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 dna_s758.Aligned.sortedByCoord.out.bam --OUTPUT dna_s758.md.bam --METRICS_FILE dna_s758.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:36:33.278 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Jun 08 07:36:33 GMT 2026] MarkDuplicates --INPUT dna_s758.Aligned.sortedByCoord.out.bam --OUTPUT dna_s758.md.bam --METRICS_FILE dna_s758.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 <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 07:36:33 GMT 2026] Executing as ?@nf-3fa640cc50ae585c647d6ab128da9ab7-5082e-pkgch on Linux 6.12.88 amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0
INFO 2026-06-08 07:36:33 MarkDuplicates Start of doWork freeMemory: 105828208; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:36:33 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:36:33 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:36:39 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 4s. Last read position: chr1:8,015,090
INFO 2026-06-08 07:36:39 MarkDuplicates Tracking 4047 as yet unmatched pairs. 1110 records in RAM.
INFO 2026-06-08 07:36:42 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 3s. Last read position: chr1:13,475,865
INFO 2026-06-08 07:36:42 MarkDuplicates Tracking 6008 as yet unmatched pairs. 462 records in RAM.
INFO 2026-06-08 07:36:45 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 2s. Last read position: chr1:18,857,304
INFO 2026-06-08 07:36:45 MarkDuplicates Tracking 9343 as yet unmatched pairs. 654 records in RAM.
INFO 2026-06-08 07:36:48 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 3s. Last read position: chr1:27,154,114
INFO 2026-06-08 07:36:48 MarkDuplicates Tracking 12963 as yet unmatched pairs. 892 records in RAM.
INFO 2026-06-08 07:36:52 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 4s. Last read position: chr1:37,592,695
INFO 2026-06-08 07:36:52 MarkDuplicates Tracking 16649 as yet unmatched pairs. 939 records in RAM.
INFO 2026-06-08 07:36:55 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 2s. Last read position: chr1:45,658,807
INFO 2026-06-08 07:36:55 MarkDuplicates Tracking 20107 as yet unmatched pairs. 1072 records in RAM.
INFO 2026-06-08 07:36:58 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 3s. Last read position: chr1:58,783,833
INFO 2026-06-08 07:36:58 MarkDuplicates Tracking 25703 as yet unmatched pairs. 2536 records in RAM.
INFO 2026-06-08 07:37:02 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 3s. Last read position: chr1:84,244,571
INFO 2026-06-08 07:37:02 MarkDuplicates Tracking 30282 as yet unmatched pairs. 1379 records in RAM.
INFO 2026-06-08 07:37:06 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 3s. Last read position: chr1:103,750,925
INFO 2026-06-08 07:37:06 MarkDuplicates Tracking 34939 as yet unmatched pairs. 1441 records in RAM.
INFO 2026-06-08 07:37:09 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 3s. Last read position: chr1:117,144,988
INFO 2026-06-08 07:37:09 MarkDuplicates Tracking 39586 as yet unmatched pairs. 2174 records in RAM.
INFO 2026-06-08 07:37:12 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 2s. Last read position: chr1:145,453,851
INFO 2026-06-08 07:37:12 MarkDuplicates Tracking 42925 as yet unmatched pairs. 1625 records in RAM.
INFO 2026-06-08 07:37:15 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 2s. Last read position: chr1:151,027,751
INFO 2026-06-08 07:37:15 MarkDuplicates Tracking 45280 as yet unmatched pairs. 1470 records in RAM.
INFO 2026-06-08 07:37:18 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chr1:155,911,247
INFO 2026-06-08 07:37:18 MarkDuplicates Tracking 48879 as yet unmatched pairs. 2252 records in RAM.
INFO 2026-06-08 07:37:20 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: chr1:161,213,798
INFO 2026-06-08 07:37:20 MarkDuplicates Tracking 51026 as yet unmatched pairs. 1395 records in RAM.
INFO 2026-06-08 07:37:23 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 3s. Last read position: chr1:178,514,118
INFO 2026-06-08 07:37:23 MarkDuplicates Tracking 55484 as yet unmatched pairs. 1155 records in RAM.
INFO 2026-06-08 07:37:27 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 3s. Last read position: chr1:200,644,322
INFO 2026-06-08 07:37:27 MarkDuplicates Tracking 60711 as yet unmatched pairs. 1027 records in RAM.
INFO 2026-06-08 07:37:30 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 3s. Last read position: chr1:205,673,724
INFO 2026-06-08 07:37:30 MarkDuplicates Tracking 64805 as yet unmatched pairs. 1899 records in RAM.
INFO 2026-06-08 07:37:33 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 2s. Last read position: chr1:222,732,504
INFO 2026-06-08 07:37:33 MarkDuplicates Tracking 68057 as yet unmatched pairs. 573 records in RAM.
INFO 2026-06-08 07:37:36 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 3s. Last read position: chr1:235,800,816
INFO 2026-06-08 07:37:36 MarkDuplicates Tracking 71985 as yet unmatched pairs. 344 records in RAM.
INFO 2026-06-08 07:37:39 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 3s. Last read position: chr2:4,628,747
INFO 2026-06-08 07:37:39 MarkDuplicates Tracking 76058 as yet unmatched pairs. 20594 records in RAM.
INFO 2026-06-08 07:37:42 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 3s. Last read position: chr2:25,281,792
INFO 2026-06-08 07:37:42 MarkDuplicates Tracking 82036 as yet unmatched pairs. 22599 records in RAM.
INFO 2026-06-08 07:37:46 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 3s. Last read position: chr2:32,478,581
INFO 2026-06-08 07:37:46 MarkDuplicates Tracking 83925 as yet unmatched pairs. 22163 records in RAM.
INFO 2026-06-08 07:37:49 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 3s. Last read position: chr2:42,492,879
INFO 2026-06-08 07:37:49 MarkDuplicates Tracking 217654 as yet unmatched pairs. 14971 records in RAM.
INFO 2026-06-08 07:37:52 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 3s. Last read position: chr2:60,891,833
INFO 2026-06-08 07:37:52 MarkDuplicates Tracking 220454 as yet unmatched pairs. 14047 records in RAM.
INFO 2026-06-08 07:37:55 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 3s. Last read position: chr2:74,370,892
INFO 2026-06-08 07:37:55 MarkDuplicates Tracking 222400 as yet unmatched pairs. 13020 records in RAM.
INFO 2026-06-08 07:37:59 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 3s. Last read position: chr2:95,574,969
INFO 2026-06-08 07:37:59 MarkDuplicates Tracking 225056 as yet unmatched pairs. 12366 records in RAM.
INFO 2026-06-08 07:38:02 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 3s. Last read position: chr2:102,218,905
INFO 2026-06-08 07:38:02 MarkDuplicates Tracking 226234 as yet unmatched pairs. 11298 records in RAM.
INFO 2026-06-08 07:38:04 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 2s. Last read position: chr2:111,898,740
INFO 2026-06-08 07:38:04 MarkDuplicates Tracking 227795 as yet unmatched pairs. 10686 records in RAM.
INFO 2026-06-08 07:38:08 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 3s. Last read position: chr2:126,425,341
INFO 2026-06-08 07:38:08 MarkDuplicates Tracking 229551 as yet unmatched pairs. 9383 records in RAM.
INFO 2026-06-08 07:38:11 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 2s. Last read position: chr2:140,993,980
INFO 2026-06-08 07:38:11 MarkDuplicates Tracking 231804 as yet unmatched pairs. 8624 records in RAM.
INFO 2026-06-08 07:38:14 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 3s. Last read position: chr2:168,859,551
INFO 2026-06-08 07:38:14 MarkDuplicates Tracking 234945 as yet unmatched pairs. 7176 records in RAM.
INFO 2026-06-08 07:38:17 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 2s. Last read position: chr2:178,659,035
INFO 2026-06-08 07:38:17 MarkDuplicates Tracking 236739 as yet unmatched pairs. 6344 records in RAM.
INFO 2026-06-08 07:38:20 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 3s. Last read position: chr2:197,459,972
INFO 2026-06-08 07:38:20 MarkDuplicates Tracking 238910 as yet unmatched pairs. 4690 records in RAM.
INFO 2026-06-08 07:38:23 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 2s. Last read position: chr2:214,734,165
INFO 2026-06-08 07:38:23 MarkDuplicates Tracking 241451 as yet unmatched pairs. 3428 records in RAM.
INFO 2026-06-08 07:38:26 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 3s. Last read position: chr2:224,470,601
INFO 2026-06-08 07:38:26 MarkDuplicates Tracking 243647 as yet unmatched pairs. 3002 records in RAM.
INFO 2026-06-08 07:38:29 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 3s. Last read position: chr2:238,163,924
INFO 2026-06-08 07:38:29 MarkDuplicates Tracking 244568 as yet unmatched pairs. 874 records in RAM.
INFO 2026-06-08 07:38:33 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 3s. Last read position: chr3:10,057,967
INFO 2026-06-08 07:38:33 MarkDuplicates Tracking 246035 as yet unmatched pairs. 18367 records in RAM.
INFO 2026-06-08 07:38:37 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 4s. Last read position: chr3:12,357,463
INFO 2026-06-08 07:38:37 MarkDuplicates Tracking 247873 as yet unmatched pairs. 18205 records in RAM.
INFO 2026-06-08 07:38:41 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 4s. Last read position: chr3:27,632,754
INFO 2026-06-08 07:38:41 MarkDuplicates Tracking 248872 as yet unmatched pairs. 15918 records in RAM.
INFO 2026-06-08 07:38:45 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 3s. Last read position: chr3:43,600,426
INFO 2026-06-08 07:38:45 MarkDuplicates Tracking 250711 as yet unmatched pairs. 14697 records in RAM.
INFO 2026-06-08 07:38:48 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 3s. Last read position: chr3:49,697,931
INFO 2026-06-08 07:38:48 MarkDuplicates Tracking 251386 as yet unmatched pairs. 13506 records in RAM.
INFO 2026-06-08 07:38:51 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 3s. Last read position: chr3:57,296,821
INFO 2026-06-08 07:38:51 MarkDuplicates Tracking 252026 as yet unmatched pairs. 12156 records in RAM.
INFO 2026-06-08 07:38:54 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 3s. Last read position: chr3:78,652,046
INFO 2026-06-08 07:38:54 MarkDuplicates Tracking 254174 as yet unmatched pairs. 10529 records in RAM.
INFO 2026-06-08 07:38:57 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 3s. Last read position: chr3:117,292,775
INFO 2026-06-08 07:38:57 MarkDuplicates Tracking 257503 as yet unmatched pairs. 8437 records in RAM.
INFO 2026-06-08 07:39:01 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 3s. Last read position: chr3:129,479,666
INFO 2026-06-08 07:39:01 MarkDuplicates Tracking 258689 as yet unmatched pairs. 6980 records in RAM.
INFO 2026-06-08 07:39:04 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 2s. Last read position: chr3:142,553,302
INFO 2026-06-08 07:39:04 MarkDuplicates Tracking 260437 as yet unmatched pairs. 5824 records in RAM.
INFO 2026-06-08 07:39:07 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 3s. Last read position: chr3:171,843,392
INFO 2026-06-08 07:39:07 MarkDuplicates Tracking 262653 as yet unmatched pairs. 3591 records in RAM.
INFO 2026-06-08 07:39:10 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 3s. Last read position: chr3:185,533,474
INFO 2026-06-08 07:39:10 MarkDuplicates Tracking 264019 as yet unmatched pairs. 1848 records in RAM.
INFO 2026-06-08 07:39:13 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 2s. Last read position: chr3:196,483,684
INFO 2026-06-08 07:39:13 MarkDuplicates Tracking 265000 as yet unmatched pairs. 291 records in RAM.
INFO 2026-06-08 07:39:17 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 3s. Last read position: chr4:6,611,067
INFO 2026-06-08 07:39:17 MarkDuplicates Tracking 265624 as yet unmatched pairs. 14609 records in RAM.
INFO 2026-06-08 07:39:19 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 2s. Last read position: chr4:20,610,087
INFO 2026-06-08 07:39:19 MarkDuplicates Tracking 266808 as yet unmatched pairs. 13349 records in RAM.
INFO 2026-06-08 07:39:22 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 2s. Last read position: chr4:53,228,628
INFO 2026-06-08 07:39:22 MarkDuplicates Tracking 268869 as yet unmatched pairs. 10990 records in RAM.
INFO 2026-06-08 07:39:25 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 3s. Last read position: chr4:70,926,797
INFO 2026-06-08 07:39:25 MarkDuplicates Tracking 270362 as yet unmatched pairs. 9328 records in RAM.
INFO 2026-06-08 07:39:28 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 2s. Last read position: chr4:94,276,370
INFO 2026-06-08 07:39:28 MarkDuplicates Tracking 272105 as yet unmatched pairs. 7473 records in RAM.
INFO 2026-06-08 07:39:32 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 3s. Last read position: chr4:121,147,015
INFO 2026-06-08 07:39:32 MarkDuplicates Tracking 274045 as yet unmatched pairs. 5375 records in RAM.
INFO 2026-06-08 07:39:34 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 2s. Last read position: chr4:152,321,118
INFO 2026-06-08 07:39:34 MarkDuplicates Tracking 276940 as yet unmatched pairs. 3726 records in RAM.
INFO 2026-06-08 07:39:38 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 3s. Last read position: chr4:186,198,900
INFO 2026-06-08 07:39:38 MarkDuplicates Tracking 278416 as yet unmatched pairs. 570 records in RAM.
INFO 2026-06-08 07:39:41 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 3s. Last read position: chr5:19,612,195
INFO 2026-06-08 07:39:41 MarkDuplicates Tracking 279636 as yet unmatched pairs. 16838 records in RAM.
INFO 2026-06-08 07:39:44 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 2s. Last read position: chr5:45,695,818
INFO 2026-06-08 07:39:44 MarkDuplicates Tracking 281372 as yet unmatched pairs. 14911 records in RAM.
INFO 2026-06-08 07:39:47 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 2s. Last read position: chr5:70,132,933
INFO 2026-06-08 07:39:47 MarkDuplicates Tracking 282635 as yet unmatched pairs. 12652 records in RAM.
INFO 2026-06-08 07:39:49 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 2s. Last read position: chr5:90,745,627
INFO 2026-06-08 07:39:49 MarkDuplicates Tracking 283916 as yet unmatched pairs. 10870 records in RAM.
INFO 2026-06-08 07:39:52 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 3s. Last read position: chr5:123,588,305
INFO 2026-06-08 07:39:52 MarkDuplicates Tracking 285557 as yet unmatched pairs. 8205 records in RAM.
INFO 2026-06-08 07:39:55 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 3s. Last read position: chr5:140,562,301
INFO 2026-06-08 07:39:55 MarkDuplicates Tracking 286439 as yet unmatched pairs. 6274 records in RAM.
INFO 2026-06-08 07:39:59 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 3s. Last read position: chr5:150,053,412
INFO 2026-06-08 07:39:59 MarkDuplicates Tracking 287520 as yet unmatched pairs. 5333 records in RAM.
INFO 2026-06-08 07:40:02 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 3s. Last read position: chr5:170,919,370
INFO 2026-06-08 07:40:02 MarkDuplicates Tracking 287359 as yet unmatched pairs. 2105 records in RAM.
INFO 2026-06-08 07:40:05 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 2s. Last read position: chr5:180,602,535
INFO 2026-06-08 07:40:05 MarkDuplicates Tracking 288506 as yet unmatched pairs. 1278 records in RAM.
INFO 2026-06-08 07:40:08 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 3s. Last read position: chr6:22,982,269
INFO 2026-06-08 07:40:08 MarkDuplicates Tracking 288403 as yet unmatched pairs. 21666 records in RAM.
INFO 2026-06-08 07:40:12 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 3s. Last read position: chr6:30,949,784
INFO 2026-06-08 07:40:12 MarkDuplicates Tracking 288772 as yet unmatched pairs. 20363 records in RAM.
INFO 2026-06-08 07:40:15 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 2s. Last read position: chr6:33,004,166
INFO 2026-06-08 07:40:15 MarkDuplicates Tracking 288819 as yet unmatched pairs. 19363 records in RAM.
INFO 2026-06-08 07:40:18 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 3s. Last read position: chr6:41,785,728
INFO 2026-06-08 07:40:18 MarkDuplicates Tracking 287972 as yet unmatched pairs. 16791 records in RAM.
INFO 2026-06-08 07:40:21 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 3s. Last read position: chr6:56,302,210
INFO 2026-06-08 07:40:21 MarkDuplicates Tracking 288275 as yet unmatched pairs. 14779 records in RAM.
INFO 2026-06-08 07:40:24 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 2s. Last read position: chr6:87,264,071
INFO 2026-06-08 07:40:24 MarkDuplicates Tracking 289815 as yet unmatched pairs. 12721 records in RAM.
INFO 2026-06-08 07:40:28 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 4s. Last read position: chr6:112,060,940
INFO 2026-06-08 07:40:28 MarkDuplicates Tracking 290148 as yet unmatched pairs. 9939 records in RAM.
INFO 2026-06-08 07:40:31 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 2s. Last read position: chr6:127,137,714
INFO 2026-06-08 07:40:31 MarkDuplicates Tracking 290737 as yet unmatched pairs. 7972 records in RAM.
INFO 2026-06-08 07:40:34 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 2s. Last read position: chr6:138,861,067
INFO 2026-06-08 07:40:34 MarkDuplicates Tracking 290053 as yet unmatched pairs. 5069 records in RAM.
INFO 2026-06-08 07:40:37 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 3s. Last read position: chr6:154,406,701
INFO 2026-06-08 07:40:37 MarkDuplicates Tracking 290298 as yet unmatched pairs. 2783 records in RAM.
INFO 2026-06-08 07:40:40 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 2s. Last read position: chr6:167,208,869
INFO 2026-06-08 07:40:40 MarkDuplicates Tracking 290082 as yet unmatched pairs. 478 records in RAM.
INFO 2026-06-08 07:40:43 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 3s. Last read position: chr7:6,930,824
INFO 2026-06-08 07:40:43 MarkDuplicates Tracking 289842 as yet unmatched pairs. 24291 records in RAM.
INFO 2026-06-08 07:40:47 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 3s. Last read position: chr7:17,310,004
INFO 2026-06-08 07:40:47 MarkDuplicates Tracking 289675 as yet unmatched pairs. 22174 records in RAM.
INFO 2026-06-08 07:40:50 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 3s. Last read position: chr7:44,039,804
INFO 2026-06-08 07:40:50 MarkDuplicates Tracking 289909 as yet unmatched pairs. 19399 records in RAM.
INFO 2026-06-08 07:40:53 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 3s. Last read position: chr7:55,186,559
INFO 2026-06-08 07:40:53 MarkDuplicates Tracking 290346 as yet unmatched pairs. 18104 records in RAM.
INFO 2026-06-08 07:40:56 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 3s. Last read position: chr7:73,748,470
INFO 2026-06-08 07:40:56 MarkDuplicates Tracking 289300 as yet unmatched pairs. 14930 records in RAM.
INFO 2026-06-08 07:40:59 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 2s. Last read position: chr7:86,552,972
INFO 2026-06-08 07:40:59 MarkDuplicates Tracking 289083 as yet unmatched pairs. 13055 records in RAM.
INFO 2026-06-08 07:41:02 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 3s. Last read position: chr7:100,309,101
INFO 2026-06-08 07:41:02 MarkDuplicates Tracking 289070 as yet unmatched pairs. 10871 records in RAM.
INFO 2026-06-08 07:41:05 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 3s. Last read position: chr7:102,749,226
INFO 2026-06-08 07:41:05 MarkDuplicates Tracking 288865 as yet unmatched pairs. 9722 records in RAM.
INFO 2026-06-08 07:41:08 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 2s. Last read position: chr7:122,837,939
INFO 2026-06-08 07:41:08 MarkDuplicates Tracking 288476 as yet unmatched pairs. 6743 records in RAM.
INFO 2026-06-08 07:41:11 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 2s. Last read position: chr7:140,343,419
INFO 2026-06-08 07:41:11 MarkDuplicates Tracking 288403 as yet unmatched pairs. 4370 records in RAM.
INFO 2026-06-08 07:41:14 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 3s. Last read position: chr7:148,883,144
INFO 2026-06-08 07:41:14 MarkDuplicates Tracking 289009 as yet unmatched pairs. 3316 records in RAM.
INFO 2026-06-08 07:41:17 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 3s. Last read position: chr8:246,078
INFO 2026-06-08 07:41:17 MarkDuplicates Tracking 287434 as yet unmatched pairs. 24643 records in RAM.
INFO 2026-06-08 07:41:20 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 2s. Last read position: chr8:8,377,108
INFO 2026-06-08 07:41:20 MarkDuplicates Tracking 287086 as yet unmatched pairs. 23271 records in RAM.
INFO 2026-06-08 07:41:24 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 3s. Last read position: chr8:27,241,060
INFO 2026-06-08 07:41:24 MarkDuplicates Tracking 286566 as yet unmatched pairs. 20638 records in RAM.
INFO 2026-06-08 07:41:27 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 3s. Last read position: chr8:32,666,986
INFO 2026-06-08 07:41:27 MarkDuplicates Tracking 286631 as yet unmatched pairs. 19338 records in RAM.
INFO 2026-06-08 07:41:30 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 3s. Last read position: chr8:32,770,258
INFO 2026-06-08 07:41:30 MarkDuplicates Tracking 285712 as yet unmatched pairs. 17183 records in RAM.
INFO 2026-06-08 07:41:33 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 3s. Last read position: chr8:38,460,809
INFO 2026-06-08 07:41:33 MarkDuplicates Tracking 285567 as yet unmatched pairs. 15672 records in RAM.
INFO 2026-06-08 07:41:36 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 3s. Last read position: chr8:56,069,804
INFO 2026-06-08 07:41:36 MarkDuplicates Tracking 283799 as yet unmatched pairs. 11894 records in RAM.
INFO 2026-06-08 07:41:39 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 3s. Last read position: chr8:89,919,512
INFO 2026-06-08 07:41:39 MarkDuplicates Tracking 283426 as yet unmatched pairs. 8213 records in RAM.
INFO 2026-06-08 07:41:43 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 3s. Last read position: chr8:116,849,010
INFO 2026-06-08 07:41:43 MarkDuplicates Tracking 282827 as yet unmatched pairs. 4889 records in RAM.
INFO 2026-06-08 07:41:46 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 2s. Last read position: chr8:143,561,973
INFO 2026-06-08 07:41:46 MarkDuplicates Tracking 282207 as yet unmatched pairs. 1413 records in RAM.
INFO 2026-06-08 07:41:49 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 3s. Last read position: chr9:2,097,237
INFO 2026-06-08 07:41:49 MarkDuplicates Tracking 281120 as yet unmatched pairs. 25115 records in RAM.
INFO 2026-06-08 07:41:52 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 2s. Last read position: chr9:21,409,324
INFO 2026-06-08 07:41:52 MarkDuplicates Tracking 280364 as yet unmatched pairs. 22255 records in RAM.
INFO 2026-06-08 07:41:56 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 3s. Last read position: chr9:36,822,016
INFO 2026-06-08 07:41:56 MarkDuplicates Tracking 279502 as yet unmatched pairs. 19556 records in RAM.
INFO 2026-06-08 07:41:59 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 2s. Last read position: chr9:61,068,296
INFO 2026-06-08 07:41:59 MarkDuplicates Tracking 278972 as yet unmatched pairs. 17973 records in RAM.
INFO 2026-06-08 07:42:01 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 2s. Last read position: chr9:71,121,249
INFO 2026-06-08 07:42:01 MarkDuplicates Tracking 278529 as yet unmatched pairs. 16623 records in RAM.
INFO 2026-06-08 07:42:04 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 3s. Last read position: chr9:84,864,566
INFO 2026-06-08 07:42:04 MarkDuplicates Tracking 278077 as yet unmatched pairs. 14347 records in RAM.
INFO 2026-06-08 07:42:07 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 3s. Last read position: chr9:86,308,247
INFO 2026-06-08 07:42:07 MarkDuplicates Tracking 276456 as yet unmatched pairs. 11653 records in RAM.
INFO 2026-06-08 07:42:11 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 3s. Last read position: chr9:99,062,245
INFO 2026-06-08 07:42:11 MarkDuplicates Tracking 275321 as yet unmatched pairs. 9032 records in RAM.
INFO 2026-06-08 07:42:13 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 2s. Last read position: chr9:120,976,878
INFO 2026-06-08 07:42:13 MarkDuplicates Tracking 274350 as yet unmatched pairs. 5841 records in RAM.
INFO 2026-06-08 07:42:16 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 2s. Last read position: chr9:130,875,049
INFO 2026-06-08 07:42:16 MarkDuplicates Tracking 273457 as yet unmatched pairs. 3627 records in RAM.
INFO 2026-06-08 07:42:19 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 2s. Last read position: chr9:136,495,169
INFO 2026-06-08 07:42:19 MarkDuplicates Tracking 273409 as yet unmatched pairs. 2451 records in RAM.
INFO 2026-06-08 07:42:23 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 3s. Last read position: chr10:8,074,290
INFO 2026-06-08 07:42:23 MarkDuplicates Tracking 271992 as yet unmatched pairs. 24156 records in RAM.
INFO 2026-06-08 07:42:26 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 2s. Last read position: chr10:32,346,692
INFO 2026-06-08 07:42:26 MarkDuplicates Tracking 269983 as yet unmatched pairs. 19956 records in RAM.
INFO 2026-06-08 07:42:29 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 3s. Last read position: chr10:46,837,874
INFO 2026-06-08 07:42:29 MarkDuplicates Tracking 268806 as yet unmatched pairs. 17336 records in RAM.
INFO 2026-06-08 07:42:31 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 2s. Last read position: chr10:68,572,984
INFO 2026-06-08 07:42:31 MarkDuplicates Tracking 268010 as yet unmatched pairs. 14631 records in RAM.
INFO 2026-06-08 07:42:33 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 2s. Last read position: chr10:86,662,293
INFO 2026-06-08 07:42:33 MarkDuplicates Tracking 265993 as yet unmatched pairs. 10958 records in RAM.
INFO 2026-06-08 07:42:36 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 2s. Last read position: chr10:95,855,851
INFO 2026-06-08 07:42:36 MarkDuplicates Tracking 264627 as yet unmatched pairs. 8309 records in RAM.
INFO 2026-06-08 07:42:39 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 3s. Last read position: chr10:105,089,783
INFO 2026-06-08 07:42:39 MarkDuplicates Tracking 263256 as yet unmatched pairs. 5755 records in RAM.
INFO 2026-06-08 07:42:42 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 2s. Last read position: chr10:121,581,108
INFO 2026-06-08 07:42:42 MarkDuplicates Tracking 262611 as yet unmatched pairs. 3430 records in RAM.
INFO 2026-06-08 07:42:46 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 3s. Last read position: chr11:381,574
INFO 2026-06-08 07:42:46 MarkDuplicates Tracking 260289 as yet unmatched pairs. 28880 records in RAM.
INFO 2026-06-08 07:42:49 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 3s. Last read position: chr11:5,323,608
INFO 2026-06-08 07:42:49 MarkDuplicates Tracking 259197 as yet unmatched pairs. 27048 records in RAM.
INFO 2026-06-08 07:42:52 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 3s. Last read position: chr11:18,403,602
INFO 2026-06-08 07:42:52 MarkDuplicates Tracking 257513 as yet unmatched pairs. 24163 records in RAM.
INFO 2026-06-08 07:42:55 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 3s. Last read position: chr11:46,890,009
INFO 2026-06-08 07:42:55 MarkDuplicates Tracking 255816 as yet unmatched pairs. 20392 records in RAM.
INFO 2026-06-08 07:42:58 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 2s. Last read position: chr11:61,532,993
INFO 2026-06-08 07:42:58 MarkDuplicates Tracking 254466 as yet unmatched pairs. 17835 records in RAM.
INFO 2026-06-08 07:43:01 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 2s. Last read position: chr11:65,965,160
INFO 2026-06-08 07:43:01 MarkDuplicates Tracking 253019 as yet unmatched pairs. 15614 records in RAM.
INFO 2026-06-08 07:43:04 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 2s. Last read position: chr11:73,977,820
INFO 2026-06-08 07:43:04 MarkDuplicates Tracking 251525 as yet unmatched pairs. 13184 records in RAM.
INFO 2026-06-08 07:43:06 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:06:31s. Time for last 1,000,000: 2s. Last read position: chr11:94,086,459
INFO 2026-06-08 07:43:06 MarkDuplicates Tracking 249714 as yet unmatched pairs. 9800 records in RAM.
INFO 2026-06-08 07:43:09 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 2s. Last read position: chr11:108,345,638
INFO 2026-06-08 07:43:09 MarkDuplicates Tracking 248321 as yet unmatched pairs. 6836 records in RAM.
INFO 2026-06-08 07:43:12 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 3s. Last read position: chr11:119,172,896
INFO 2026-06-08 07:43:12 MarkDuplicates Tracking 246486 as yet unmatched pairs. 3708 records in RAM.
INFO 2026-06-08 07:43:15 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 2s. Last read position: chr11:131,911,534
INFO 2026-06-08 07:43:15 MarkDuplicates Tracking 244835 as yet unmatched pairs. 742 records in RAM.
INFO 2026-06-08 07:43:19 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:06:44s. Time for last 1,000,000: 4s. Last read position: chr12:6,933,968
INFO 2026-06-08 07:43:19 MarkDuplicates Tracking 242845 as yet unmatched pairs. 31135 records in RAM.
INFO 2026-06-08 07:43:22 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:06:47s. Time for last 1,000,000: 3s. Last read position: chr12:11,792,761
INFO 2026-06-08 07:43:22 MarkDuplicates Tracking 241536 as yet unmatched pairs. 29008 records in RAM.
INFO 2026-06-08 07:43:25 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 2s. Last read position: chr12:11,881,517
INFO 2026-06-08 07:43:25 MarkDuplicates Tracking 240779 as yet unmatched pairs. 27582 records in RAM.
INFO 2026-06-08 07:43:28 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 3s. Last read position: chr12:30,740,829
INFO 2026-06-08 07:43:28 MarkDuplicates Tracking 237600 as yet unmatched pairs. 23073 records in RAM.
INFO 2026-06-08 07:43:31 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 3s. Last read position: chr12:49,034,478
INFO 2026-06-08 07:43:31 MarkDuplicates Tracking 235992 as yet unmatched pairs. 20126 records in RAM.
INFO 2026-06-08 07:43:35 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 3s. Last read position: chr12:53,307,370
INFO 2026-06-08 07:43:35 MarkDuplicates Tracking 234139 as yet unmatched pairs. 17610 records in RAM.
INFO 2026-06-08 07:43:38 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:07:03s. Time for last 1,000,000: 3s. Last read position: chr12:57,625,315
INFO 2026-06-08 07:43:38 MarkDuplicates Tracking 232844 as yet unmatched pairs. 15622 records in RAM.
INFO 2026-06-08 07:43:41 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 3s. Last read position: chr12:80,605,080
INFO 2026-06-08 07:43:41 MarkDuplicates Tracking 230076 as yet unmatched pairs. 11162 records in RAM.
INFO 2026-06-08 07:43:44 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:07:09s. Time for last 1,000,000: 3s. Last read position: chr12:106,067,501
INFO 2026-06-08 07:43:44 MarkDuplicates Tracking 228155 as yet unmatched pairs. 7503 records in RAM.
INFO 2026-06-08 07:43:47 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:07:12s. Time for last 1,000,000: 3s. Last read position: chr12:118,246,427
INFO 2026-06-08 07:43:47 MarkDuplicates Tracking 225646 as yet unmatched pairs. 3969 records in RAM.
INFO 2026-06-08 07:43:51 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:07:16s. Time for last 1,000,000: 3s. Last read position: chr12:132,030,057
INFO 2026-06-08 07:43:51 MarkDuplicates Tracking 223578 as yet unmatched pairs. 779 records in RAM.
INFO 2026-06-08 07:43:54 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:07:19s. Time for last 1,000,000: 3s. Last read position: chr13:28,300,427
INFO 2026-06-08 07:43:54 MarkDuplicates Tracking 222936 as yet unmatched pairs. 15614 records in RAM.
INFO 2026-06-08 07:43:58 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:07:22s. Time for last 1,000,000: 3s. Last read position: chr13:45,988,812
INFO 2026-06-08 07:43:58 MarkDuplicates Tracking 219208 as yet unmatched pairs. 10570 records in RAM.
INFO 2026-06-08 07:44:01 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:07:26s. Time for last 1,000,000: 3s. Last read position: chr13:87,676,794
INFO 2026-06-08 07:44:01 MarkDuplicates Tracking 215822 as yet unmatched pairs. 4948 records in RAM.
INFO 2026-06-08 07:44:04 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:07:29s. Time for last 1,000,000: 2s. Last read position: chr13:113,483,892
INFO 2026-06-08 07:44:04 MarkDuplicates Tracking 212824 as yet unmatched pairs. 326 records in RAM.
INFO 2026-06-08 07:44:07 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:07:32s. Time for last 1,000,000: 3s. Last read position: chr14:27,300,720
INFO 2026-06-08 07:44:07 MarkDuplicates Tracking 210565 as yet unmatched pairs. 15905 records in RAM.
INFO 2026-06-08 07:44:10 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:07:35s. Time for last 1,000,000: 3s. Last read position: chr14:56,229,974
INFO 2026-06-08 07:44:10 MarkDuplicates Tracking 207059 as yet unmatched pairs. 10973 records in RAM.
INFO 2026-06-08 07:44:13 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:07:38s. Time for last 1,000,000: 2s. Last read position: chr14:75,014,246
INFO 2026-06-08 07:44:13 MarkDuplicates Tracking 205417 as yet unmatched pairs. 8272 records in RAM.
INFO 2026-06-08 07:44:17 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:07:41s. Time for last 1,000,000: 3s. Last read position: chr14:96,306,744
INFO 2026-06-08 07:44:17 MarkDuplicates Tracking 201282 as yet unmatched pairs. 2822 records in RAM.
INFO 2026-06-08 07:44:20 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:07:45s. Time for last 1,000,000: 3s. Last read position: chr15:21,164,633
INFO 2026-06-08 07:44:20 MarkDuplicates Tracking 198891 as yet unmatched pairs. 29549 records in RAM.
INFO 2026-06-08 07:44:23 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:07:48s. Time for last 1,000,000: 2s. Last read position: chr15:30,477,897
INFO 2026-06-08 07:44:23 MarkDuplicates Tracking 197227 as yet unmatched pairs. 27401 records in RAM.
INFO 2026-06-08 07:44:26 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:07:51s. Time for last 1,000,000: 3s. Last read position: chr15:41,049,255
INFO 2026-06-08 07:44:26 MarkDuplicates Tracking 194956 as yet unmatched pairs. 24462 records in RAM.
INFO 2026-06-08 07:44:29 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:07:54s. Time for last 1,000,000: 3s. Last read position: chr15:47,759,897
INFO 2026-06-08 07:44:29 MarkDuplicates Tracking 192735 as yet unmatched pairs. 21645 records in RAM.
INFO 2026-06-08 07:44:32 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:07:57s. Time for last 1,000,000: 3s. Last read position: chr15:65,922,336
INFO 2026-06-08 07:44:32 MarkDuplicates Tracking 189913 as yet unmatched pairs. 17821 records in RAM.
INFO 2026-06-08 07:44:35 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:08:00s. Time for last 1,000,000: 3s. Last read position: chr15:76,862,463
INFO 2026-06-08 07:44:35 MarkDuplicates Tracking 187453 as yet unmatched pairs. 14701 records in RAM.
INFO 2026-06-08 07:44:38 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:08:03s. Time for last 1,000,000: 2s. Last read position: chr15:87,950,030
INFO 2026-06-08 07:44:38 MarkDuplicates Tracking 186004 as yet unmatched pairs. 12538 records in RAM.
INFO 2026-06-08 07:44:41 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:08:06s. Time for last 1,000,000: 2s. Last read position: chr15:88,025,318
INFO 2026-06-08 07:44:41 MarkDuplicates Tracking 183675 as yet unmatched pairs. 9791 records in RAM.
INFO 2026-06-08 07:44:44 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:08:09s. Time for last 1,000,000: 3s. Last read position: chr15:88,085,788
INFO 2026-06-08 07:44:44 MarkDuplicates Tracking 181580 as yet unmatched pairs. 7216 records in RAM.
INFO 2026-06-08 07:44:47 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:08:12s. Time for last 1,000,000: 3s. Last read position: chr15:89,115,153
INFO 2026-06-08 07:44:47 MarkDuplicates Tracking 178445 as yet unmatched pairs. 3653 records in RAM.
INFO 2026-06-08 07:44:51 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 3s. Last read position: chr16:17,246
INFO 2026-06-08 07:44:51 MarkDuplicates Tracking 175587 as yet unmatched pairs. 27320 records in RAM.
INFO 2026-06-08 07:44:54 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 3s. Last read position: chr16:2,598,242
INFO 2026-06-08 07:44:54 MarkDuplicates Tracking 174930 as yet unmatched pairs. 26320 records in RAM.
INFO 2026-06-08 07:44:56 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 2s. Last read position: chr16:10,430,621
INFO 2026-06-08 07:44:56 MarkDuplicates Tracking 170877 as yet unmatched pairs. 21794 records in RAM.
INFO 2026-06-08 07:44:59 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:08:24s. Time for last 1,000,000: 2s. Last read position: chr16:18,391,316
INFO 2026-06-08 07:44:59 MarkDuplicates Tracking 169315 as yet unmatched pairs. 19840 records in RAM.
INFO 2026-06-08 07:45:02 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:08:27s. Time for last 1,000,000: 3s. Last read position: chr16:28,349,080
INFO 2026-06-08 07:45:02 MarkDuplicates Tracking 166881 as yet unmatched pairs. 16871 records in RAM.
INFO 2026-06-08 07:45:05 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:08:30s. Time for last 1,000,000: 2s. Last read position: chr16:31,381,518
INFO 2026-06-08 07:45:05 MarkDuplicates Tracking 165181 as yet unmatched pairs. 14900 records in RAM.
INFO 2026-06-08 07:45:08 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:08:33s. Time for last 1,000,000: 2s. Last read position: chr16:56,847,442
INFO 2026-06-08 07:45:08 MarkDuplicates Tracking 162382 as yet unmatched pairs. 11150 records in RAM.
INFO 2026-06-08 07:45:11 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:08:36s. Time for last 1,000,000: 2s. Last read position: chr16:69,351,755
INFO 2026-06-08 07:45:11 MarkDuplicates Tracking 158826 as yet unmatched pairs. 7032 records in RAM.
INFO 2026-06-08 07:45:14 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:08:39s. Time for last 1,000,000: 3s. Last read position: chr16:81,701,527
INFO 2026-06-08 07:45:14 MarkDuplicates Tracking 156033 as yet unmatched pairs. 3581 records in RAM.
INFO 2026-06-08 07:45:17 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:08:41s. Time for last 1,000,000: 2s. Last read position: chr16:89,784,867
INFO 2026-06-08 07:45:17 MarkDuplicates Tracking 153558 as yet unmatched pairs. 593 records in RAM.
INFO 2026-06-08 07:45:19 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:08:44s. Time for last 1,000,000: 2s. Last read position: chr17:5,468,504
INFO 2026-06-08 07:45:19 MarkDuplicates Tracking 151194 as yet unmatched pairs. 33763 records in RAM.
INFO 2026-06-08 07:45:22 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:08:47s. Time for last 1,000,000: 3s. Last read position: chr17:10,414,354
INFO 2026-06-08 07:45:22 MarkDuplicates Tracking 148780 as yet unmatched pairs. 31030 records in RAM.
INFO 2026-06-08 07:45:26 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 3s. Last read position: chr17:18,492,438
INFO 2026-06-08 07:45:26 MarkDuplicates Tracking 146273 as yet unmatched pairs. 28133 records in RAM.
INFO 2026-06-08 07:45:29 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 3s. Last read position: chr17:31,226,469
INFO 2026-06-08 07:45:29 MarkDuplicates Tracking 143615 as yet unmatched pairs. 25013 records in RAM.
INFO 2026-06-08 07:45:32 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:08:57s. Time for last 1,000,000: 3s. Last read position: chr17:38,335,549
INFO 2026-06-08 07:45:32 MarkDuplicates Tracking 140829 as yet unmatched pairs. 21861 records in RAM.
INFO 2026-06-08 07:45:35 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:09:00s. Time for last 1,000,000: 3s. Last read position: chr17:40,625,813
INFO 2026-06-08 07:45:35 MarkDuplicates Tracking 138813 as yet unmatched pairs. 19522 records in RAM.
INFO 2026-06-08 07:45:38 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:09:03s. Time for last 1,000,000: 3s. Last read position: chr17:43,027,343
INFO 2026-06-08 07:45:38 MarkDuplicates Tracking 136244 as yet unmatched pairs. 16668 records in RAM.
INFO 2026-06-08 07:45:42 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:09:06s. Time for last 1,000,000: 3s. Last read position: chr17:46,032,041
INFO 2026-06-08 07:45:42 MarkDuplicates Tracking 133874 as yet unmatched pairs. 14002 records in RAM.
INFO 2026-06-08 07:45:45 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:09:09s. Time for last 1,000,000: 2s. Last read position: chr17:56,437,787
INFO 2026-06-08 07:45:45 MarkDuplicates Tracking 131007 as yet unmatched pairs. 10759 records in RAM.
INFO 2026-06-08 07:45:48 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:09:13s. Time for last 1,000,000: 3s. Last read position: chr17:64,000,634
INFO 2026-06-08 07:45:48 MarkDuplicates Tracking 128193 as yet unmatched pairs. 7541 records in RAM.
INFO 2026-06-08 07:45:51 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 3s. Last read position: chr17:75,487,863
INFO 2026-06-08 07:45:51 MarkDuplicates Tracking 125218 as yet unmatched pairs. 4156 records in RAM.
INFO 2026-06-08 07:45:54 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:09:19s. Time for last 1,000,000: 2s. Last read position: chr17:81,250,987
INFO 2026-06-08 07:45:54 MarkDuplicates Tracking 122407 as yet unmatched pairs. 1024 records in RAM.
INFO 2026-06-08 07:45:57 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 3s. Last read position: chr18:21,023,554
INFO 2026-06-08 07:45:57 MarkDuplicates Tracking 118592 as yet unmatched pairs. 13335 records in RAM.
INFO 2026-06-08 07:46:01 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:09:26s. Time for last 1,000,000: 3s. Last read position: chr18:46,963,361
INFO 2026-06-08 07:46:01 MarkDuplicates Tracking 114298 as yet unmatched pairs. 8324 records in RAM.
INFO 2026-06-08 07:46:04 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:09:29s. Time for last 1,000,000: 3s. Last read position: chr18:61,550,058
INFO 2026-06-08 07:46:04 MarkDuplicates Tracking 110202 as yet unmatched pairs. 3755 records in RAM.
INFO 2026-06-08 07:46:07 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:09:32s. Time for last 1,000,000: 3s. Last read position: chr19:1,611,108
INFO 2026-06-08 07:46:07 MarkDuplicates Tracking 106864 as yet unmatched pairs. 29907 records in RAM.
INFO 2026-06-08 07:46:10 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 3s. Last read position: chr19:5,695,750
INFO 2026-06-08 07:46:10 MarkDuplicates Tracking 103076 as yet unmatched pairs. 25947 records in RAM.
INFO 2026-06-08 07:46:13 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:09:38s. Time for last 1,000,000: 2s. Last read position: chr19:8,972,996
INFO 2026-06-08 07:46:13 MarkDuplicates Tracking 100968 as yet unmatched pairs. 23587 records in RAM.
INFO 2026-06-08 07:46:16 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:09:41s. Time for last 1,000,000: 2s. Last read position: chr19:13,100,712
INFO 2026-06-08 07:46:16 MarkDuplicates Tracking 98047 as yet unmatched pairs. 20462 records in RAM.
INFO 2026-06-08 07:46:19 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 3s. Last read position: chr19:17,500,583
INFO 2026-06-08 07:46:19 MarkDuplicates Tracking 95340 as yet unmatched pairs. 17574 records in RAM.
INFO 2026-06-08 07:46:24 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:09:48s. Time for last 1,000,000: 4s. Last read position: chr19:35,359,607
INFO 2026-06-08 07:46:24 MarkDuplicates Tracking 92116 as yet unmatched pairs. 14017 records in RAM.
INFO 2026-06-08 07:46:28 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:09:52s. Time for last 1,000,000: 3s. Last read position: chr19:40,285,284
INFO 2026-06-08 07:46:28 MarkDuplicates Tracking 89043 as yet unmatched pairs. 10738 records in RAM.
INFO 2026-06-08 07:46:31 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:09:56s. Time for last 1,000,000: 3s. Last read position: chr19:45,350,002
INFO 2026-06-08 07:46:31 MarkDuplicates Tracking 86550 as yet unmatched pairs. 8026 records in RAM.
INFO 2026-06-08 07:46:34 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 3s. Last read position: chr19:49,799,432
INFO 2026-06-08 07:46:34 MarkDuplicates Tracking 83468 as yet unmatched pairs. 4766 records in RAM.
INFO 2026-06-08 07:46:37 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:10:02s. Time for last 1,000,000: 3s. Last read position: chr19:55,079,782
INFO 2026-06-08 07:46:37 MarkDuplicates Tracking 80717 as yet unmatched pairs. 1802 records in RAM.
INFO 2026-06-08 07:46:40 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:10:05s. Time for last 1,000,000: 3s. Last read position: chr20:5,954,745
INFO 2026-06-08 07:46:40 MarkDuplicates Tracking 77482 as yet unmatched pairs. 17077 records in RAM.
INFO 2026-06-08 07:46:43 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:10:08s. Time for last 1,000,000: 2s. Last read position: chr20:32,359,509
INFO 2026-06-08 07:46:43 MarkDuplicates Tracking 73382 as yet unmatched pairs. 12590 records in RAM.
INFO 2026-06-08 07:46:47 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 3s. Last read position: chr20:41,358,720
INFO 2026-06-08 07:46:47 MarkDuplicates Tracking 69095 as yet unmatched pairs. 8128 records in RAM.
INFO 2026-06-08 07:46:50 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:10:15s. Time for last 1,000,000: 2s. Last read position: chr20:51,130,743
INFO 2026-06-08 07:46:50 MarkDuplicates Tracking 65452 as yet unmatched pairs. 4259 records in RAM.
INFO 2026-06-08 07:46:53 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:10:18s. Time for last 1,000,000: 2s. Last read position: chr20:64,010,299
INFO 2026-06-08 07:46:53 MarkDuplicates Tracking 61627 as yet unmatched pairs. 205 records in RAM.
INFO 2026-06-08 07:46:56 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:10:21s. Time for last 1,000,000: 2s. Last read position: chr21:13,427,636
INFO 2026-06-08 07:46:56 MarkDuplicates Tracking 59254 as yet unmatched pairs. 10136 records in RAM.
INFO 2026-06-08 07:46:59 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:10:24s. Time for last 1,000,000: 3s. Last read position: chr21:40,055,729
INFO 2026-06-08 07:46:59 MarkDuplicates Tracking 53719 as yet unmatched pairs. 4314 records in RAM.
INFO 2026-06-08 07:47:02 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:10:27s. Time for last 1,000,000: 2s. Last read position: chr21:44,250,537
INFO 2026-06-08 07:47:02 MarkDuplicates Tracking 50643 as yet unmatched pairs. 1084 records in RAM.
INFO 2026-06-08 07:47:05 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:10:30s. Time for last 1,000,000: 3s. Last read position: chr22:19,142,660
INFO 2026-06-08 07:47:05 MarkDuplicates Tracking 47953 as yet unmatched pairs. 16483 records in RAM.
INFO 2026-06-08 07:47:08 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:10:33s. Time for last 1,000,000: 2s. Last read position: chr22:22,488,406
INFO 2026-06-08 07:47:08 MarkDuplicates Tracking 45841 as yet unmatched pairs. 14288 records in RAM.
INFO 2026-06-08 07:47:10 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:10:35s. Time for last 1,000,000: 2s. Last read position: chr22:23,800,980
INFO 2026-06-08 07:47:10 MarkDuplicates Tracking 43490 as yet unmatched pairs. 11845 records in RAM.
INFO 2026-06-08 07:47:13 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:10:38s. Time for last 1,000,000: 2s. Last read position: chr22:29,682,940
INFO 2026-06-08 07:47:13 MarkDuplicates Tracking 40091 as yet unmatched pairs. 8340 records in RAM.
INFO 2026-06-08 07:47:16 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:10:41s. Time for last 1,000,000: 3s. Last read position: chr22:39,223,388
INFO 2026-06-08 07:47:16 MarkDuplicates Tracking 36994 as yet unmatched pairs. 5152 records in RAM.
INFO 2026-06-08 07:47:19 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:10:44s. Time for last 1,000,000: 2s. Last read position: chr22:50,283,854
INFO 2026-06-08 07:47:19 MarkDuplicates Tracking 32611 as yet unmatched pairs. 658 records in RAM.
INFO 2026-06-08 07:47:22 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:10:47s. Time for last 1,000,000: 2s. Last read position: chrX:34,393,638
INFO 2026-06-08 07:47:22 MarkDuplicates Tracking 27860 as yet unmatched pairs. 19263 records in RAM.
INFO 2026-06-08 07:47:24 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:10:49s. Time for last 1,000,000: 2s. Last read position: chrX:52,972,346
INFO 2026-06-08 07:47:24 MarkDuplicates Tracking 24438 as yet unmatched pairs. 15824 records in RAM.
INFO 2026-06-08 07:47:27 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:10:52s. Time for last 1,000,000: 2s. Last read position: chrX:71,250,373
INFO 2026-06-08 07:47:27 MarkDuplicates Tracking 21131 as yet unmatched pairs. 12471 records in RAM.
INFO 2026-06-08 07:47:30 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:10:55s. Time for last 1,000,000: 2s. Last read position: chrX:110,455,298
INFO 2026-06-08 07:47:30 MarkDuplicates Tracking 15971 as yet unmatched pairs. 7275 records in RAM.
INFO 2026-06-08 07:47:33 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 3s. Last read position: chrX:135,985,712
INFO 2026-06-08 07:47:33 MarkDuplicates Tracking 11988 as yet unmatched pairs. 3250 records in RAM.
INFO 2026-06-08 07:47:36 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:11:01s. Time for last 1,000,000: 2s. Last read position: chrY:9,340,076
INFO 2026-06-08 07:47:36 MarkDuplicates Tracking 8281 as yet unmatched pairs. 3054 records in RAM.
INFO 2026-06-08 07:47:38 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:11:03s. Time for last 1,000,000: 2s. Last read position: chrY:24,805,013
INFO 2026-06-08 07:47:38 MarkDuplicates Tracking 6294 as yet unmatched pairs. 1047 records in RAM.
INFO 2026-06-08 07:47:41 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:11:05s. Time for last 1,000,000: 2s. Last read position: KI270731.1:6,027
INFO 2026-06-08 07:47:41 MarkDuplicates Tracking 2805 as yet unmatched pairs. 1251 records in RAM.
INFO 2026-06-08 07:47:42 MarkDuplicates Read 214547106 records. 0 pairs never matched.
INFO 2026-06-08 07:47:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 25856856280; totalMemory: 50801410048; maxMemory: 63585648640
INFO 2026-06-08 07:47:57 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 07:47:59 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 07:48:16 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 07:48:31 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 07:48:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 34851405816; totalMemory: 50801410048; maxMemory: 63585648640
INFO 2026-06-08 07:48:33 MarkDuplicates Marking 36769915 records as duplicates.
INFO 2026-06-08 07:48:33 MarkDuplicates Found 8093432 optical duplicate clusters.
INFO 2026-06-08 07:48:33 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 07:49:04 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:30s. Time for last 10,000,000: 30s. Last read position: chr1:117,144,988
INFO 2026-06-08 07:49:34 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:01:00s. Time for last 10,000,000: 30s. Last read position: chr2:4,628,747
INFO 2026-06-08 07:50:03 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:29s. Time for last 10,000,000: 29s. Last read position: chr2:140,993,980
INFO 2026-06-08 07:50:34 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:02:00s. Time for last 10,000,000: 30s. Last read position: chr3:43,600,426
INFO 2026-06-08 07:51:04 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:02:30s. Time for last 10,000,000: 30s. Last read position: chr4:6,611,067
INFO 2026-06-08 07:51:34 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:03:00s. Time for last 10,000,000: 29s. Last read position: chr5:70,132,933
INFO 2026-06-08 07:52:03 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:03:30s. Time for last 10,000,000: 29s. Last read position: chr6:41,785,728
INFO 2026-06-08 07:52:33 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:03:59s. Time for last 10,000,000: 29s. Last read position: chr7:44,039,804
INFO 2026-06-08 07:53:02 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:04:29s. Time for last 10,000,000: 29s. Last read position: chr8:8,377,108
INFO 2026-06-08 07:53:33 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:04:59s. Time for last 10,000,000: 30s. Last read position: chr9:21,409,324
INFO 2026-06-08 07:54:02 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:05:28s. Time for last 10,000,000: 29s. Last read position: chr10:8,074,290
INFO 2026-06-08 07:54:33 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:05:59s. Time for last 10,000,000: 30s. Last read position: chr11:18,403,602
INFO 2026-06-08 07:55:02 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:06:28s. Time for last 10,000,000: 29s. Last read position: chr12:11,792,761
INFO 2026-06-08 07:55:32 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:06:58s. Time for last 10,000,000: 29s. Last read position: chr13:28,300,427
INFO 2026-06-08 07:56:02 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:07:28s. Time for last 10,000,000: 29s. Last read position: chr15:41,049,255
INFO 2026-06-08 07:56:31 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:07:57s. Time for last 10,000,000: 29s. Last read position: chr16:10,430,621
INFO 2026-06-08 07:57:00 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:08:26s. Time for last 10,000,000: 29s. Last read position: chr17:18,492,438
INFO 2026-06-08 07:57:30 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:08:56s. Time for last 10,000,000: 29s. Last read position: chr18:21,023,554
INFO 2026-06-08 07:57:59 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:09:25s. Time for last 10,000,000: 29s. Last read position: chr19:45,350,002
INFO 2026-06-08 07:58:28 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:09:55s. Time for last 10,000,000: 29s. Last read position: chr21:44,250,537
INFO 2026-06-08 07:58:58 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:10:24s. Time for last 10,000,000: 29s. Last read position: chrX:110,455,298
INFO 2026-06-08 07:59:19 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 07:59:19 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 07:59:19 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 07:59:19 MarkDuplicates Before output close freeMemory: 201880552; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 07:59:19 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 07:59:19 MarkDuplicates After output close freeMemory: 104367296; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 07:59:19 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 22.77 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory