Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT 659_bMa-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bam --METRICS_FILE 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT 20:50:30.081 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so [Thu Jun 04 20:50:30 GMT 2026] MarkDuplicates --INPUT 659_bMa-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bam --METRICS_FILE 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Jun 04 20:50:30 GMT 2026] Executing as ?@nf-bf0d67dff87d6c5050d9ca1997ced295-cea35-fbnsb on Linux 6.12.88 amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0 INFO 2026-06-04 20:50:30 MarkDuplicates Start of doWork freeMemory: 105829560; totalMemory: 134217728; maxMemory: 63585648640 INFO 2026-06-04 20:50:30 MarkDuplicates Reading input file and constructing read end information. INFO 2026-06-04 20:50:30 MarkDuplicates Will retain up to 230382784 data points before spilling to disk. INFO 2026-06-04 20:50:33 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:01s. Time for last 1,000,000: 1s. Last read position: chr1:1,623,911 INFO 2026-06-04 20:50:33 MarkDuplicates Tracking 1719 as yet unmatched pairs. 5 records in RAM. INFO 2026-06-04 20:50:35 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: chr1:6,593,470 INFO 2026-06-04 20:50:35 MarkDuplicates Tracking 3675 as yet unmatched pairs. 19 records in RAM. INFO 2026-06-04 20:50:37 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: chr1:11,676,099 INFO 2026-06-04 20:50:37 MarkDuplicates Tracking 5533 as yet unmatched pairs. 28 records in RAM. INFO 2026-06-04 20:50:38 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: chr1:16,930,332 INFO 2026-06-04 20:50:38 MarkDuplicates Tracking 7492 as yet unmatched pairs. 15 records in RAM. INFO 2026-06-04 20:50:40 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: chr1:21,598,053 INFO 2026-06-04 20:50:40 MarkDuplicates Tracking 9363 as yet unmatched pairs. 3 records in RAM. INFO 2026-06-04 20:50:41 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: chr1:23,751,484 INFO 2026-06-04 20:50:41 MarkDuplicates Tracking 11018 as yet unmatched pairs. 31 records in RAM. INFO 2026-06-04 20:50:43 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: chr1:26,946,130 INFO 2026-06-04 20:50:43 MarkDuplicates Tracking 12610 as yet unmatched pairs. 35 records in RAM. INFO 2026-06-04 20:50:45 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: chr1:31,585,159 INFO 2026-06-04 20:50:45 MarkDuplicates Tracking 14468 as yet unmatched pairs. 110 records in RAM. INFO 2026-06-04 20:50:46 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: chr1:35,192,517 INFO 2026-06-04 20:50:46 MarkDuplicates Tracking 16282 as yet unmatched pairs. 97 records in RAM. INFO 2026-06-04 20:50:48 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: chr1:39,388,509 INFO 2026-06-04 20:50:48 MarkDuplicates Tracking 17986 as yet unmatched pairs. 5 records in RAM. INFO 2026-06-04 20:50:50 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 2s. Last read position: chr1:43,447,026 INFO 2026-06-04 20:50:50 MarkDuplicates Tracking 19927 as yet unmatched pairs. 5 records in RAM. INFO 2026-06-04 20:50:51 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: chr1:47,333,933 INFO 2026-06-04 20:50:51 MarkDuplicates Tracking 22089 as yet unmatched pairs. 170 records in RAM. INFO 2026-06-04 20:50:52 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 1s. Last read position: chr1:62,578,831 INFO 2026-06-04 20:50:52 MarkDuplicates Tracking 23802 as yet unmatched pairs. 5 records in RAM. INFO 2026-06-04 20:50:54 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: chr1:93,154,781 INFO 2026-06-04 20:50:54 MarkDuplicates Tracking 25438 as yet unmatched pairs. 28 records in RAM. INFO 2026-06-04 20:50:55 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 1s. Last read position: chr1:111,704,397 INFO 2026-06-04 20:50:55 MarkDuplicates Tracking 27056 as yet unmatched pairs. 58 records in RAM. INFO 2026-06-04 20:50:57 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 1s. Last read position: chr1:119,915,941 INFO 2026-06-04 20:50:57 MarkDuplicates Tracking 28921 as yet unmatched pairs. 88 records in RAM. INFO 2026-06-04 20:50:58 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 1s. Last read position: chr1:147,622,308 INFO 2026-06-04 20:50:58 MarkDuplicates Tracking 29963 as yet unmatched pairs. 5 records in RAM. INFO 2026-06-04 20:50:59 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 1s. Last read position: chr1:150,554,527 INFO 2026-06-04 20:50:59 MarkDuplicates Tracking 31331 as yet unmatched pairs. 109 records in RAM. INFO 2026-06-04 20:51:01 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 1s. Last read position: chr1:153,607,532 INFO 2026-06-04 20:51:01 MarkDuplicates Tracking 33008 as yet unmatched pairs. 62 records in RAM. INFO 2026-06-04 20:51:02 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 1s. Last read position: chr1:154,176,162 INFO 2026-06-04 20:51:02 MarkDuplicates Tracking 35505 as yet unmatched pairs. 841 records in RAM. INFO 2026-06-04 20:51:04 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 1s. Last read position: chr1:155,190,775 INFO 2026-06-04 20:51:04 MarkDuplicates Tracking 36202 as yet unmatched pairs. 44 records in RAM. INFO 2026-06-04 20:51:05 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 1s. Last read position: chr1:156,135,185 INFO 2026-06-04 20:51:05 MarkDuplicates Tracking 38372 as yet unmatched pairs. 621 records in RAM. INFO 2026-06-04 20:51:07 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 1s. Last read position: chr1:160,541,888 INFO 2026-06-04 20:51:07 MarkDuplicates Tracking 39714 as yet unmatched pairs. 4 records in RAM. INFO 2026-06-04 20:51:08 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 1s. Last read position: chr1:169,130,016 INFO 2026-06-04 20:51:08 MarkDuplicates Tracking 42109 as yet unmatched pairs. 604 records in RAM. INFO 2026-06-04 20:51:09 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 1s. Last read position: chr1:180,935,353 INFO 2026-06-04 20:51:09 MarkDuplicates Tracking 42967 as yet unmatched pairs. 25 records in RAM. INFO 2026-06-04 20:51:11 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 1s. Last read position: chr1:192,809,150 INFO 2026-06-04 20:51:11 MarkDuplicates Tracking 44754 as yet unmatched pairs. 63 records in RAM. INFO 2026-06-04 20:51:12 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 1s. Last read position: chr1:203,848,331 INFO 2026-06-04 20:51:12 MarkDuplicates Tracking 46379 as yet unmatched pairs. 89 records in RAM. INFO 2026-06-04 20:51:13 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 1s. Last read position: chr1:207,783,297 INFO 2026-06-04 20:51:13 MarkDuplicates Tracking 48053 as yet unmatched pairs. 213 records in RAM. INFO 2026-06-04 20:51:14 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 1s. Last read position: chr1:224,433,838 INFO 2026-06-04 20:51:14 MarkDuplicates Tracking 49917 as yet unmatched pairs. 238 records in RAM. INFO 2026-06-04 20:51:15 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 1s. Last read position: chr1:232,514,079 INFO 2026-06-04 20:51:15 MarkDuplicates Tracking 51555 as yet unmatched pairs. 24 records in RAM. INFO 2026-06-04 20:51:18 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 2s. Last read position: chr1:247,100,564 INFO 2026-06-04 20:51:18 MarkDuplicates Tracking 53437 as yet unmatched pairs. 12 records in RAM. INFO 2026-06-04 20:51:20 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 2s. Last read position: chr2:17,666,438 INFO 2026-06-04 20:51:20 MarkDuplicates Tracking 55203 as yet unmatched pairs. 55114 records in RAM. INFO 2026-06-04 20:51:21 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 1s. Last read position: chr2:27,201,743 INFO 2026-06-04 20:51:21 MarkDuplicates Tracking 57206 as yet unmatched pairs. 57115 records in RAM. INFO 2026-06-04 20:51:23 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,261 INFO 2026-06-04 20:51:23 MarkDuplicates Tracking 78142 as yet unmatched pairs. 57522 records in RAM. INFO 2026-06-04 20:51:24 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,406 INFO 2026-06-04 20:51:24 MarkDuplicates Tracking 519057 as yet unmatched pairs. 42730 records in RAM. INFO 2026-06-04 20:51:26 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 1s. Last read position: chr2:39,024,128 INFO 2026-06-04 20:51:26 MarkDuplicates Tracking 545135 as yet unmatched pairs. 41218 records in RAM. INFO 2026-06-04 20:51:27 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 1s. Last read position: chr2:47,373,890 INFO 2026-06-04 20:51:27 MarkDuplicates Tracking 543240 as yet unmatched pairs. 39322 records in RAM. INFO 2026-06-04 20:51:28 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 1s. Last read position: chr2:55,601,445 INFO 2026-06-04 20:51:28 MarkDuplicates Tracking 541104 as yet unmatched pairs. 37185 records in RAM. INFO 2026-06-04 20:51:30 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 1s. Last read position: chr2:70,281,654 INFO 2026-06-04 20:51:30 MarkDuplicates Tracking 539359 as yet unmatched pairs. 35437 records in RAM. INFO 2026-06-04 20:51:32 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 1s. Last read position: chr2:84,821,952 INFO 2026-06-04 20:51:32 MarkDuplicates Tracking 537647 as yet unmatched pairs. 33724 records in RAM. INFO 2026-06-04 20:51:33 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 1s. Last read position: chr2:96,144,352 INFO 2026-06-04 20:51:33 MarkDuplicates Tracking 535837 as yet unmatched pairs. 31912 records in RAM. INFO 2026-06-04 20:51:35 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 1s. Last read position: chr2:102,024,504 INFO 2026-06-04 20:51:35 MarkDuplicates Tracking 534143 as yet unmatched pairs. 30218 records in RAM. INFO 2026-06-04 20:51:36 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 1s. Last read position: chr2:110,115,719 INFO 2026-06-04 20:51:36 MarkDuplicates Tracking 532781 as yet unmatched pairs. 28854 records in RAM. INFO 2026-06-04 20:51:38 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 1s. Last read position: chr2:119,370,753 INFO 2026-06-04 20:51:38 MarkDuplicates Tracking 531448 as yet unmatched pairs. 27521 records in RAM. INFO 2026-06-04 20:51:39 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 1s. Last read position: chr2:148,469,713 INFO 2026-06-04 20:51:39 MarkDuplicates Tracking 529933 as yet unmatched pairs. 25996 records in RAM. INFO 2026-06-04 20:51:40 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 1s. Last read position: chr2:171,867,415 INFO 2026-06-04 20:51:40 MarkDuplicates Tracking 528275 as yet unmatched pairs. 24332 records in RAM. INFO 2026-06-04 20:51:41 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 1s. Last read position: chr2:186,507,433 INFO 2026-06-04 20:51:41 MarkDuplicates Tracking 526350 as yet unmatched pairs. 22407 records in RAM. INFO 2026-06-04 20:51:43 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 1s. Last read position: chr2:189,001,543 INFO 2026-06-04 20:51:43 MarkDuplicates Tracking 526097 as yet unmatched pairs. 22154 records in RAM. INFO 2026-06-04 20:51:44 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 1s. Last read position: chr2:190,497,468 INFO 2026-06-04 20:51:44 MarkDuplicates Tracking 522443 as yet unmatched pairs. 18498 records in RAM. INFO 2026-06-04 20:51:46 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 1s. Last read position: chr2:203,396,865 INFO 2026-06-04 20:51:46 MarkDuplicates Tracking 520860 as yet unmatched pairs. 16914 records in RAM. INFO 2026-06-04 20:51:47 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 1s. Last read position: chr2:215,367,983 INFO 2026-06-04 20:51:47 MarkDuplicates Tracking 520027 as yet unmatched pairs. 16081 records in RAM. INFO 2026-06-04 20:51:49 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 1s. Last read position: chr2:215,376,625 INFO 2026-06-04 20:51:49 MarkDuplicates Tracking 519321 as yet unmatched pairs. 15375 records in RAM. INFO 2026-06-04 20:51:50 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 1s. Last read position: chr2:215,394,707 INFO 2026-06-04 20:51:50 MarkDuplicates Tracking 518025 as yet unmatched pairs. 14078 records in RAM. INFO 2026-06-04 20:51:51 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 1s. Last read position: chr2:215,414,837 INFO 2026-06-04 20:51:51 MarkDuplicates Tracking 514933 as yet unmatched pairs. 10986 records in RAM. INFO 2026-06-04 20:51:53 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 1s. Last read position: chr2:215,433,348 INFO 2026-06-04 20:51:53 MarkDuplicates Tracking 515425 as yet unmatched pairs. 11476 records in RAM. INFO 2026-06-04 20:51:54 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 1s. Last read position: chr2:218,644,321 INFO 2026-06-04 20:51:54 MarkDuplicates Tracking 510867 as yet unmatched pairs. 6916 records in RAM. INFO 2026-06-04 20:51:55 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 1s. Last read position: chr2:230,442,944 INFO 2026-06-04 20:51:55 MarkDuplicates Tracking 508929 as yet unmatched pairs. 4950 records in RAM. INFO 2026-06-04 20:51:56 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 1s. Last read position: chr2:232,790,746 INFO 2026-06-04 20:51:56 MarkDuplicates Tracking 507083 as yet unmatched pairs. 3103 records in RAM. INFO 2026-06-04 20:51:58 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 1s. Last read position: chr2:238,035,888 INFO 2026-06-04 20:51:58 MarkDuplicates Tracking 505340 as yet unmatched pairs. 1343 records in RAM. INFO 2026-06-04 20:51:59 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 1s. Last read position: chr3:9,429,865 INFO 2026-06-04 20:51:59 MarkDuplicates Tracking 503680 as yet unmatched pairs. 27219 records in RAM. INFO 2026-06-04 20:52:01 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 1s. Last read position: chr3:22,382,171 INFO 2026-06-04 20:52:01 MarkDuplicates Tracking 502191 as yet unmatched pairs. 25726 records in RAM. INFO 2026-06-04 20:52:02 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 1s. Last read position: chr3:39,411,943 INFO 2026-06-04 20:52:02 MarkDuplicates Tracking 501293 as yet unmatched pairs. 24825 records in RAM. INFO 2026-06-04 20:52:03 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 1s. Last read position: chr3:47,009,223 INFO 2026-06-04 20:52:03 MarkDuplicates Tracking 498584 as yet unmatched pairs. 22115 records in RAM. INFO 2026-06-04 20:52:05 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 1s. Last read position: chr3:48,591,684 INFO 2026-06-04 20:52:05 MarkDuplicates Tracking 496936 as yet unmatched pairs. 20465 records in RAM. INFO 2026-06-04 20:52:06 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 1s. Last read position: chr3:49,903,277 INFO 2026-06-04 20:52:06 MarkDuplicates Tracking 494968 as yet unmatched pairs. 18495 records in RAM. INFO 2026-06-04 20:52:08 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 1s. Last read position: chr3:52,523,550 INFO 2026-06-04 20:52:08 MarkDuplicates Tracking 492957 as yet unmatched pairs. 16483 records in RAM. INFO 2026-06-04 20:52:09 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 1s. Last read position: chr3:68,951,275 INFO 2026-06-04 20:52:09 MarkDuplicates Tracking 491297 as yet unmatched pairs. 14822 records in RAM. INFO 2026-06-04 20:52:10 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 1s. Last read position: chr3:108,047,245 INFO 2026-06-04 20:52:10 MarkDuplicates Tracking 489939 as yet unmatched pairs. 13461 records in RAM. INFO 2026-06-04 20:52:11 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 1s. Last read position: chr3:124,413,423 INFO 2026-06-04 20:52:11 MarkDuplicates Tracking 487909 as yet unmatched pairs. 11430 records in RAM. INFO 2026-06-04 20:52:13 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 1s. Last read position: chr3:132,474,984 INFO 2026-06-04 20:52:13 MarkDuplicates Tracking 486017 as yet unmatched pairs. 9536 records in RAM. INFO 2026-06-04 20:52:14 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 1s. Last read position: chr3:156,543,228 INFO 2026-06-04 20:52:14 MarkDuplicates Tracking 484364 as yet unmatched pairs. 7879 records in RAM. INFO 2026-06-04 20:52:15 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 1s. Last read position: chr3:184,117,477 INFO 2026-06-04 20:52:15 MarkDuplicates Tracking 482670 as yet unmatched pairs. 6184 records in RAM. INFO 2026-06-04 20:52:17 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 1s. Last read position: chr3:188,609,242 INFO 2026-06-04 20:52:17 MarkDuplicates Tracking 481389 as yet unmatched pairs. 4900 records in RAM. INFO 2026-06-04 20:52:18 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 1s. Last read position: chr3:195,779,502 INFO 2026-06-04 20:52:18 MarkDuplicates Tracking 481235 as yet unmatched pairs. 4745 records in RAM. INFO 2026-06-04 20:52:19 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 1s. Last read position: chr3:195,781,767 INFO 2026-06-04 20:52:19 MarkDuplicates Tracking 481120 as yet unmatched pairs. 4622 records in RAM. INFO 2026-06-04 20:52:20 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 1s. Last read position: chr3:195,784,338 INFO 2026-06-04 20:52:20 MarkDuplicates Tracking 480581 as yet unmatched pairs. 4083 records in RAM. INFO 2026-06-04 20:52:22 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 1s. Last read position: chr3:195,786,957 INFO 2026-06-04 20:52:22 MarkDuplicates Tracking 478479 as yet unmatched pairs. 1980 records in RAM. INFO 2026-06-04 20:52:23 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 1s. Last read position: chr4:769,054 INFO 2026-06-04 20:52:23 MarkDuplicates Tracking 476622 as yet unmatched pairs. 11643 records in RAM. INFO 2026-06-04 20:52:24 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 1s. Last read position: chr4:6,861,475 INFO 2026-06-04 20:52:24 MarkDuplicates Tracking 474878 as yet unmatched pairs. 9896 records in RAM. INFO 2026-06-04 20:52:26 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 1s. Last read position: chr4:40,502,545 INFO 2026-06-04 20:52:26 MarkDuplicates Tracking 473173 as yet unmatched pairs. 8188 records in RAM. INFO 2026-06-04 20:52:28 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 1s. Last read position: chr4:73,741,606 INFO 2026-06-04 20:52:28 MarkDuplicates Tracking 476244 as yet unmatched pairs. 11252 records in RAM. INFO 2026-06-04 20:52:29 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 1s. Last read position: chr4:87,108,161 INFO 2026-06-04 20:52:29 MarkDuplicates Tracking 469633 as yet unmatched pairs. 4640 records in RAM. INFO 2026-06-04 20:52:31 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 1s. Last read position: chr4:119,031,206 INFO 2026-06-04 20:52:31 MarkDuplicates Tracking 467775 as yet unmatched pairs. 2774 records in RAM. INFO 2026-06-04 20:52:32 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 1s. Last read position: chr4:153,788,803 INFO 2026-06-04 20:52:32 MarkDuplicates Tracking 466465 as yet unmatched pairs. 1458 records in RAM. INFO 2026-06-04 20:52:33 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 1s. Last read position: chr5:491,861 INFO 2026-06-04 20:52:33 MarkDuplicates Tracking 464718 as yet unmatched pairs. 25544 records in RAM. INFO 2026-06-04 20:52:35 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 1s. Last read position: chr5:14,488,158 INFO 2026-06-04 20:52:35 MarkDuplicates Tracking 462408 as yet unmatched pairs. 23230 records in RAM. INFO 2026-06-04 20:52:36 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 1s. Last read position: chr5:43,527,317 INFO 2026-06-04 20:52:36 MarkDuplicates Tracking 460697 as yet unmatched pairs. 21517 records in RAM. INFO 2026-06-04 20:52:38 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 1s. Last read position: chr5:76,173,757 INFO 2026-06-04 20:52:38 MarkDuplicates Tracking 459129 as yet unmatched pairs. 19946 records in RAM. INFO 2026-06-04 20:52:39 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 1s. Last read position: chr5:96,881,391 INFO 2026-06-04 20:52:39 MarkDuplicates Tracking 457609 as yet unmatched pairs. 18421 records in RAM. INFO 2026-06-04 20:52:41 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 1s. Last read position: chr5:131,429,107 INFO 2026-06-04 20:52:41 MarkDuplicates Tracking 455911 as yet unmatched pairs. 16721 records in RAM. INFO 2026-06-04 20:52:42 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 1s. Last read position: chr5:138,386,068 INFO 2026-06-04 20:52:42 MarkDuplicates Tracking 454287 as yet unmatched pairs. 15096 records in RAM. INFO 2026-06-04 20:52:43 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 1s. Last read position: chr5:140,877,405 INFO 2026-06-04 20:52:43 MarkDuplicates Tracking 452659 as yet unmatched pairs. 13352 records in RAM. INFO 2026-06-04 20:52:44 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 1s. Last read position: chr5:149,242,440 INFO 2026-06-04 20:52:44 MarkDuplicates Tracking 451036 as yet unmatched pairs. 11729 records in RAM. INFO 2026-06-04 20:52:46 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 1s. Last read position: chr5:150,406,263 INFO 2026-06-04 20:52:46 MarkDuplicates Tracking 450839 as yet unmatched pairs. 11532 records in RAM. INFO 2026-06-04 20:52:47 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 1s. Last read position: chr5:154,793,928 INFO 2026-06-04 20:52:47 MarkDuplicates Tracking 447352 as yet unmatched pairs. 8044 records in RAM. INFO 2026-06-04 20:52:48 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 1s. Last read position: chr5:171,391,724 INFO 2026-06-04 20:52:48 MarkDuplicates Tracking 448021 as yet unmatched pairs. 8710 records in RAM. INFO 2026-06-04 20:52:50 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 1s. Last read position: chr5:172,770,845 INFO 2026-06-04 20:52:50 MarkDuplicates Tracking 444111 as yet unmatched pairs. 4800 records in RAM. INFO 2026-06-04 20:52:51 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 1s. Last read position: chr5:178,120,407 INFO 2026-06-04 20:52:51 MarkDuplicates Tracking 442203 as yet unmatched pairs. 2892 records in RAM. INFO 2026-06-04 20:52:52 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 1s. Last read position: chr5:179,836,448 INFO 2026-06-04 20:52:52 MarkDuplicates Tracking 442000 as yet unmatched pairs. 2688 records in RAM. INFO 2026-06-04 20:52:54 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr6:7,229,232 INFO 2026-06-04 20:52:54 MarkDuplicates Tracking 438636 as yet unmatched pairs. 25810 records in RAM. INFO 2026-06-04 20:52:55 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 1s. Last read position: chr6:18,258,403 INFO 2026-06-04 20:52:55 MarkDuplicates Tracking 437093 as yet unmatched pairs. 24260 records in RAM. INFO 2026-06-04 20:52:56 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 1s. Last read position: chr6:29,889,375 INFO 2026-06-04 20:52:56 MarkDuplicates Tracking 435530 as yet unmatched pairs. 22694 records in RAM. INFO 2026-06-04 20:52:58 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 1s. Last read position: chr6:30,744,109 INFO 2026-06-04 20:52:58 MarkDuplicates Tracking 434736 as yet unmatched pairs. 21900 records in RAM. INFO 2026-06-04 20:52:59 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 1s. Last read position: chr6:31,649,232 INFO 2026-06-04 20:52:59 MarkDuplicates Tracking 432085 as yet unmatched pairs. 19249 records in RAM. INFO 2026-06-04 20:53:00 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 1s. Last read position: chr6:31,993,794 INFO 2026-06-04 20:53:00 MarkDuplicates Tracking 430413 as yet unmatched pairs. 17575 records in RAM. INFO 2026-06-04 20:53:02 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 1s. Last read position: chr6:33,313,238 INFO 2026-06-04 20:53:02 MarkDuplicates Tracking 428951 as yet unmatched pairs. 16113 records in RAM. INFO 2026-06-04 20:53:03 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 1s. Last read position: chr6:36,899,480 INFO 2026-06-04 20:53:03 MarkDuplicates Tracking 426789 as yet unmatched pairs. 13950 records in RAM. INFO 2026-06-04 20:53:04 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 1s. Last read position: chr6:43,512,257 INFO 2026-06-04 20:53:04 MarkDuplicates Tracking 425183 as yet unmatched pairs. 12341 records in RAM. INFO 2026-06-04 20:53:06 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 1s. Last read position: chr6:56,569,856 INFO 2026-06-04 20:53:06 MarkDuplicates Tracking 423250 as yet unmatched pairs. 10406 records in RAM. INFO 2026-06-04 20:53:07 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 1s. Last read position: chr6:87,501,270 INFO 2026-06-04 20:53:07 MarkDuplicates Tracking 421779 as yet unmatched pairs. 8933 records in RAM. INFO 2026-06-04 20:53:08 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 1s. Last read position: chr6:111,020,593 INFO 2026-06-04 20:53:08 MarkDuplicates Tracking 420373 as yet unmatched pairs. 7518 records in RAM. INFO 2026-06-04 20:53:09 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 1s. Last read position: chr6:135,037,034 INFO 2026-06-04 20:53:09 MarkDuplicates Tracking 418640 as yet unmatched pairs. 5781 records in RAM. INFO 2026-06-04 20:53:10 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 1s. Last read position: chr6:149,683,585 INFO 2026-06-04 20:53:10 MarkDuplicates Tracking 416726 as yet unmatched pairs. 3867 records in RAM. INFO 2026-06-04 20:53:12 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 1s. Last read position: chr6:158,783,557 INFO 2026-06-04 20:53:12 MarkDuplicates Tracking 416723 as yet unmatched pairs. 3862 records in RAM. INFO 2026-06-04 20:53:13 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 1s. Last read position: chr6:169,234,872 INFO 2026-06-04 20:53:13 MarkDuplicates Tracking 413311 as yet unmatched pairs. 450 records in RAM. INFO 2026-06-04 20:53:14 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 1s. Last read position: chr7:2,731,361 INFO 2026-06-04 20:53:14 MarkDuplicates Tracking 411200 as yet unmatched pairs. 31304 records in RAM. INFO 2026-06-04 20:53:16 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 1s. Last read position: chr7:5,528,528 INFO 2026-06-04 20:53:16 MarkDuplicates Tracking 411055 as yet unmatched pairs. 31157 records in RAM. INFO 2026-06-04 20:53:18 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 1s. Last read position: chr7:20,003,014 INFO 2026-06-04 20:53:18 MarkDuplicates Tracking 407185 as yet unmatched pairs. 27286 records in RAM. INFO 2026-06-04 20:53:19 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 1s. Last read position: chr7:39,833,861 INFO 2026-06-04 20:53:19 MarkDuplicates Tracking 405859 as yet unmatched pairs. 25942 records in RAM. INFO 2026-06-04 20:53:20 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 1s. Last read position: chr7:47,368,889 INFO 2026-06-04 20:53:20 MarkDuplicates Tracking 404432 as yet unmatched pairs. 24514 records in RAM. INFO 2026-06-04 20:53:22 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 1s. Last read position: chr7:73,027,811 INFO 2026-06-04 20:53:22 MarkDuplicates Tracking 402945 as yet unmatched pairs. 23023 records in RAM. INFO 2026-06-04 20:53:23 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 1s. Last read position: chr7:75,286,815 INFO 2026-06-04 20:53:23 MarkDuplicates Tracking 401886 as yet unmatched pairs. 21963 records in RAM. INFO 2026-06-04 20:53:25 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 1s. Last read position: chr7:76,626,166 INFO 2026-06-04 20:53:25 MarkDuplicates Tracking 400440 as yet unmatched pairs. 20517 records in RAM. INFO 2026-06-04 20:53:26 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 1s. Last read position: chr7:94,401,605 INFO 2026-06-04 20:53:26 MarkDuplicates Tracking 401511 as yet unmatched pairs. 21587 records in RAM. INFO 2026-06-04 20:53:28 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 1s. Last read position: chr7:96,191,131 INFO 2026-06-04 20:53:28 MarkDuplicates Tracking 396983 as yet unmatched pairs. 17055 records in RAM. INFO 2026-06-04 20:53:29 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 1s. Last read position: chr7:100,433,029 INFO 2026-06-04 20:53:29 MarkDuplicates Tracking 395115 as yet unmatched pairs. 15186 records in RAM. INFO 2026-06-04 20:53:30 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 1s. Last read position: chr7:100,992,605 INFO 2026-06-04 20:53:30 MarkDuplicates Tracking 393703 as yet unmatched pairs. 13772 records in RAM. INFO 2026-06-04 20:53:31 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 0s. Last read position: chr7:100,996,006 INFO 2026-06-04 20:53:31 MarkDuplicates Tracking 393190 as yet unmatched pairs. 13259 records in RAM. INFO 2026-06-04 20:53:32 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 1s. Last read position: chr7:100,997,636 INFO 2026-06-04 20:53:32 MarkDuplicates Tracking 392185 as yet unmatched pairs. 12254 records in RAM. INFO 2026-06-04 20:53:33 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 0s. Last read position: chr7:100,999,596 INFO 2026-06-04 20:53:33 MarkDuplicates Tracking 392856 as yet unmatched pairs. 12925 records in RAM. INFO 2026-06-04 20:53:34 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 1s. Last read position: chr7:101,001,575 INFO 2026-06-04 20:53:34 MarkDuplicates Tracking 391222 as yet unmatched pairs. 11291 records in RAM. INFO 2026-06-04 20:53:35 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 0s. Last read position: chr7:101,128,473 INFO 2026-06-04 20:53:35 MarkDuplicates Tracking 390907 as yet unmatched pairs. 10976 records in RAM. INFO 2026-06-04 20:53:37 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 1s. Last read position: chr7:105,055,199 INFO 2026-06-04 20:53:37 MarkDuplicates Tracking 389407 as yet unmatched pairs. 9476 records in RAM. INFO 2026-06-04 20:53:38 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 1s. Last read position: chr7:123,692,719 INFO 2026-06-04 20:53:38 MarkDuplicates Tracking 387769 as yet unmatched pairs. 7834 records in RAM. INFO 2026-06-04 20:53:39 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 1s. Last read position: chr7:134,933,291 INFO 2026-06-04 20:53:39 MarkDuplicates Tracking 385719 as yet unmatched pairs. 5782 records in RAM. INFO 2026-06-04 20:53:40 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 1s. Last read position: chr7:143,381,704 INFO 2026-06-04 20:53:40 MarkDuplicates Tracking 384330 as yet unmatched pairs. 4390 records in RAM. INFO 2026-06-04 20:53:41 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 1s. Last read position: chr7:149,266,882 INFO 2026-06-04 20:53:41 MarkDuplicates Tracking 383044 as yet unmatched pairs. 3104 records in RAM. INFO 2026-06-04 20:53:43 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 1s. Last read position: chr7:152,205,132 INFO 2026-06-04 20:53:43 MarkDuplicates Tracking 381006 as yet unmatched pairs. 1065 records in RAM. INFO 2026-06-04 20:53:44 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 1s. Last read position: chr8:20,197,447 INFO 2026-06-04 20:53:44 MarkDuplicates Tracking 378859 as yet unmatched pairs. 23096 records in RAM. INFO 2026-06-04 20:53:45 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 1s. Last read position: chr8:37,697,492 INFO 2026-06-04 20:53:45 MarkDuplicates Tracking 377555 as yet unmatched pairs. 21791 records in RAM. INFO 2026-06-04 20:53:47 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 1s. Last read position: chr8:41,941,157 INFO 2026-06-04 20:53:47 MarkDuplicates Tracking 375668 as yet unmatched pairs. 19901 records in RAM. INFO 2026-06-04 20:53:48 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 1s. Last read position: chr8:67,172,945 INFO 2026-06-04 20:53:48 MarkDuplicates Tracking 374042 as yet unmatched pairs. 18263 records in RAM. INFO 2026-06-04 20:53:49 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 1s. Last read position: chr8:96,231,912 INFO 2026-06-04 20:53:49 MarkDuplicates Tracking 372275 as yet unmatched pairs. 16493 records in RAM. INFO 2026-06-04 20:53:50 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 1s. Last read position: chr8:102,651,460 INFO 2026-06-04 20:53:50 MarkDuplicates Tracking 370672 as yet unmatched pairs. 14889 records in RAM. INFO 2026-06-04 20:53:52 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 1s. Last read position: chr8:127,738,807 INFO 2026-06-04 20:53:52 MarkDuplicates Tracking 368897 as yet unmatched pairs. 13113 records in RAM. INFO 2026-06-04 20:53:53 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: chr8:143,576,811 INFO 2026-06-04 20:53:53 MarkDuplicates Tracking 367412 as yet unmatched pairs. 11623 records in RAM. INFO 2026-06-04 20:53:54 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 1s. Last read position: chr8:143,858,536 INFO 2026-06-04 20:53:54 MarkDuplicates Tracking 366378 as yet unmatched pairs. 10589 records in RAM. INFO 2026-06-04 20:53:55 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 1s. Last read position: chr8:143,859,923 INFO 2026-06-04 20:53:55 MarkDuplicates Tracking 365827 as yet unmatched pairs. 10038 records in RAM. INFO 2026-06-04 20:53:57 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 1s. Last read position: chr8:143,861,228 INFO 2026-06-04 20:53:57 MarkDuplicates Tracking 364623 as yet unmatched pairs. 8833 records in RAM. INFO 2026-06-04 20:53:58 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 0s. Last read position: chr8:143,862,228 INFO 2026-06-04 20:53:58 MarkDuplicates Tracking 364240 as yet unmatched pairs. 8449 records in RAM. INFO 2026-06-04 20:53:59 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 1s. Last read position: chr8:143,863,585 INFO 2026-06-04 20:53:59 MarkDuplicates Tracking 363838 as yet unmatched pairs. 8047 records in RAM. INFO 2026-06-04 20:54:00 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 0s. Last read position: chr8:143,864,839 INFO 2026-06-04 20:54:00 MarkDuplicates Tracking 363238 as yet unmatched pairs. 7446 records in RAM. INFO 2026-06-04 20:54:01 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 1s. Last read position: chr8:143,866,192 INFO 2026-06-04 20:54:01 MarkDuplicates Tracking 361796 as yet unmatched pairs. 6003 records in RAM. INFO 2026-06-04 20:54:02 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 1s. Last read position: chr8:143,919,564 INFO 2026-06-04 20:54:02 MarkDuplicates Tracking 360883 as yet unmatched pairs. 5090 records in RAM. INFO 2026-06-04 20:54:04 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 1s. Last read position: chr8:143,985,064 INFO 2026-06-04 20:54:04 MarkDuplicates Tracking 358412 as yet unmatched pairs. 2619 records in RAM. INFO 2026-06-04 20:54:05 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 1s. Last read position: chr8:144,509,820 INFO 2026-06-04 20:54:05 MarkDuplicates Tracking 356143 as yet unmatched pairs. 349 records in RAM. INFO 2026-06-04 20:54:07 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 1s. Last read position: chr9:19,376,337 INFO 2026-06-04 20:54:07 MarkDuplicates Tracking 354693 as yet unmatched pairs. 20458 records in RAM. INFO 2026-06-04 20:54:08 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 1s. Last read position: chr9:35,684,531 INFO 2026-06-04 20:54:08 MarkDuplicates Tracking 352946 as yet unmatched pairs. 18711 records in RAM. INFO 2026-06-04 20:54:10 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 1s. Last read position: chr9:73,163,515 INFO 2026-06-04 20:54:10 MarkDuplicates Tracking 351212 as yet unmatched pairs. 16926 records in RAM. INFO 2026-06-04 20:54:11 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 1s. Last read position: chr9:93,253,034 INFO 2026-06-04 20:54:11 MarkDuplicates Tracking 349736 as yet unmatched pairs. 15448 records in RAM. INFO 2026-06-04 20:54:12 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 1s. Last read position: chr9:104,786,891 INFO 2026-06-04 20:54:12 MarkDuplicates Tracking 347890 as yet unmatched pairs. 13598 records in RAM. INFO 2026-06-04 20:54:14 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 1s. Last read position: chr9:114,406,410 INFO 2026-06-04 20:54:14 MarkDuplicates Tracking 346005 as yet unmatched pairs. 11713 records in RAM. INFO 2026-06-04 20:54:15 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 1s. Last read position: chr9:125,672,397 INFO 2026-06-04 20:54:15 MarkDuplicates Tracking 344304 as yet unmatched pairs. 10010 records in RAM. INFO 2026-06-04 20:54:16 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 1s. Last read position: chr9:128,615,702 INFO 2026-06-04 20:54:16 MarkDuplicates Tracking 342573 as yet unmatched pairs. 8279 records in RAM. INFO 2026-06-04 20:54:17 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 1s. Last read position: chr9:131,476,345 INFO 2026-06-04 20:54:17 MarkDuplicates Tracking 340883 as yet unmatched pairs. 6572 records in RAM. INFO 2026-06-04 20:54:19 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 1s. Last read position: chr9:134,768,361 INFO 2026-06-04 20:54:19 MarkDuplicates Tracking 339461 as yet unmatched pairs. 5148 records in RAM. INFO 2026-06-04 20:54:20 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 1s. Last read position: chr9:136,823,555 INFO 2026-06-04 20:54:20 MarkDuplicates Tracking 337044 as yet unmatched pairs. 2730 records in RAM. INFO 2026-06-04 20:54:21 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 1s. Last read position: chr9:137,555,476 INFO 2026-06-04 20:54:21 MarkDuplicates Tracking 334622 as yet unmatched pairs. 306 records in RAM. INFO 2026-06-04 20:54:23 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 1s. Last read position: chr10:13,118,972 INFO 2026-06-04 20:54:23 MarkDuplicates Tracking 332961 as yet unmatched pairs. 18867 records in RAM. INFO 2026-06-04 20:54:24 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 1s. Last read position: chr10:30,349,195 INFO 2026-06-04 20:54:24 MarkDuplicates Tracking 331475 as yet unmatched pairs. 17376 records in RAM. INFO 2026-06-04 20:54:25 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 1s. Last read position: chr10:43,387,512 INFO 2026-06-04 20:54:25 MarkDuplicates Tracking 329839 as yet unmatched pairs. 15738 records in RAM. INFO 2026-06-04 20:54:26 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 1s. Last read position: chr10:59,852,678 INFO 2026-06-04 20:54:26 MarkDuplicates Tracking 329002 as yet unmatched pairs. 14900 records in RAM. INFO 2026-06-04 20:54:28 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 1s. Last read position: chr10:72,375,858 INFO 2026-06-04 20:54:28 MarkDuplicates Tracking 327046 as yet unmatched pairs. 12942 records in RAM. INFO 2026-06-04 20:54:29 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 1s. Last read position: chr10:79,347,498 INFO 2026-06-04 20:54:29 MarkDuplicates Tracking 326104 as yet unmatched pairs. 12000 records in RAM. INFO 2026-06-04 20:54:30 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 1s. Last read position: chr10:95,238,028 INFO 2026-06-04 20:54:30 MarkDuplicates Tracking 323419 as yet unmatched pairs. 9312 records in RAM. INFO 2026-06-04 20:54:32 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 1s. Last read position: chr10:102,141,020 INFO 2026-06-04 20:54:32 MarkDuplicates Tracking 321739 as yet unmatched pairs. 7629 records in RAM. INFO 2026-06-04 20:54:33 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 1s. Last read position: chr10:112,426,385 INFO 2026-06-04 20:54:33 MarkDuplicates Tracking 320289 as yet unmatched pairs. 6176 records in RAM. INFO 2026-06-04 20:54:35 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 1s. Last read position: chr10:121,479,908 INFO 2026-06-04 20:54:35 MarkDuplicates Tracking 318531 as yet unmatched pairs. 4414 records in RAM. INFO 2026-06-04 20:54:36 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 1s. Last read position: chr10:122,595,515 INFO 2026-06-04 20:54:36 MarkDuplicates Tracking 317963 as yet unmatched pairs. 3846 records in RAM. INFO 2026-06-04 20:54:37 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 1s. Last read position: chr10:122,621,111 INFO 2026-06-04 20:54:37 MarkDuplicates Tracking 317518 as yet unmatched pairs. 3401 records in RAM. INFO 2026-06-04 20:54:38 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 1s. Last read position: chr10:132,351,648 INFO 2026-06-04 20:54:38 MarkDuplicates Tracking 314821 as yet unmatched pairs. 697 records in RAM. INFO 2026-06-04 20:54:40 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 1s. Last read position: chr11:319,961 INFO 2026-06-04 20:54:40 MarkDuplicates Tracking 314824 as yet unmatched pairs. 34679 records in RAM. INFO 2026-06-04 20:54:42 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 1s. Last read position: chr11:834,576 INFO 2026-06-04 20:54:42 MarkDuplicates Tracking 311221 as yet unmatched pairs. 31075 records in RAM. INFO 2026-06-04 20:54:43 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 1s. Last read position: chr11:1,242,852 INFO 2026-06-04 20:54:43 MarkDuplicates Tracking 310008 as yet unmatched pairs. 29861 records in RAM. INFO 2026-06-04 20:54:45 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 1s. Last read position: chr11:1,246,750 INFO 2026-06-04 20:54:45 MarkDuplicates Tracking 309255 as yet unmatched pairs. 29108 records in RAM. INFO 2026-06-04 20:54:46 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 1s. Last read position: chr11:1,250,920 INFO 2026-06-04 20:54:46 MarkDuplicates Tracking 308401 as yet unmatched pairs. 28253 records in RAM. INFO 2026-06-04 20:54:47 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 1s. Last read position: chr11:6,217,621 INFO 2026-06-04 20:54:47 MarkDuplicates Tracking 306623 as yet unmatched pairs. 26472 records in RAM. INFO 2026-06-04 20:54:48 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 1s. Last read position: chr11:12,220,409 INFO 2026-06-04 20:54:48 MarkDuplicates Tracking 304569 as yet unmatched pairs. 24416 records in RAM. INFO 2026-06-04 20:54:50 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 1s. Last read position: chr11:34,079,665 INFO 2026-06-04 20:54:50 MarkDuplicates Tracking 303211 as yet unmatched pairs. 23057 records in RAM. INFO 2026-06-04 20:54:51 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 1s. Last read position: chr11:46,808,112 INFO 2026-06-04 20:54:51 MarkDuplicates Tracking 301534 as yet unmatched pairs. 21379 records in RAM. INFO 2026-06-04 20:54:52 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 1s. Last read position: chr11:59,576,828 INFO 2026-06-04 20:54:52 MarkDuplicates Tracking 299685 as yet unmatched pairs. 19530 records in RAM. INFO 2026-06-04 20:54:53 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 1s. Last read position: chr11:62,525,656 INFO 2026-06-04 20:54:53 MarkDuplicates Tracking 298211 as yet unmatched pairs. 18039 records in RAM. INFO 2026-06-04 20:54:55 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 1s. Last read position: chr11:64,230,825 INFO 2026-06-04 20:54:55 MarkDuplicates Tracking 296116 as yet unmatched pairs. 15942 records in RAM. INFO 2026-06-04 20:54:56 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 1s. Last read position: chr11:65,182,751 INFO 2026-06-04 20:54:56 MarkDuplicates Tracking 294376 as yet unmatched pairs. 14200 records in RAM. INFO 2026-06-04 20:54:57 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr11:65,861,425 INFO 2026-06-04 20:54:57 MarkDuplicates Tracking 292343 as yet unmatched pairs. 12165 records in RAM. INFO 2026-06-04 20:54:59 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 1s. Last read position: chr11:67,285,295 INFO 2026-06-04 20:54:59 MarkDuplicates Tracking 290909 as yet unmatched pairs. 10731 records in RAM. INFO 2026-06-04 20:55:00 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr11:68,936,882 INFO 2026-06-04 20:55:00 MarkDuplicates Tracking 288841 as yet unmatched pairs. 8663 records in RAM. INFO 2026-06-04 20:55:01 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 1s. Last read position: chr11:73,310,430 INFO 2026-06-04 20:55:01 MarkDuplicates Tracking 287089 as yet unmatched pairs. 6909 records in RAM. INFO 2026-06-04 20:55:03 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 1s. Last read position: chr11:85,958,967 INFO 2026-06-04 20:55:03 MarkDuplicates Tracking 285311 as yet unmatched pairs. 5131 records in RAM. INFO 2026-06-04 20:55:04 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 1s. Last read position: chr11:117,091,159 INFO 2026-06-04 20:55:04 MarkDuplicates Tracking 283702 as yet unmatched pairs. 3521 records in RAM. INFO 2026-06-04 20:55:05 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 1s. Last read position: chr11:121,558,633 INFO 2026-06-04 20:55:05 MarkDuplicates Tracking 281907 as yet unmatched pairs. 1726 records in RAM. INFO 2026-06-04 20:55:07 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 1s. Last read position: chr12:753,613 INFO 2026-06-04 20:55:07 MarkDuplicates Tracking 280431 as yet unmatched pairs. 31988 records in RAM. INFO 2026-06-04 20:55:09 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 1s. Last read position: chr12:6,769,939 INFO 2026-06-04 20:55:09 MarkDuplicates Tracking 278707 as yet unmatched pairs. 30263 records in RAM. INFO 2026-06-04 20:55:10 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 1s. Last read position: chr12:10,702,091 INFO 2026-06-04 20:55:10 MarkDuplicates Tracking 276596 as yet unmatched pairs. 28150 records in RAM. INFO 2026-06-04 20:55:12 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 1s. Last read position: chr12:32,576,288 INFO 2026-06-04 20:55:12 MarkDuplicates Tracking 275020 as yet unmatched pairs. 26573 records in RAM. INFO 2026-06-04 20:55:13 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 1s. Last read position: chr12:49,040,911 INFO 2026-06-04 20:55:13 MarkDuplicates Tracking 273440 as yet unmatched pairs. 24990 records in RAM. INFO 2026-06-04 20:55:15 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 1s. Last read position: chr12:49,741,590 INFO 2026-06-04 20:55:15 MarkDuplicates Tracking 271946 as yet unmatched pairs. 23496 records in RAM. INFO 2026-06-04 20:55:16 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 1s. Last read position: chr12:52,949,213 INFO 2026-06-04 20:55:16 MarkDuplicates Tracking 270967 as yet unmatched pairs. 22516 records in RAM. INFO 2026-06-04 20:55:18 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 1s. Last read position: chr12:54,281,871 INFO 2026-06-04 20:55:18 MarkDuplicates Tracking 269234 as yet unmatched pairs. 20781 records in RAM. INFO 2026-06-04 20:55:19 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 1s. Last read position: chr12:56,231,408 INFO 2026-06-04 20:55:19 MarkDuplicates Tracking 266898 as yet unmatched pairs. 18445 records in RAM. INFO 2026-06-04 20:55:20 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 1s. Last read position: chr12:57,175,946 INFO 2026-06-04 20:55:20 MarkDuplicates Tracking 265241 as yet unmatched pairs. 16788 records in RAM. INFO 2026-06-04 20:55:21 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 1s. Last read position: chr12:68,553,441 INFO 2026-06-04 20:55:21 MarkDuplicates Tracking 263432 as yet unmatched pairs. 14978 records in RAM. INFO 2026-06-04 20:55:23 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 1s. Last read position: chr12:95,474,209 INFO 2026-06-04 20:55:23 MarkDuplicates Tracking 261732 as yet unmatched pairs. 13274 records in RAM. INFO 2026-06-04 20:55:24 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 1s. Last read position: chr12:108,623,639 INFO 2026-06-04 20:55:24 MarkDuplicates Tracking 260010 as yet unmatched pairs. 11552 records in RAM. INFO 2026-06-04 20:55:25 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 1s. Last read position: chr12:112,314,527 INFO 2026-06-04 20:55:25 MarkDuplicates Tracking 258298 as yet unmatched pairs. 9839 records in RAM. INFO 2026-06-04 20:55:27 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 1s. Last read position: chr12:118,052,348 INFO 2026-06-04 20:55:27 MarkDuplicates Tracking 256432 as yet unmatched pairs. 7972 records in RAM. INFO 2026-06-04 20:55:28 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 1s. Last read position: chr12:121,004,146 INFO 2026-06-04 20:55:28 MarkDuplicates Tracking 254629 as yet unmatched pairs. 6169 records in RAM. INFO 2026-06-04 20:55:29 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 1s. Last read position: chr12:122,702,459 INFO 2026-06-04 20:55:29 MarkDuplicates Tracking 253536 as yet unmatched pairs. 5074 records in RAM. INFO 2026-06-04 20:55:30 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 1s. Last read position: chr12:124,346,635 INFO 2026-06-04 20:55:30 MarkDuplicates Tracking 251362 as yet unmatched pairs. 2900 records in RAM. INFO 2026-06-04 20:55:32 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 1s. Last read position: chr12:132,571,441 INFO 2026-06-04 20:55:32 MarkDuplicates Tracking 249299 as yet unmatched pairs. 835 records in RAM. INFO 2026-06-04 20:55:33 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 1s. Last read position: chr13:27,256,446 INFO 2026-06-04 20:55:33 MarkDuplicates Tracking 247424 as yet unmatched pairs. 8827 records in RAM. INFO 2026-06-04 20:55:34 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 1s. Last read position: chr13:39,013,652 INFO 2026-06-04 20:55:34 MarkDuplicates Tracking 245775 as yet unmatched pairs. 7176 records in RAM. INFO 2026-06-04 20:55:35 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 1s. Last read position: chr13:48,045,666 INFO 2026-06-04 20:55:35 MarkDuplicates Tracking 243715 as yet unmatched pairs. 5113 records in RAM. INFO 2026-06-04 20:55:37 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 1s. Last read position: chr13:75,359,837 INFO 2026-06-04 20:55:37 MarkDuplicates Tracking 242175 as yet unmatched pairs. 3572 records in RAM. INFO 2026-06-04 20:55:38 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 1s. Last read position: chr13:110,174,492 INFO 2026-06-04 20:55:38 MarkDuplicates Tracking 240731 as yet unmatched pairs. 2122 records in RAM. INFO 2026-06-04 20:55:39 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 1s. Last read position: chr14:20,408,320 INFO 2026-06-04 20:55:39 MarkDuplicates Tracking 238506 as yet unmatched pairs. 14106 records in RAM. INFO 2026-06-04 20:55:41 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr14:23,323,447 INFO 2026-06-04 20:55:41 MarkDuplicates Tracking 236744 as yet unmatched pairs. 12342 records in RAM. INFO 2026-06-04 20:55:43 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 1s. Last read position: chr14:35,401,997 INFO 2026-06-04 20:55:43 MarkDuplicates Tracking 234773 as yet unmatched pairs. 10371 records in RAM. INFO 2026-06-04 20:55:44 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 1s. Last read position: chr14:57,246,786 INFO 2026-06-04 20:55:44 MarkDuplicates Tracking 233129 as yet unmatched pairs. 8724 records in RAM. INFO 2026-06-04 20:55:45 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 1s. Last read position: chr14:69,053,851 INFO 2026-06-04 20:55:45 MarkDuplicates Tracking 231434 as yet unmatched pairs. 7029 records in RAM. INFO 2026-06-04 20:55:47 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 1s. Last read position: chr14:76,763,001 INFO 2026-06-04 20:55:47 MarkDuplicates Tracking 229610 as yet unmatched pairs. 5203 records in RAM. INFO 2026-06-04 20:55:48 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 1s. Last read position: chr14:99,517,108 INFO 2026-06-04 20:55:48 MarkDuplicates Tracking 228330 as yet unmatched pairs. 3880 records in RAM. INFO 2026-06-04 20:55:50 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 1s. Last read position: chr14:104,770,777 INFO 2026-06-04 20:55:50 MarkDuplicates Tracking 226672 as yet unmatched pairs. 2221 records in RAM. INFO 2026-06-04 20:55:51 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:05:20s. Time for last 1,000,000: 1s. Last read position: chr14:105,708,067 INFO 2026-06-04 20:55:51 MarkDuplicates Tracking 225040 as yet unmatched pairs. 587 records in RAM. INFO 2026-06-04 20:55:53 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 1s. Last read position: chr15:32,732,141 INFO 2026-06-04 20:55:53 MarkDuplicates Tracking 224704 as yet unmatched pairs. 12926 records in RAM. INFO 2026-06-04 20:55:54 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 1s. Last read position: chr15:40,844,754 INFO 2026-06-04 20:55:54 MarkDuplicates Tracking 222172 as yet unmatched pairs. 10392 records in RAM. INFO 2026-06-04 20:55:55 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 1s. Last read position: chr15:44,651,712 INFO 2026-06-04 20:55:55 MarkDuplicates Tracking 220319 as yet unmatched pairs. 8537 records in RAM. INFO 2026-06-04 20:55:56 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 1s. Last read position: chr15:59,769,077 INFO 2026-06-04 20:55:56 MarkDuplicates Tracking 218727 as yet unmatched pairs. 6943 records in RAM. INFO 2026-06-04 20:55:58 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 1s. Last read position: chr15:69,360,017 INFO 2026-06-04 20:55:58 MarkDuplicates Tracking 217014 as yet unmatched pairs. 5229 records in RAM. INFO 2026-06-04 20:55:59 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 1s. Last read position: chr15:75,206,055 INFO 2026-06-04 20:55:59 MarkDuplicates Tracking 215494 as yet unmatched pairs. 3706 records in RAM. INFO 2026-06-04 20:56:00 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 1s. Last read position: chr15:84,669,996 INFO 2026-06-04 20:56:00 MarkDuplicates Tracking 214419 as yet unmatched pairs. 2629 records in RAM. INFO 2026-06-04 20:56:01 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 1s. Last read position: chr15:92,162,963 INFO 2026-06-04 20:56:01 MarkDuplicates Tracking 212264 as yet unmatched pairs. 474 records in RAM. INFO 2026-06-04 20:56:03 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 1s. Last read position: chr16:666,518 INFO 2026-06-04 20:56:03 MarkDuplicates Tracking 210784 as yet unmatched pairs. 29087 records in RAM. INFO 2026-06-04 20:56:04 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 1s. Last read position: chr16:2,009,575 INFO 2026-06-04 20:56:04 MarkDuplicates Tracking 208625 as yet unmatched pairs. 26927 records in RAM. INFO 2026-06-04 20:56:05 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 1s. Last read position: chr16:2,763,002 INFO 2026-06-04 20:56:05 MarkDuplicates Tracking 206870 as yet unmatched pairs. 25172 records in RAM. INFO 2026-06-04 20:56:07 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 1s. Last read position: chr16:3,549,191 INFO 2026-06-04 20:56:07 MarkDuplicates Tracking 205014 as yet unmatched pairs. 23316 records in RAM. INFO 2026-06-04 20:56:08 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 1s. Last read position: chr16:11,387,221 INFO 2026-06-04 20:56:08 MarkDuplicates Tracking 203232 as yet unmatched pairs. 21533 records in RAM. INFO 2026-06-04 20:56:09 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 1s. Last read position: chr16:15,130,285 INFO 2026-06-04 20:56:09 MarkDuplicates Tracking 202127 as yet unmatched pairs. 20428 records in RAM. INFO 2026-06-04 20:56:10 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 0s. Last read position: chr16:16,393,625 INFO 2026-06-04 20:56:10 MarkDuplicates Tracking 201569 as yet unmatched pairs. 19870 records in RAM. INFO 2026-06-04 20:56:11 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 1s. Last read position: chr16:18,890,877 INFO 2026-06-04 20:56:11 MarkDuplicates Tracking 200481 as yet unmatched pairs. 18782 records in RAM. INFO 2026-06-04 20:56:12 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 1s. Last read position: chr16:21,448,574 INFO 2026-06-04 20:56:12 MarkDuplicates Tracking 199718 as yet unmatched pairs. 18018 records in RAM. INFO 2026-06-04 20:56:13 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 1s. Last read position: chr16:22,429,840 INFO 2026-06-04 20:56:13 MarkDuplicates Tracking 199011 as yet unmatched pairs. 17311 records in RAM. INFO 2026-06-04 20:56:14 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:05:43s. Time for last 1,000,000: 0s. Last read position: chr16:23,105,449 INFO 2026-06-04 20:56:14 MarkDuplicates Tracking 198700 as yet unmatched pairs. 17000 records in RAM. INFO 2026-06-04 20:56:16 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 1s. Last read position: chr16:28,826,377 INFO 2026-06-04 20:56:16 MarkDuplicates Tracking 197193 as yet unmatched pairs. 15493 records in RAM. INFO 2026-06-04 20:56:17 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 1s. Last read position: chr16:29,483,897 INFO 2026-06-04 20:56:17 MarkDuplicates Tracking 196646 as yet unmatched pairs. 14945 records in RAM. INFO 2026-06-04 20:56:19 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 1s. Last read position: chr16:29,990,949 INFO 2026-06-04 20:56:19 MarkDuplicates Tracking 194995 as yet unmatched pairs. 13294 records in RAM. INFO 2026-06-04 20:56:20 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 1s. Last read position: chr16:30,262,071 INFO 2026-06-04 20:56:20 MarkDuplicates Tracking 193743 as yet unmatched pairs. 12041 records in RAM. INFO 2026-06-04 20:56:21 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 1s. Last read position: chr16:31,078,783 INFO 2026-06-04 20:56:21 MarkDuplicates Tracking 192022 as yet unmatched pairs. 10306 records in RAM. INFO 2026-06-04 20:56:23 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 1s. Last read position: chr16:50,749,579 INFO 2026-06-04 20:56:23 MarkDuplicates Tracking 190508 as yet unmatched pairs. 8783 records in RAM. INFO 2026-06-04 20:56:24 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 1s. Last read position: chr16:58,197,678 INFO 2026-06-04 20:56:24 MarkDuplicates Tracking 188886 as yet unmatched pairs. 7160 records in RAM. INFO 2026-06-04 20:56:26 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 1s. Last read position: chr16:69,566,269 INFO 2026-06-04 20:56:26 MarkDuplicates Tracking 186913 as yet unmatched pairs. 5185 records in RAM. INFO 2026-06-04 20:56:27 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 1s. Last read position: chr16:81,724,502 INFO 2026-06-04 20:56:27 MarkDuplicates Tracking 185059 as yet unmatched pairs. 3327 records in RAM. INFO 2026-06-04 20:56:28 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 1s. Last read position: chr16:88,735,202 INFO 2026-06-04 20:56:28 MarkDuplicates Tracking 183012 as yet unmatched pairs. 1278 records in RAM. INFO 2026-06-04 20:57:27 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 58s. Last read position: chr17:1,422,895 INFO 2026-06-04 20:57:27 MarkDuplicates Tracking 181352 as yet unmatched pairs. 64474 records in RAM. INFO 2026-06-04 20:57:28 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:06:57s. Time for last 1,000,000: 1s. Last read position: chr17:4,789,526 INFO 2026-06-04 20:57:28 MarkDuplicates Tracking 179368 as yet unmatched pairs. 62490 records in RAM. INFO 2026-06-04 20:57:30 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 1s. Last read position: chr17:7,343,400 INFO 2026-06-04 20:57:30 MarkDuplicates Tracking 177715 as yet unmatched pairs. 60834 records in RAM. INFO 2026-06-04 20:57:31 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 1s. Last read position: chr17:7,848,344 INFO 2026-06-04 20:57:31 MarkDuplicates Tracking 176367 as yet unmatched pairs. 59486 records in RAM. INFO 2026-06-04 20:57:33 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 1s. Last read position: chr17:16,382,366 INFO 2026-06-04 20:57:33 MarkDuplicates Tracking 174645 as yet unmatched pairs. 57763 records in RAM. INFO 2026-06-04 20:57:34 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:07:03s. Time for last 1,000,000: 1s. Last read position: chr17:28,043,011 INFO 2026-06-04 20:57:34 MarkDuplicates Tracking 173006 as yet unmatched pairs. 56123 records in RAM. INFO 2026-06-04 20:57:36 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:07:04s. Time for last 1,000,000: 1s. Last read position: chr17:31,488,215 INFO 2026-06-04 20:57:36 MarkDuplicates Tracking 171235 as yet unmatched pairs. 54351 records in RAM. INFO 2026-06-04 20:57:37 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 1s. Last read position: chr17:38,122,829 INFO 2026-06-04 20:57:37 MarkDuplicates Tracking 169487 as yet unmatched pairs. 52601 records in RAM. INFO 2026-06-04 20:57:38 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:07:07s. Time for last 1,000,000: 1s. Last read position: chr17:39,711,937 INFO 2026-06-04 20:57:38 MarkDuplicates Tracking 168049 as yet unmatched pairs. 51162 records in RAM. INFO 2026-06-04 20:57:40 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:07:09s. Time for last 1,000,000: 1s. Last read position: chr17:40,630,714 INFO 2026-06-04 20:57:40 MarkDuplicates Tracking 166112 as yet unmatched pairs. 49225 records in RAM. INFO 2026-06-04 20:57:42 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 1s. Last read position: chr17:42,795,151 INFO 2026-06-04 20:57:42 MarkDuplicates Tracking 164561 as yet unmatched pairs. 47673 records in RAM. INFO 2026-06-04 20:57:43 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:07:12s. Time for last 1,000,000: 1s. Last read position: chr17:45,453,558 INFO 2026-06-04 20:57:43 MarkDuplicates Tracking 162582 as yet unmatched pairs. 45694 records in RAM. INFO 2026-06-04 20:57:44 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 1s. Last read position: chr17:50,140,146 INFO 2026-06-04 20:57:44 MarkDuplicates Tracking 160889 as yet unmatched pairs. 43999 records in RAM. INFO 2026-06-04 20:57:46 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:07:14s. Time for last 1,000,000: 1s. Last read position: chr17:50,186,699 INFO 2026-06-04 20:57:46 MarkDuplicates Tracking 162876 as yet unmatched pairs. 45986 records in RAM. INFO 2026-06-04 20:57:47 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:07:16s. Time for last 1,000,000: 1s. Last read position: chr17:50,187,483 INFO 2026-06-04 20:57:47 MarkDuplicates Tracking 166819 as yet unmatched pairs. 49929 records in RAM. INFO 2026-06-04 20:57:48 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:07:17s. Time for last 1,000,000: 1s. Last read position: chr17:50,188,542 INFO 2026-06-04 20:57:48 MarkDuplicates Tracking 163395 as yet unmatched pairs. 46505 records in RAM. INFO 2026-06-04 20:57:50 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:07:18s. Time for last 1,000,000: 1s. Last read position: chr17:50,188,980 INFO 2026-06-04 20:57:50 MarkDuplicates Tracking 160818 as yet unmatched pairs. 43927 records in RAM. INFO 2026-06-04 20:57:51 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:07:20s. Time for last 1,000,000: 1s. Last read position: chr17:50,189,496 INFO 2026-06-04 20:57:51 MarkDuplicates Tracking 160267 as yet unmatched pairs. 43374 records in RAM. INFO 2026-06-04 20:57:53 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:07:21s. Time for last 1,000,000: 1s. Last read position: chr17:50,190,007 INFO 2026-06-04 20:57:53 MarkDuplicates Tracking 157484 as yet unmatched pairs. 40591 records in RAM. INFO 2026-06-04 20:57:54 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:07:23s. Time for last 1,000,000: 1s. Last read position: chr17:50,190,445 INFO 2026-06-04 20:57:54 MarkDuplicates Tracking 155835 as yet unmatched pairs. 38942 records in RAM. INFO 2026-06-04 20:57:56 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:07:24s. Time for last 1,000,000: 1s. Last read position: chr17:50,192,004 INFO 2026-06-04 20:57:56 MarkDuplicates Tracking 158247 as yet unmatched pairs. 41354 records in RAM. INFO 2026-06-04 20:57:57 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:07:26s. Time for last 1,000,000: 1s. Last read position: chr17:50,193,942 INFO 2026-06-04 20:57:57 MarkDuplicates Tracking 151031 as yet unmatched pairs. 34138 records in RAM. INFO 2026-06-04 20:57:59 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 1s. Last read position: chr17:50,194,415 INFO 2026-06-04 20:57:59 MarkDuplicates Tracking 152327 as yet unmatched pairs. 35434 records in RAM. INFO 2026-06-04 20:58:00 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:07:28s. Time for last 1,000,000: 1s. Last read position: chr17:50,195,268 INFO 2026-06-04 20:58:00 MarkDuplicates Tracking 147406 as yet unmatched pairs. 30513 records in RAM. INFO 2026-06-04 20:58:01 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:07:30s. Time for last 1,000,000: 1s. Last read position: chr17:50,195,961 INFO 2026-06-04 20:58:01 MarkDuplicates Tracking 152128 as yet unmatched pairs. 35235 records in RAM. INFO 2026-06-04 20:58:03 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:07:31s. Time for last 1,000,000: 1s. Last read position: chr17:50,196,334 INFO 2026-06-04 20:58:03 MarkDuplicates Tracking 150983 as yet unmatched pairs. 34090 records in RAM. INFO 2026-06-04 20:58:05 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:07:33s. Time for last 1,000,000: 1s. Last read position: chr17:50,197,215 INFO 2026-06-04 20:58:05 MarkDuplicates Tracking 146993 as yet unmatched pairs. 30100 records in RAM. INFO 2026-06-04 20:58:06 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:07:35s. Time for last 1,000,000: 1s. Last read position: chr17:50,199,259 INFO 2026-06-04 20:58:06 MarkDuplicates Tracking 135928 as yet unmatched pairs. 19035 records in RAM. INFO 2026-06-04 20:58:07 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:07:36s. Time for last 1,000,000: 1s. Last read position: chr17:50,385,160 INFO 2026-06-04 20:58:07 MarkDuplicates Tracking 130656 as yet unmatched pairs. 13763 records in RAM. INFO 2026-06-04 20:58:09 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:07:38s. Time for last 1,000,000: 2s. Last read position: chr17:59,647,401 INFO 2026-06-04 20:58:09 MarkDuplicates Tracking 129154 as yet unmatched pairs. 12260 records in RAM. INFO 2026-06-04 20:58:11 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:07:39s. Time for last 1,000,000: 1s. Last read position: chr17:64,506,104 INFO 2026-06-04 20:58:11 MarkDuplicates Tracking 126834 as yet unmatched pairs. 9940 records in RAM. INFO 2026-06-04 20:58:12 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:07:41s. Time for last 1,000,000: 1s. Last read position: chr17:75,238,122 INFO 2026-06-04 20:58:12 MarkDuplicates Tracking 125358 as yet unmatched pairs. 8454 records in RAM. INFO 2026-06-04 20:58:14 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:07:42s. Time for last 1,000,000: 1s. Last read position: chr17:76,280,345 INFO 2026-06-04 20:58:14 MarkDuplicates Tracking 123625 as yet unmatched pairs. 6721 records in RAM. INFO 2026-06-04 20:58:15 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:07:44s. Time for last 1,000,000: 1s. Last read position: chr17:80,073,808 INFO 2026-06-04 20:58:15 MarkDuplicates Tracking 121765 as yet unmatched pairs. 4860 records in RAM. INFO 2026-06-04 20:58:16 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:07:45s. Time for last 1,000,000: 1s. Last read position: chr17:81,512,275 INFO 2026-06-04 20:58:16 MarkDuplicates Tracking 119693 as yet unmatched pairs. 2782 records in RAM. INFO 2026-06-04 20:58:18 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:07:46s. Time for last 1,000,000: 1s. Last read position: chr17:82,322,162 INFO 2026-06-04 20:58:18 MarkDuplicates Tracking 117518 as yet unmatched pairs. 607 records in RAM. INFO 2026-06-04 20:58:19 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:07:48s. Time for last 1,000,000: 1s. Last read position: chr18:13,030,447 INFO 2026-06-04 20:58:19 MarkDuplicates Tracking 115860 as yet unmatched pairs. 3632 records in RAM. INFO 2026-06-04 20:58:20 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:07:49s. Time for last 1,000,000: 1s. Last read position: chr18:49,488,544 INFO 2026-06-04 20:58:20 MarkDuplicates Tracking 114446 as yet unmatched pairs. 2215 records in RAM. INFO 2026-06-04 20:58:22 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:07:50s. Time for last 1,000,000: 1s. Last read position: chr19:66,245 INFO 2026-06-04 20:58:22 MarkDuplicates Tracking 112230 as yet unmatched pairs. 51534 records in RAM. INFO 2026-06-04 20:58:23 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:07:52s. Time for last 1,000,000: 1s. Last read position: chr19:1,113,537 INFO 2026-06-04 20:58:23 MarkDuplicates Tracking 110070 as yet unmatched pairs. 49372 records in RAM. INFO 2026-06-04 20:58:24 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:07:53s. Time for last 1,000,000: 1s. Last read position: chr19:1,854,567 INFO 2026-06-04 20:58:24 MarkDuplicates Tracking 108496 as yet unmatched pairs. 47798 records in RAM. INFO 2026-06-04 20:58:26 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:07:54s. Time for last 1,000,000: 1s. Last read position: chr19:3,449,094 INFO 2026-06-04 20:58:26 MarkDuplicates Tracking 106374 as yet unmatched pairs. 45676 records in RAM. INFO 2026-06-04 20:58:27 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:07:56s. Time for last 1,000,000: 1s. Last read position: chr19:5,119,660 INFO 2026-06-04 20:58:27 MarkDuplicates Tracking 104563 as yet unmatched pairs. 43862 records in RAM. INFO 2026-06-04 20:58:28 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:07:57s. Time for last 1,000,000: 1s. Last read position: chr19:6,751,237 INFO 2026-06-04 20:58:28 MarkDuplicates Tracking 102942 as yet unmatched pairs. 42241 records in RAM. INFO 2026-06-04 20:58:30 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:07:58s. Time for last 1,000,000: 1s. Last read position: chr19:9,969,893 INFO 2026-06-04 20:58:30 MarkDuplicates Tracking 100621 as yet unmatched pairs. 39919 records in RAM. INFO 2026-06-04 20:58:31 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:07:59s. Time for last 1,000,000: 1s. Last read position: chr19:11,030,871 INFO 2026-06-04 20:58:31 MarkDuplicates Tracking 98947 as yet unmatched pairs. 38245 records in RAM. INFO 2026-06-04 20:58:33 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:08:01s. Time for last 1,000,000: 1s. Last read position: chr19:12,943,844 INFO 2026-06-04 20:58:33 MarkDuplicates Tracking 97573 as yet unmatched pairs. 36871 records in RAM. INFO 2026-06-04 20:58:34 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:08:03s. Time for last 1,000,000: 1s. Last read position: chr19:14,516,796 INFO 2026-06-04 20:58:34 MarkDuplicates Tracking 96442 as yet unmatched pairs. 35739 records in RAM. INFO 2026-06-04 20:58:35 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:08:04s. Time for last 1,000,000: 1s. Last read position: chr19:15,272,978 INFO 2026-06-04 20:58:35 MarkDuplicates Tracking 94146 as yet unmatched pairs. 33443 records in RAM. INFO 2026-06-04 20:58:36 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 1s. Last read position: chr19:17,520,958 INFO 2026-06-04 20:58:36 MarkDuplicates Tracking 91827 as yet unmatched pairs. 31122 records in RAM. INFO 2026-06-04 20:58:37 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:08:06s. Time for last 1,000,000: 1s. Last read position: chr19:18,856,036 INFO 2026-06-04 20:58:37 MarkDuplicates Tracking 90171 as yet unmatched pairs. 29453 records in RAM. INFO 2026-06-04 20:58:39 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:08:07s. Time for last 1,000,000: 1s. Last read position: chr19:35,011,466 INFO 2026-06-04 20:58:39 MarkDuplicates Tracking 88346 as yet unmatched pairs. 27627 records in RAM. INFO 2026-06-04 20:58:40 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:08:09s. Time for last 1,000,000: 1s. Last read position: chr19:38,082,913 INFO 2026-06-04 20:58:40 MarkDuplicates Tracking 85982 as yet unmatched pairs. 25262 records in RAM. INFO 2026-06-04 20:58:41 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:08:10s. Time for last 1,000,000: 1s. Last read position: chr19:39,407,894 INFO 2026-06-04 20:58:41 MarkDuplicates Tracking 84754 as yet unmatched pairs. 24034 records in RAM. INFO 2026-06-04 20:58:43 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:08:11s. Time for last 1,000,000: 1s. Last read position: chr19:39,877,918 INFO 2026-06-04 20:58:43 MarkDuplicates Tracking 82353 as yet unmatched pairs. 21633 records in RAM. INFO 2026-06-04 20:58:44 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:08:13s. Time for last 1,000,000: 1s. Last read position: chr19:39,943,532 INFO 2026-06-04 20:58:44 MarkDuplicates Tracking 80550 as yet unmatched pairs. 19830 records in RAM. INFO 2026-06-04 20:58:46 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:08:15s. Time for last 1,000,000: 1s. Last read position: chr19:41,715,109 INFO 2026-06-04 20:58:46 MarkDuplicates Tracking 79251 as yet unmatched pairs. 18531 records in RAM. INFO 2026-06-04 20:58:47 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 1s. Last read position: chr19:42,272,927 INFO 2026-06-04 20:58:47 MarkDuplicates Tracking 77117 as yet unmatched pairs. 16397 records in RAM. INFO 2026-06-04 20:58:49 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:08:18s. Time for last 1,000,000: 1s. Last read position: chr19:44,759,464 INFO 2026-06-04 20:58:49 MarkDuplicates Tracking 75336 as yet unmatched pairs. 14604 records in RAM. INFO 2026-06-04 20:58:51 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 1s. Last read position: chr19:45,825,219 INFO 2026-06-04 20:58:51 MarkDuplicates Tracking 73096 as yet unmatched pairs. 12360 records in RAM. INFO 2026-06-04 20:58:52 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 1s. Last read position: chr19:48,470,606 INFO 2026-06-04 20:58:52 MarkDuplicates Tracking 71049 as yet unmatched pairs. 10312 records in RAM. INFO 2026-06-04 20:58:53 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:08:22s. Time for last 1,000,000: 1s. Last read position: chr19:49,459,827 INFO 2026-06-04 20:58:53 MarkDuplicates Tracking 69074 as yet unmatched pairs. 8337 records in RAM. INFO 2026-06-04 20:58:55 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 1s. Last read position: chr19:49,861,804 INFO 2026-06-04 20:58:55 MarkDuplicates Tracking 67420 as yet unmatched pairs. 6682 records in RAM. INFO 2026-06-04 20:58:56 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:08:24s. Time for last 1,000,000: 1s. Last read position: chr19:52,212,749 INFO 2026-06-04 20:58:56 MarkDuplicates Tracking 65353 as yet unmatched pairs. 4615 records in RAM. INFO 2026-06-04 20:58:57 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:08:26s. Time for last 1,000,000: 1s. Last read position: chr19:54,666,298 INFO 2026-06-04 20:58:57 MarkDuplicates Tracking 63650 as yet unmatched pairs. 2911 records in RAM. INFO 2026-06-04 20:58:58 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:08:27s. Time for last 1,000,000: 1s. Last read position: chr19:56,087,962 INFO 2026-06-04 20:58:58 MarkDuplicates Tracking 61813 as yet unmatched pairs. 1073 records in RAM. INFO 2026-06-04 20:59:00 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:08:28s. Time for last 1,000,000: 1s. Last read position: chr20:2,838,365 INFO 2026-06-04 20:59:00 MarkDuplicates Tracking 60024 as yet unmatched pairs. 14136 records in RAM. INFO 2026-06-04 20:59:01 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 1s. Last read position: chr20:17,641,856 INFO 2026-06-04 20:59:01 MarkDuplicates Tracking 58300 as yet unmatched pairs. 12411 records in RAM. INFO 2026-06-04 20:59:02 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:08:31s. Time for last 1,000,000: 1s. Last read position: chr20:31,547,940 INFO 2026-06-04 20:59:02 MarkDuplicates Tracking 56699 as yet unmatched pairs. 10808 records in RAM. INFO 2026-06-04 20:59:04 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 1s. Last read position: chr20:35,714,221 INFO 2026-06-04 20:59:04 MarkDuplicates Tracking 55147 as yet unmatched pairs. 9255 records in RAM. INFO 2026-06-04 20:59:05 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:08:33s. Time for last 1,000,000: 1s. Last read position: chr20:44,746,256 INFO 2026-06-04 20:59:05 MarkDuplicates Tracking 53117 as yet unmatched pairs. 7224 records in RAM. INFO 2026-06-04 20:59:06 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 1s. Last read position: chr20:50,096,720 INFO 2026-06-04 20:59:06 MarkDuplicates Tracking 51248 as yet unmatched pairs. 5353 records in RAM. INFO 2026-06-04 20:59:07 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:08:36s. Time for last 1,000,000: 1s. Last read position: chr20:62,139,679 INFO 2026-06-04 20:59:07 MarkDuplicates Tracking 49128 as yet unmatched pairs. 3230 records in RAM. INFO 2026-06-04 20:59:09 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 1s. Last read position: chr20:63,563,936 INFO 2026-06-04 20:59:09 MarkDuplicates Tracking 47329 as yet unmatched pairs. 1429 records in RAM. INFO 2026-06-04 20:59:10 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:08:38s. Time for last 1,000,000: 1s. Last read position: chr21:8,214,506 INFO 2026-06-04 20:59:10 MarkDuplicates Tracking 45744 as yet unmatched pairs. 11540 records in RAM. INFO 2026-06-04 20:59:11 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 1s. Last read position: chr21:8,217,192 INFO 2026-06-04 20:59:11 MarkDuplicates Tracking 44556 as yet unmatched pairs. 10333 records in RAM. INFO 2026-06-04 20:59:12 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:08:41s. Time for last 1,000,000: 1s. Last read position: chr21:8,258,974 INFO 2026-06-04 20:59:12 MarkDuplicates Tracking 44295 as yet unmatched pairs. 10071 records in RAM. INFO 2026-06-04 20:59:13 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:08:42s. Time for last 1,000,000: 1s. Last read position: chr21:8,399,091 INFO 2026-06-04 20:59:13 MarkDuplicates Tracking 44561 as yet unmatched pairs. 10335 records in RAM. INFO 2026-06-04 20:59:15 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:08:44s. Time for last 1,000,000: 1s. Last read position: chr21:8,441,961 INFO 2026-06-04 20:59:15 MarkDuplicates Tracking 43664 as yet unmatched pairs. 9430 records in RAM. INFO 2026-06-04 20:59:16 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:08:45s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,595 INFO 2026-06-04 20:59:16 MarkDuplicates Tracking 41477 as yet unmatched pairs. 7242 records in RAM. INFO 2026-06-04 20:59:18 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:08:46s. Time for last 1,000,000: 1s. Last read position: chr21:33,557,206 INFO 2026-06-04 20:59:18 MarkDuplicates Tracking 39869 as yet unmatched pairs. 5634 records in RAM. INFO 2026-06-04 20:59:19 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 1s. Last read position: chr21:41,942,144 INFO 2026-06-04 20:59:19 MarkDuplicates Tracking 37782 as yet unmatched pairs. 3547 records in RAM. INFO 2026-06-04 20:59:20 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 1s. Last read position: chr21:45,512,208 INFO 2026-06-04 20:59:20 MarkDuplicates Tracking 36304 as yet unmatched pairs. 2068 records in RAM. INFO 2026-06-04 20:59:22 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 1s. Last read position: chr22:17,582,690 INFO 2026-06-04 20:59:22 MarkDuplicates Tracking 34175 as yet unmatched pairs. 12018 records in RAM. INFO 2026-06-04 20:59:23 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:08:52s. Time for last 1,000,000: 1s. Last read position: chr22:23,767,536 INFO 2026-06-04 20:59:23 MarkDuplicates Tracking 32630 as yet unmatched pairs. 10473 records in RAM. INFO 2026-06-04 20:59:24 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:08:53s. Time for last 1,000,000: 1s. Last read position: chr22:29,419,167 INFO 2026-06-04 20:59:24 MarkDuplicates Tracking 30384 as yet unmatched pairs. 8227 records in RAM. INFO 2026-06-04 20:59:26 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 1s. Last read position: chr22:36,289,224 INFO 2026-06-04 20:59:26 MarkDuplicates Tracking 28761 as yet unmatched pairs. 6604 records in RAM. INFO 2026-06-04 20:59:27 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:08:56s. Time for last 1,000,000: 1s. Last read position: chr22:38,486,409 INFO 2026-06-04 20:59:27 MarkDuplicates Tracking 26768 as yet unmatched pairs. 4611 records in RAM. INFO 2026-06-04 20:59:28 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:08:57s. Time for last 1,000,000: 1s. Last read position: chr22:42,384,545 INFO 2026-06-04 20:59:28 MarkDuplicates Tracking 24997 as yet unmatched pairs. 2840 records in RAM. INFO 2026-06-04 20:59:29 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:08:58s. Time for last 1,000,000: 1s. Last read position: chr22:50,468,406 INFO 2026-06-04 20:59:29 MarkDuplicates Tracking 23103 as yet unmatched pairs. 946 records in RAM. INFO 2026-06-04 20:59:31 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:08:59s. Time for last 1,000,000: 1s. Last read position: chrX:16,595,472 INFO 2026-06-04 20:59:31 MarkDuplicates Tracking 20859 as yet unmatched pairs. 12056 records in RAM. INFO 2026-06-04 20:59:32 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:09:01s. Time for last 1,000,000: 1s. Last read position: chrX:41,923,000 INFO 2026-06-04 20:59:32 MarkDuplicates Tracking 19324 as yet unmatched pairs. 10506 records in RAM. INFO 2026-06-04 20:59:33 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:09:02s. Time for last 1,000,000: 1s. Last read position: chrX:49,174,392 INFO 2026-06-04 20:59:33 MarkDuplicates Tracking 17759 as yet unmatched pairs. 8936 records in RAM. INFO 2026-06-04 20:59:35 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:09:03s. Time for last 1,000,000: 1s. Last read position: chrX:68,600,230 INFO 2026-06-04 20:59:35 MarkDuplicates Tracking 15838 as yet unmatched pairs. 7015 records in RAM. INFO 2026-06-04 20:59:36 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:09:04s. Time for last 1,000,000: 1s. Last read position: chrX:95,131,958 INFO 2026-06-04 20:59:36 MarkDuplicates Tracking 14263 as yet unmatched pairs. 5439 records in RAM. INFO 2026-06-04 20:59:37 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:09:06s. Time for last 1,000,000: 1s. Last read position: chrX:129,925,945 INFO 2026-06-04 20:59:37 MarkDuplicates Tracking 12635 as yet unmatched pairs. 3811 records in RAM. INFO 2026-06-04 20:59:38 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:09:07s. Time for last 1,000,000: 1s. Last read position: chrX:153,955,278 INFO 2026-06-04 20:59:38 MarkDuplicates Tracking 10893 as yet unmatched pairs. 2067 records in RAM. INFO 2026-06-04 20:59:40 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 1s. Last read position: chrX:154,645,841 INFO 2026-06-04 20:59:40 MarkDuplicates Tracking 9018 as yet unmatched pairs. 192 records in RAM. INFO 2026-06-04 20:59:41 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:09:09s. Time for last 1,000,000: 0s. Last read position: GL000220.1:114,206 INFO 2026-06-04 20:59:41 MarkDuplicates Tracking 8604 as yet unmatched pairs. 3767 records in RAM. INFO 2026-06-04 20:59:42 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:09:10s. Time for last 1,000,000: 1s. Last read position: GL000220.1:157,836 INFO 2026-06-04 20:59:42 MarkDuplicates Tracking 5075 as yet unmatched pairs. 237 records in RAM. INFO 2026-06-04 20:59:43 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:09:12s. Time for last 1,000,000: 1s. Last read position: GL000220.1:160,314 INFO 2026-06-04 20:59:43 MarkDuplicates Tracking 4843 as yet unmatched pairs. 5 records in RAM. INFO 2026-06-04 20:59:44 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:09:13s. Time for last 1,000,000: 1s. Last read position: KI270733.1:131,060 INFO 2026-06-04 20:59:44 MarkDuplicates Tracking 2214 as yet unmatched pairs. 2212 records in RAM. INFO 2026-06-04 20:59:45 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 0s. Last read position: KI270733.1:176,047 INFO 2026-06-04 20:59:45 MarkDuplicates Tracking 93 as yet unmatched pairs. 91 records in RAM. INFO 2026-06-04 20:59:46 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:09:15s. Time for last 1,000,000: 1s. Last read position: KI270733.1:178,689 INFO 2026-06-04 20:59:46 MarkDuplicates Tracking 6 as yet unmatched pairs. 4 records in RAM. INFO 2026-06-04 20:59:47 MarkDuplicates Read 367248533 records. 0 pairs never matched. INFO 2026-06-04 21:00:15 MarkDuplicates After buildSortedReadEndLists freeMemory: 31348400304; totalMemory: 44761612288; maxMemory: 63585648640 INFO 2026-06-04 21:00:15 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk. INFO 2026-06-04 21:00:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2026-06-04 21:00:32 OpticalDuplicateFinder Large duplicate set. size = 1083 INFO 2026-06-04 21:00:32 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,660 INFO 2026-06-04 21:00:35 OpticalDuplicateFinder Large duplicate set. size = 1652 INFO 2026-06-04 21:00:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,280 INFO 2026-06-04 21:00:35 OpticalDuplicateFinder Large duplicate set. size = 1682 INFO 2026-06-04 21:00:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,419 INFO 2026-06-04 21:00:35 OpticalDuplicateFinder Large duplicate set. size = 1017 INFO 2026-06-04 21:00:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,930 INFO 2026-06-04 21:00:38 OpticalDuplicateFinder Large duplicate set. size = 1137 INFO 2026-06-04 21:00:38 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,995 INFO 2026-06-04 21:00:53 OpticalDuplicateFinder Large duplicate set. size = 1088 INFO 2026-06-04 21:00:53 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-19,143 INFO 2026-06-04 21:00:53 OpticalDuplicateFinder Large duplicate set. size = 1253 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,378 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder Large duplicate set. size = 1222 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,717 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder Large duplicate set. size = 1058 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,350 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder Large duplicate set. size = 1689 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,686 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder Large duplicate set. size = 1115 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,745 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder Large duplicate set. size = 1268 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:10,546 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder Large duplicate set. size = 1395 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,816 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder Large duplicate set. size = 1041 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,496 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder Large duplicate set. size = 1382 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:24,137 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder Large duplicate set. size = 1450 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,556 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder Large duplicate set. size = 1637 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,531 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder Large duplicate set. size = 1109 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,015 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder Large duplicate set. size = 1017 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:7,367 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder Large duplicate set. size = 1216 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:17,746 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder Large duplicate set. size = 1023 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,873 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder Large duplicate set. size = 1016 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:8,702 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder Large duplicate set. size = 1032 INFO 2026-06-04 21:00:54 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,952 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder Large duplicate set. size = 1482 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,515 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder Large duplicate set. size = 1282 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-22,897 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder Large duplicate set. size = 1390 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,341 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder Large duplicate set. size = 1431 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,771 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder Large duplicate set. size = 1214 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:5,805 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder Large duplicate set. size = 1026 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:31,240 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder Large duplicate set. size = 1562 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:8,912 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder Large duplicate set. size = 1004 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,011 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder Large duplicate set. size = 1521 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,286 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder Large duplicate set. size = 1389 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,223 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder Large duplicate set. size = 1337 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,325 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder Large duplicate set. size = 1156 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,227 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder Large duplicate set. size = 1070 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:7,723 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder Large duplicate set. size = 1224 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:14,397 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder Large duplicate set. size = 1514 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:2,125 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder Large duplicate set. size = 1202 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,772 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder Large duplicate set. size = 1153 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,414 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder Large duplicate set. size = 1087 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,195 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder Large duplicate set. size = 1136 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,103 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder Large duplicate set. size = 1768 INFO 2026-06-04 21:00:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,153 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1139 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:1,445 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1257 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,580 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1290 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,390 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1095 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,636 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 2478 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,058 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,279 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1083 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:21,460 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 4223 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:24,963 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:6,550 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 3,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,492 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 4,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:8,896 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1005 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,978 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1064 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,181 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1089 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-22,970 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1353 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-21,918 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1147 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:24,129 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1025 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,466 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1394 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,161 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1064 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:26,306 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1282 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,147 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1448 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,219 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1065 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:8,985 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1805 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,427 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1584 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,276 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1565 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,535 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1933 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,114 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 2361 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,713 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,093 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 2298 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:2,828 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,685 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1022 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,609 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1784 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,201 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 2649 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,867 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:5,199 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1064 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:25,925 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1088 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,942 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1367 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,080 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1422 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:5,716 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1650 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:8,483 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1624 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,822 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1121 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,237 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1031 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,365 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1125 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,334 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1201 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-14,289 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1174 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,026 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1411 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:7,035 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1184 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-25,162 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1226 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,228 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder Large duplicate set. size = 1622 INFO 2026-06-04 21:00:56 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,631 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder Large duplicate set. size = 1114 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:26,484 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder Large duplicate set. size = 1099 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:15,214 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder Large duplicate set. size = 1019 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,959 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder Large duplicate set. size = 1624 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,168 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder Large duplicate set. size = 1936 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-13,512 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder Large duplicate set. size = 1228 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,295 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder Large duplicate set. size = 1474 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,506 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder Large duplicate set. size = 1265 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:2,214 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder Large duplicate set. size = 1053 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,755 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder Large duplicate set. size = 1157 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,163 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder Large duplicate set. size = 2550 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,358 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,834 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder Large duplicate set. size = 1589 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:15,449 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder Large duplicate set. size = 1579 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,155 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder Large duplicate set. size = 1147 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-13,982 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder Large duplicate set. size = 1198 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,491 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder Large duplicate set. size = 1417 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-18,908 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder Large duplicate set. size = 1052 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,494 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder Large duplicate set. size = 1509 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,737 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder Large duplicate set. size = 1346 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,402 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder Large duplicate set. size = 1102 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,306 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder Large duplicate set. size = 1103 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,013 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder Large duplicate set. size = 1014 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,737 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder Large duplicate set. size = 1785 INFO 2026-06-04 21:00:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-13,569 INFO 2026-06-04 21:01:18 MarkDuplicates Traversing fragment information and detecting duplicates. WARNING 2026-06-04 21:01:18 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered. INFO 2026-06-04 21:01:53 MarkDuplicates Sorting list of duplicate records. INFO 2026-06-04 21:01:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 203902040; totalMemory: 234881024; maxMemory: 63585648640 INFO 2026-06-04 21:01:54 MarkDuplicates Marking 282041987 records as duplicates. INFO 2026-06-04 21:01:54 MarkDuplicates Found 3737777 optical duplicate clusters. INFO 2026-06-04 21:01:54 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2026-06-04 21:02:09 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:14s. Time for last 10,000,000: 14s. Last read position: chr1:39,388,509 INFO 2026-06-04 21:02:24 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:29s. Time for last 10,000,000: 14s. Last read position: chr1:154,176,162 INFO 2026-06-04 21:02:38 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:44s. Time for last 10,000,000: 14s. Last read position: chr1:232,514,079 INFO 2026-06-04 21:02:53 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:00:58s. Time for last 10,000,000: 14s. Last read position: chr2:84,821,952 INFO 2026-06-04 21:03:08 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:13s. Time for last 10,000,000: 14s. Last read position: chr2:203,396,865 INFO 2026-06-04 21:03:22 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:28s. Time for last 10,000,000: 14s. Last read position: chr3:9,429,865 INFO 2026-06-04 21:03:37 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:01:42s. Time for last 10,000,000: 14s. Last read position: chr3:132,474,984 INFO 2026-06-04 21:03:52 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:01:57s. Time for last 10,000,000: 14s. Last read position: chr4:40,502,545 INFO 2026-06-04 21:04:06 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:12s. Time for last 10,000,000: 14s. Last read position: chr5:131,429,107 INFO 2026-06-04 21:04:21 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:26s. Time for last 10,000,000: 14s. Last read position: chr6:7,229,232 INFO 2026-06-04 21:04:35 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:02:41s. Time for last 10,000,000: 14s. Last read position: chr6:87,501,270 INFO 2026-06-04 21:04:50 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:02:55s. Time for last 10,000,000: 14s. Last read position: chr7:47,368,889 INFO 2026-06-04 21:05:04 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:10s. Time for last 10,000,000: 14s. Last read position: chr7:100,999,596 INFO 2026-06-04 21:05:19 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:03:24s. Time for last 10,000,000: 14s. Last read position: chr8:37,697,492 INFO 2026-06-04 21:05:33 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:03:39s. Time for last 10,000,000: 14s. Last read position: chr8:143,862,228 INFO 2026-06-04 21:05:48 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:03:53s. Time for last 10,000,000: 14s. Last read position: chr9:93,253,034 INFO 2026-06-04 21:06:02 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:04:08s. Time for last 10,000,000: 14s. Last read position: chr10:30,349,195 INFO 2026-06-04 21:06:17 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:04:22s. Time for last 10,000,000: 14s. Last read position: chr10:122,621,111 INFO 2026-06-04 21:06:31 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:04:37s. Time for last 10,000,000: 14s. Last read position: chr11:46,808,112 INFO 2026-06-04 21:06:46 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:04:51s. Time for last 10,000,000: 14s. Last read position: chr11:117,091,159 INFO 2026-06-04 21:07:00 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:05:06s. Time for last 10,000,000: 14s. Last read position: chr12:56,231,408 INFO 2026-06-04 21:07:15 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:05:20s. Time for last 10,000,000: 14s. Last read position: chr12:132,571,441 INFO 2026-06-04 21:07:29 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:05:35s. Time for last 10,000,000: 14s. Last read position: chr14:69,053,851 INFO 2026-06-04 21:07:44 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:05:49s. Time for last 10,000,000: 14s. Last read position: chr15:75,206,055 INFO 2026-06-04 21:07:59 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:06:04s. Time for last 10,000,000: 14s. Last read position: chr16:18,890,877 INFO 2026-06-04 21:08:14 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:06:19s. Time for last 10,000,000: 14s. Last read position: chr16:58,197,678 INFO 2026-06-04 21:08:29 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:06:34s. Time for last 10,000,000: 14s. Last read position: chr17:31,488,215 INFO 2026-06-04 21:08:44 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:06:49s. Time for last 10,000,000: 15s. Last read position: chr17:50,188,980 INFO 2026-06-04 21:08:59 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:07:04s. Time for last 10,000,000: 15s. Last read position: chr17:50,197,215 INFO 2026-06-04 21:09:13 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:07:19s. Time for last 10,000,000: 14s. Last read position: chr18:13,030,447 INFO 2026-06-04 21:09:27 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:07:33s. Time for last 10,000,000: 14s. Last read position: chr19:12,943,844 INFO 2026-06-04 21:09:42 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:07:47s. Time for last 10,000,000: 14s. Last read position: chr19:41,715,109 INFO 2026-06-04 21:09:56 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:08:02s. Time for last 10,000,000: 14s. Last read position: chr20:2,838,365 INFO 2026-06-04 21:10:10 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:08:16s. Time for last 10,000,000: 14s. Last read position: chr21:8,258,974 INFO 2026-06-04 21:10:25 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:08:30s. Time for last 10,000,000: 14s. Last read position: chr22:36,289,224 INFO 2026-06-04 21:10:39 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:08:45s. Time for last 10,000,000: 14s. Last read position: chrX:153,955,278 INFO 2026-06-04 21:10:55 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:09:01s. Time for last 10,000,000: 15s. Last read position: */* INFO 2026-06-04 21:10:56 MarkDuplicates Writing complete. Closing input iterator. INFO 2026-06-04 21:10:56 MarkDuplicates Duplicate Index cleanup. INFO 2026-06-04 21:10:56 MarkDuplicates Getting Memory Stats. INFO 2026-06-04 21:10:56 MarkDuplicates Before output close freeMemory: 203871920; totalMemory: 234881024; maxMemory: 63585648640 INFO 2026-06-04 21:10:56 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2026-06-04 21:10:56 MarkDuplicates After output close freeMemory: 104114008; totalMemory: 134217728; maxMemory: 63585648640 [Thu Jun 04 21:10:56 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 20.45 minutes. Runtime.totalMemory()=134217728 ls: *cram: No such file or directory ls: *.crai: No such file or directory