:09 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 3s. Last read position: chr1:207,883,362 INFO 2026-06-08 07:58:09 MarkDuplicates Tracking 24167 as yet unmatched pairs. 1 records in RAM. INFO 2026-06-08 07:58:13 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 3s. Last read position: chr1:222,633,166 INFO 2026-06-08 07:58:13 MarkDuplicates Tracking 24949 as yet unmatched pairs. 108 records in RAM. INFO 2026-06-08 07:58:16 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 3s. Last read position: chr1:226,071,350 INFO 2026-06-08 07:58:16 MarkDuplicates Tracking 25451 as yet unmatched pairs. 40 records in RAM. INFO 2026-06-08 07:58:18 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 2s. Last read position: chr1:228,406,369 INFO 2026-06-08 07:58:18 MarkDuplicates Tracking 26440 as yet unmatched pairs. 164 records in RAM. INFO 2026-06-08 07:58:21 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 2s. Last read position: chr1:235,806,552 INFO 2026-06-08 07:58:21 MarkDuplicates Tracking 27333 as yet unmatched pairs. 61 records in RAM. INFO 2026-06-08 07:58:23 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 2s. Last read position: chr1:246,851,135 INFO 2026-06-08 07:58:23 MarkDuplicates Tracking 28035 as yet unmatched pairs. 108 records in RAM. INFO 2026-06-08 07:58:27 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 3s. Last read position: chr2:15,474,140 INFO 2026-06-08 07:58:27 MarkDuplicates Tracking 28621 as yet unmatched pairs. 28423 records in RAM. INFO 2026-06-08 07:58:30 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 2s. Last read position: chr2:26,268,951 INFO 2026-06-08 07:58:30 MarkDuplicates Tracking 29329 as yet unmatched pairs. 29127 records in RAM. INFO 2026-06-08 07:58:33 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 2s. Last read position: chr2:32,595,092 INFO 2026-06-08 07:58:33 MarkDuplicates Tracking 30174 as yet unmatched pairs. 29966 records in RAM. INFO 2026-06-08 07:58:37 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 4s. Last read position: chr2:36,849,736 INFO 2026-06-08 07:58:37 MarkDuplicates Tracking 242668 as yet unmatched pairs. 14193 records in RAM. INFO 2026-06-08 07:58:40 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 2s. Last read position: chr2:43,549,357 INFO 2026-06-08 07:58:40 MarkDuplicates Tracking 242554 as yet unmatched pairs. 14075 records in RAM. INFO 2026-06-08 07:58:42 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 2s. Last read position: chr2:55,049,742 INFO 2026-06-08 07:58:42 MarkDuplicates Tracking 241191 as yet unmatched pairs. 12700 records in RAM. INFO 2026-06-08 07:58:46 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 3s. Last read position: chr2:67,000,005 INFO 2026-06-08 07:58:46 MarkDuplicates Tracking 240430 as yet unmatched pairs. 11937 records in RAM. INFO 2026-06-08 07:58:48 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 2s. Last read position: chr2:74,415,629 INFO 2026-06-08 07:58:48 MarkDuplicates Tracking 239838 as yet unmatched pairs. 11332 records in RAM. INFO 2026-06-08 07:58:51 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 3s. Last read position: chr2:86,914,337 INFO 2026-06-08 07:58:51 MarkDuplicates Tracking 239185 as yet unmatched pairs. 10671 records in RAM. INFO 2026-06-08 07:58:54 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 2s. Last read position: chr2:97,545,716 INFO 2026-06-08 07:58:54 MarkDuplicates Tracking 238738 as yet unmatched pairs. 10220 records in RAM. INFO 2026-06-08 07:58:56 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 2s. Last read position: chr2:108,489,894 INFO 2026-06-08 07:58:56 MarkDuplicates Tracking 238031 as yet unmatched pairs. 9503 records in RAM. INFO 2026-06-08 07:58:58 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 2s. Last read position: chr2:110,569,716 INFO 2026-06-08 07:58:58 MarkDuplicates Tracking 237811 as yet unmatched pairs. 9282 records in RAM. INFO 2026-06-08 07:59:00 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 2s. Last read position: chr2:127,481,025 INFO 2026-06-08 07:59:00 MarkDuplicates Tracking 237172 as yet unmatched pairs. 8628 records in RAM. INFO 2026-06-08 07:59:02 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 2s. Last read position: chr2:136,114,872 INFO 2026-06-08 07:59:02 MarkDuplicates Tracking 237014 as yet unmatched pairs. 8466 records in RAM. INFO 2026-06-08 07:59:06 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 3s. Last read position: chr2:159,431,096 INFO 2026-06-08 07:59:06 MarkDuplicates Tracking 236055 as yet unmatched pairs. 7501 records in RAM. INFO 2026-06-08 07:59:09 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 2s. Last read position: chr2:173,913,150 INFO 2026-06-08 07:59:09 MarkDuplicates Tracking 235321 as yet unmatched pairs. 6764 records in RAM. INFO 2026-06-08 07:59:12 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 3s. Last read position: chr2:182,736,248 INFO 2026-06-08 07:59:12 MarkDuplicates Tracking 234828 as yet unmatched pairs. 6261 records in RAM. INFO 2026-06-08 07:59:15 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 3s. Last read position: chr2:190,997,893 INFO 2026-06-08 07:59:15 MarkDuplicates Tracking 233891 as yet unmatched pairs. 5323 records in RAM. INFO 2026-06-08 07:59:17 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 2s. Last read position: chr2:203,440,384 INFO 2026-06-08 07:59:17 MarkDuplicates Tracking 233665 as yet unmatched pairs. 5094 records in RAM. INFO 2026-06-08 07:59:20 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 3s. Last read position: chr2:215,376,505 INFO 2026-06-08 07:59:20 MarkDuplicates Tracking 233193 as yet unmatched pairs. 4620 records in RAM. INFO 2026-06-08 07:59:23 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 2s. Last read position: chr2:216,679,015 INFO 2026-06-08 07:59:23 MarkDuplicates Tracking 232024 as yet unmatched pairs. 3451 records in RAM. INFO 2026-06-08 07:59:25 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 2s. Last read position: chr2:221,560,969 INFO 2026-06-08 07:59:25 MarkDuplicates Tracking 230984 as yet unmatched pairs. 2406 records in RAM. INFO 2026-06-08 07:59:27 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 2s. Last read position: chr2:233,251,778 INFO 2026-06-08 07:59:27 MarkDuplicates Tracking 230436 as yet unmatched pairs. 1823 records in RAM. INFO 2026-06-08 07:59:30 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 2s. Last read position: chr2:237,542,602 INFO 2026-06-08 07:59:30 MarkDuplicates Tracking 230287 as yet unmatched pairs. 1674 records in RAM. INFO 2026-06-08 07:59:32 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 2s. Last read position: chr2:241,445,603 INFO 2026-06-08 07:59:32 MarkDuplicates Tracking 228844 as yet unmatched pairs. 229 records in RAM. INFO 2026-06-08 07:59:36 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 3s. Last read position: chr3:9,820,569 INFO 2026-06-08 07:59:36 MarkDuplicates Tracking 228183 as yet unmatched pairs. 12425 records in RAM. INFO 2026-06-08 07:59:39 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 3s. Last read position: chr3:15,030,382 INFO 2026-06-08 07:59:39 MarkDuplicates Tracking 227058 as yet unmatched pairs. 11299 records in RAM. INFO 2026-06-08 07:59:42 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 2s. Last read position: chr3:31,683,699 INFO 2026-06-08 07:59:42 MarkDuplicates Tracking 226473 as yet unmatched pairs. 10710 records in RAM. INFO 2026-06-08 07:59:45 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 3s. Last read position: chr3:40,461,432 INFO 2026-06-08 07:59:45 MarkDuplicates Tracking 226480 as yet unmatched pairs. 10716 records in RAM. INFO 2026-06-08 07:59:47 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 2s. Last read position: chr3:46,996,005 INFO 2026-06-08 07:59:47 MarkDuplicates Tracking 225366 as yet unmatched pairs. 9601 records in RAM. INFO 2026-06-08 07:59:50 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 2s. Last read position: chr3:48,600,120 INFO 2026-06-08 07:59:50 MarkDuplicates Tracking 224517 as yet unmatched pairs. 8751 records in RAM. INFO 2026-06-08 07:59:52 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 2s. Last read position: chr3:49,809,700 INFO 2026-06-08 07:59:52 MarkDuplicates Tracking 223666 as yet unmatched pairs. 7899 records in RAM. INFO 2026-06-08 07:59:55 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 2s. Last read position: chr3:52,476,484 INFO 2026-06-08 07:59:55 MarkDuplicates Tracking 222894 as yet unmatched pairs. 7126 records in RAM. INFO 2026-06-08 07:59:57 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 2s. Last read position: chr3:58,135,988 INFO 2026-06-08 07:59:57 MarkDuplicates Tracking 222243 as yet unmatched pairs. 6474 records in RAM. INFO 2026-06-08 08:00:00 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 3s. Last read position: chr3:71,584,157 INFO 2026-06-08 08:00:00 MarkDuplicates Tracking 221551 as yet unmatched pairs. 5778 records in RAM. INFO 2026-06-08 08:00:03 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 2s. Last read position: chr3:107,728,763 INFO 2026-06-08 08:00:03 MarkDuplicates Tracking 220932 as yet unmatched pairs. 5155 records in RAM. INFO 2026-06-08 08:00:06 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 3s. Last read position: chr3:121,692,391 INFO 2026-06-08 08:00:06 MarkDuplicates Tracking 220456 as yet unmatched pairs. 4673 records in RAM. INFO 2026-06-08 08:00:09 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 3s. Last read position: chr3:128,408,294 INFO 2026-06-08 08:00:09 MarkDuplicates Tracking 219591 as yet unmatched pairs. 3804 records in RAM. INFO 2026-06-08 08:00:13 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 3s. Last read position: chr3:136,315,502 INFO 2026-06-08 08:00:13 MarkDuplicates Tracking 218750 as yet unmatched pairs. 2958 records in RAM. INFO 2026-06-08 08:00:15 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 2s. Last read position: chr3:152,401,328 INFO 2026-06-08 08:00:15 MarkDuplicates Tracking 218198 as yet unmatched pairs. 2397 records in RAM. INFO 2026-06-08 08:00:17 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 2s. Last read position: chr3:179,220,986 INFO 2026-06-08 08:00:17 MarkDuplicates Tracking 217833 as yet unmatched pairs. 2025 records in RAM. INFO 2026-06-08 08:00:19 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 2s. Last read position: chr3:187,729,252 INFO 2026-06-08 08:00:19 MarkDuplicates Tracking 217226 as yet unmatched pairs. 1416 records in RAM. INFO 2026-06-08 08:00:21 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 2s. Last read position: chr3:195,975,751 INFO 2026-06-08 08:00:21 MarkDuplicates Tracking 216213 as yet unmatched pairs. 397 records in RAM. INFO 2026-06-08 08:00:24 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 2s. Last read position: chr4:1,212,228 INFO 2026-06-08 08:00:24 MarkDuplicates Tracking 215476 as yet unmatched pairs. 7075 records in RAM. INFO 2026-06-08 08:00:26 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 2s. Last read position: chr4:5,294,160 INFO 2026-06-08 08:00:26 MarkDuplicates Tracking 214618 as yet unmatched pairs. 6216 records in RAM. INFO 2026-06-08 08:00:28 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 2s. Last read position: chr4:17,803,679 INFO 2026-06-08 08:00:28 MarkDuplicates Tracking 214156 as yet unmatched pairs. 5752 records in RAM. INFO 2026-06-08 08:00:30 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 2s. Last read position: chr4:41,938,647 INFO 2026-06-08 08:00:30 MarkDuplicates Tracking 213117 as yet unmatched pairs. 4705 records in RAM. INFO 2026-06-08 08:00:33 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 2s. Last read position: chr4:73,090,928 INFO 2026-06-08 08:00:33 MarkDuplicates Tracking 212667 as yet unmatched pairs. 4246 records in RAM. INFO 2026-06-08 08:00:35 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 2s. Last read position: chr4:82,918,464 INFO 2026-06-08 08:00:35 MarkDuplicates Tracking 211803 as yet unmatched pairs. 3380 records in RAM. INFO 2026-06-08 08:00:37 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 2s. Last read position: chr4:95,148,790 INFO 2026-06-08 08:00:37 MarkDuplicates Tracking 211656 as yet unmatched pairs. 3230 records in RAM. INFO 2026-06-08 08:00:40 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 2s. Last read position: chr4:111,316,628 INFO 2026-06-08 08:00:40 MarkDuplicates Tracking 210710 as yet unmatched pairs. 2282 records in RAM. INFO 2026-06-08 08:00:43 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 2s. Last read position: chr4:139,480,685 INFO 2026-06-08 08:00:43 MarkDuplicates Tracking 210141 as yet unmatched pairs. 1707 records in RAM. INFO 2026-06-08 08:00:45 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 2s. Last read position: chr4:151,175,262 INFO 2026-06-08 08:00:45 MarkDuplicates Tracking 209855 as yet unmatched pairs. 1409 records in RAM. INFO 2026-06-08 08:00:47 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 2s. Last read position: chr4:182,898,691 INFO 2026-06-08 08:00:47 MarkDuplicates Tracking 208719 as yet unmatched pairs. 268 records in RAM. INFO 2026-06-08 08:00:50 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 2s. Last read position: chr5:10,290,650 INFO 2026-06-08 08:00:50 MarkDuplicates Tracking 208005 as yet unmatched pairs. 12679 records in RAM. INFO 2026-06-08 08:00:54 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 3s. Last read position: chr5:14,471,369 INFO 2026-06-08 08:00:54 MarkDuplicates Tracking 207249 as yet unmatched pairs. 11922 records in RAM. INFO 2026-06-08 08:00:57 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 3s. Last read position: chr5:33,576,466 INFO 2026-06-08 08:00:57 MarkDuplicates Tracking 206165 as yet unmatched pairs. 10836 records in RAM. INFO 2026-06-08 08:01:00 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 3s. Last read position: chr5:39,392,361 INFO 2026-06-08 08:01:00 MarkDuplicates Tracking 205670 as yet unmatched pairs. 10339 records in RAM. INFO 2026-06-08 08:01:03 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 2s. Last read position: chr5:57,249,444 INFO 2026-06-08 08:01:03 MarkDuplicates Tracking 205223 as yet unmatched pairs. 9888 records in RAM. INFO 2026-06-08 08:01:06 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 2s. Last read position: chr5:70,815,619 INFO 2026-06-08 08:01:06 MarkDuplicates Tracking 204531 as yet unmatched pairs. 9193 records in RAM. INFO 2026-06-08 08:01:09 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 2s. Last read position: chr5:79,737,749 INFO 2026-06-08 08:01:09 MarkDuplicates Tracking 203975 as yet unmatched pairs. 8625 records in RAM. INFO 2026-06-08 08:01:11 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 2s. Last read position: chr5:96,730,786 INFO 2026-06-08 08:01:11 MarkDuplicates Tracking 203494 as yet unmatched pairs. 8143 records in RAM. INFO 2026-06-08 08:01:14 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 2s. Last read position: chr5:122,423,034 INFO 2026-06-08 08:01:14 MarkDuplicates Tracking 202619 as yet unmatched pairs. 7266 records in RAM. INFO 2026-06-08 08:01:17 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 2s. Last read position: chr5:132,824,401 INFO 2026-06-08 08:01:17 MarkDuplicates Tracking 202834 as yet unmatched pairs. 7479 records in RAM. INFO 2026-06-08 08:01:19 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 2s. Last read position: chr5:138,465,968 INFO 2026-06-08 08:01:19 MarkDuplicates Tracking 200973 as yet unmatched pairs. 5611 records in RAM. INFO 2026-06-08 08:01:22 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 2s. Last read position: chr5:140,674,682 INFO 2026-06-08 08:01:22 MarkDuplicates Tracking 200052 as yet unmatched pairs. 4625 records in RAM. INFO 2026-06-08 08:01:24 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 2s. Last read position: chr5:141,928,180 INFO 2026-06-08 08:01:24 MarkDuplicates Tracking 199325 as yet unmatched pairs. 3897 records in RAM. INFO 2026-06-08 08:01:27 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 2s. Last read position: chr5:150,402,133 INFO 2026-06-08 08:01:27 MarkDuplicates Tracking 201416 as yet unmatched pairs. 5984 records in RAM. INFO 2026-06-08 08:01:30 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 3s. Last read position: chr5:151,525,899 INFO 2026-06-08 08:01:30 MarkDuplicates Tracking 197803 as yet unmatched pairs. 2371 records in RAM. INFO 2026-06-08 08:01:33 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 2s. Last read position: chr5:171,391,307 INFO 2026-06-08 08:01:33 MarkDuplicates Tracking 198231 as yet unmatched pairs. 2778 records in RAM. INFO 2026-06-08 08:01:35 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 2s. Last read position: chr5:177,269,794 INFO 2026-06-08 08:01:35 MarkDuplicates Tracking 196645 as yet unmatched pairs. 1181 records in RAM. INFO 2026-06-08 08:01:38 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 2s. Last read position: chr5:179,824,186 INFO 2026-06-08 08:01:38 MarkDuplicates Tracking 195987 as yet unmatched pairs. 521 records in RAM. INFO 2026-06-08 08:01:40 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:05:20s. Time for last 1,000,000: 2s. Last read position: chr6:7,181,934 INFO 2026-06-08 08:01:40 MarkDuplicates Tracking 195623 as yet unmatched pairs. 11903 records in RAM. INFO 2026-06-08 08:01:42 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 2s. Last read position: chr6:14,890,973 INFO 2026-06-08 08:01:42 MarkDuplicates Tracking 194295 as yet unmatched pairs. 10574 records in RAM. INFO 2026-06-08 08:01:44 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 2s. Last read position: chr6:26,413,565 INFO 2026-06-08 08:01:44 MarkDuplicates Tracking 193831 as yet unmatched pairs. 10105 records in RAM. INFO 2026-06-08 08:01:46 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 1s. Last read position: chr6:30,895,470 INFO 2026-06-08 08:01:46 MarkDuplicates Tracking 193167 as yet unmatched pairs. 9440 records in RAM. INFO 2026-06-08 08:01:49 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 2s. Last read position: chr6:31,882,716 INFO 2026-06-08 08:01:49 MarkDuplicates Tracking 192429 as yet unmatched pairs. 8699 records in RAM. INFO 2026-06-08 08:01:51 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 2s. Last read position: chr6:32,056,650 INFO 2026-06-08 08:01:51 MarkDuplicates Tracking 191946 as yet unmatched pairs. 8215 records in RAM. INFO 2026-06-08 08:01:53 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 2s. Last read position: chr6:33,293,134 INFO 2026-06-08 08:01:53 MarkDuplicates Tracking 191892 as yet unmatched pairs. 8161 records in RAM. INFO 2026-06-08 08:01:55 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 2s. Last read position: chr6:35,470,653 INFO 2026-06-08 08:01:55 MarkDuplicates Tracking 190262 as yet unmatched pairs. 6529 records in RAM. INFO 2026-06-08 08:01:58 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 3s. Last read position: chr6:42,262,470 INFO 2026-06-08 08:01:58 MarkDuplicates Tracking 189567 as yet unmatched pairs. 5831 records in RAM. INFO 2026-06-08 08:02:00 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 1s. Last read position: chr6:47,478,146 INFO 2026-06-08 08:02:00 MarkDuplicates Tracking 188780 as yet unmatched pairs. 5042 records in RAM. INFO 2026-06-08 08:02:02 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:05:43s. Time for last 1,000,000: 2s. Last read position: chr6:63,685,334 INFO 2026-06-08 08:02:02 MarkDuplicates Tracking 188389 as yet unmatched pairs. 4649 records in RAM. INFO 2026-06-08 08:02:04 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 2s. Last read position: chr6:89,081,002 INFO 2026-06-08 08:02:04 MarkDuplicates Tracking 187806 as yet unmatched pairs. 4058 records in RAM. INFO 2026-06-08 08:02:06 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 1s. Last read position: chr6:109,691,344 INFO 2026-06-08 08:02:06 MarkDuplicates Tracking 186940 as yet unmatched pairs. 3188 records in RAM. INFO 2026-06-08 08:02:09 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 2s. Last read position: chr6:131,598,657 INFO 2026-06-08 08:02:09 MarkDuplicates Tracking 186292 as yet unmatched pairs. 2535 records in RAM. INFO 2026-06-08 08:02:11 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 2s. Last read position: chr6:143,941,881 INFO 2026-06-08 08:02:11 MarkDuplicates Tracking 185613 as yet unmatched pairs. 1856 records in RAM. INFO 2026-06-08 08:02:14 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 2s. Last read position: chr6:152,318,869 INFO 2026-06-08 08:02:14 MarkDuplicates Tracking 184843 as yet unmatched pairs. 1085 records in RAM. INFO 2026-06-08 08:02:17 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 2s. Last read position: chr6:163,478,801 INFO 2026-06-08 08:02:17 MarkDuplicates Tracking 184282 as yet unmatched pairs. 521 records in RAM. INFO 2026-06-08 08:02:20 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 2s. Last read position: chr7:2,433,616 INFO 2026-06-08 08:02:20 MarkDuplicates Tracking 183351 as yet unmatched pairs. 12465 records in RAM. INFO 2026-06-08 08:02:22 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 2s. Last read position: chr7:5,527,773 INFO 2026-06-08 08:02:22 MarkDuplicates Tracking 183439 as yet unmatched pairs. 12552 records in RAM. INFO 2026-06-08 08:02:26 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 3s. Last read position: chr7:19,708,849 INFO 2026-06-08 08:02:26 MarkDuplicates Tracking 181436 as yet unmatched pairs. 10546 records in RAM. INFO 2026-06-08 08:02:28 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:06:09s. Time for last 1,000,000: 2s. Last read position: chr7:37,021,912 INFO 2026-06-08 08:02:28 MarkDuplicates Tracking 180710 as yet unmatched pairs. 9817 records in RAM. INFO 2026-06-08 08:02:31 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 2s. Last read position: chr7:44,573,702 INFO 2026-06-08 08:02:31 MarkDuplicates Tracking 179980 as yet unmatched pairs. 9077 records in RAM. INFO 2026-06-08 08:02:33 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 2s. Last read position: chr7:65,979,776 INFO 2026-06-08 08:02:33 MarkDuplicates Tracking 179286 as yet unmatched pairs. 8377 records in RAM. INFO 2026-06-08 08:02:35 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 2s. Last read position: chr7:73,245,822 INFO 2026-06-08 08:02:35 MarkDuplicates Tracking 178787 as yet unmatched pairs. 7871 records in RAM. INFO 2026-06-08 08:02:37 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 2s. Last read position: chr7:75,422,630 INFO 2026-06-08 08:02:37 MarkDuplicates Tracking 178395 as yet unmatched pairs. 7478 records in RAM. INFO 2026-06-08 08:02:39 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 2s. Last read position: chr7:86,947,842 INFO 2026-06-08 08:02:39 MarkDuplicates Tracking 177708 as yet unmatched pairs. 6788 records in RAM. INFO 2026-06-08 08:02:42 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 2s. Last read position: chr7:92,102,624 INFO 2026-06-08 08:02:42 MarkDuplicates Tracking 177502 as yet unmatched pairs. 6582 records in RAM. INFO 2026-06-08 08:02:45 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 2s. Last read position: chr7:98,970,189 INFO 2026-06-08 08:02:45 MarkDuplicates Tracking 176475 as yet unmatched pairs. 5553 records in RAM. INFO 2026-06-08 08:02:48 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 3s. Last read position: chr7:100,578,154 INFO 2026-06-08 08:02:48 MarkDuplicates Tracking 175678 as yet unmatched pairs. 4756 records in RAM. INFO 2026-06-08 08:02:51 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:06:31s. Time for last 1,000,000: 2s. Last read position: chr7:102,555,304 INFO 2026-06-08 08:02:51 MarkDuplicates Tracking 175235 as yet unmatched pairs. 4313 records in RAM. INFO 2026-06-08 08:02:53 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 2s. Last read position: chr7:107,196,015 INFO 2026-06-08 08:02:53 MarkDuplicates Tracking 174467 as yet unmatched pairs. 3545 records in RAM. INFO 2026-06-08 08:02:56 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 2s. Last read position: chr7:128,544,835 INFO 2026-06-08 08:02:56 MarkDuplicates Tracking 173932 as yet unmatched pairs. 2989 records in RAM. INFO 2026-06-08 08:02:58 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 2s. Last read position: chr7:138,579,331 INFO 2026-06-08 08:02:58 MarkDuplicates Tracking 173445 as yet unmatched pairs. 2501 records in RAM. INFO 2026-06-08 08:03:00 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 2s. Last read position: chr7:143,600,692 INFO 2026-06-08 08:03:00 MarkDuplicates Tracking 172559 as yet unmatched pairs. 1614 records in RAM. INFO 2026-06-08 08:03:03 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 2s. Last read position: chr7:150,339,025 INFO 2026-06-08 08:03:03 MarkDuplicates Tracking 172065 as yet unmatched pairs. 1120 records in RAM. INFO 2026-06-08 08:03:05 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 2s. Last read position: chr7:155,711,203 INFO 2026-06-08 08:03:05 MarkDuplicates Tracking 171603 as yet unmatched pairs. 656 records in RAM. INFO 2026-06-08 08:03:07 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:06:47s. Time for last 1,000,000: 2s. Last read position: chr8:16,150,302 INFO 2026-06-08 08:03:07 MarkDuplicates Tracking 170497 as yet unmatched pairs. 8336 records in RAM. INFO 2026-06-08 08:03:10 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 2s. Last read position: chr8:27,432,300 INFO 2026-06-08 08:03:10 MarkDuplicates Tracking 169919 as yet unmatched pairs. 7756 records in RAM. INFO 2026-06-08 08:03:12 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 2s. Last read position: chr8:37,835,616 INFO 2026-06-08 08:03:12 MarkDuplicates Tracking 169277 as yet unmatched pairs. 7112 records in RAM. INFO 2026-06-08 08:03:14 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 2s. Last read position: chr8:42,403,371 INFO 2026-06-08 08:03:14 MarkDuplicates Tracking 168756 as yet unmatched pairs. 6591 records in RAM. INFO 2026-06-08 08:03:18 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 3s. Last read position: chr8:67,202,982 INFO 2026-06-08 08:03:18 MarkDuplicates Tracking 168106 as yet unmatched pairs. 5933 records in RAM. INFO 2026-06-08 08:03:20 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:07:00s. Time for last 1,000,000: 2s. Last read position: chr8:93,733,996 INFO 2026-06-08 08:03:20 MarkDuplicates Tracking 167683 as yet unmatched pairs. 5497 records in RAM. INFO 2026-06-08 08:03:22 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 2s. Last read position: chr8:102,411,214 INFO 2026-06-08 08:03:22 MarkDuplicates Tracking 166877 as yet unmatched pairs. 4676 records in RAM. INFO 2026-06-08 08:03:24 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 2s. Last read position: chr8:120,003,102 INFO 2026-06-08 08:03:24 MarkDuplicates Tracking 166285 as yet unmatched pairs. 4084 records in RAM. INFO 2026-06-08 08:03:27 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 2s. Last read position: chr8:139,491,807 INFO 2026-06-08 08:03:27 MarkDuplicates Tracking 165667 as yet unmatched pairs. 3463 records in RAM. INFO 2026-06-08 08:03:30 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 2s. Last read position: chr8:143,840,129 INFO 2026-06-08 08:03:30 MarkDuplicates Tracking 164829 as yet unmatched pairs. 2614 records in RAM. INFO 2026-06-08 08:03:32 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:07:12s. Time for last 1,000,000: 1s. Last read position: chr8:143,862,319 INFO 2026-06-08 08:03:32 MarkDuplicates Tracking 164783 as yet unmatched pairs. 2567 records in RAM. INFO 2026-06-08 08:03:34 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:07:15s. Time for last 1,000,000: 2s. Last read position: chr8:143,868,187 INFO 2026-06-08 08:03:34 MarkDuplicates Tracking 164317 as yet unmatched pairs. 2101 records in RAM. INFO 2026-06-08 08:03:38 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:07:18s. Time for last 1,000,000: 3s. Last read position: chr8:144,105,950 INFO 2026-06-08 08:03:38 MarkDuplicates Tracking 163161 as yet unmatched pairs. 945 records in RAM. INFO 2026-06-08 08:03:41 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:07:21s. Time for last 1,000,000: 3s. Last read position: chr9:2,047,359 INFO 2026-06-08 08:03:41 MarkDuplicates Tracking 162317 as yet unmatched pairs. 10077 records in RAM. INFO 2026-06-08 08:03:44 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:07:24s. Time for last 1,000,000: 2s. Last read position: chr9:16,451,257 INFO 2026-06-08 08:03:44 MarkDuplicates Tracking 161522 as yet unmatched pairs. 9278 records in RAM. INFO 2026-06-08 08:03:46 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:07:26s. Time for last 1,000,000: 1s. Last read position: chr9:35,376,180 INFO 2026-06-08 08:03:46 MarkDuplicates Tracking 160815 as yet unmatched pairs. 8571 records in RAM. INFO 2026-06-08 08:03:48 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:07:28s. Time for last 1,000,000: 2s. Last read position: chr9:65,143,886 INFO 2026-06-08 08:03:48 MarkDuplicates Tracking 160183 as yet unmatched pairs. 7915 records in RAM. INFO 2026-06-08 08:03:51 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:07:31s. Time for last 1,000,000: 2s. Last read position: chr9:86,328,355 INFO 2026-06-08 08:03:51 MarkDuplicates Tracking 159732 as yet unmatched pairs. 7462 records in RAM. INFO 2026-06-08 08:03:54 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:07:34s. Time for last 1,000,000: 2s. Last read position: chr9:94,760,128 INFO 2026-06-08 08:03:54 MarkDuplicates Tracking 158933 as yet unmatched pairs. 6661 records in RAM. INFO 2026-06-08 08:03:56 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:07:37s. Time for last 1,000,000: 2s. Last read position: chr9:110,579,181 INFO 2026-06-08 08:03:56 MarkDuplicates Tracking 158219 as yet unmatched pairs. 5946 records in RAM. INFO 2026-06-08 08:03:59 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:07:39s. Time for last 1,000,000: 2s. Last read position: chr9:114,643,132 INFO 2026-06-08 08:03:59 MarkDuplicates Tracking 157410 as yet unmatched pairs. 5137 records in RAM. INFO 2026-06-08 08:04:02 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:07:42s. Time for last 1,000,000: 2s. Last read position: chr9:124,459,391 INFO 2026-06-08 08:04:02 MarkDuplicates Tracking 156607 as yet unmatched pairs. 4332 records in RAM. INFO 2026-06-08 08:04:04 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:07:45s. Time for last 1,000,000: 2s. Last read position: chr9:128,387,822 INFO 2026-06-08 08:04:04 MarkDuplicates Tracking 155949 as yet unmatched pairs. 3673 records in RAM. INFO 2026-06-08 08:04:07 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:07:47s. Time for last 1,000,000: 2s. Last read position: chr9:131,189,117 INFO 2026-06-08 08:04:07 MarkDuplicates Tracking 155317 as yet unmatched pairs. 3040 records in RAM. INFO 2026-06-08 08:04:09 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:07:49s. Time for last 1,000,000: 2s. Last read position: chr9:134,053,266 INFO 2026-06-08 08:04:09 MarkDuplicates Tracking 155103 as yet unmatched pairs. 2825 records in RAM. INFO 2026-06-08 08:04:12 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:07:52s. Time for last 1,000,000: 3s. Last read position: chr9:136,740,841 INFO 2026-06-08 08:04:12 MarkDuplicates Tracking 153629 as yet unmatched pairs. 1350 records in RAM. INFO 2026-06-08 08:04:14 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:07:54s. Time for last 1,000,000: 2s. Last read position: chr9:137,462,032 INFO 2026-06-08 08:04:14 MarkDuplicates Tracking 152685 as yet unmatched pairs. 394 records in RAM. INFO 2026-06-08 08:04:17 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:07:57s. Time for last 1,000,000: 3s. Last read position: chr10:7,573,177 INFO 2026-06-08 08:04:17 MarkDuplicates Tracking 151759 as yet unmatched pairs. 9107 records in RAM. INFO 2026-06-08 08:04:20 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:08:00s. Time for last 1,000,000: 2s. Last read position: chr10:18,542,928 INFO 2026-06-08 08:04:20 MarkDuplicates Tracking 151096 as yet unmatched pairs. 8443 records in RAM. INFO 2026-06-08 08:04:22 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:08:02s. Time for last 1,000,000: 2s. Last read position: chr10:29,550,678 INFO 2026-06-08 08:04:22 MarkDuplicates Tracking 150678 as yet unmatched pairs. 8017 records in RAM. INFO 2026-06-08 08:04:24 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 2s. Last read position: chr10:37,141,936 INFO 2026-06-08 08:04:24 MarkDuplicates Tracking 150866 as yet unmatched pairs. 8204 records in RAM. INFO 2026-06-08 08:04:27 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:08:08s. Time for last 1,000,000: 3s. Last read position: chr10:37,181,500 INFO 2026-06-08 08:04:27 MarkDuplicates Tracking 151157 as yet unmatched pairs. 8494 records in RAM. INFO 2026-06-08 08:04:31 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:08:11s. Time for last 1,000,000: 3s. Last read position: chr10:37,837,672 INFO 2026-06-08 08:04:31 MarkDuplicates Tracking 149331 as yet unmatched pairs. 6661 records in RAM. INFO 2026-06-08 08:04:34 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:08:14s. Time for last 1,000,000: 3s. Last read position: chr10:47,525,618 INFO 2026-06-08 08:04:34 MarkDuplicates Tracking 148587 as yet unmatched pairs. 5912 records in RAM. INFO 2026-06-08 08:04:36 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 2s. Last read position: chr10:63,207,292 INFO 2026-06-08 08:04:36 MarkDuplicates Tracking 148025 as yet unmatched pairs. 5348 records in RAM. INFO 2026-06-08 08:04:38 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 2s. Last read position: chr10:73,495,809 INFO 2026-06-08 08:04:38 MarkDuplicates Tracking 147176 as yet unmatched pairs. 4496 records in RAM. INFO 2026-06-08 08:04:41 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 2s. Last read position: chr10:79,292,201 INFO 2026-06-08 08:04:41 MarkDuplicates Tracking 146598 as yet unmatched pairs. 3917 records in RAM. INFO 2026-06-08 08:04:43 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 2s. Last read position: chr10:89,403,035 INFO 2026-06-08 08:04:43 MarkDuplicates Tracking 145882 as yet unmatched pairs. 3200 records in RAM. INFO 2026-06-08 08:04:45 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 2s. Last read position: chr10:98,425,974 INFO 2026-06-08 08:04:45 MarkDuplicates Tracking 145317 as yet unmatched pairs. 2632 records in RAM. INFO 2026-06-08 08:04:48 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:08:28s. Time for last 1,000,000: 2s. Last read position: chr10:103,421,369 INFO 2026-06-08 08:04:48 MarkDuplicates Tracking 144378 as yet unmatched pairs. 1692 records in RAM. INFO 2026-06-08 08:04:50 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:08:30s. Time for last 1,000,000: 2s. Last read position: chr10:117,284,433 INFO 2026-06-08 08:04:50 MarkDuplicates Tracking 143777 as yet unmatched pairs. 1071 records in RAM. INFO 2026-06-08 08:04:52 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 1s. Last read position: chr10:126,101,203 INFO 2026-06-08 08:04:52 MarkDuplicates Tracking 143114 as yet unmatched pairs. 402 records in RAM. INFO 2026-06-08 08:04:54 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 2s. Last read position: chr11:534,224 INFO 2026-06-08 08:04:54 MarkDuplicates Tracking 142428 as yet unmatched pairs. 15450 records in RAM. INFO 2026-06-08 08:04:57 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 2s. Last read position: chr11:1,249,203 INFO 2026-06-08 08:04:57 MarkDuplicates Tracking 141476 as yet unmatched pairs. 14496 records in RAM. INFO 2026-06-08 08:04:59 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:08:39s. Time for last 1,000,000: 2s. Last read position: chr11:6,546,230 INFO 2026-06-08 08:04:59 MarkDuplicates Tracking 140717 as yet unmatched pairs. 13737 records in RAM. INFO 2026-06-08 08:05:02 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:08:42s. Time for last 1,000,000: 2s. Last read position: chr11:13,010,031 INFO 2026-06-08 08:05:02 MarkDuplicates Tracking 139955 as yet unmatched pairs. 12975 records in RAM. INFO 2026-06-08 08:05:04 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:08:44s. Time for last 1,000,000: 2s. Last read position: chr11:34,197,324 INFO 2026-06-08 08:05:04 MarkDuplicates Tracking 139231 as yet unmatched pairs. 12249 records in RAM. INFO 2026-06-08 08:05:06 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:08:46s. Time for last 1,000,000: 2s. Last read position: chr11:46,751,178 INFO 2026-06-08 08:05:06 MarkDuplicates Tracking 138646 as yet unmatched pairs. 11661 records in RAM. INFO 2026-06-08 08:05:08 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 2s. Last read position: chr11:57,811,472 INFO 2026-06-08 08:05:08 MarkDuplicates Tracking 138374 as yet unmatched pairs. 11388 records in RAM. INFO 2026-06-08 08:05:11 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 2s. Last read position: chr11:62,271,156 INFO 2026-06-08 08:05:11 MarkDuplicates Tracking 138280 as yet unmatched pairs. 11270 records in RAM. INFO 2026-06-08 08:05:13 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:08:53s. Time for last 1,000,000: 2s. Last read position: chr11:62,535,945 INFO 2026-06-08 08:05:13 MarkDuplicates Tracking 136688 as yet unmatched pairs. 9677 records in RAM. INFO 2026-06-08 08:05:15 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:08:55s. Time for last 1,000,000: 2s. Last read position: chr11:64,343,178 INFO 2026-06-08 08:05:15 MarkDuplicates Tracking 135789 as yet unmatched pairs. 8776 records in RAM. INFO 2026-06-08 08:05:18 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:08:58s. Time for last 1,000,000: 2s. Last read position: chr11:65,500,779 INFO 2026-06-08 08:05:18 MarkDuplicates Tracking 134976 as yet unmatched pairs. 7962 records in RAM. INFO 2026-06-08 08:05:21 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:09:02s. Time for last 1,000,000: 3s. Last read position: chr11:65,641,412 INFO 2026-06-08 08:05:21 MarkDuplicates Tracking 134161 as yet unmatched pairs. 7146 records in RAM. INFO 2026-06-08 08:05:25 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 3s. Last read position: chr11:66,858,226 INFO 2026-06-08 08:05:25 MarkDuplicates Tracking 133181 as yet unmatched pairs. 6165 records in RAM. INFO 2026-06-08 08:05:28 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 2s. Last read position: chr11:68,762,625 INFO 2026-06-08 08:05:28 MarkDuplicates Tracking 132159 as yet unmatched pairs. 5143 records in RAM. INFO 2026-06-08 08:05:30 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:09:10s. Time for last 1,000,000: 2s. Last read position: chr11:72,095,378 INFO 2026-06-08 08:05:30 MarkDuplicates Tracking 131559 as yet unmatched pairs. 4543 records in RAM. INFO 2026-06-08 08:05:32 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:09:12s. Time for last 1,000,000: 2s. Last read position: chr11:76,089,418 INFO 2026-06-08 08:05:32 MarkDuplicates Tracking 130727 as yet unmatched pairs. 3710 records in RAM. INFO 2026-06-08 08:05:34 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:09:15s. Time for last 1,000,000: 2s. Last read position: chr11:95,128,480 INFO 2026-06-08 08:05:34 MarkDuplicates Tracking 130084 as yet unmatched pairs. 3063 records in RAM. INFO 2026-06-08 08:05:36 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:09:17s. Time for last 1,000,000: 2s. Last read position: chr11:111,883,148 INFO 2026-06-08 08:05:36 MarkDuplicates Tracking 129576 as yet unmatched pairs. 2554 records in RAM. INFO 2026-06-08 08:05:39 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:09:19s. Time for last 1,000,000: 2s. Last read position: chr11:117,820,674 INFO 2026-06-08 08:05:39 MarkDuplicates Tracking 128829 as yet unmatched pairs. 1800 records in RAM. INFO 2026-06-08 08:05:41 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:09:21s. Time for last 1,000,000: 2s. Last read position: chr11:119,114,088 INFO 2026-06-08 08:05:41 MarkDuplicates Tracking 128105 as yet unmatched pairs. 1076 records in RAM. INFO 2026-06-08 08:05:43 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:09:24s. Time for last 1,000,000: 2s. Last read position: chr11:129,376,198 INFO 2026-06-08 08:05:43 MarkDuplicates Tracking 127470 as yet unmatched pairs. 435 records in RAM. INFO 2026-06-08 08:05:46 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:09:26s. Time for last 1,000,000: 2s. Last read position: chr12:5,949,762 INFO 2026-06-08 08:05:46 MarkDuplicates Tracking 126618 as yet unmatched pairs. 12194 records in RAM. INFO 2026-06-08 08:05:48 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:09:29s. Time for last 1,000,000: 2s. Last read position: chr12:7,487,503 INFO 2026-06-08 08:05:48 MarkDuplicates Tracking 125918 as yet unmatched pairs. 11494 records in RAM. INFO 2026-06-08 08:05:51 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:09:31s. Time for last 1,000,000: 2s. Last read position: chr12:14,582,326 INFO 2026-06-08 08:05:51 MarkDuplicates Tracking 125287 as yet unmatched pairs. 10861 records in RAM. INFO 2026-06-08 08:05:54 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:09:34s. Time for last 1,000,000: 2s. Last read position: chr12:39,356,859 INFO 2026-06-08 08:05:54 MarkDuplicates Tracking 124740 as yet unmatched pairs. 10308 records in RAM. INFO 2026-06-08 08:05:57 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 2s. Last read position: chr12:49,029,218 INFO 2026-06-08 08:05:57 MarkDuplicates Tracking 124245 as yet unmatched pairs. 9812 records in RAM. INFO 2026-06-08 08:05:59 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:09:40s. Time for last 1,000,000: 2s. Last read position: chr12:50,780,180 INFO 2026-06-08 08:05:59 MarkDuplicates Tracking 123774 as yet unmatched pairs. 9341 records in RAM. INFO 2026-06-08 08:06:02 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:09:42s. Time for last 1,000,000: 2s. Last read position: chr12:53,059,441 INFO 2026-06-08 08:06:02 MarkDuplicates Tracking 123300 as yet unmatched pairs. 8866 records in RAM. INFO 2026-06-08 08:06:05 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:09:46s. Time for last 1,000,000: 3s. Last read position: chr12:54,342,217 INFO 2026-06-08 08:06:05 MarkDuplicates Tracking 122163 as yet unmatched pairs. 7728 records in RAM. INFO 2026-06-08 08:06:08 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:09:48s. Time for last 1,000,000: 2s. Last read position: chr12:56,417,740 INFO 2026-06-08 08:06:08 MarkDuplicates Tracking 121359 as yet unmatched pairs. 6914 records in RAM. INFO 2026-06-08 08:06:10 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:09:50s. Time for last 1,000,000: 2s. Last read position: chr12:57,205,142 INFO 2026-06-08 08:06:10 MarkDuplicates Tracking 120805 as yet unmatched pairs. 6360 records in RAM. INFO 2026-06-08 08:06:12 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:09:52s. Time for last 1,000,000: 1s. Last read position: chr12:65,333,308 INFO 2026-06-08 08:06:12 MarkDuplicates Tracking 119961 as yet unmatched pairs. 5514 records in RAM. INFO 2026-06-08 08:06:15 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:09:55s. Time for last 1,000,000: 2s. Last read position: chr12:82,391,167 INFO 2026-06-08 08:06:15 MarkDuplicates Tracking 119328 as yet unmatched pairs. 4876 records in RAM. INFO 2026-06-08 08:06:18 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:09:58s. Time for last 1,000,000: 3s. Last read position: chr12:101,338,916 INFO 2026-06-08 08:06:18 MarkDuplicates Tracking 118646 as yet unmatched pairs. 4191 records in RAM. INFO 2026-06-08 08:06:20 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:10:00s. Time for last 1,000,000: 2s. Last read position: chr12:110,190,971 INFO 2026-06-08 08:06:20 MarkDuplicates Tracking 118021 as yet unmatched pairs. 3563 records in RAM. INFO 2026-06-08 08:06:23 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:10:03s. Time for last 1,000,000: 2s. Last read position: chr12:114,674,387 INFO 2026-06-08 08:06:23 MarkDuplicates Tracking 117471 as yet unmatched pairs. 3013 records in RAM. INFO 2026-06-08 08:06:26 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 3s. Last read position: chr12:121,810,117 INFO 2026-06-08 08:06:26 MarkDuplicates Tracking 116702 as yet unmatched pairs. 2243 records in RAM. INFO 2026-06-08 08:06:29 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 2s. Last read position: chr12:124,344,798 INFO 2026-06-08 08:06:29 MarkDuplicates Tracking 115836 as yet unmatched pairs. 1377 records in RAM. INFO 2026-06-08 08:06:31 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 2s. Last read position: chr12:132,583,472 INFO 2026-06-08 08:06:31 MarkDuplicates Tracking 114816 as yet unmatched pairs. 353 records in RAM. INFO 2026-06-08 08:06:34 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:10:14s. Time for last 1,000,000: 2s. Last read position: chr13:27,665,752 INFO 2026-06-08 08:06:34 MarkDuplicates Tracking 113960 as yet unmatched pairs. 2593 records in RAM. INFO 2026-06-08 08:06:37 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:10:17s. Time for last 1,000,000: 3s. Last read position: chr13:41,949,960 INFO 2026-06-08 08:06:37 MarkDuplicates Tracking 113239 as yet unmatched pairs. 1866 records in RAM. INFO 2026-06-08 08:06:40 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:10:20s. Time for last 1,000,000: 2s. Last read position: chr13:77,018,626 INFO 2026-06-08 08:06:40 MarkDuplicates Tracking 112542 as yet unmatched pairs. 1167 records in RAM. INFO 2026-06-08 08:06:42 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:10:23s. Time for last 1,000,000: 2s. Last read position: chr13:110,205,353 INFO 2026-06-08 08:06:42 MarkDuplicates Tracking 111930 as yet unmatched pairs. 552 records in RAM. INFO 2026-06-08 08:06:45 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:10:25s. Time for last 1,000,000: 2s. Last read position: chr14:21,260,260 INFO 2026-06-08 08:06:45 MarkDuplicates Tracking 111134 as yet unmatched pairs. 7808 records in RAM. INFO 2026-06-08 08:06:48 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:10:28s. Time for last 1,000,000: 2s. Last read position: chr14:24,162,267 INFO 2026-06-08 08:06:48 MarkDuplicates Tracking 110454 as yet unmatched pairs. 7128 records in RAM. INFO 2026-06-08 08:06:50 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:10:31s. Time for last 1,000,000: 2s. Last read position: chr14:35,081,106 INFO 2026-06-08 08:06:50 MarkDuplicates Tracking 109812 as yet unmatched pairs. 6482 records in RAM. INFO 2026-06-08 08:06:53 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:10:34s. Time for last 1,000,000: 2s. Last read position: chr14:49,586,734 INFO 2026-06-08 08:06:53 MarkDuplicates Tracking 109312 as yet unmatched pairs. 5976 records in RAM. INFO 2026-06-08 08:06:55 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:10:36s. Time for last 1,000,000: 2s. Last read position: chr14:53,397,856 INFO 2026-06-08 08:06:55 MarkDuplicates Tracking 108826 as yet unmatched pairs. 5485 records in RAM. INFO 2026-06-08 08:06:58 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:10:39s. Time for last 1,000,000: 2s. Last read position: chr14:64,202,954 INFO 2026-06-08 08:06:58 MarkDuplicates Tracking 108282 as yet unmatched pairs. 4940 records in RAM. INFO 2026-06-08 08:07:02 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:10:42s. Time for last 1,000,000: 3s. Last read position: chr14:70,978,431 INFO 2026-06-08 08:07:02 MarkDuplicates Tracking 107584 as yet unmatched pairs. 4241 records in RAM. INFO 2026-06-08 08:07:04 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:10:44s. Time for last 1,000,000: 2s. Last read position: chr14:75,048,874 INFO 2026-06-08 08:07:04 MarkDuplicates Tracking 106897 as yet unmatched pairs. 3554 records in RAM. INFO 2026-06-08 08:07:08 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:10:48s. Time for last 1,000,000: 3s. Last read position: chr14:91,273,017 INFO 2026-06-08 08:07:08 MarkDuplicates Tracking 106275 as yet unmatched pairs. 2926 records in RAM. INFO 2026-06-08 08:07:12 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:10:52s. Time for last 1,000,000: 3s. Last read position: chr14:100,016,895 INFO 2026-06-08 08:07:12 MarkDuplicates Tracking 105488 as yet unmatched pairs. 2119 records in RAM. INFO 2026-06-08 08:07:14 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:10:54s. Time for last 1,000,000: 2s. Last read position: chr14:103,475,035 INFO 2026-06-08 08:07:14 MarkDuplicates Tracking 104654 as yet unmatched pairs. 1284 records in RAM. INFO 2026-06-08 08:07:17 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:10:57s. Time for last 1,000,000: 2s. Last read position: chr14:105,587,641 INFO 2026-06-08 08:07:17 MarkDuplicates Tracking 103850 as yet unmatched pairs. 476 records in RAM. INFO 2026-06-08 08:07:21 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:11:01s. Time for last 1,000,000: 3s. Last read position: chr15:28,206,263 INFO 2026-06-08 08:07:21 MarkDuplicates Tracking 103128 as yet unmatched pairs. 6860 records in RAM. INFO 2026-06-08 08:07:23 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:11:03s. Time for last 1,000,000: 2s. Last read position: chr15:38,266,515 INFO 2026-06-08 08:07:23 MarkDuplicates Tracking 102694 as yet unmatched pairs. 6426 records in RAM. INFO 2026-06-08 08:07:25 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:11:06s. Time for last 1,000,000: 2s. Last read position: chr15:42,360,475 INFO 2026-06-08 08:07:25 MarkDuplicates Tracking 101963 as yet unmatched pairs. 5692 records in RAM. INFO 2026-06-08 08:07:28 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:11:08s. Time for last 1,000,000: 2s. Last read position: chr15:48,165,896 INFO 2026-06-08 08:07:28 MarkDuplicates Tracking 101351 as yet unmatched pairs. 5078 records in RAM. INFO 2026-06-08 08:07:31 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:11:11s. Time for last 1,000,000: 2s. Last read position: chr15:58,518,186 INFO 2026-06-08 08:07:31 MarkDuplicates Tracking 100624 as yet unmatched pairs. 4350 records in RAM. INFO 2026-06-08 08:07:34 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:11:14s. Time for last 1,000,000: 3s. Last read position: chr15:64,491,713 INFO 2026-06-08 08:07:34 MarkDuplicates Tracking 99959 as yet unmatched pairs. 3684 records in RAM. INFO 2026-06-08 08:07:37 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:11:17s. Time for last 1,000,000: 2s. Last read position: chr15:71,129,040 INFO 2026-06-08 08:07:37 MarkDuplicates Tracking 99542 as yet unmatched pairs. 3265 records in RAM. INFO 2026-06-08 08:08:51 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:12:31s. Time for last 1,000,000: 73s. Last read position: chr15:74,840,481 INFO 2026-06-08 08:08:51 MarkDuplicates Tracking 98451 as yet unmatched pairs. 2173 records in RAM. INFO 2026-06-08 08:08:53 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:12:33s. Time for last 1,000,000: 2s. Last read position: chr15:81,436,534 INFO 2026-06-08 08:08:53 MarkDuplicates Tracking 97714 as yet unmatched pairs. 1434 records in RAM. INFO 2026-06-08 08:08:55 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:12:36s. Time for last 1,000,000: 2s. Last read position: chr15:89,665,628 INFO 2026-06-08 08:08:55 MarkDuplicates Tracking 97089 as yet unmatched pairs. 804 records in RAM. INFO 2026-06-08 08:08:57 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:12:38s. Time for last 1,000,000: 2s. Last read position: chr15:101,010,688 INFO 2026-06-08 08:08:57 MarkDuplicates Tracking 96386 as yet unmatched pairs. 96 records in RAM. INFO 2026-06-08 08:09:00 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:12:40s. Time for last 1,000,000: 2s. Last read position: chr16:869,047 INFO 2026-06-08 08:09:00 MarkDuplicates Tracking 95476 as yet unmatched pairs. 12969 records in RAM. INFO 2026-06-08 08:09:02 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:12:42s. Time for last 1,000,000: 2s. Last read position: chr16:2,100,531 INFO 2026-06-08 08:09:02 MarkDuplicates Tracking 94462 as yet unmatched pairs. 11955 records in RAM. INFO 2026-06-08 08:09:04 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:12:45s. Time for last 1,000,000: 2s. Last read position: chr16:2,765,552 INFO 2026-06-08 08:09:04 MarkDuplicates Tracking 94049 as yet unmatched pairs. 11541 records in RAM. INFO 2026-06-08 08:09:06 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:12:47s. Time for last 1,000,000: 1s. Last read position: chr16:3,782,824 INFO 2026-06-08 08:09:06 MarkDuplicates Tracking 93042 as yet unmatched pairs. 10534 records in RAM. INFO 2026-06-08 08:09:09 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:12:49s. Time for last 1,000,000: 2s. Last read position: chr16:11,850,292 INFO 2026-06-08 08:09:09 MarkDuplicates Tracking 92400 as yet unmatched pairs. 9891 records in RAM. INFO 2026-06-08 08:09:11 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:12:51s. Time for last 1,000,000: 2s. Last read position: chr16:15,130,290 INFO 2026-06-08 08:09:11 MarkDuplicates Tracking 91925 as yet unmatched pairs. 9414 records in RAM. INFO 2026-06-08 08:09:12 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:12:52s. Time for last 1,000,000: 1s. Last read position: chr16:18,318,335 INFO 2026-06-08 08:09:12 MarkDuplicates Tracking 91404 as yet unmatched pairs. 8892 records in RAM. INFO 2026-06-08 08:09:14 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:12:54s. Time for last 1,000,000: 1s. Last read position: chr16:21,402,428 INFO 2026-06-08 08:09:14 MarkDuplicates Tracking 90920 as yet unmatched pairs. 8408 records in RAM. INFO 2026-06-08 08:09:16 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:12:56s. Time for last 1,000,000: 1s. Last read position: chr16:21,835,809 INFO 2026-06-08 08:09:16 MarkDuplicates Tracking 92594 as yet unmatched pairs. 10081 records in RAM. INFO 2026-06-08 08:09:18 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:12:58s. Time for last 1,000,000: 1s. Last read position: chr16:22,533,626 INFO 2026-06-08 08:09:18 MarkDuplicates Tracking 90523 as yet unmatched pairs. 8010 records in RAM. INFO 2026-06-08 08:09:20 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:13:00s. Time for last 1,000,000: 1s. Last read position: chr16:27,363,688 INFO 2026-06-08 08:09:20 MarkDuplicates Tracking 90166 as yet unmatched pairs. 7652 records in RAM. INFO 2026-06-08 08:09:22 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:13:02s. Time for last 1,000,000: 2s. Last read position: chr16:29,381,522 INFO 2026-06-08 08:09:22 MarkDuplicates Tracking 89493 as yet unmatched pairs. 6979 records in RAM. INFO 2026-06-08 08:09:24 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:13:04s. Time for last 1,000,000: 1s. Last read position: chr16:29,833,846 INFO 2026-06-08 08:09:24 MarkDuplicates Tracking 89049 as yet unmatched pairs. 6534 records in RAM. INFO 2026-06-08 08:09:26 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:13:06s. Time for last 1,000,000: 1s. Last read position: chr16:30,417,784 INFO 2026-06-08 08:09:26 MarkDuplicates Tracking 88526 as yet unmatched pairs. 6011 records in RAM. INFO 2026-06-08 08:09:28 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:13:08s. Time for last 1,000,000: 2s. Last read position: chr16:31,182,614 INFO 2026-06-08 08:09:28 MarkDuplicates Tracking 88210 as yet unmatched pairs. 5693 records in RAM. INFO 2026-06-08 08:09:30 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:13:10s. Time for last 1,000,000: 2s. Last read position: chr16:53,157,404 INFO 2026-06-08 08:09:30 MarkDuplicates Tracking 87159 as yet unmatched pairs. 4590 records in RAM. INFO 2026-06-08 08:09:32 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:13:13s. Time for last 1,000,000: 2s. Last read position: chr16:57,798,119 INFO 2026-06-08 08:09:32 MarkDuplicates Tracking 86707 as yet unmatched pairs. 4138 records in RAM. INFO 2026-06-08 08:09:35 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:13:15s. Time for last 1,000,000: 2s. Last read position: chr16:68,296,747 INFO 2026-06-08 08:09:35 MarkDuplicates Tracking 85371 as yet unmatched pairs. 2801 records in RAM. INFO 2026-06-08 08:09:38 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:13:18s. Time for last 1,000,000: 2s. Last read position: chr16:74,695,322 INFO 2026-06-08 08:09:38 MarkDuplicates Tracking 84790 as yet unmatched pairs. 2217 records in RAM. INFO 2026-06-08 08:09:41 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:13:21s. Time for last 1,000,000: 2s. Last read position: chr16:87,411,879 INFO 2026-06-08 08:09:41 MarkDuplicates Tracking 84195 as yet unmatched pairs. 1617 records in RAM. INFO 2026-06-08 08:09:44 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:13:24s. Time for last 1,000,000: 3s. Last read position: chr16:89,303,538 INFO 2026-06-08 08:09:44 MarkDuplicates Tracking 83139 as yet unmatched pairs. 554 records in RAM. INFO 2026-06-08 08:09:47 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:13:27s. Time for last 1,000,000: 2s. Last read position: chr17:1,679,069 INFO 2026-06-08 08:09:47 MarkDuplicates Tracking 82446 as yet unmatched pairs. 20296 records in RAM. INFO 2026-06-08 08:09:49 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:13:29s. Time for last 1,000,000: 2s. Last read position: chr17:4,539,664 INFO 2026-06-08 08:09:49 MarkDuplicates Tracking 81708 as yet unmatched pairs. 19557 records in RAM. INFO 2026-06-08 08:09:51 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:13:31s. Time for last 1,000,000: 2s. Last read position: chr17:7,222,737 INFO 2026-06-08 08:09:51 MarkDuplicates Tracking 80980 as yet unmatched pairs. 18829 records in RAM. INFO 2026-06-08 08:09:53 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:13:34s. Time for last 1,000,000: 2s. Last read position: chr17:7,587,226 INFO 2026-06-08 08:09:53 MarkDuplicates Tracking 80149 as yet unmatched pairs. 17998 records in RAM. INFO 2026-06-08 08:09:56 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:13:37s. Time for last 1,000,000: 2s. Last read position: chr17:8,893,667 INFO 2026-06-08 08:09:56 MarkDuplicates Tracking 79248 as yet unmatched pairs. 17096 records in RAM. INFO 2026-06-08 08:09:59 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:13:40s. Time for last 1,000,000: 3s. Last read position: chr17:17,797,831 INFO 2026-06-08 08:09:59 MarkDuplicates Tracking 78635 as yet unmatched pairs. 16483 records in RAM. INFO 2026-06-08 08:10:02 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:13:42s. Time for last 1,000,000: 2s. Last read position: chr17:27,749,796 INFO 2026-06-08 08:10:02 MarkDuplicates Tracking 77949 as yet unmatched pairs. 15797 records in RAM. INFO 2026-06-08 08:10:04 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:13:44s. Time for last 1,000,000: 1s. Last read position: chr17:30,786,832 INFO 2026-06-08 08:10:04 MarkDuplicates Tracking 77155 as yet unmatched pairs. 15003 records in RAM. INFO 2026-06-08 08:10:06 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:13:46s. Time for last 1,000,000: 2s. Last read position: chr17:36,378,131 INFO 2026-06-08 08:10:06 MarkDuplicates Tracking 76659 as yet unmatched pairs. 14505 records in RAM. INFO 2026-06-08 08:10:09 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:13:49s. Time for last 1,000,000: 2s. Last read position: chr17:39,067,865 INFO 2026-06-08 08:10:09 MarkDuplicates Tracking 75789 as yet unmatched pairs. 13633 records in RAM. INFO 2026-06-08 08:10:12 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:13:52s. Time for last 1,000,000: 2s. Last read position: chr17:40,164,153 INFO 2026-06-08 08:10:12 MarkDuplicates Tracking 74926 as yet unmatched pairs. 12769 records in RAM. INFO 2026-06-08 08:10:14 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:13:54s. Time for last 1,000,000: 2s. Last read position: chr17:42,659,541 INFO 2026-06-08 08:10:14 MarkDuplicates Tracking 74115 as yet unmatched pairs. 11957 records in RAM. INFO 2026-06-08 08:10:16 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:13:56s. Time for last 1,000,000: 2s. Last read position: chr17:45,149,599 INFO 2026-06-08 08:10:16 MarkDuplicates Tracking 73511 as yet unmatched pairs. 11353 records in RAM. INFO 2026-06-08 08:10:18 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:13:58s. Time for last 1,000,000: 2s. Last read position: chr17:47,656,980 INFO 2026-06-08 08:10:18 MarkDuplicates Tracking 72919 as yet unmatched pairs. 10761 records in RAM. INFO 2026-06-08 08:10:20 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:14:00s. Time for last 1,000,000: 2s. Last read position: chr17:50,185,805 INFO 2026-06-08 08:10:20 MarkDuplicates Tracking 72517 as yet unmatched pairs. 10358 records in RAM. INFO 2026-06-08 08:10:22 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:14:03s. Time for last 1,000,000: 2s. Last read position: chr17:50,189,223 INFO 2026-06-08 08:10:22 MarkDuplicates Tracking 72505 as yet unmatched pairs. 10346 records in RAM. INFO 2026-06-08 08:10:25 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:14:05s. Time for last 1,000,000: 2s. Last read position: chr17:50,192,677 INFO 2026-06-08 08:10:25 MarkDuplicates Tracking 75719 as yet unmatched pairs. 13560 records in RAM. INFO 2026-06-08 08:10:27 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:14:07s. Time for last 1,000,000: 2s. Last read position: chr17:50,196,177 INFO 2026-06-08 08:10:27 MarkDuplicates Tracking 74594 as yet unmatched pairs. 12435 records in RAM. INFO 2026-06-08 08:10:30 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:14:10s. Time for last 1,000,000: 3s. Last read position: chr17:50,199,900 INFO 2026-06-08 08:10:30 MarkDuplicates Tracking 69349 as yet unmatched pairs. 7190 records in RAM. INFO 2026-06-08 08:10:33 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:14:13s. Time for last 1,000,000: 2s. Last read position: chr17:59,644,288 INFO 2026-06-08 08:10:33 MarkDuplicates Tracking 68397 as yet unmatched pairs. 6237 records in RAM. INFO 2026-06-08 08:10:35 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:14:15s. Time for last 1,000,000: 1s. Last read position: chr17:64,360,235 INFO 2026-06-08 08:10:35 MarkDuplicates Tracking 67208 as yet unmatched pairs. 5047 records in RAM. INFO 2026-06-08 08:10:37 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:14:17s. Time for last 1,000,000: 2s. Last read position: chr17:68,529,976 INFO 2026-06-08 08:10:37 MarkDuplicates Tracking 66759 as yet unmatched pairs. 4598 records in RAM. INFO 2026-06-08 08:10:40 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:14:20s. Time for last 1,000,000: 2s. Last read position: chr17:75,614,255 INFO 2026-06-08 08:10:40 MarkDuplicates Tracking 65802 as yet unmatched pairs. 3634 records in RAM. INFO 2026-06-08 08:10:42 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:14:22s. Time for last 1,000,000: 2s. Last read position: chr17:77,297,821 INFO 2026-06-08 08:10:42 MarkDuplicates Tracking 64793 as yet unmatched pairs. 2624 records in RAM. INFO 2026-06-08 08:10:44 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:14:25s. Time for last 1,000,000: 2s. Last read position: chr17:80,221,708 INFO 2026-06-08 08:10:44 MarkDuplicates Tracking 64057 as yet unmatched pairs. 1888 records in RAM. INFO 2026-06-08 08:10:46 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:14:27s. Time for last 1,000,000: 1s. Last read position: chr17:81,701,062 INFO 2026-06-08 08:10:46 MarkDuplicates Tracking 63219 as yet unmatched pairs. 1050 records in RAM. INFO 2026-06-08 08:10:48 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:14:29s. Time for last 1,000,000: 2s. Last read position: chr17:82,929,402 INFO 2026-06-08 08:10:48 MarkDuplicates Tracking 62228 as yet unmatched pairs. 59 records in RAM. INFO 2026-06-08 08:10:51 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:14:31s. Time for last 1,000,000: 2s. Last read position: chr18:13,427,042 INFO 2026-06-08 08:10:51 MarkDuplicates Tracking 61477 as yet unmatched pairs. 2693 records in RAM. INFO 2026-06-08 08:10:53 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:14:33s. Time for last 1,000,000: 2s. Last read position: chr18:24,443,063 INFO 2026-06-08 08:10:53 MarkDuplicates Tracking 60901 as yet unmatched pairs. 2117 records in RAM. INFO 2026-06-08 08:10:55 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:14:35s. Time for last 1,000,000: 2s. Last read position: chr18:49,843,373 INFO 2026-06-08 08:10:55 MarkDuplicates Tracking 60272 as yet unmatched pairs. 1485 records in RAM. INFO 2026-06-08 08:10:57 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:14:37s. Time for last 1,000,000: 1s. Last read position: chr18:63,318,174 INFO 2026-06-08 08:10:57 MarkDuplicates Tracking 60897 as yet unmatched pairs. 2110 records in RAM. INFO 2026-06-08 08:11:00 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:14:40s. Time for last 1,000,000: 2s. Last read position: chr19:805,133 INFO 2026-06-08 08:11:00 MarkDuplicates Tracking 58796 as yet unmatched pairs. 21774 records in RAM. INFO 2026-06-08 08:11:02 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:14:42s. Time for last 1,000,000: 2s. Last read position: chr19:1,417,499 INFO 2026-06-08 08:11:02 MarkDuplicates Tracking 57506 as yet unmatched pairs. 20482 records in RAM. INFO 2026-06-08 08:11:04 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:14:44s. Time for last 1,000,000: 2s. Last read position: chr19:2,433,862 INFO 2026-06-08 08:11:04 MarkDuplicates Tracking 56513 as yet unmatched pairs. 19488 records in RAM. INFO 2026-06-08 08:11:06 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:14:46s. Time for last 1,000,000: 2s. Last read position: chr19:4,501,945 INFO 2026-06-08 08:11:06 MarkDuplicates Tracking 55644 as yet unmatched pairs. 18619 records in RAM. INFO 2026-06-08 08:11:08 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:14:49s. Time for last 1,000,000: 2s. Last read position: chr19:6,685,099 INFO 2026-06-08 08:11:08 MarkDuplicates Tracking 54850 as yet unmatched pairs. 17825 records in RAM. INFO 2026-06-08 08:11:10 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:14:51s. Time for last 1,000,000: 2s. Last read position: chr19:8,490,597 INFO 2026-06-08 08:11:10 MarkDuplicates Tracking 53669 as yet unmatched pairs. 16644 records in RAM. INFO 2026-06-08 08:11:13 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:14:53s. Time for last 1,000,000: 2s. Last read position: chr19:10,929,215 INFO 2026-06-08 08:11:13 MarkDuplicates Tracking 52904 as yet unmatched pairs. 15879 records in RAM. INFO 2026-06-08 08:11:15 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:14:55s. Time for last 1,000,000: 2s. Last read position: chr19:13,025,207 INFO 2026-06-08 08:11:15 MarkDuplicates Tracking 52291 as yet unmatched pairs. 15266 records in RAM. INFO 2026-06-08 08:11:17 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:14:58s. Time for last 1,000,000: 2s. Last read position: chr19:15,239,253 INFO 2026-06-08 08:11:17 MarkDuplicates Tracking 51505 as yet unmatched pairs. 14480 records in RAM. INFO 2026-06-08 08:11:19 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:15:00s. Time for last 1,000,000: 2s. Last read position: chr19:16,326,932 INFO 2026-06-08 08:11:19 MarkDuplicates Tracking 50552 as yet unmatched pairs. 13526 records in RAM. INFO 2026-06-08 08:11:22 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:15:02s. Time for last 1,000,000: 2s. Last read position: chr19:18,265,480 INFO 2026-06-08 08:11:22 MarkDuplicates Tracking 49762 as yet unmatched pairs. 12736 records in RAM. INFO 2026-06-08 08:11:24 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:15:04s. Time for last 1,000,000: 2s. Last read position: chr19:19,657,318 INFO 2026-06-08 08:11:24 MarkDuplicates Tracking 48402 as yet unmatched pairs. 11375 records in RAM. INFO 2026-06-08 08:11:26 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:15:06s. Time for last 1,000,000: 2s. Last read position: chr19:35,269,078 INFO 2026-06-08 08:11:26 MarkDuplicates Tracking 47501 as yet unmatched pairs. 10474 records in RAM. INFO 2026-06-08 08:11:28 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:15:08s. Time for last 1,000,000: 1s. Last read position: chr19:38,081,690 INFO 2026-06-08 08:11:28 MarkDuplicates Tracking 46762 as yet unmatched pairs. 9734 records in RAM. INFO 2026-06-08 08:11:30 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:15:11s. Time for last 1,000,000: 2s. Last read position: chr19:39,408,435 INFO 2026-06-08 08:11:30 MarkDuplicates Tracking 46140 as yet unmatched pairs. 9112 records in RAM. INFO 2026-06-08 08:11:33 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:15:13s. Time for last 1,000,000: 2s. Last read position: chr19:41,292,308 INFO 2026-06-08 08:11:33 MarkDuplicates Tracking 45025 as yet unmatched pairs. 7997 records in RAM. INFO 2026-06-08 08:11:35 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:15:15s. Time for last 1,000,000: 1s. Last read position: chr19:42,286,774 INFO 2026-06-08 08:11:35 MarkDuplicates Tracking 44264 as yet unmatched pairs. 7236 records in RAM. INFO 2026-06-08 08:11:37 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:15:17s. Time for last 1,000,000: 2s. Last read position: chr19:44,777,896 INFO 2026-06-08 08:11:37 MarkDuplicates Tracking 43429 as yet unmatched pairs. 6392 records in RAM. INFO 2026-06-08 08:11:39 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:15:20s. Time for last 1,000,000: 2s. Last read position: chr19:45,785,786 INFO 2026-06-08 08:11:39 MarkDuplicates Tracking 42503 as yet unmatched pairs. 5465 records in RAM. INFO 2026-06-08 08:11:42 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:15:22s. Time for last 1,000,000: 2s. Last read position: chr19:47,754,768 INFO 2026-06-08 08:11:42 MarkDuplicates Tracking 41565 as yet unmatched pairs. 4526 records in RAM. INFO 2026-06-08 08:11:44 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:15:24s. Time for last 1,000,000: 2s. Last read position: chr19:49,491,476 INFO 2026-06-08 08:11:44 MarkDuplicates Tracking 40693 as yet unmatched pairs. 3654 records in RAM. INFO 2026-06-08 08:11:46 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:15:26s. Time for last 1,000,000: 2s. Last read position: chr19:50,334,910 INFO 2026-06-08 08:11:46 MarkDuplicates Tracking 39731 as yet unmatched pairs. 2692 records in RAM. INFO 2026-06-08 08:11:48 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:15:29s. Time for last 1,000,000: 2s. Last read position: chr19:54,454,518 INFO 2026-06-08 08:11:48 MarkDuplicates Tracking 39631 as yet unmatched pairs. 2592 records in RAM. INFO 2026-06-08 08:11:50 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:15:31s. Time for last 1,000,000: 1s. Last read position: chr19:55,673,936 INFO 2026-06-08 08:11:50 MarkDuplicates Tracking 38019 as yet unmatched pairs. 980 records in RAM. INFO 2026-06-08 08:11:52 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:15:33s. Time for last 1,000,000: 2s. Last read position: chr19:58,088,718 INFO 2026-06-08 08:11:52 MarkDuplicates Tracking 37444 as yet unmatched pairs. 404 records in RAM. INFO 2026-06-08 08:11:55 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:15:35s. Time for last 1,000,000: 2s. Last read position: chr20:3,671,291 INFO 2026-06-08 08:11:55 MarkDuplicates Tracking 36640 as yet unmatched pairs. 5570 records in RAM. INFO 2026-06-08 08:11:57 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:15:37s. Time for last 1,000,000: 2s. Last read position: chr20:19,880,811 INFO 2026-06-08 08:11:57 MarkDuplicates Tracking 35808 as yet unmatched pairs. 4737 records in RAM. INFO 2026-06-08 08:11:59 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:15:39s. Time for last 1,000,000: 2s. Last read position: chr20:34,492,562 INFO 2026-06-08 08:11:59 MarkDuplicates Tracking 35033 as yet unmatched pairs. 3960 records in RAM. INFO 2026-06-08 08:12:01 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:15:41s. Time for last 1,000,000: 1s. Last read position: chr20:38,521,313 INFO 2026-06-08 08:12:01 MarkDuplicates Tracking 34343 as yet unmatched pairs. 3270 records in RAM. INFO 2026-06-08 08:12:03 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:15:43s. Time for last 1,000,000: 2s. Last read position: chr20:46,062,765 INFO 2026-06-08 08:12:03 MarkDuplicates Tracking 33604 as yet unmatched pairs. 2530 records in RAM. INFO 2026-06-08 08:12:05 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:15:46s. Time for last 1,000,000: 2s. Last read position: chr20:53,255,576 INFO 2026-06-08 08:12:05 MarkDuplicates Tracking 32847 as yet unmatched pairs. 1772 records in RAM. INFO 2026-06-08 08:12:08 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:15:48s. Time for last 1,000,000: 2s. Last read position: chr20:62,671,762 INFO 2026-06-08 08:12:08 MarkDuplicates Tracking 32067 as yet unmatched pairs. 991 records in RAM. INFO 2026-06-08 08:12:10 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:15:50s. Time for last 1,000,000: 2s. Last read position: chr20:64,255,857 INFO 2026-06-08 08:12:10 MarkDuplicates Tracking 31149 as yet unmatched pairs. 70 records in RAM. INFO 2026-06-08 08:12:12 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:15:52s. Time for last 1,000,000: 1s. Last read position: chr21:8,214,783 INFO 2026-06-08 08:12:12 MarkDuplicates Tracking 30609 as yet unmatched pairs. 8600 records in RAM. INFO 2026-06-08 08:12:13 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:15:54s. Time for last 1,000,000: 1s. Last read position: chr21:8,217,389 INFO 2026-06-08 08:12:13 MarkDuplicates Tracking 29146 as yet unmatched pairs. 7119 records in RAM. INFO 2026-06-08 08:12:15 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:15:55s. Time for last 1,000,000: 1s. Last read position: chr21:8,260,222 INFO 2026-06-08 08:12:15 MarkDuplicates Tracking 28845 as yet unmatched pairs. 6818 records in RAM. INFO 2026-06-08 08:12:16 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:15:56s. Time for last 1,000,000: 1s. Last read position: chr21:8,399,068 INFO 2026-06-08 08:12:16 MarkDuplicates Tracking 28389 as yet unmatched pairs. 6361 records in RAM. INFO 2026-06-08 08:12:18 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:15:58s. Time for last 1,000,000: 1s. Last read position: chr21:8,435,388 INFO 2026-06-08 08:12:18 MarkDuplicates Tracking 27019 as yet unmatched pairs. 4982 records in RAM. INFO 2026-06-08 08:12:19 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:16:00s. Time for last 1,000,000: 1s. Last read position: chr21:8,443,280 INFO 2026-06-08 08:12:19 MarkDuplicates Tracking 26480 as yet unmatched pairs. 4443 records in RAM. INFO 2026-06-08 08:12:21 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:16:01s. Time for last 1,000,000: 1s. Last read position: chr21:8,448,078 INFO 2026-06-08 08:12:21 MarkDuplicates Tracking 25364 as yet unmatched pairs. 3327 records in RAM. INFO 2026-06-08 08:12:23 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:16:03s. Time for last 1,000,000: 2s. Last read position: chr21:33,550,988 INFO 2026-06-08 08:12:23 MarkDuplicates Tracking 24653 as yet unmatched pairs. 2615 records in RAM. INFO 2026-06-08 08:12:25 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:16:05s. Time for last 1,000,000: 2s. Last read position: chr21:39,259,616 INFO 2026-06-08 08:12:25 MarkDuplicates Tracking 23965 as yet unmatched pairs. 1927 records in RAM. INFO 2026-06-08 08:12:27 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:16:07s. Time for last 1,000,000: 2s. Last read position: chr21:44,910,636 INFO 2026-06-08 08:12:27 MarkDuplicates Tracking 23148 as yet unmatched pairs. 1110 records in RAM. INFO 2026-06-08 08:12:29 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:16:09s. Time for last 1,000,000: 2s. Last read position: chr21:46,411,872 INFO 2026-06-08 08:12:29 MarkDuplicates Tracking 22284 as yet unmatched pairs. 246 records in RAM. INFO 2026-06-08 08:12:31 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:16:12s. Time for last 1,000,000: 2s. Last read position: chr22:20,584,854 INFO 2026-06-08 08:12:31 MarkDuplicates Tracking 21350 as yet unmatched pairs. 7464 records in RAM. INFO 2026-06-08 08:12:34 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:16:14s. Time for last 1,000,000: 2s. Last read position: chr22:24,166,975 INFO 2026-06-08 08:12:34 MarkDuplicates Tracking 20808 as yet unmatched pairs. 6921 records in RAM. INFO 2026-06-08 08:12:36 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:16:16s. Time for last 1,000,000: 1s. Last read position: chr22:29,286,979 INFO 2026-06-08 08:12:36 MarkDuplicates Tracking 20809 as yet unmatched pairs. 6921 records in RAM. INFO 2026-06-08 08:12:37 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:16:18s. Time for last 1,000,000: 1s. Last read position: chr22:31,290,084 INFO 2026-06-08 08:12:37 MarkDuplicates Tracking 19203 as yet unmatched pairs. 5315 records in RAM. INFO 2026-06-08 08:12:40 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:16:20s. Time for last 1,000,000: 2s. Last read position: chr22:36,938,211 INFO 2026-06-08 08:12:40 MarkDuplicates Tracking 18260 as yet unmatched pairs. 4372 records in RAM. INFO 2026-06-08 08:12:42 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:16:22s. Time for last 1,000,000: 2s. Last read position: chr22:38,740,422 INFO 2026-06-08 08:12:42 MarkDuplicates Tracking 17385 as yet unmatched pairs. 3497 records in RAM. INFO 2026-06-08 08:12:44 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:16:24s. Time for last 1,000,000: 1s. Last read position: chr22:41,283,727 INFO 2026-06-08 08:12:44 MarkDuplicates Tracking 16580 as yet unmatched pairs. 2692 records in RAM. INFO 2026-06-08 08:12:46 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:16:27s. Time for last 1,000,000: 2s. Last read position: chr22:45,705,956 INFO 2026-06-08 08:12:46 MarkDuplicates Tracking 15837 as yet unmatched pairs. 1949 records in RAM. INFO 2026-06-08 08:12:48 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:16:29s. Time for last 1,000,000: 2s. Last read position: chr22:50,287,126 INFO 2026-06-08 08:12:48 MarkDuplicates Tracking 15153 as yet unmatched pairs. 1265 records in RAM. INFO 2026-06-08 08:12:50 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:16:31s. Time for last 1,000,000: 2s. Last read position: chrX:1,366,781 INFO 2026-06-08 08:12:50 MarkDuplicates Tracking 13799 as yet unmatched pairs. 6036 records in RAM. INFO 2026-06-08 08:12:53 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:16:33s. Time for last 1,000,000: 2s. Last read position: chrX:19,355,375 INFO 2026-06-08 08:12:53 MarkDuplicates Tracking 13105 as yet unmatched pairs. 5328 records in RAM. INFO 2026-06-08 08:12:55 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:16:35s. Time for last 1,000,000: 2s. Last read position: chrX:45,059,004 INFO 2026-06-08 08:12:55 MarkDuplicates Tracking 12479 as yet unmatched pairs. 4701 records in RAM. INFO 2026-06-08 08:12:57 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:16:37s. Time for last 1,000,000: 2s. Last read position: chrX:53,085,783 INFO 2026-06-08 08:12:57 MarkDuplicates Tracking 11819 as yet unmatched pairs. 4041 records in RAM. INFO 2026-06-08 08:12:59 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:16:39s. Time for last 1,000,000: 2s. Last read position: chrX:68,430,339 INFO 2026-06-08 08:12:59 MarkDuplicates Tracking 10888 as yet unmatched pairs. 3110 records in RAM. INFO 2026-06-08 08:13:01 MarkDuplicates Read 368,000,000 records. Elapsed time: 00:16:42s. Time for last 1,000,000: 2s. Last read position: chrX:77,681,540 INFO 2026-06-08 08:13:01 MarkDuplicates Tracking 10479 as yet unmatched pairs. 2700 records in RAM. INFO 2026-06-08 08:13:03 MarkDuplicates Read 369,000,000 records. Elapsed time: 00:16:44s. Time for last 1,000,000: 2s. Last read position: chrX:110,721,502 INFO 2026-06-08 08:13:03 MarkDuplicates Tracking 9713 as yet unmatched pairs. 1934 records in RAM. INFO 2026-06-08 08:13:05 MarkDuplicates Read 370,000,000 records. Elapsed time: 00:16:46s. Time for last 1,000,000: 1s. Last read position: chrX:139,922,788 INFO 2026-06-08 08:13:05 MarkDuplicates Tracking 8915 as yet unmatched pairs. 1136 records in RAM. INFO 2026-06-08 08:13:07 MarkDuplicates Read 371,000,000 records. Elapsed time: 00:16:48s. Time for last 1,000,000: 2s. Last read position: chrX:154,368,032 INFO 2026-06-08 08:13:07 MarkDuplicates Tracking 8246 as yet unmatched pairs. 466 records in RAM. INFO 2026-06-08 08:13:10 MarkDuplicates Read 372,000,000 records. Elapsed time: 00:16:50s. Time for last 1,000,000: 2s. Last read position: GL000220.1:108,605 INFO 2026-06-08 08:13:10 MarkDuplicates Tracking 7583 as yet unmatched pairs. 2044 records in RAM. INFO 2026-06-08 08:13:11 MarkDuplicates Read 373,000,000 records. Elapsed time: 00:16:52s. Time for last 1,000,000: 1s. Last read position: GL000220.1:115,494 INFO 2026-06-08 08:13:11 MarkDuplicates Tracking 7368 as yet unmatched pairs. 1829 records in RAM. INFO 2026-06-08 08:13:13 MarkDuplicates Read 374,000,000 records. Elapsed time: 00:16:53s. Time for last 1,000,000: 1s. Last read position: GL000220.1:151,929 INFO 2026-06-08 08:13:13 MarkDuplicates Tracking 5742 as yet unmatched pairs. 203 records in RAM. INFO 2026-06-08 08:13:14 MarkDuplicates Read 375,000,000 records. Elapsed time: 00:16:54s. Time for last 1,000,000: 1s. Last read position: GL000220.1:159,460 INFO 2026-06-08 08:13:14 MarkDuplicates Tracking 5699 as yet unmatched pairs. 160 records in RAM. INFO 2026-06-08 08:13:15 MarkDuplicates Read 376,000,000 records. Elapsed time: 00:16:56s. Time for last 1,000,000: 1s. Last read position: KI270712.1:157,876 INFO 2026-06-08 08:13:15 MarkDuplicates Tracking 5518 as yet unmatched pairs. 0 records in RAM. INFO 2026-06-08 08:13:17 MarkDuplicates Read 377,000,000 records. Elapsed time: 00:16:57s. Time for last 1,000,000: 1s. Last read position: KI270733.1:131,052 INFO 2026-06-08 08:13:17 MarkDuplicates Tracking 3256 as yet unmatched pairs. 3212 records in RAM. INFO 2026-06-08 08:13:18 MarkDuplicates Read 378,000,000 records. Elapsed time: 00:16:59s. Time for last 1,000,000: 1s. Last read position: KI270733.1:134,986 INFO 2026-06-08 08:13:18 MarkDuplicates Tracking 2052 as yet unmatched pairs. 2008 records in RAM. INFO 2026-06-08 08:13:20 MarkDuplicates Read 379,000,000 records. Elapsed time: 00:17:00s. Time for last 1,000,000: 1s. Last read position: KI270733.1:176,128 INFO 2026-06-08 08:13:20 MarkDuplicates Tracking 108 as yet unmatched pairs. 64 records in RAM. INFO 2026-06-08 08:13:21 MarkDuplicates Read 380,000,000 records. Elapsed time: 00:17:02s. Time for last 1,000,000: 1s. Last read position: KI270734.1:138,407 INFO 2026-06-08 08:13:21 MarkDuplicates Tracking 330 as yet unmatched pairs. 328 records in RAM. INFO 2026-06-08 08:13:21 MarkDuplicates Read 380061596 records. 0 pairs never matched. INFO 2026-06-08 08:13:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 32410591376; totalMemory: 46305116160; maxMemory: 63585648640 INFO 2026-06-08 08:13:58 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk. INFO 2026-06-08 08:14:00 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2026-06-08 08:14:16 OpticalDuplicateFinder Large duplicate set. size = 1067 INFO 2026-06-08 08:14:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,482 INFO 2026-06-08 08:14:50 MarkDuplicates Traversing fragment information and detecting duplicates. WARNING 2026-06-08 08:14:51 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered. INFO 2026-06-08 08:15:41 MarkDuplicates Sorting list of duplicate records. INFO 2026-06-08 08:15:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300718480; totalMemory: 53250883584; maxMemory: 63585648640 INFO 2026-06-08 08:15:51 MarkDuplicates Marking 246508729 records as duplicates. INFO 2026-06-08 08:15:51 MarkDuplicates Found 13431592 optical duplicate clusters. INFO 2026-06-08 08:15:51 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2026-06-08 08:16:15 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:23s. Time for last 10,000,000: 23s. Last read position: chr1:36,172,576 INFO 2026-06-08 08:16:35 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:43s. Time for last 10,000,000: 20s. Last read position: chr1:143,729,502 INFO 2026-06-08 08:16:54 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:03s. Time for last 10,000,000: 19s. Last read position: chr1:161,048,060 INFO 2026-06-08 08:17:15 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:24s. Time for last 10,000,000: 20s. Last read position: chr1:235,806,552 INFO 2026-06-08 08:17:36 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:44s. Time for last 10,000,000: 20s. Last read position: chr2:86,914,337 INFO 2026-06-08 08:17:56 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:05s. Time for last 10,000,000: 20s. Last read position: chr2:203,440,384 INFO 2026-06-08 08:18:19 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:27s. Time for last 10,000,000: 22s. Last read position: chr3:40,461,432 INFO 2026-06-08 08:18:40 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:48s. Time for last 10,000,000: 21s. Last read position: chr3:136,315,502 INFO 2026-06-08 08:19:01 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:03:09s. Time for last 10,000,000: 20s. Last read position: chr4:82,918,464 INFO 2026-06-08 08:19:22 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:03:31s. Time for last 10,000,000: 21s. Last read position: chr5:57,249,444 INFO 2026-06-08 08:19:45 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:03:54s. Time for last 10,000,000: 22s. Last read position: chr5:151,525,899 INFO 2026-06-08 08:20:07 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:04:16s. Time for last 10,000,000: 21s. Last read position: chr6:33,293,134 INFO 2026-06-08 08:20:29 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:04:37s. Time for last 10,000,000: 21s. Last read position: chr6:163,478,801 INFO 2026-06-08 08:20:52 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:05:01s. Time for last 10,000,000: 23s. Last read position: chr7:92,102,624 INFO 2026-06-08 08:21:14 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:05:23s. Time for last 10,000,000: 22s. Last read position: chr8:16,150,302 INFO 2026-06-08 08:21:35 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:05:43s. Time for last 10,000,000: 20s. Last read position: chr8:143,862,319 INFO 2026-06-08 08:21:56 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:06:04s. Time for last 10,000,000: 21s. Last read position: chr9:114,643,132 INFO 2026-06-08 08:22:18 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:06:26s. Time for last 10,000,000: 21s. Last read position: chr10:37,141,936 INFO 2026-06-08 08:22:39 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:06:47s. Time for last 10,000,000: 20s. Last read position: chr10:117,284,433 INFO 2026-06-08 08:23:00 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:07:08s. Time for last 10,000,000: 21s. Last read position: chr11:62,535,945 INFO 2026-06-08 08:23:20 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:07:28s. Time for last 10,000,000: 20s. Last read position: chr11:117,820,674 INFO 2026-06-08 08:23:43 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:07:51s. Time for last 10,000,000: 23s. Last read position: chr12:54,342,217 INFO 2026-06-08 08:24:06 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:08:14s. Time for last 10,000,000: 23s. Last read position: chr12:132,583,472 INFO 2026-06-08 08:24:29 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:08:37s. Time for last 10,000,000: 22s. Last read position: chr14:64,202,954 INFO 2026-06-08 08:24:52 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:09:01s. Time for last 10,000,000: 23s. Last read position: chr15:48,165,896 INFO 2026-06-08 08:25:14 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:09:23s. Time for last 10,000,000: 22s. Last read position: chr16:2,765,552 INFO 2026-06-08 08:25:36 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:09:45s. Time for last 10,000,000: 21s. Last read position: chr16:29,833,846 INFO 2026-06-08 08:26:01 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:10:10s. Time for last 10,000,000: 25s. Last read position: chr17:4,539,664 INFO 2026-06-08 08:26:27 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:10:36s. Time for last 10,000,000: 26s. Last read position: chr17:42,659,541 INFO 2026-06-08 08:26:54 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:11:02s. Time for last 10,000,000: 26s. Last read position: chr17:68,529,976 INFO 2026-06-08 08:27:18 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:11:27s. Time for last 10,000,000: 24s. Last read position: chr19:805,133 INFO 2026-06-08 08:27:43 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:11:52s. Time for last 10,000,000: 24s. Last read position: chr19:18,265,480 INFO 2026-06-08 08:28:08 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:12:17s. Time for last 10,000,000: 24s. Last read position: chr19:49,491,476 INFO 2026-06-08 08:28:32 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:12:41s. Time for last 10,000,000: 24s. Last read position: chr20:53,255,576 INFO 2026-06-08 08:28:55 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:13:03s. Time for last 10,000,000: 22s. Last read position: chr21:33,550,988 INFO 2026-06-08 08:29:21 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:13:29s. Time for last 10,000,000: 26s. Last read position: chr22:41,283,727 INFO 2026-06-08 08:29:46 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:13:55s. Time for last 10,000,000: 25s. Last read position: chrX:139,922,788 INFO 2026-06-08 08:30:12 MarkDuplicates Written 380,000,000 records. Elapsed time: 00:14:20s. Time for last 10,000,000: 25s. Last read position: KI270734.1:138,407 INFO 2026-06-08 08:30:26 MarkDuplicates Writing complete. Closing input iterator. INFO 2026-06-08 08:30:26 MarkDuplicates Duplicate Index cleanup. INFO 2026-06-08 08:30:26 MarkDuplicates Getting Memory Stats. INFO 2026-06-08 08:30:26 MarkDuplicates Before output close freeMemory: 201372864; totalMemory: 234881024; maxMemory: 63585648640 INFO 2026-06-08 08:30:26 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2026-06-08 08:30:26 MarkDuplicates After output close freeMemory: 104187376; totalMemory: 134217728; maxMemory: 63585648640 [Mon Jun 08 08:30:26 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 34.15 minutes. Runtime.totalMemory()=134217728 ls: *cram: No such file or directory ls: *.crai: No such file or directory