Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bam --METRICS_FILE aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:52:39.059 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 07:52:39 GMT 2026] MarkDuplicates --INPUT aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-20b7e4-R1_B23WHYVLT4_1.md.bam --METRICS_FILE aih-tih-sc-20b7e4-R1_B23WHYVLT4_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 <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 07:52:39 GMT 2026] Executing as ?@nf-6f6f68937af1ee9ca5c19c3c0f4d07c0-1326e-rnvx4 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 07:52:39 MarkDuplicates Start of doWork freeMemory: 105828688; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:52:39 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:52:39 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:52:43 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:6,477,548
INFO 2026-06-08 07:52:43 MarkDuplicates Tracking 2642 as yet unmatched pairs. 53 records in RAM.
INFO 2026-06-08 07:52:46 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: chr1:12,611,476
INFO 2026-06-08 07:52:46 MarkDuplicates Tracking 5133 as yet unmatched pairs. 10 records in RAM.
INFO 2026-06-08 07:52:48 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 2s. Last read position: chr1:20,941,556
INFO 2026-06-08 07:52:48 MarkDuplicates Tracking 7451 as yet unmatched pairs. 72 records in RAM.
INFO 2026-06-08 07:52:51 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 2s. Last read position: chr1:26,696,496
INFO 2026-06-08 07:52:51 MarkDuplicates Tracking 9852 as yet unmatched pairs. 10 records in RAM.
INFO 2026-06-08 07:52:53 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 2s. Last read position: chr1:32,228,514
INFO 2026-06-08 07:52:53 MarkDuplicates Tracking 12390 as yet unmatched pairs. 60 records in RAM.
INFO 2026-06-08 07:52:56 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 2s. Last read position: chr1:39,324,235
INFO 2026-06-08 07:52:56 MarkDuplicates Tracking 14643 as yet unmatched pairs. 15 records in RAM.
INFO 2026-06-08 07:52:58 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: chr1:43,688,962
INFO 2026-06-08 07:52:58 MarkDuplicates Tracking 17122 as yet unmatched pairs. 22 records in RAM.
INFO 2026-06-08 07:53:00 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: chr1:55,125,394
INFO 2026-06-08 07:53:00 MarkDuplicates Tracking 19424 as yet unmatched pairs. 8 records in RAM.
INFO 2026-06-08 07:53:03 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 2s. Last read position: chr1:84,939,649
INFO 2026-06-08 07:53:03 MarkDuplicates Tracking 21974 as yet unmatched pairs. 4 records in RAM.
INFO 2026-06-08 07:53:06 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 2s. Last read position: chr1:109,250,945
INFO 2026-06-08 07:53:06 MarkDuplicates Tracking 24151 as yet unmatched pairs. 27 records in RAM.
INFO 2026-06-08 07:53:08 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 1s. Last read position: chr1:116,399,514
INFO 2026-06-08 07:53:08 MarkDuplicates Tracking 26412 as yet unmatched pairs. 67 records in RAM.
INFO 2026-06-08 07:53:10 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 2s. Last read position: chr1:144,435,228
INFO 2026-06-08 07:53:10 MarkDuplicates Tracking 28297 as yet unmatched pairs. 50 records in RAM.
INFO 2026-06-08 07:53:12 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 1s. Last read position: chr1:148,559,025
INFO 2026-06-08 07:53:12 MarkDuplicates Tracking 29261 as yet unmatched pairs. 22 records in RAM.
INFO 2026-06-08 07:53:13 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 1s. Last read position: chr1:150,492,360
INFO 2026-06-08 07:53:13 MarkDuplicates Tracking 30600 as yet unmatched pairs. 3 records in RAM.
INFO 2026-06-08 07:53:15 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 1s. Last read position: chr1:153,669,849
INFO 2026-06-08 07:53:15 MarkDuplicates Tracking 33051 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 07:53:17 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 2s. Last read position: chr1:155,169,464
INFO 2026-06-08 07:53:17 MarkDuplicates Tracking 35303 as yet unmatched pairs. 49 records in RAM.
INFO 2026-06-08 07:53:19 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 2s. Last read position: chr1:155,191,581
INFO 2026-06-08 07:53:19 MarkDuplicates Tracking 36971 as yet unmatched pairs. 114 records in RAM.
INFO 2026-06-08 07:53:22 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 2s. Last read position: chr1:156,130,636
INFO 2026-06-08 07:53:22 MarkDuplicates Tracking 40021 as yet unmatched pairs. 990 records in RAM.
INFO 2026-06-08 07:53:25 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 3s. Last read position: chr1:160,339,962
INFO 2026-06-08 07:53:25 MarkDuplicates Tracking 41775 as yet unmatched pairs. 12 records in RAM.
INFO 2026-06-08 07:53:27 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 2s. Last read position: chr1:171,541,034
INFO 2026-06-08 07:53:27 MarkDuplicates Tracking 44304 as yet unmatched pairs. 12 records in RAM.
INFO 2026-06-08 07:53:29 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 1s. Last read position: chr1:185,300,436
INFO 2026-06-08 07:53:29 MarkDuplicates Tracking 46464 as yet unmatched pairs. 14 records in RAM.
INFO 2026-06-08 07:53:31 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 1s. Last read position: chr1:202,746,196
INFO 2026-06-08 07:53:31 MarkDuplicates Tracking 48419 as yet unmatched pairs. 99 records in RAM.
INFO 2026-06-08 07:53:33 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 1s. Last read position: chr1:211,313,487
INFO 2026-06-08 07:53:33 MarkDuplicates Tracking 50844 as yet unmatched pairs. 82 records in RAM.
INFO 2026-06-08 07:53:35 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 1s. Last read position: chr1:226,707,796
INFO 2026-06-08 07:53:35 MarkDuplicates Tracking 52816 as yet unmatched pairs. 5 records in RAM.
INFO 2026-06-08 07:53:37 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 2s. Last read position: chr1:236,862,325
INFO 2026-06-08 07:53:37 MarkDuplicates Tracking 55441 as yet unmatched pairs. 24 records in RAM.
INFO 2026-06-08 07:53:39 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 2s. Last read position: chr2:11,576,394
INFO 2026-06-08 07:53:39 MarkDuplicates Tracking 57657 as yet unmatched pairs. 57576 records in RAM.
INFO 2026-06-08 07:53:42 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 2s. Last read position: chr2:27,234,590
INFO 2026-06-08 07:53:42 MarkDuplicates Tracking 60053 as yet unmatched pairs. 59971 records in RAM.
INFO 2026-06-08 07:53:44 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,264
INFO 2026-06-08 07:53:44 MarkDuplicates Tracking 170101 as yet unmatched pairs. 54614 records in RAM.
INFO 2026-06-08 07:53:46 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,406
INFO 2026-06-08 07:53:46 MarkDuplicates Tracking 456383 as yet unmatched pairs. 37647 records in RAM.
INFO 2026-06-08 07:53:50 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 3s. Last read position: chr2:47,161,774
INFO 2026-06-08 07:53:50 MarkDuplicates Tracking 485928 as yet unmatched pairs. 34277 records in RAM.
INFO 2026-06-08 07:53:52 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 2s. Last read position: chr2:69,514,601
INFO 2026-06-08 07:53:52 MarkDuplicates Tracking 483432 as yet unmatched pairs. 31779 records in RAM.
INFO 2026-06-08 07:53:55 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 2s. Last read position: chr2:86,464,071
INFO 2026-06-08 07:53:55 MarkDuplicates Tracking 481180 as yet unmatched pairs. 29525 records in RAM.
INFO 2026-06-08 07:53:57 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 2s. Last read position: chr2:99,551,536
INFO 2026-06-08 07:53:57 MarkDuplicates Tracking 479616 as yet unmatched pairs. 27961 records in RAM.
INFO 2026-06-08 07:53:59 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 1s. Last read position: chr2:108,782,206
INFO 2026-06-08 07:53:59 MarkDuplicates Tracking 478014 as yet unmatched pairs. 26357 records in RAM.
INFO 2026-06-08 07:54:01 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 1s. Last read position: chr2:120,933,834
INFO 2026-06-08 07:54:01 MarkDuplicates Tracking 476883 as yet unmatched pairs. 25225 records in RAM.
INFO 2026-06-08 07:54:03 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 2s. Last read position: chr2:144,424,824
INFO 2026-06-08 07:54:03 MarkDuplicates Tracking 474957 as yet unmatched pairs. 23293 records in RAM.
INFO 2026-06-08 07:54:07 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 3s. Last read position: chr2:171,468,889
INFO 2026-06-08 07:54:07 MarkDuplicates Tracking 472624 as yet unmatched pairs. 20957 records in RAM.
INFO 2026-06-08 07:54:09 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 2s. Last read position: chr2:188,995,763
INFO 2026-06-08 07:54:09 MarkDuplicates Tracking 470651 as yet unmatched pairs. 18982 records in RAM.
INFO 2026-06-08 07:54:11 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 2s. Last read position: chr2:201,761,287
INFO 2026-06-08 07:54:11 MarkDuplicates Tracking 468109 as yet unmatched pairs. 16439 records in RAM.
INFO 2026-06-08 07:54:14 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 2s. Last read position: chr2:215,364,950
INFO 2026-06-08 07:54:14 MarkDuplicates Tracking 466609 as yet unmatched pairs. 14929 records in RAM.
INFO 2026-06-08 07:54:17 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 3s. Last read position: chr2:215,376,518
INFO 2026-06-08 07:54:17 MarkDuplicates Tracking 465878 as yet unmatched pairs. 14198 records in RAM.
INFO 2026-06-08 07:54:19 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 2s. Last read position: chr2:215,394,605
INFO 2026-06-08 07:54:19 MarkDuplicates Tracking 462273 as yet unmatched pairs. 10593 records in RAM.
INFO 2026-06-08 07:54:22 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 2s. Last read position: chr2:215,410,075
INFO 2026-06-08 07:54:22 MarkDuplicates Tracking 461385 as yet unmatched pairs. 9705 records in RAM.
INFO 2026-06-08 07:54:25 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 3s. Last read position: chr2:216,161,986
INFO 2026-06-08 07:54:25 MarkDuplicates Tracking 457574 as yet unmatched pairs. 5894 records in RAM.
INFO 2026-06-08 07:54:28 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 2s. Last read position: chr2:231,461,795
INFO 2026-06-08 07:54:28 MarkDuplicates Tracking 455202 as yet unmatched pairs. 3517 records in RAM.
INFO 2026-06-08 07:54:30 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 2s. Last read position: chr2:238,348,768
INFO 2026-06-08 07:54:30 MarkDuplicates Tracking 452775 as yet unmatched pairs. 1090 records in RAM.
INFO 2026-06-08 07:54:32 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 2s. Last read position: chr3:9,475,734
INFO 2026-06-08 07:54:32 MarkDuplicates Tracking 450444 as yet unmatched pairs. 18876 records in RAM.
INFO 2026-06-08 07:54:35 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 2s. Last read position: chr3:38,221,576
INFO 2026-06-08 07:54:35 MarkDuplicates Tracking 448245 as yet unmatched pairs. 16672 records in RAM.
INFO 2026-06-08 07:54:38 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 2s. Last read position: chr3:48,694,974
INFO 2026-06-08 07:54:38 MarkDuplicates Tracking 445764 as yet unmatched pairs. 14191 records in RAM.
INFO 2026-06-08 07:54:39 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 1s. Last read position: chr3:56,646,524
INFO 2026-06-08 07:54:39 MarkDuplicates Tracking 443364 as yet unmatched pairs. 11790 records in RAM.
INFO 2026-06-08 07:54:41 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 1s. Last read position: chr3:105,552,554
INFO 2026-06-08 07:54:41 MarkDuplicates Tracking 441444 as yet unmatched pairs. 9867 records in RAM.
INFO 2026-06-08 07:54:43 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 2s. Last read position: chr3:126,461,726
INFO 2026-06-08 07:54:43 MarkDuplicates Tracking 439182 as yet unmatched pairs. 7602 records in RAM.
INFO 2026-06-08 07:54:45 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 1s. Last read position: chr3:143,016,259
INFO 2026-06-08 07:54:45 MarkDuplicates Tracking 436874 as yet unmatched pairs. 5293 records in RAM.
INFO 2026-06-08 07:54:47 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 1s. Last read position: chr3:179,259,548
INFO 2026-06-08 07:54:47 MarkDuplicates Tracking 434864 as yet unmatched pairs. 3282 records in RAM.
INFO 2026-06-08 07:54:49 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 2s. Last read position: chr3:193,502,526
INFO 2026-06-08 07:54:49 MarkDuplicates Tracking 432688 as yet unmatched pairs. 1105 records in RAM.
INFO 2026-06-08 07:54:52 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 2s. Last read position: chr4:1,814,462
INFO 2026-06-08 07:54:52 MarkDuplicates Tracking 430363 as yet unmatched pairs. 13307 records in RAM.
INFO 2026-06-08 07:54:54 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 2s. Last read position: chr4:15,007,370
INFO 2026-06-08 07:54:54 MarkDuplicates Tracking 427898 as yet unmatched pairs. 10840 records in RAM.
INFO 2026-06-08 07:54:57 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 2s. Last read position: chr4:70,705,253
INFO 2026-06-08 07:54:57 MarkDuplicates Tracking 425682 as yet unmatched pairs. 8623 records in RAM.
INFO 2026-06-08 07:54:59 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 2s. Last read position: chr4:88,467,096
INFO 2026-06-08 07:54:59 MarkDuplicates Tracking 423496 as yet unmatched pairs. 6436 records in RAM.
INFO 2026-06-08 07:55:02 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 2s. Last read position: chr4:121,802,913
INFO 2026-06-08 07:55:02 MarkDuplicates Tracking 421371 as yet unmatched pairs. 4309 records in RAM.
INFO 2026-06-08 07:55:04 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 2s. Last read position: chr4:150,831,817
INFO 2026-06-08 07:55:04 MarkDuplicates Tracking 419230 as yet unmatched pairs. 2162 records in RAM.
INFO 2026-06-08 07:55:06 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 2s. Last read position: chr5:1,038,227
INFO 2026-06-08 07:55:06 MarkDuplicates Tracking 416792 as yet unmatched pairs. 22843 records in RAM.
INFO 2026-06-08 07:55:08 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 2s. Last read position: chr5:17,354,224
INFO 2026-06-08 07:55:08 MarkDuplicates Tracking 414712 as yet unmatched pairs. 20762 records in RAM.
INFO 2026-06-08 07:55:11 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 2s. Last read position: chr5:56,882,419
INFO 2026-06-08 07:55:11 MarkDuplicates Tracking 412745 as yet unmatched pairs. 18793 records in RAM.
INFO 2026-06-08 07:55:13 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 2s. Last read position: chr5:73,503,050
INFO 2026-06-08 07:55:13 MarkDuplicates Tracking 410950 as yet unmatched pairs. 16990 records in RAM.
INFO 2026-06-08 07:55:16 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 2s. Last read position: chr5:96,702,872
INFO 2026-06-08 07:55:16 MarkDuplicates Tracking 408842 as yet unmatched pairs. 14877 records in RAM.
INFO 2026-06-08 07:55:18 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 2s. Last read position: chr5:132,824,710
INFO 2026-06-08 07:55:18 MarkDuplicates Tracking 406541 as yet unmatched pairs. 12573 records in RAM.
INFO 2026-06-08 07:55:21 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 2s. Last read position: chr5:139,322,739
INFO 2026-06-08 07:55:21 MarkDuplicates Tracking 404229 as yet unmatched pairs. 10261 records in RAM.
INFO 2026-06-08 07:55:23 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 1s. Last read position: chr5:149,978,314
INFO 2026-06-08 07:55:23 MarkDuplicates Tracking 401787 as yet unmatched pairs. 7788 records in RAM.
INFO 2026-06-08 07:55:25 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 2s. Last read position: chr5:151,663,548
INFO 2026-06-08 07:55:25 MarkDuplicates Tracking 399503 as yet unmatched pairs. 5504 records in RAM.
INFO 2026-06-08 07:55:27 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 2s. Last read position: chr5:175,961,365
INFO 2026-06-08 07:55:27 MarkDuplicates Tracking 396920 as yet unmatched pairs. 2919 records in RAM.
INFO 2026-06-08 07:55:30 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 2s. Last read position: chr5:179,891,431
INFO 2026-06-08 07:55:30 MarkDuplicates Tracking 394556 as yet unmatched pairs. 555 records in RAM.
INFO 2026-06-08 07:55:32 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 2s. Last read position: chr6:10,529,528
INFO 2026-06-08 07:55:32 MarkDuplicates Tracking 392111 as yet unmatched pairs. 29219 records in RAM.
INFO 2026-06-08 07:55:34 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 2s. Last read position: chr6:27,815,122
INFO 2026-06-08 07:55:34 MarkDuplicates Tracking 389760 as yet unmatched pairs. 26866 records in RAM.
INFO 2026-06-08 07:55:36 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 2s. Last read position: chr6:31,625,186
INFO 2026-06-08 07:55:36 MarkDuplicates Tracking 387702 as yet unmatched pairs. 24808 records in RAM.
INFO 2026-06-08 07:55:38 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 1s. Last read position: chr6:31,982,780
INFO 2026-06-08 07:55:38 MarkDuplicates Tracking 385785 as yet unmatched pairs. 22890 records in RAM.
INFO 2026-06-08 07:55:40 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 1s. Last read position: chr6:31,995,177
INFO 2026-06-08 07:55:40 MarkDuplicates Tracking 386414 as yet unmatched pairs. 23519 records in RAM.
INFO 2026-06-08 07:55:42 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 1s. Last read position: chr6:32,007,049
INFO 2026-06-08 07:55:42 MarkDuplicates Tracking 386756 as yet unmatched pairs. 23861 records in RAM.
INFO 2026-06-08 07:55:45 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 3s. Last read position: chr6:32,026,981
INFO 2026-06-08 07:55:45 MarkDuplicates Tracking 384126 as yet unmatched pairs. 21231 records in RAM.
INFO 2026-06-08 07:55:47 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 2s. Last read position: chr6:32,034,328
INFO 2026-06-08 07:55:47 MarkDuplicates Tracking 381253 as yet unmatched pairs. 18357 records in RAM.
INFO 2026-06-08 07:55:49 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 2s. Last read position: chr6:33,413,736
INFO 2026-06-08 07:55:49 MarkDuplicates Tracking 378054 as yet unmatched pairs. 15158 records in RAM.
INFO 2026-06-08 07:55:52 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 2s. Last read position: chr6:43,037,914
INFO 2026-06-08 07:55:52 MarkDuplicates Tracking 375853 as yet unmatched pairs. 12954 records in RAM.
INFO 2026-06-08 07:55:54 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 2s. Last read position: chr6:57,101,346
INFO 2026-06-08 07:55:54 MarkDuplicates Tracking 373510 as yet unmatched pairs. 10608 records in RAM.
INFO 2026-06-08 07:55:56 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 2s. Last read position: chr6:89,867,045
INFO 2026-06-08 07:55:56 MarkDuplicates Tracking 371245 as yet unmatched pairs. 8341 records in RAM.
INFO 2026-06-08 07:55:58 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 2s. Last read position: chr6:128,368,926
INFO 2026-06-08 07:55:58 MarkDuplicates Tracking 369041 as yet unmatched pairs. 6132 records in RAM.
INFO 2026-06-08 07:56:00 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 2s. Last read position: chr6:144,437,592
INFO 2026-06-08 07:56:00 MarkDuplicates Tracking 366671 as yet unmatched pairs. 3760 records in RAM.
INFO 2026-06-08 07:56:02 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 2s. Last read position: chr6:158,785,409
INFO 2026-06-08 07:56:02 MarkDuplicates Tracking 364637 as yet unmatched pairs. 1723 records in RAM.
INFO 2026-06-08 07:56:05 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 2s. Last read position: chr7:4,788,207
INFO 2026-06-08 07:56:05 MarkDuplicates Tracking 361903 as yet unmatched pairs. 23713 records in RAM.
INFO 2026-06-08 07:56:07 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 2s. Last read position: chr7:8,128,005
INFO 2026-06-08 07:56:07 MarkDuplicates Tracking 359623 as yet unmatched pairs. 21430 records in RAM.
INFO 2026-06-08 07:56:10 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 2s. Last read position: chr7:42,223,154
INFO 2026-06-08 07:56:10 MarkDuplicates Tracking 357408 as yet unmatched pairs. 19212 records in RAM.
INFO 2026-06-08 07:56:12 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 2s. Last read position: chr7:70,709,000
INFO 2026-06-08 07:56:12 MarkDuplicates Tracking 355024 as yet unmatched pairs. 16823 records in RAM.
INFO 2026-06-08 07:56:14 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 1s. Last read position: chr7:75,395,254
INFO 2026-06-08 07:56:14 MarkDuplicates Tracking 353450 as yet unmatched pairs. 15246 records in RAM.
INFO 2026-06-08 07:56:16 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 2s. Last read position: chr7:92,001,103
INFO 2026-06-08 07:56:16 MarkDuplicates Tracking 351414 as yet unmatched pairs. 13209 records in RAM.
INFO 2026-06-08 07:56:18 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 2s. Last read position: chr7:94,417,797
INFO 2026-06-08 07:56:18 MarkDuplicates Tracking 349315 as yet unmatched pairs. 11109 records in RAM.
INFO 2026-06-08 07:56:20 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 2s. Last read position: chr7:100,607,689
INFO 2026-06-08 07:56:20 MarkDuplicates Tracking 346682 as yet unmatched pairs. 8472 records in RAM.
INFO 2026-06-08 07:56:22 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 2s. Last read position: chr7:112,455,816
INFO 2026-06-08 07:56:22 MarkDuplicates Tracking 344606 as yet unmatched pairs. 6392 records in RAM.
INFO 2026-06-08 07:56:24 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 1s. Last read position: chr7:137,908,425
INFO 2026-06-08 07:56:24 MarkDuplicates Tracking 342813 as yet unmatched pairs. 4597 records in RAM.
INFO 2026-06-08 07:56:27 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 2s. Last read position: chr7:144,365,099
INFO 2026-06-08 07:56:27 MarkDuplicates Tracking 340498 as yet unmatched pairs. 2280 records in RAM.
INFO 2026-06-08 07:56:29 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 2s. Last read position: chr8:8,377,350
INFO 2026-06-08 07:56:29 MarkDuplicates Tracking 338075 as yet unmatched pairs. 17498 records in RAM.
INFO 2026-06-08 07:56:32 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 2s. Last read position: chr8:37,772,792
INFO 2026-06-08 07:56:32 MarkDuplicates Tracking 335715 as yet unmatched pairs. 15136 records in RAM.
INFO 2026-06-08 07:56:35 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 2s. Last read position: chr8:58,588,377
INFO 2026-06-08 07:56:35 MarkDuplicates Tracking 333237 as yet unmatched pairs. 12658 records in RAM.
INFO 2026-06-08 07:56:37 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 2s. Last read position: chr8:94,726,298
INFO 2026-06-08 07:56:37 MarkDuplicates Tracking 330819 as yet unmatched pairs. 10237 records in RAM.
INFO 2026-06-08 07:56:39 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 2s. Last read position: chr8:115,604,021
INFO 2026-06-08 07:56:39 MarkDuplicates Tracking 328812 as yet unmatched pairs. 8230 records in RAM.
INFO 2026-06-08 07:56:42 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 2s. Last read position: chr8:134,602,455
INFO 2026-06-08 07:56:42 MarkDuplicates Tracking 326239 as yet unmatched pairs. 5654 records in RAM.
INFO 2026-06-08 07:56:44 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 1s. Last read position: chr8:143,861,004
INFO 2026-06-08 07:56:44 MarkDuplicates Tracking 324944 as yet unmatched pairs. 4357 records in RAM.
INFO 2026-06-08 07:56:45 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 1s. Last read position: chr8:143,866,199
INFO 2026-06-08 07:56:45 MarkDuplicates Tracking 323650 as yet unmatched pairs. 3063 records in RAM.
INFO 2026-06-08 07:56:47 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 1s. Last read position: chr8:144,545,399
INFO 2026-06-08 07:56:47 MarkDuplicates Tracking 320818 as yet unmatched pairs. 231 records in RAM.
INFO 2026-06-08 07:56:49 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 2s. Last read position: chr9:32,526,079
INFO 2026-06-08 07:56:49 MarkDuplicates Tracking 318857 as yet unmatched pairs. 15786 records in RAM.
INFO 2026-06-08 07:56:51 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 2s. Last read position: chr9:70,259,064
INFO 2026-06-08 07:56:51 MarkDuplicates Tracking 316836 as yet unmatched pairs. 13761 records in RAM.
INFO 2026-06-08 07:56:54 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 2s. Last read position: chr9:95,928,718
INFO 2026-06-08 07:56:54 MarkDuplicates Tracking 314598 as yet unmatched pairs. 11522 records in RAM.
INFO 2026-06-08 07:56:56 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 2s. Last read position: chr9:115,024,125
INFO 2026-06-08 07:56:56 MarkDuplicates Tracking 312189 as yet unmatched pairs. 9111 records in RAM.
INFO 2026-06-08 07:56:59 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 2s. Last read position: chr9:128,258,498
INFO 2026-06-08 07:56:59 MarkDuplicates Tracking 309715 as yet unmatched pairs. 6633 records in RAM.
INFO 2026-06-08 07:57:01 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 2s. Last read position: chr9:131,629,231
INFO 2026-06-08 07:57:01 MarkDuplicates Tracking 307314 as yet unmatched pairs. 4231 records in RAM.
INFO 2026-06-08 07:57:03 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 2s. Last read position: chr9:136,507,343
INFO 2026-06-08 07:57:03 MarkDuplicates Tracking 304778 as yet unmatched pairs. 1692 records in RAM.
INFO 2026-06-08 07:57:06 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 2s. Last read position: chr10:5,921,321
INFO 2026-06-08 07:57:06 MarkDuplicates Tracking 302201 as yet unmatched pairs. 16834 records in RAM.
INFO 2026-06-08 07:57:08 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 1s. Last read position: chr10:27,043,502
INFO 2026-06-08 07:57:08 MarkDuplicates Tracking 300075 as yet unmatched pairs. 14706 records in RAM.
INFO 2026-06-08 07:57:09 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr10:37,185,638
INFO 2026-06-08 07:57:09 MarkDuplicates Tracking 299066 as yet unmatched pairs. 13690 records in RAM.
INFO 2026-06-08 07:57:11 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 1s. Last read position: chr10:50,009,403
INFO 2026-06-08 07:57:11 MarkDuplicates Tracking 296534 as yet unmatched pairs. 11158 records in RAM.
INFO 2026-06-08 07:57:13 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 1s. Last read position: chr10:73,517,068
INFO 2026-06-08 07:57:13 MarkDuplicates Tracking 294326 as yet unmatched pairs. 8947 records in RAM.
INFO 2026-06-08 07:57:15 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 1s. Last read position: chr10:87,366,461
INFO 2026-06-08 07:57:15 MarkDuplicates Tracking 292233 as yet unmatched pairs. 6854 records in RAM.
INFO 2026-06-08 07:57:17 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 2s. Last read position: chr10:100,999,925
INFO 2026-06-08 07:57:17 MarkDuplicates Tracking 290195 as yet unmatched pairs. 4815 records in RAM.
INFO 2026-06-08 07:57:19 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 2s. Last read position: chr10:116,269,505
INFO 2026-06-08 07:57:19 MarkDuplicates Tracking 288046 as yet unmatched pairs. 2661 records in RAM.
INFO 2026-06-08 07:57:21 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 2s. Last read position: chr10:132,405,445
INFO 2026-06-08 07:57:21 MarkDuplicates Tracking 285664 as yet unmatched pairs. 277 records in RAM.
INFO 2026-06-08 07:57:23 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 2s. Last read position: chr11:1,754,982
INFO 2026-06-08 07:57:23 MarkDuplicates Tracking 283228 as yet unmatched pairs. 27684 records in RAM.
INFO 2026-06-08 07:57:26 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 2s. Last read position: chr11:16,871,104
INFO 2026-06-08 07:57:26 MarkDuplicates Tracking 280722 as yet unmatched pairs. 25177 records in RAM.
INFO 2026-06-08 07:57:28 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 2s. Last read position: chr11:46,669,490
INFO 2026-06-08 07:57:28 MarkDuplicates Tracking 278480 as yet unmatched pairs. 22934 records in RAM.
INFO 2026-06-08 07:57:30 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 2s. Last read position: chr11:61,680,476
INFO 2026-06-08 07:57:30 MarkDuplicates Tracking 276174 as yet unmatched pairs. 20626 records in RAM.
INFO 2026-06-08 07:57:32 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 2s. Last read position: chr11:62,762,942
INFO 2026-06-08 07:57:32 MarkDuplicates Tracking 274039 as yet unmatched pairs. 18491 records in RAM.
INFO 2026-06-08 07:57:34 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 2s. Last read position: chr11:65,582,695
INFO 2026-06-08 07:57:34 MarkDuplicates Tracking 271710 as yet unmatched pairs. 16162 records in RAM.
INFO 2026-06-08 07:57:37 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 2s. Last read position: chr11:67,250,634
INFO 2026-06-08 07:57:37 MarkDuplicates Tracking 269129 as yet unmatched pairs. 13579 records in RAM.
INFO 2026-06-08 07:57:39 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 2s. Last read position: chr11:69,648,093
INFO 2026-06-08 07:57:39 MarkDuplicates Tracking 266453 as yet unmatched pairs. 10903 records in RAM.
INFO 2026-06-08 07:57:41 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 2s. Last read position: chr11:73,235,062
INFO 2026-06-08 07:57:41 MarkDuplicates Tracking 263691 as yet unmatched pairs. 8140 records in RAM.
INFO 2026-06-08 07:57:43 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 1s. Last read position: chr11:89,862,593
INFO 2026-06-08 07:57:43 MarkDuplicates Tracking 261232 as yet unmatched pairs. 5678 records in RAM.
INFO 2026-06-08 07:57:45 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 2s. Last read position: chr11:118,482,070
INFO 2026-06-08 07:57:45 MarkDuplicates Tracking 259120 as yet unmatched pairs. 3565 records in RAM.
INFO 2026-06-08 07:57:47 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 2s. Last read position: chr11:128,970,122
INFO 2026-06-08 07:57:47 MarkDuplicates Tracking 257077 as yet unmatched pairs. 1522 records in RAM.
INFO 2026-06-08 07:57:50 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 2s. Last read position: chr12:6,347,934
INFO 2026-06-08 07:57:50 MarkDuplicates Tracking 254394 as yet unmatched pairs. 24992 records in RAM.
INFO 2026-06-08 07:57:52 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 2s. Last read position: chr12:11,133,542
INFO 2026-06-08 07:57:52 MarkDuplicates Tracking 252470 as yet unmatched pairs. 23068 records in RAM.
INFO 2026-06-08 07:57:54 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 2s. Last read position: chr12:31,981,519
INFO 2026-06-08 07:57:54 MarkDuplicates Tracking 250317 as yet unmatched pairs. 20914 records in RAM.
INFO 2026-06-08 07:57:56 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 2s. Last read position: chr12:49,129,248
INFO 2026-06-08 07:57:56 MarkDuplicates Tracking 248168 as yet unmatched pairs. 18763 records in RAM.
INFO 2026-06-08 07:57:58 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 2s. Last read position: chr12:52,235,374
INFO 2026-06-08 07:57:58 MarkDuplicates Tracking 245923 as yet unmatched pairs. 16517 records in RAM.
INFO 2026-06-08 07:58:01 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:05:20s. Time for last 1,000,000: 2s. Last read position: chr12:56,027,790
INFO 2026-06-08 07:58:01 MarkDuplicates Tracking 243709 as yet unmatched pairs. 14301 records in RAM.
INFO 2026-06-08 07:58:03 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 2s. Last read position: chr12:57,154,149
INFO 2026-06-08 07:58:03 MarkDuplicates Tracking 241476 as yet unmatched pairs. 12068 records in RAM.
INFO 2026-06-08 07:58:05 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 2s. Last read position: chr12:69,239,615
INFO 2026-06-08 07:58:05 MarkDuplicates Tracking 239229 as yet unmatched pairs. 9819 records in RAM.
INFO 2026-06-08 07:58:08 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 2s. Last read position: chr12:100,059,134
INFO 2026-06-08 07:58:08 MarkDuplicates Tracking 237036 as yet unmatched pairs. 7626 records in RAM.
INFO 2026-06-08 07:58:10 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 2s. Last read position: chr12:112,453,285
INFO 2026-06-08 07:58:10 MarkDuplicates Tracking 234696 as yet unmatched pairs. 5286 records in RAM.
INFO 2026-06-08 07:58:12 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 2s. Last read position: chr12:122,279,051
INFO 2026-06-08 07:58:12 MarkDuplicates Tracking 232258 as yet unmatched pairs. 2846 records in RAM.
INFO 2026-06-08 07:58:14 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 2s. Last read position: chr12:132,774,199
INFO 2026-06-08 07:58:14 MarkDuplicates Tracking 229810 as yet unmatched pairs. 397 records in RAM.
INFO 2026-06-08 07:58:16 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 2s. Last read position: chr13:37,563,268
INFO 2026-06-08 07:58:16 MarkDuplicates Tracking 228081 as yet unmatched pairs. 5700 records in RAM.
INFO 2026-06-08 07:58:18 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 2s. Last read position: chr13:71,559,899
INFO 2026-06-08 07:58:18 MarkDuplicates Tracking 225286 as yet unmatched pairs. 2904 records in RAM.
INFO 2026-06-08 07:58:20 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 2s. Last read position: chr13:113,118,447
INFO 2026-06-08 07:58:20 MarkDuplicates Tracking 222884 as yet unmatched pairs. 501 records in RAM.
INFO 2026-06-08 07:58:22 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 1s. Last read position: chr14:24,207,387
INFO 2026-06-08 07:58:22 MarkDuplicates Tracking 220492 as yet unmatched pairs. 11014 records in RAM.
INFO 2026-06-08 07:58:24 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:05:43s. Time for last 1,000,000: 2s. Last read position: chr14:50,109,591
INFO 2026-06-08 07:58:24 MarkDuplicates Tracking 218180 as yet unmatched pairs. 8701 records in RAM.
INFO 2026-06-08 07:58:26 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 2s. Last read position: chr14:68,921,073
INFO 2026-06-08 07:58:26 MarkDuplicates Tracking 216117 as yet unmatched pairs. 6637 records in RAM.
INFO 2026-06-08 07:58:28 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 1s. Last read position: chr14:89,412,047
INFO 2026-06-08 07:58:28 MarkDuplicates Tracking 213621 as yet unmatched pairs. 4138 records in RAM.
INFO 2026-06-08 07:58:30 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 1s. Last read position: chr14:104,706,101
INFO 2026-06-08 07:58:30 MarkDuplicates Tracking 211252 as yet unmatched pairs. 1764 records in RAM.
INFO 2026-06-08 07:58:31 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 1s. Last read position: chr15:28,163,210
INFO 2026-06-08 07:58:31 MarkDuplicates Tracking 209055 as yet unmatched pairs. 14973 records in RAM.
INFO 2026-06-08 07:58:33 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 1s. Last read position: chr15:40,383,031
INFO 2026-06-08 07:58:33 MarkDuplicates Tracking 207127 as yet unmatched pairs. 13045 records in RAM.
INFO 2026-06-08 07:58:34 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 1s. Last read position: chr15:44,490,889
INFO 2026-06-08 07:58:34 MarkDuplicates Tracking 204848 as yet unmatched pairs. 10766 records in RAM.
INFO 2026-06-08 07:58:36 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 1s. Last read position: chr15:59,081,034
INFO 2026-06-08 07:58:36 MarkDuplicates Tracking 202576 as yet unmatched pairs. 8492 records in RAM.
INFO 2026-06-08 07:58:38 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 2s. Last read position: chr15:68,208,298
INFO 2026-06-08 07:58:38 MarkDuplicates Tracking 200186 as yet unmatched pairs. 6102 records in RAM.
INFO 2026-06-08 07:58:40 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 2s. Last read position: chr15:75,527,207
INFO 2026-06-08 07:58:40 MarkDuplicates Tracking 197759 as yet unmatched pairs. 3674 records in RAM.
INFO 2026-06-08 07:58:43 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 2s. Last read position: chr15:90,090,509
INFO 2026-06-08 07:58:43 MarkDuplicates Tracking 195775 as yet unmatched pairs. 1687 records in RAM.
INFO 2026-06-08 07:58:45 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 2s. Last read position: chr16:682,049
INFO 2026-06-08 07:58:45 MarkDuplicates Tracking 193133 as yet unmatched pairs. 28029 records in RAM.
INFO 2026-06-08 07:58:47 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 2s. Last read position: chr16:2,760,382
INFO 2026-06-08 07:58:47 MarkDuplicates Tracking 190530 as yet unmatched pairs. 25426 records in RAM.
INFO 2026-06-08 07:58:50 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:06:09s. Time for last 1,000,000: 2s. Last read position: chr16:3,021,787
INFO 2026-06-08 07:58:50 MarkDuplicates Tracking 188085 as yet unmatched pairs. 22981 records in RAM.
INFO 2026-06-08 07:58:52 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 1s. Last read position: chr16:14,246,614
INFO 2026-06-08 07:58:52 MarkDuplicates Tracking 185927 as yet unmatched pairs. 20822 records in RAM.
INFO 2026-06-08 07:58:53 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 1s. Last read position: chr16:16,315,718
INFO 2026-06-08 07:58:53 MarkDuplicates Tracking 184067 as yet unmatched pairs. 18961 records in RAM.
INFO 2026-06-08 07:58:55 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 1s. Last read position: chr16:18,380,584
INFO 2026-06-08 07:58:55 MarkDuplicates Tracking 183563 as yet unmatched pairs. 18456 records in RAM.
INFO 2026-06-08 07:58:58 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 2s. Last read position: chr16:21,405,231
INFO 2026-06-08 07:58:58 MarkDuplicates Tracking 182489 as yet unmatched pairs. 17382 records in RAM.
INFO 2026-06-08 07:59:00 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 2s. Last read position: chr16:22,532,125
INFO 2026-06-08 07:59:00 MarkDuplicates Tracking 181518 as yet unmatched pairs. 16410 records in RAM.
INFO 2026-06-08 07:59:02 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 1s. Last read position: chr16:28,638,390
INFO 2026-06-08 07:59:02 MarkDuplicates Tracking 180208 as yet unmatched pairs. 15100 records in RAM.
INFO 2026-06-08 07:59:03 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 1s. Last read position: chr16:29,872,234
INFO 2026-06-08 07:59:03 MarkDuplicates Tracking 179067 as yet unmatched pairs. 13959 records in RAM.
INFO 2026-06-08 07:59:05 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 1s. Last read position: chr16:30,768,720
INFO 2026-06-08 07:59:05 MarkDuplicates Tracking 177316 as yet unmatched pairs. 12208 records in RAM.
INFO 2026-06-08 07:59:07 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 2s. Last read position: chr16:54,284,885
INFO 2026-06-08 07:59:07 MarkDuplicates Tracking 175240 as yet unmatched pairs. 10130 records in RAM.
INFO 2026-06-08 07:59:09 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 1s. Last read position: chr16:67,542,290
INFO 2026-06-08 07:59:09 MarkDuplicates Tracking 172514 as yet unmatched pairs. 7404 records in RAM.
INFO 2026-06-08 07:59:10 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 1s. Last read position: chr16:71,649,966
INFO 2026-06-08 07:59:10 MarkDuplicates Tracking 169995 as yet unmatched pairs. 4884 records in RAM.
INFO 2026-06-08 07:59:12 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:06:31s. Time for last 1,000,000: 1s. Last read position: chr16:87,331,269
INFO 2026-06-08 07:59:12 MarkDuplicates Tracking 167543 as yet unmatched pairs. 2432 records in RAM.
INFO 2026-06-08 07:59:14 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:06:33s. Time for last 1,000,000: 2s. Last read position: chr17:1,420,189
INFO 2026-06-08 07:59:14 MarkDuplicates Tracking 164715 as yet unmatched pairs. 70401 records in RAM.
INFO 2026-06-08 07:59:15 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 1s. Last read position: chr17:7,462,526
INFO 2026-06-08 07:59:15 MarkDuplicates Tracking 162371 as yet unmatched pairs. 68057 records in RAM.
INFO 2026-06-08 07:59:17 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 1s. Last read position: chr17:16,048,975
INFO 2026-06-08 07:59:17 MarkDuplicates Tracking 160229 as yet unmatched pairs. 65914 records in RAM.
INFO 2026-06-08 07:59:19 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 1s. Last read position: chr17:28,624,301
INFO 2026-06-08 07:59:19 MarkDuplicates Tracking 158120 as yet unmatched pairs. 63805 records in RAM.
INFO 2026-06-08 07:59:21 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 1s. Last read position: chr17:30,423,626
INFO 2026-06-08 07:59:21 MarkDuplicates Tracking 155997 as yet unmatched pairs. 61682 records in RAM.
INFO 2026-06-08 07:59:23 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 2s. Last read position: chr17:37,538,295
INFO 2026-06-08 07:59:23 MarkDuplicates Tracking 153901 as yet unmatched pairs. 59586 records in RAM.
INFO 2026-06-08 07:59:26 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 2s. Last read position: chr17:39,673,982
INFO 2026-06-08 07:59:26 MarkDuplicates Tracking 152172 as yet unmatched pairs. 57857 records in RAM.
INFO 2026-06-08 07:59:29 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 2s. Last read position: chr17:39,708,366
INFO 2026-06-08 07:59:29 MarkDuplicates Tracking 150553 as yet unmatched pairs. 56230 records in RAM.
INFO 2026-06-08 07:59:31 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 2s. Last read position: chr17:39,710,129
INFO 2026-06-08 07:59:31 MarkDuplicates Tracking 155850 as yet unmatched pairs. 61527 records in RAM.
INFO 2026-06-08 07:59:33 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 2s. Last read position: chr17:39,712,001
INFO 2026-06-08 07:59:33 MarkDuplicates Tracking 150028 as yet unmatched pairs. 55705 records in RAM.
INFO 2026-06-08 07:59:35 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 2s. Last read position: chr17:39,715,890
INFO 2026-06-08 07:59:35 MarkDuplicates Tracking 145134 as yet unmatched pairs. 50811 records in RAM.
INFO 2026-06-08 07:59:37 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 1s. Last read position: chr17:39,717,417
INFO 2026-06-08 07:59:37 MarkDuplicates Tracking 141206 as yet unmatched pairs. 46883 records in RAM.
INFO 2026-06-08 07:59:39 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 1s. Last read position: chr17:39,724,726
INFO 2026-06-08 07:59:39 MarkDuplicates Tracking 137803 as yet unmatched pairs. 43480 records in RAM.
INFO 2026-06-08 07:59:40 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 1s. Last read position: chr17:39,726,583
INFO 2026-06-08 07:59:40 MarkDuplicates Tracking 136486 as yet unmatched pairs. 42162 records in RAM.
INFO 2026-06-08 07:59:42 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 1s. Last read position: chr17:39,727,702
INFO 2026-06-08 07:59:42 MarkDuplicates Tracking 139326 as yet unmatched pairs. 45002 records in RAM.
INFO 2026-06-08 07:59:43 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 1s. Last read position: chr17:39,923,148
INFO 2026-06-08 07:59:43 MarkDuplicates Tracking 128979 as yet unmatched pairs. 34641 records in RAM.
INFO 2026-06-08 07:59:45 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:07:04s. Time for last 1,000,000: 1s. Last read position: chr17:42,419,701
INFO 2026-06-08 07:59:45 MarkDuplicates Tracking 126144 as yet unmatched pairs. 31806 records in RAM.
INFO 2026-06-08 07:59:46 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 1s. Last read position: chr17:48,058,886
INFO 2026-06-08 07:59:46 MarkDuplicates Tracking 124075 as yet unmatched pairs. 29737 records in RAM.
INFO 2026-06-08 07:59:48 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:07:07s. Time for last 1,000,000: 1s. Last read position: chr17:50,186,758
INFO 2026-06-08 07:59:48 MarkDuplicates Tracking 122664 as yet unmatched pairs. 28325 records in RAM.
INFO 2026-06-08 07:59:50 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:07:09s. Time for last 1,000,000: 2s. Last read position: chr17:50,188,626
INFO 2026-06-08 07:59:50 MarkDuplicates Tracking 122116 as yet unmatched pairs. 27777 records in RAM.
INFO 2026-06-08 07:59:52 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:07:11s. Time for last 1,000,000: 2s. Last read position: chr17:50,190,006
INFO 2026-06-08 07:59:52 MarkDuplicates Tracking 117739 as yet unmatched pairs. 23400 records in RAM.
INFO 2026-06-08 07:59:54 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 2s. Last read position: chr17:50,192,674
INFO 2026-06-08 07:59:54 MarkDuplicates Tracking 115918 as yet unmatched pairs. 21579 records in RAM.
INFO 2026-06-08 07:59:56 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:07:16s. Time for last 1,000,000: 2s. Last read position: chr17:50,194,753
INFO 2026-06-08 07:59:56 MarkDuplicates Tracking 113107 as yet unmatched pairs. 18768 records in RAM.
INFO 2026-06-08 07:59:59 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:07:18s. Time for last 1,000,000: 2s. Last read position: chr17:50,196,500
INFO 2026-06-08 07:59:59 MarkDuplicates Tracking 111030 as yet unmatched pairs. 16691 records in RAM.
INFO 2026-06-08 08:00:01 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:07:20s. Time for last 1,000,000: 2s. Last read position: chr17:50,199,283
INFO 2026-06-08 08:00:01 MarkDuplicates Tracking 108335 as yet unmatched pairs. 13995 records in RAM.
INFO 2026-06-08 08:00:04 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:07:23s. Time for last 1,000,000: 2s. Last read position: chr17:59,648,319
INFO 2026-06-08 08:00:04 MarkDuplicates Tracking 103078 as yet unmatched pairs. 8738 records in RAM.
INFO 2026-06-08 08:00:06 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:07:25s. Time for last 1,000,000: 2s. Last read position: chr17:68,523,761
INFO 2026-06-08 08:00:06 MarkDuplicates Tracking 101500 as yet unmatched pairs. 7160 records in RAM.
INFO 2026-06-08 08:00:08 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 1s. Last read position: chr17:78,873,819
INFO 2026-06-08 08:00:08 MarkDuplicates Tracking 98518 as yet unmatched pairs. 4177 records in RAM.
INFO 2026-06-08 08:00:10 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:07:29s. Time for last 1,000,000: 1s. Last read position: chr17:82,083,842
INFO 2026-06-08 08:00:10 MarkDuplicates Tracking 96143 as yet unmatched pairs. 1801 records in RAM.
INFO 2026-06-08 08:00:12 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:07:31s. Time for last 1,000,000: 1s. Last read position: chr18:12,802,103
INFO 2026-06-08 08:00:12 MarkDuplicates Tracking 93323 as yet unmatched pairs. 5072 records in RAM.
INFO 2026-06-08 08:00:14 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:07:33s. Time for last 1,000,000: 1s. Last read position: chr18:48,670,679
INFO 2026-06-08 08:00:14 MarkDuplicates Tracking 91010 as yet unmatched pairs. 2759 records in RAM.
INFO 2026-06-08 08:00:16 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:07:35s. Time for last 1,000,000: 2s. Last read position: chr18:77,016,958
INFO 2026-06-08 08:00:16 MarkDuplicates Tracking 88624 as yet unmatched pairs. 373 records in RAM.
INFO 2026-06-08 08:00:18 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:07:37s. Time for last 1,000,000: 2s. Last read position: chr19:3,061,166
INFO 2026-06-08 08:00:18 MarkDuplicates Tracking 85612 as yet unmatched pairs. 40935 records in RAM.
INFO 2026-06-08 08:00:20 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:07:39s. Time for last 1,000,000: 1s. Last read position: chr19:8,586,177
INFO 2026-06-08 08:00:20 MarkDuplicates Tracking 82836 as yet unmatched pairs. 38158 records in RAM.
INFO 2026-06-08 08:00:22 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:07:42s. Time for last 1,000,000: 2s. Last read position: chr19:14,093,112
INFO 2026-06-08 08:00:22 MarkDuplicates Tracking 80215 as yet unmatched pairs. 35536 records in RAM.
INFO 2026-06-08 08:00:25 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:07:44s. Time for last 1,000,000: 2s. Last read position: chr19:15,265,392
INFO 2026-06-08 08:00:25 MarkDuplicates Tracking 77793 as yet unmatched pairs. 33113 records in RAM.
INFO 2026-06-08 08:00:27 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:07:46s. Time for last 1,000,000: 2s. Last read position: chr19:18,396,525
INFO 2026-06-08 08:00:27 MarkDuplicates Tracking 74471 as yet unmatched pairs. 29788 records in RAM.
INFO 2026-06-08 08:00:29 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:07:49s. Time for last 1,000,000: 2s. Last read position: chr19:18,768,583
INFO 2026-06-08 08:00:29 MarkDuplicates Tracking 71784 as yet unmatched pairs. 27101 records in RAM.
INFO 2026-06-08 08:00:32 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:07:51s. Time for last 1,000,000: 2s. Last read position: chr19:19,537,461
INFO 2026-06-08 08:00:32 MarkDuplicates Tracking 68674 as yet unmatched pairs. 23991 records in RAM.
INFO 2026-06-08 08:00:33 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:07:52s. Time for last 1,000,000: 1s. Last read position: chr19:32,918,233
INFO 2026-06-08 08:00:33 MarkDuplicates Tracking 66639 as yet unmatched pairs. 21955 records in RAM.
INFO 2026-06-08 08:00:35 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:07:54s. Time for last 1,000,000: 1s. Last read position: chr19:37,363,448
INFO 2026-06-08 08:00:35 MarkDuplicates Tracking 64148 as yet unmatched pairs. 19464 records in RAM.
INFO 2026-06-08 08:00:37 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:07:56s. Time for last 1,000,000: 1s. Last read position: chr19:39,408,001
INFO 2026-06-08 08:00:37 MarkDuplicates Tracking 62154 as yet unmatched pairs. 17470 records in RAM.
INFO 2026-06-08 08:00:38 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:07:57s. Time for last 1,000,000: 1s. Last read position: chr19:41,294,349
INFO 2026-06-08 08:00:38 MarkDuplicates Tracking 59128 as yet unmatched pairs. 14444 records in RAM.
INFO 2026-06-08 08:00:39 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:07:59s. Time for last 1,000,000: 1s. Last read position: chr19:42,406,331
INFO 2026-06-08 08:00:39 MarkDuplicates Tracking 56705 as yet unmatched pairs. 12012 records in RAM.
INFO 2026-06-08 08:00:41 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:08:00s. Time for last 1,000,000: 1s. Last read position: chr19:45,786,134
INFO 2026-06-08 08:00:41 MarkDuplicates Tracking 54186 as yet unmatched pairs. 9493 records in RAM.
INFO 2026-06-08 08:00:43 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:08:03s. Time for last 1,000,000: 2s. Last read position: chr19:49,108,231
INFO 2026-06-08 08:00:43 MarkDuplicates Tracking 51707 as yet unmatched pairs. 7013 records in RAM.
INFO 2026-06-08 08:00:45 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:08:04s. Time for last 1,000,000: 1s. Last read position: chr19:52,034,955
INFO 2026-06-08 08:00:45 MarkDuplicates Tracking 49027 as yet unmatched pairs. 4332 records in RAM.
INFO 2026-06-08 08:00:48 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:08:07s. Time for last 1,000,000: 2s. Last read position: chr19:55,602,116
INFO 2026-06-08 08:00:48 MarkDuplicates Tracking 46749 as yet unmatched pairs. 2054 records in RAM.
INFO 2026-06-08 08:00:50 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:08:09s. Time for last 1,000,000: 2s. Last read position: chr20:427,312
INFO 2026-06-08 08:00:50 MarkDuplicates Tracking 44643 as yet unmatched pairs. 11081 records in RAM.
INFO 2026-06-08 08:00:52 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:08:11s. Time for last 1,000,000: 2s. Last read position: chr20:24,973,727
INFO 2026-06-08 08:00:52 MarkDuplicates Tracking 42478 as yet unmatched pairs. 8914 records in RAM.
INFO 2026-06-08 08:00:54 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:08:13s. Time for last 1,000,000: 2s. Last read position: chr20:37,393,909
INFO 2026-06-08 08:00:54 MarkDuplicates Tracking 39984 as yet unmatched pairs. 6419 records in RAM.
INFO 2026-06-08 08:00:57 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 2s. Last read position: chr20:49,115,792
INFO 2026-06-08 08:00:57 MarkDuplicates Tracking 37573 as yet unmatched pairs. 4008 records in RAM.
INFO 2026-06-08 08:00:59 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:08:18s. Time for last 1,000,000: 2s. Last read position: chr20:62,330,766
INFO 2026-06-08 08:00:59 MarkDuplicates Tracking 35131 as yet unmatched pairs. 1566 records in RAM.
INFO 2026-06-08 08:01:00 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 1s. Last read position: chr21:8,254,148
INFO 2026-06-08 08:01:00 MarkDuplicates Tracking 33060 as yet unmatched pairs. 6500 records in RAM.
INFO 2026-06-08 08:01:02 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 1s. Last read position: chr21:29,553,589
INFO 2026-06-08 08:01:02 MarkDuplicates Tracking 31796 as yet unmatched pairs. 5233 records in RAM.
INFO 2026-06-08 08:01:03 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:08:22s. Time for last 1,000,000: 1s. Last read position: chr21:41,452,743
INFO 2026-06-08 08:01:03 MarkDuplicates Tracking 29662 as yet unmatched pairs. 3099 records in RAM.
INFO 2026-06-08 08:01:05 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:08:24s. Time for last 1,000,000: 1s. Last read position: chr21:46,266,136
INFO 2026-06-08 08:01:05 MarkDuplicates Tracking 26830 as yet unmatched pairs. 266 records in RAM.
INFO 2026-06-08 08:01:06 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 1s. Last read position: chr22:28,745,903
INFO 2026-06-08 08:01:06 MarkDuplicates Tracking 24405 as yet unmatched pairs. 8842 records in RAM.
INFO 2026-06-08 08:01:08 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:08:27s. Time for last 1,000,000: 1s. Last read position: chr22:32,859,296
INFO 2026-06-08 08:01:08 MarkDuplicates Tracking 21967 as yet unmatched pairs. 6404 records in RAM.
INFO 2026-06-08 08:01:09 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:08:28s. Time for last 1,000,000: 1s. Last read position: chr22:41,177,291
INFO 2026-06-08 08:01:09 MarkDuplicates Tracking 19283 as yet unmatched pairs. 3720 records in RAM.
INFO 2026-06-08 08:01:11 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:08:30s. Time for last 1,000,000: 1s. Last read position: chr22:50,220,807
INFO 2026-06-08 08:01:11 MarkDuplicates Tracking 16969 as yet unmatched pairs. 1406 records in RAM.
INFO 2026-06-08 08:01:12 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:08:31s. Time for last 1,000,000: 1s. Last read position: chrX:13,923,580
INFO 2026-06-08 08:01:12 MarkDuplicates Tracking 14209 as yet unmatched pairs. 12120 records in RAM.
INFO 2026-06-08 08:01:14 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:08:33s. Time for last 1,000,000: 1s. Last read position: chrX:47,202,745
INFO 2026-06-08 08:01:14 MarkDuplicates Tracking 11997 as yet unmatched pairs. 9906 records in RAM.
INFO 2026-06-08 08:01:16 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 1s. Last read position: chrX:54,807,723
INFO 2026-06-08 08:01:16 MarkDuplicates Tracking 9635 as yet unmatched pairs. 7544 records in RAM.
INFO 2026-06-08 08:01:18 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 2s. Last read position: chrX:77,717,144
INFO 2026-06-08 08:01:18 MarkDuplicates Tracking 7176 as yet unmatched pairs. 5085 records in RAM.
INFO 2026-06-08 08:01:19 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:08:39s. Time for last 1,000,000: 1s. Last read position: chrX:124,090,576
INFO 2026-06-08 08:01:19 MarkDuplicates Tracking 5052 as yet unmatched pairs. 2961 records in RAM.
INFO 2026-06-08 08:01:21 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 1s. Last read position: chrX:154,432,270
INFO 2026-06-08 08:01:21 MarkDuplicates Tracking 2622 as yet unmatched pairs. 530 records in RAM.
INFO 2026-06-08 08:01:22 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:08:41s. Time for last 1,000,000: 1s. Last read position: KI270733.1:130,975
INFO 2026-06-08 08:01:22 MarkDuplicates Tracking 1441 as yet unmatched pairs. 1434 records in RAM.
INFO 2026-06-08 08:01:23 MarkDuplicates Read 245501330 records. 0 pairs never matched.
INFO 2026-06-08 08:01:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 35424115632; totalMemory: 62981668864; maxMemory: 63585648640
INFO 2026-06-08 08:01:40 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:01:46 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:01:59 OpticalDuplicateFinder Large duplicate set. size = 1470
INFO 2026-06-08 08:01:59 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:21,249
INFO 2026-06-08 08:02:11 OpticalDuplicateFinder Large duplicate set. size = 1194
INFO 2026-06-08 08:02:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,600
INFO 2026-06-08 08:02:11 OpticalDuplicateFinder Large duplicate set. size = 1164
INFO 2026-06-08 08:02:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,064
INFO 2026-06-08 08:02:11 OpticalDuplicateFinder Large duplicate set. size = 1157
INFO 2026-06-08 08:02:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:17,544
INFO 2026-06-08 08:02:11 OpticalDuplicateFinder Large duplicate set. size = 1511
INFO 2026-06-08 08:02:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,356
INFO 2026-06-08 08:02:11 OpticalDuplicateFinder Large duplicate set. size = 2232
INFO 2026-06-08 08:02:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:2,230
INFO 2026-06-08 08:02:11 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-14,443
INFO 2026-06-08 08:02:12 OpticalDuplicateFinder Large duplicate set. size = 1235
INFO 2026-06-08 08:02:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,397
INFO 2026-06-08 08:02:12 OpticalDuplicateFinder Large duplicate set. size = 2045
INFO 2026-06-08 08:02:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:15,780
INFO 2026-06-08 08:02:12 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:24,542
INFO 2026-06-08 08:02:12 OpticalDuplicateFinder Large duplicate set. size = 2470
INFO 2026-06-08 08:02:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-18,431
INFO 2026-06-08 08:02:12 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:2,618
INFO 2026-06-08 08:02:12 OpticalDuplicateFinder Large duplicate set. size = 1410
INFO 2026-06-08 08:02:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:6,461
INFO 2026-06-08 08:02:12 OpticalDuplicateFinder Large duplicate set. size = 1007
INFO 2026-06-08 08:02:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:26,864
INFO 2026-06-08 08:02:12 OpticalDuplicateFinder Large duplicate set. size = 1053
INFO 2026-06-08 08:02:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,866
INFO 2026-06-08 08:02:12 OpticalDuplicateFinder Large duplicate set. size = 1183
INFO 2026-06-08 08:02:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,106
INFO 2026-06-08 08:02:12 OpticalDuplicateFinder Large duplicate set. size = 1382
INFO 2026-06-08 08:02:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:10,870
INFO 2026-06-08 08:02:12 OpticalDuplicateFinder Large duplicate set. size = 1045
INFO 2026-06-08 08:02:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,115
INFO 2026-06-08 08:02:13 OpticalDuplicateFinder Large duplicate set. size = 1250
INFO 2026-06-08 08:02:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:6,445
INFO 2026-06-08 08:02:13 OpticalDuplicateFinder Large duplicate set. size = 1971
INFO 2026-06-08 08:02:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:24,048
INFO 2026-06-08 08:02:13 OpticalDuplicateFinder Large duplicate set. size = 2032
INFO 2026-06-08 08:02:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:4,818
INFO 2026-06-08 08:02:13 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,028
INFO 2026-06-08 08:02:14 OpticalDuplicateFinder Large duplicate set. size = 1048
INFO 2026-06-08 08:02:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,998
INFO 2026-06-08 08:02:14 OpticalDuplicateFinder Large duplicate set. size = 1331
INFO 2026-06-08 08:02:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-22,953
INFO 2026-06-08 08:02:15 OpticalDuplicateFinder Large duplicate set. size = 1474
INFO 2026-06-08 08:02:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,553
INFO 2026-06-08 08:02:15 OpticalDuplicateFinder Large duplicate set. size = 2035
INFO 2026-06-08 08:02:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:21,945
INFO 2026-06-08 08:02:15 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,306
INFO 2026-06-08 08:02:15 OpticalDuplicateFinder Large duplicate set. size = 1077
INFO 2026-06-08 08:02:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,144
INFO 2026-06-08 08:02:15 OpticalDuplicateFinder Large duplicate set. size = 1321
INFO 2026-06-08 08:02:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:23,256
INFO 2026-06-08 08:02:15 OpticalDuplicateFinder Large duplicate set. size = 1137
INFO 2026-06-08 08:02:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:31,960
INFO 2026-06-08 08:02:19 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 08:02:40 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:02:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300759784; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-08 08:02:47 MarkDuplicates Marking 171342887 records as duplicates.
INFO 2026-06-08 08:02:47 MarkDuplicates Found 4908889 optical duplicate clusters.
INFO 2026-06-08 08:02:47 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 08:03:09 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:21s. Time for last 10,000,000: 21s. Last read position: chr1:109,250,945
INFO 2026-06-08 08:03:32 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:44s. Time for last 10,000,000: 22s. Last read position: chr1:171,541,034
INFO 2026-06-08 08:03:54 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:07s. Time for last 10,000,000: 22s. Last read position: chr2:47,161,774
INFO 2026-06-08 08:04:16 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:29s. Time for last 10,000,000: 21s. Last read position: chr2:215,364,950
INFO 2026-06-08 08:04:38 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:51s. Time for last 10,000,000: 22s. Last read position: chr3:56,646,524
INFO 2026-06-08 08:05:00 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:13s. Time for last 10,000,000: 21s. Last read position: chr4:121,802,913
INFO 2026-06-08 08:05:23 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:35s. Time for last 10,000,000: 22s. Last read position: chr5:151,663,548
INFO 2026-06-08 08:05:46 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:58s. Time for last 10,000,000: 22s. Last read position: chr6:32,034,328
INFO 2026-06-08 08:06:08 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:03:20s. Time for last 10,000,000: 21s. Last read position: chr7:42,223,154
INFO 2026-06-08 08:06:29 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:03:42s. Time for last 10,000,000: 21s. Last read position: chr8:37,772,792
INFO 2026-06-08 08:06:49 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:04:02s. Time for last 10,000,000: 19s. Last read position: chr9:95,928,718
INFO 2026-06-08 08:07:09 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:04:22s. Time for last 10,000,000: 20s. Last read position: chr10:87,366,461
INFO 2026-06-08 08:07:29 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:04:42s. Time for last 10,000,000: 20s. Last read position: chr11:67,250,634
INFO 2026-06-08 08:07:49 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:05:01s. Time for last 10,000,000: 19s. Last read position: chr12:52,235,374
INFO 2026-06-08 08:08:11 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:05:23s. Time for last 10,000,000: 21s. Last read position: chr13:113,118,447
INFO 2026-06-08 08:08:30 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:05:43s. Time for last 10,000,000: 19s. Last read position: chr15:68,208,298
INFO 2026-06-08 08:08:48 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:06:01s. Time for last 10,000,000: 18s. Last read position: chr16:22,532,125
INFO 2026-06-08 08:09:07 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:06:19s. Time for last 10,000,000: 18s. Last read position: chr17:16,048,975
INFO 2026-06-08 08:09:27 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:06:40s. Time for last 10,000,000: 20s. Last read position: chr17:39,724,726
INFO 2026-06-08 08:09:48 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:07:01s. Time for last 10,000,000: 21s. Last read position: chr17:50,194,753
INFO 2026-06-08 08:10:10 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:07:23s. Time for last 10,000,000: 21s. Last read position: chr19:3,061,166
INFO 2026-06-08 08:10:31 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:07:44s. Time for last 10,000,000: 21s. Last read position: chr19:41,294,349
INFO 2026-06-08 08:10:52 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:08:04s. Time for last 10,000,000: 20s. Last read position: chr20:62,330,766
INFO 2026-06-08 08:11:10 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:08:23s. Time for last 10,000,000: 18s. Last read position: chrX:47,202,745
INFO 2026-06-08 08:11:25 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:11:25 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:11:25 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:11:26 MarkDuplicates Before output close freeMemory: 201647096; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:11:26 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:11:26 MarkDuplicates After output close freeMemory: 104233616; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 08:11:26 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 18.79 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory