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 RGB_RLP_lowDV_1ststrand_25C_1.Aligned.sortedByCoord.out.bam --OUTPUT RGB_RLP_lowDV_1ststrand_25C_1.md.bam --METRICS_FILE RGB_RLP_lowDV_1ststrand_25C_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:05:02.968 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Thu Jun 04 07:05:02 GMT 2026] MarkDuplicates --INPUT RGB_RLP_lowDV_1ststrand_25C_1.Aligned.sortedByCoord.out.bam --OUTPUT RGB_RLP_lowDV_1ststrand_25C_1.md.bam --METRICS_FILE RGB_RLP_lowDV_1ststrand_25C_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
[Thu Jun 04 07:05:02 GMT 2026] Executing as ?@nf-afa2a838012fc263e56a58bbc9fa389d-2c4bb-hzbpt on Linux 6.12.88 amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0
INFO 2026-06-04 07:05:03 MarkDuplicates Start of doWork freeMemory: 105827616; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-04 07:05:03 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-04 07:05:03 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-04 07:05:06 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:2,589,460
INFO 2026-06-04 07:05:06 MarkDuplicates Tracking 759 as yet unmatched pairs. 43 records in RAM.
INFO 2026-06-04 07:05:10 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 3s. Last read position: chr1:11,966,262
INFO 2026-06-04 07:05:10 MarkDuplicates Tracking 1475 as yet unmatched pairs. 135 records in RAM.
INFO 2026-06-04 07:05:12 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 2s. Last read position: chr1:19,657,004
INFO 2026-06-04 07:05:12 MarkDuplicates Tracking 2019 as yet unmatched pairs. 108 records in RAM.
INFO 2026-06-04 07:05:13 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: chr1:23,971,910
INFO 2026-06-04 07:05:13 MarkDuplicates Tracking 2420 as yet unmatched pairs. 27 records in RAM.
INFO 2026-06-04 07:05:15 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: chr1:30,964,815
INFO 2026-06-04 07:05:15 MarkDuplicates Tracking 3154 as yet unmatched pairs. 157 records in RAM.
INFO 2026-06-04 07:05:17 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: chr1:36,287,114
INFO 2026-06-04 07:05:17 MarkDuplicates Tracking 3805 as yet unmatched pairs. 218 records in RAM.
INFO 2026-06-04 07:05:18 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: chr1:43,578,907
INFO 2026-06-04 07:05:18 MarkDuplicates Tracking 4498 as yet unmatched pairs. 316 records in RAM.
INFO 2026-06-04 07:05:21 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr1:54,242,164
INFO 2026-06-04 07:05:21 MarkDuplicates Tracking 4915 as yet unmatched pairs. 165 records in RAM.
INFO 2026-06-04 07:05:22 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: chr1:92,297,461
INFO 2026-06-04 07:05:22 MarkDuplicates Tracking 5280 as yet unmatched pairs. 18 records in RAM.
INFO 2026-06-04 07:05:24 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: chr1:113,672,680
INFO 2026-06-04 07:05:24 MarkDuplicates Tracking 5851 as yet unmatched pairs. 51 records in RAM.
INFO 2026-06-04 07:05:25 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 1s. Last read position: chr1:120,578,818
INFO 2026-06-04 07:05:25 MarkDuplicates Tracking 6274 as yet unmatched pairs. 30 records in RAM.
INFO 2026-06-04 07:05:28 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 2s. Last read position: chr1:148,562,278
INFO 2026-06-04 07:05:28 MarkDuplicates Tracking 6547 as yet unmatched pairs. 54 records in RAM.
INFO 2026-06-04 07:05:30 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 2s. Last read position: chr1:150,627,517
INFO 2026-06-04 07:05:30 MarkDuplicates Tracking 7323 as yet unmatched pairs. 455 records in RAM.
INFO 2026-06-04 07:05:31 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 1s. Last read position: chr1:153,390,116
INFO 2026-06-04 07:05:31 MarkDuplicates Tracking 7907 as yet unmatched pairs. 518 records in RAM.
INFO 2026-06-04 07:05:33 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 1s. Last read position: chr1:154,945,847
INFO 2026-06-04 07:05:33 MarkDuplicates Tracking 8095 as yet unmatched pairs. 142 records in RAM.
INFO 2026-06-04 07:05:35 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 1s. Last read position: chr1:155,765,009
INFO 2026-06-04 07:05:35 MarkDuplicates Tracking 8556 as yet unmatched pairs. 118 records in RAM.
INFO 2026-06-04 07:05:36 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 1s. Last read position: chr1:158,089,784
INFO 2026-06-04 07:05:36 MarkDuplicates Tracking 9103 as yet unmatched pairs. 38 records in RAM.
INFO 2026-06-04 07:05:38 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 1s. Last read position: chr1:169,127,356
INFO 2026-06-04 07:05:38 MarkDuplicates Tracking 9825 as yet unmatched pairs. 208 records in RAM.
INFO 2026-06-04 07:05:40 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 1s. Last read position: chr1:185,098,070
INFO 2026-06-04 07:05:40 MarkDuplicates Tracking 10165 as yet unmatched pairs. 76 records in RAM.
INFO 2026-06-04 07:05:43 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 2s. Last read position: chr1:203,348,002
INFO 2026-06-04 07:05:43 MarkDuplicates Tracking 10582 as yet unmatched pairs. 11 records in RAM.
INFO 2026-06-04 07:05:45 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 1s. Last read position: chr1:217,620,260
INFO 2026-06-04 07:05:45 MarkDuplicates Tracking 11140 as yet unmatched pairs. 43 records in RAM.
INFO 2026-06-04 07:05:46 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 1s. Last read position: chr1:228,305,265
INFO 2026-06-04 07:05:46 MarkDuplicates Tracking 11703 as yet unmatched pairs. 39 records in RAM.
INFO 2026-06-04 07:05:48 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 1s. Last read position: chr1:245,687,996
INFO 2026-06-04 07:05:48 MarkDuplicates Tracking 12312 as yet unmatched pairs. 23 records in RAM.
INFO 2026-06-04 07:05:50 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 1s. Last read position: chr2:24,665,760
INFO 2026-06-04 07:05:50 MarkDuplicates Tracking 12896 as yet unmatched pairs. 12742 records in RAM.
INFO 2026-06-04 07:05:52 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,264
INFO 2026-06-04 07:05:52 MarkDuplicates Tracking 43261 as yet unmatched pairs. 11228 records in RAM.
INFO 2026-06-04 07:05:53 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 1s. Last read position: chr2:47,783,223
INFO 2026-06-04 07:05:53 MarkDuplicates Tracking 104298 as yet unmatched pairs. 6813 records in RAM.
INFO 2026-06-04 07:05:55 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 1s. Last read position: chr2:71,068,661
INFO 2026-06-04 07:05:55 MarkDuplicates Tracking 103705 as yet unmatched pairs. 6219 records in RAM.
INFO 2026-06-04 07:05:57 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 1s. Last read position: chr2:88,590,591
INFO 2026-06-04 07:05:57 MarkDuplicates Tracking 103229 as yet unmatched pairs. 5742 records in RAM.
INFO 2026-06-04 07:05:58 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 1s. Last read position: chr2:108,751,331
INFO 2026-06-04 07:05:58 MarkDuplicates Tracking 102978 as yet unmatched pairs. 5489 records in RAM.
INFO 2026-06-04 07:05:59 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 1s. Last read position: chr2:127,636,556
INFO 2026-06-04 07:05:59 MarkDuplicates Tracking 102420 as yet unmatched pairs. 4928 records in RAM.
INFO 2026-06-04 07:06:01 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 1s. Last read position: chr2:168,456,592
INFO 2026-06-04 07:06:01 MarkDuplicates Tracking 101970 as yet unmatched pairs. 4476 records in RAM.
INFO 2026-06-04 07:06:02 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 1s. Last read position: chr2:188,992,925
INFO 2026-06-04 07:06:02 MarkDuplicates Tracking 102345 as yet unmatched pairs. 4845 records in RAM.
INFO 2026-06-04 07:06:04 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 1s. Last read position: chr2:199,433,471
INFO 2026-06-04 07:06:04 MarkDuplicates Tracking 100853 as yet unmatched pairs. 3351 records in RAM.
INFO 2026-06-04 07:06:05 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 1s. Last read position: chr2:215,370,353
INFO 2026-06-04 07:06:05 MarkDuplicates Tracking 106883 as yet unmatched pairs. 9380 records in RAM.
INFO 2026-06-04 07:06:07 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 2s. Last read position: chr2:215,383,367
INFO 2026-06-04 07:06:07 MarkDuplicates Tracking 102784 as yet unmatched pairs. 5281 records in RAM.
INFO 2026-06-04 07:06:09 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 2s. Last read position: chr2:215,408,321
INFO 2026-06-04 07:06:09 MarkDuplicates Tracking 104152 as yet unmatched pairs. 6649 records in RAM.
INFO 2026-06-04 07:06:11 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 1s. Last read position: chr2:215,435,689
INFO 2026-06-04 07:06:11 MarkDuplicates Tracking 102371 as yet unmatched pairs. 4864 records in RAM.
INFO 2026-06-04 07:06:12 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 1s. Last read position: chr2:222,639,579
INFO 2026-06-04 07:06:12 MarkDuplicates Tracking 98523 as yet unmatched pairs. 1013 records in RAM.
INFO 2026-06-04 07:06:14 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 1s. Last read position: chr2:237,371,818
INFO 2026-06-04 07:06:14 MarkDuplicates Tracking 98517 as yet unmatched pairs. 1000 records in RAM.
INFO 2026-06-04 07:06:15 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 1s. Last read position: chr3:9,834,738
INFO 2026-06-04 07:06:15 MarkDuplicates Tracking 97533 as yet unmatched pairs. 5220 records in RAM.
INFO 2026-06-04 07:06:18 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 2s. Last read position: chr3:33,865,261
INFO 2026-06-04 07:06:18 MarkDuplicates Tracking 96849 as yet unmatched pairs. 4527 records in RAM.
INFO 2026-06-04 07:06:19 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 1s. Last read position: chr3:47,736,087
INFO 2026-06-04 07:06:19 MarkDuplicates Tracking 96353 as yet unmatched pairs. 4031 records in RAM.
INFO 2026-06-04 07:06:21 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 1s. Last read position: chr3:50,302,029
INFO 2026-06-04 07:06:21 MarkDuplicates Tracking 95667 as yet unmatched pairs. 3345 records in RAM.
INFO 2026-06-04 07:06:23 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 2s. Last read position: chr3:70,970,795
INFO 2026-06-04 07:06:23 MarkDuplicates Tracking 95138 as yet unmatched pairs. 2814 records in RAM.
INFO 2026-06-04 07:06:25 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 1s. Last read position: chr3:121,490,303
INFO 2026-06-04 07:06:25 MarkDuplicates Tracking 94621 as yet unmatched pairs. 2292 records in RAM.
INFO 2026-06-04 07:06:27 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 1s. Last read position: chr3:129,573,593
INFO 2026-06-04 07:06:27 MarkDuplicates Tracking 94162 as yet unmatched pairs. 1826 records in RAM.
INFO 2026-06-04 07:06:28 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 1s. Last read position: chr3:152,456,269
INFO 2026-06-04 07:06:28 MarkDuplicates Tracking 93701 as yet unmatched pairs. 1358 records in RAM.
INFO 2026-06-04 07:06:31 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 2s. Last read position: chr3:184,322,716
INFO 2026-06-04 07:06:31 MarkDuplicates Tracking 93018 as yet unmatched pairs. 673 records in RAM.
INFO 2026-06-04 07:06:32 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 1s. Last read position: chr3:195,867,442
INFO 2026-06-04 07:06:32 MarkDuplicates Tracking 92611 as yet unmatched pairs. 264 records in RAM.
INFO 2026-06-04 07:06:33 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 1s. Last read position: chr4:3,439,454
INFO 2026-06-04 07:06:33 MarkDuplicates Tracking 91893 as yet unmatched pairs. 2190 records in RAM.
INFO 2026-06-04 07:06:35 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 1s. Last read position: chr4:41,650,422
INFO 2026-06-04 07:06:35 MarkDuplicates Tracking 91427 as yet unmatched pairs. 1715 records in RAM.
INFO 2026-06-04 07:06:36 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 1s. Last read position: chr4:81,046,218
INFO 2026-06-04 07:06:36 MarkDuplicates Tracking 90861 as yet unmatched pairs. 1144 records in RAM.
INFO 2026-06-04 07:06:38 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 1s. Last read position: chr4:119,271,447
INFO 2026-06-04 07:06:38 MarkDuplicates Tracking 90496 as yet unmatched pairs. 766 records in RAM.
INFO 2026-06-04 07:06:39 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 1s. Last read position: chr4:168,236,351
INFO 2026-06-04 07:06:39 MarkDuplicates Tracking 89976 as yet unmatched pairs. 246 records in RAM.
INFO 2026-06-04 07:06:41 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 1s. Last read position: chr5:14,387,810
INFO 2026-06-04 07:06:41 MarkDuplicates Tracking 89808 as yet unmatched pairs. 4500 records in RAM.
INFO 2026-06-04 07:06:43 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 1s. Last read position: chr5:54,519,018
INFO 2026-06-04 07:06:43 MarkDuplicates Tracking 88935 as yet unmatched pairs. 3620 records in RAM.
INFO 2026-06-04 07:06:44 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 1s. Last read position: chr5:83,512,306
INFO 2026-06-04 07:06:44 MarkDuplicates Tracking 88855 as yet unmatched pairs. 3533 records in RAM.
INFO 2026-06-04 07:06:45 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 1s. Last read position: chr5:132,934,158
INFO 2026-06-04 07:06:45 MarkDuplicates Tracking 87955 as yet unmatched pairs. 2630 records in RAM.
INFO 2026-06-04 07:06:47 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 1s. Last read position: chr5:141,355,330
INFO 2026-06-04 07:06:47 MarkDuplicates Tracking 87477 as yet unmatched pairs. 2119 records in RAM.
INFO 2026-06-04 07:06:49 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 2s. Last read position: chr5:150,402,564
INFO 2026-06-04 07:06:49 MarkDuplicates Tracking 92994 as yet unmatched pairs. 7630 records in RAM.
INFO 2026-06-04 07:06:51 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 1s. Last read position: chr5:157,491,678
INFO 2026-06-04 07:06:51 MarkDuplicates Tracking 86405 as yet unmatched pairs. 1041 records in RAM.
INFO 2026-06-04 07:06:52 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 1s. Last read position: chr5:177,524,627
INFO 2026-06-04 07:06:52 MarkDuplicates Tracking 85881 as yet unmatched pairs. 509 records in RAM.
INFO 2026-06-04 07:06:53 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 1s. Last read position: chr6:3,850,558
INFO 2026-06-04 07:06:53 MarkDuplicates Tracking 85276 as yet unmatched pairs. 5277 records in RAM.
INFO 2026-06-04 07:06:55 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 1s. Last read position: chr6:26,156,763
INFO 2026-06-04 07:06:55 MarkDuplicates Tracking 84808 as yet unmatched pairs. 4805 records in RAM.
INFO 2026-06-04 07:06:57 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 1s. Last read position: chr6:31,269,117
INFO 2026-06-04 07:06:57 MarkDuplicates Tracking 84833 as yet unmatched pairs. 4830 records in RAM.
INFO 2026-06-04 07:06:58 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 1s. Last read position: chr6:31,947,998
INFO 2026-06-04 07:06:58 MarkDuplicates Tracking 83906 as yet unmatched pairs. 3898 records in RAM.
INFO 2026-06-04 07:06:59 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 1s. Last read position: chr6:33,085,095
INFO 2026-06-04 07:06:59 MarkDuplicates Tracking 83330 as yet unmatched pairs. 3322 records in RAM.
INFO 2026-06-04 07:07:01 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 1s. Last read position: chr6:38,575,514
INFO 2026-06-04 07:07:01 MarkDuplicates Tracking 82731 as yet unmatched pairs. 2720 records in RAM.
INFO 2026-06-04 07:07:03 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 1s. Last read position: chr6:50,823,529
INFO 2026-06-04 07:07:03 MarkDuplicates Tracking 82328 as yet unmatched pairs. 2313 records in RAM.
INFO 2026-06-04 07:07:04 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 1s. Last read position: chr6:89,338,240
INFO 2026-06-04 07:07:04 MarkDuplicates Tracking 81736 as yet unmatched pairs. 1706 records in RAM.
INFO 2026-06-04 07:07:06 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 1s. Last read position: chr6:131,950,098
INFO 2026-06-04 07:07:06 MarkDuplicates Tracking 81370 as yet unmatched pairs. 1331 records in RAM.
INFO 2026-06-04 07:07:07 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 1s. Last read position: chr6:152,098,784
INFO 2026-06-04 07:07:07 MarkDuplicates Tracking 80804 as yet unmatched pairs. 765 records in RAM.
INFO 2026-06-04 07:07:09 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 1s. Last read position: chr6:169,659,456
INFO 2026-06-04 07:07:09 MarkDuplicates Tracking 80120 as yet unmatched pairs. 81 records in RAM.
INFO 2026-06-04 07:07:11 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 2s. Last read position: chr7:5,529,534
INFO 2026-06-04 07:07:11 MarkDuplicates Tracking 80461 as yet unmatched pairs. 5633 records in RAM.
INFO 2026-06-04 07:07:13 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 1s. Last read position: chr7:43,792,745
INFO 2026-06-04 07:07:13 MarkDuplicates Tracking 78930 as yet unmatched pairs. 4092 records in RAM.
INFO 2026-06-04 07:07:15 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 1s. Last read position: chr7:57,003,539
INFO 2026-06-04 07:07:15 MarkDuplicates Tracking 78351 as yet unmatched pairs. 3513 records in RAM.
INFO 2026-06-04 07:07:16 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 1s. Last read position: chr7:75,393,187
INFO 2026-06-04 07:07:16 MarkDuplicates Tracking 77966 as yet unmatched pairs. 3123 records in RAM.
INFO 2026-06-04 07:07:18 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 1s. Last read position: chr7:94,405,215
INFO 2026-06-04 07:07:18 MarkDuplicates Tracking 78025 as yet unmatched pairs. 3182 records in RAM.
INFO 2026-06-04 07:07:20 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 1s. Last read position: chr7:100,033,665
INFO 2026-06-04 07:07:20 MarkDuplicates Tracking 77008 as yet unmatched pairs. 2163 records in RAM.
INFO 2026-06-04 07:07:21 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 1s. Last read position: chr7:100,998,997
INFO 2026-06-04 07:07:21 MarkDuplicates Tracking 76602 as yet unmatched pairs. 1757 records in RAM.
INFO 2026-06-04 07:07:23 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 1s. Last read position: chr7:107,758,626
INFO 2026-06-04 07:07:23 MarkDuplicates Tracking 76341 as yet unmatched pairs. 1489 records in RAM.
INFO 2026-06-04 07:07:24 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 1s. Last read position: chr7:137,880,447
INFO 2026-06-04 07:07:24 MarkDuplicates Tracking 75882 as yet unmatched pairs. 1026 records in RAM.
INFO 2026-06-04 07:07:26 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 1s. Last read position: chr7:150,340,540
INFO 2026-06-04 07:07:26 MarkDuplicates Tracking 75246 as yet unmatched pairs. 385 records in RAM.
INFO 2026-06-04 07:07:27 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 1s. Last read position: chr8:17,563,699
INFO 2026-06-04 07:07:27 MarkDuplicates Tracking 74780 as yet unmatched pairs. 5252 records in RAM.
INFO 2026-06-04 07:07:29 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 1s. Last read position: chr8:37,698,579
INFO 2026-06-04 07:07:29 MarkDuplicates Tracking 74357 as yet unmatched pairs. 4829 records in RAM.
INFO 2026-06-04 07:07:30 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 1s. Last read position: chr8:42,321,910
INFO 2026-06-04 07:07:30 MarkDuplicates Tracking 73664 as yet unmatched pairs. 4136 records in RAM.
INFO 2026-06-04 07:07:32 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 1s. Last read position: chr8:69,564,042
INFO 2026-06-04 07:07:32 MarkDuplicates Tracking 73167 as yet unmatched pairs. 3638 records in RAM.
INFO 2026-06-04 07:07:33 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 1s. Last read position: chr8:100,715,461
INFO 2026-06-04 07:07:33 MarkDuplicates Tracking 73153 as yet unmatched pairs. 3622 records in RAM.
INFO 2026-06-04 07:07:35 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 1s. Last read position: chr8:123,346,245
INFO 2026-06-04 07:07:35 MarkDuplicates Tracking 72092 as yet unmatched pairs. 2558 records in RAM.
INFO 2026-06-04 07:07:37 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 1s. Last read position: chr8:143,738,087
INFO 2026-06-04 07:07:37 MarkDuplicates Tracking 71429 as yet unmatched pairs. 1893 records in RAM.
INFO 2026-06-04 07:07:38 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 1s. Last read position: chr8:143,860,460
INFO 2026-06-04 07:07:38 MarkDuplicates Tracking 71304 as yet unmatched pairs. 1766 records in RAM.
INFO 2026-06-04 07:07:39 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 1s. Last read position: chr8:143,862,878
INFO 2026-06-04 07:07:39 MarkDuplicates Tracking 71819 as yet unmatched pairs. 2281 records in RAM.
INFO 2026-06-04 07:07:40 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 1s. Last read position: chr8:143,865,409
INFO 2026-06-04 07:07:40 MarkDuplicates Tracking 70606 as yet unmatched pairs. 1061 records in RAM.
INFO 2026-06-04 07:07:41 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 1s. Last read position: chr8:143,924,352
INFO 2026-06-04 07:07:41 MarkDuplicates Tracking 70250 as yet unmatched pairs. 705 records in RAM.
INFO 2026-06-04 07:07:43 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 2s. Last read position: chr9:5,080,579
INFO 2026-06-04 07:07:43 MarkDuplicates Tracking 69501 as yet unmatched pairs. 3657 records in RAM.
INFO 2026-06-04 07:07:45 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 1s. Last read position: chr9:35,707,794
INFO 2026-06-04 07:07:45 MarkDuplicates Tracking 69038 as yet unmatched pairs. 3193 records in RAM.
INFO 2026-06-04 07:07:46 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 1s. Last read position: chr9:93,075,579
INFO 2026-06-04 07:07:46 MarkDuplicates Tracking 68607 as yet unmatched pairs. 2755 records in RAM.
INFO 2026-06-04 07:07:48 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 1s. Last read position: chr9:114,205,110
INFO 2026-06-04 07:07:48 MarkDuplicates Tracking 68031 as yet unmatched pairs. 2176 records in RAM.
INFO 2026-06-04 07:07:49 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 1s. Last read position: chr9:127,914,727
INFO 2026-06-04 07:07:49 MarkDuplicates Tracking 67496 as yet unmatched pairs. 1640 records in RAM.
INFO 2026-06-04 07:07:51 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 1s. Last read position: chr9:131,487,166
INFO 2026-06-04 07:07:51 MarkDuplicates Tracking 66977 as yet unmatched pairs. 1115 records in RAM.
INFO 2026-06-04 07:07:52 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 1s. Last read position: chr9:136,508,015
INFO 2026-06-04 07:07:52 MarkDuplicates Tracking 66342 as yet unmatched pairs. 479 records in RAM.
INFO 2026-06-04 07:07:53 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 1s. Last read position: chr10:7,585,894
INFO 2026-06-04 07:07:53 MarkDuplicates Tracking 65659 as yet unmatched pairs. 3270 records in RAM.
INFO 2026-06-04 07:07:55 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 1s. Last read position: chr10:32,037,331
INFO 2026-06-04 07:07:55 MarkDuplicates Tracking 66050 as yet unmatched pairs. 3659 records in RAM.
INFO 2026-06-04 07:07:56 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 1s. Last read position: chr10:48,873,611
INFO 2026-06-04 07:07:56 MarkDuplicates Tracking 64770 as yet unmatched pairs. 2379 records in RAM.
INFO 2026-06-04 07:07:58 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 1s. Last read position: chr10:73,799,245
INFO 2026-06-04 07:07:58 MarkDuplicates Tracking 64292 as yet unmatched pairs. 1900 records in RAM.
INFO 2026-06-04 07:07:59 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 1s. Last read position: chr10:91,981,681
INFO 2026-06-04 07:07:59 MarkDuplicates Tracking 63796 as yet unmatched pairs. 1404 records in RAM.
INFO 2026-06-04 07:08:01 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 1s. Last read position: chr10:102,812,796
INFO 2026-06-04 07:08:01 MarkDuplicates Tracking 63221 as yet unmatched pairs. 822 records in RAM.
INFO 2026-06-04 07:08:02 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 1s. Last read position: chr10:124,498,050
INFO 2026-06-04 07:08:02 MarkDuplicates Tracking 62645 as yet unmatched pairs. 238 records in RAM.
INFO 2026-06-04 07:08:04 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 1s. Last read position: chr11:610,321
INFO 2026-06-04 07:08:04 MarkDuplicates Tracking 62141 as yet unmatched pairs. 6342 records in RAM.
INFO 2026-06-04 07:08:05 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 1s. Last read position: chr11:2,138,069
INFO 2026-06-04 07:08:05 MarkDuplicates Tracking 61628 as yet unmatched pairs. 5824 records in RAM.
INFO 2026-06-04 07:08:07 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 1s. Last read position: chr11:14,457,842
INFO 2026-06-04 07:08:07 MarkDuplicates Tracking 61038 as yet unmatched pairs. 5231 records in RAM.
INFO 2026-06-04 07:08:09 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 2s. Last read position: chr11:46,379,515
INFO 2026-06-04 07:08:09 MarkDuplicates Tracking 60606 as yet unmatched pairs. 4798 records in RAM.
INFO 2026-06-04 07:08:11 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 1s. Last read position: chr11:60,951,147
INFO 2026-06-04 07:08:11 MarkDuplicates Tracking 59981 as yet unmatched pairs. 4173 records in RAM.
INFO 2026-06-04 07:08:13 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 2s. Last read position: chr11:62,690,484
INFO 2026-06-04 07:08:13 MarkDuplicates Tracking 59574 as yet unmatched pairs. 3762 records in RAM.
INFO 2026-06-04 07:08:15 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 1s. Last read position: chr11:65,527,022
INFO 2026-06-04 07:08:15 MarkDuplicates Tracking 58804 as yet unmatched pairs. 2983 records in RAM.
INFO 2026-06-04 07:08:17 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 1s. Last read position: chr11:66,625,064
INFO 2026-06-04 07:08:17 MarkDuplicates Tracking 58258 as yet unmatched pairs. 2437 records in RAM.
INFO 2026-06-04 07:08:18 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 1s. Last read position: chr11:70,429,151
INFO 2026-06-04 07:08:18 MarkDuplicates Tracking 57823 as yet unmatched pairs. 1995 records in RAM.
INFO 2026-06-04 07:08:19 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 1s. Last read position: chr11:77,340,682
INFO 2026-06-04 07:08:19 MarkDuplicates Tracking 57008 as yet unmatched pairs. 1177 records in RAM.
INFO 2026-06-04 07:08:21 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 1s. Last read position: chr11:117,206,052
INFO 2026-06-04 07:08:21 MarkDuplicates Tracking 56496 as yet unmatched pairs. 665 records in RAM.
INFO 2026-06-04 07:08:22 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 1s. Last read position: chr11:130,196,413
INFO 2026-06-04 07:08:22 MarkDuplicates Tracking 55929 as yet unmatched pairs. 95 records in RAM.
INFO 2026-06-04 07:08:24 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 1s. Last read position: chr12:6,871,188
INFO 2026-06-04 07:08:24 MarkDuplicates Tracking 55378 as yet unmatched pairs. 4902 records in RAM.
INFO 2026-06-04 07:08:26 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 1s. Last read position: chr12:15,640,724
INFO 2026-06-04 07:08:26 MarkDuplicates Tracking 54918 as yet unmatched pairs. 4438 records in RAM.
INFO 2026-06-04 07:08:27 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 1s. Last read position: chr12:47,077,617
INFO 2026-06-04 07:08:27 MarkDuplicates Tracking 54411 as yet unmatched pairs. 3930 records in RAM.
INFO 2026-06-04 07:08:29 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 2s. Last read position: chr12:50,991,606
INFO 2026-06-04 07:08:29 MarkDuplicates Tracking 53981 as yet unmatched pairs. 3499 records in RAM.
INFO 2026-06-04 07:08:31 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 1s. Last read position: chr12:54,283,946
INFO 2026-06-04 07:08:31 MarkDuplicates Tracking 53714 as yet unmatched pairs. 3231 records in RAM.
INFO 2026-06-04 07:08:32 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 1s. Last read position: chr12:57,105,151
INFO 2026-06-04 07:08:32 MarkDuplicates Tracking 53454 as yet unmatched pairs. 2971 records in RAM.
INFO 2026-06-04 07:08:34 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 1s. Last read position: chr12:71,504,618
INFO 2026-06-04 07:08:34 MarkDuplicates Tracking 52338 as yet unmatched pairs. 1849 records in RAM.
INFO 2026-06-04 07:08:35 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 1s. Last read position: chr12:108,564,356
INFO 2026-06-04 07:08:35 MarkDuplicates Tracking 51909 as yet unmatched pairs. 1420 records in RAM.
INFO 2026-06-04 07:08:37 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 1s. Last read position: chr12:120,197,395
INFO 2026-06-04 07:08:37 MarkDuplicates Tracking 51819 as yet unmatched pairs. 1330 records in RAM.
INFO 2026-06-04 07:08:39 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 1s. Last read position: chr12:131,909,779
INFO 2026-06-04 07:08:39 MarkDuplicates Tracking 50899 as yet unmatched pairs. 408 records in RAM.
INFO 2026-06-04 07:08:40 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 1s. Last read position: chr13:28,713,359
INFO 2026-06-04 07:08:40 MarkDuplicates Tracking 50254 as yet unmatched pairs. 1589 records in RAM.
INFO 2026-06-04 07:08:42 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 1s. Last read position: chr13:77,126,422
INFO 2026-06-04 07:08:42 MarkDuplicates Tracking 49813 as yet unmatched pairs. 1145 records in RAM.
INFO 2026-06-04 07:08:43 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 1s. Last read position: chr13:112,545,775
INFO 2026-06-04 07:08:43 MarkDuplicates Tracking 49254 as yet unmatched pairs. 577 records in RAM.
INFO 2026-06-04 07:08:46 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 2s. Last read position: chr14:21,359,530
INFO 2026-06-04 07:08:46 MarkDuplicates Tracking 48594 as yet unmatched pairs. 3307 records in RAM.
INFO 2026-06-04 07:08:48 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 2s. Last read position: chr14:34,713,367
INFO 2026-06-04 07:08:48 MarkDuplicates Tracking 47990 as yet unmatched pairs. 2702 records in RAM.
INFO 2026-06-04 07:08:50 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 1s. Last read position: chr14:60,124,308
INFO 2026-06-04 07:08:50 MarkDuplicates Tracking 47452 as yet unmatched pairs. 2160 records in RAM.
INFO 2026-06-04 07:08:51 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 1s. Last read position: chr14:74,713,181
INFO 2026-06-04 07:08:51 MarkDuplicates Tracking 46907 as yet unmatched pairs. 1615 records in RAM.
INFO 2026-06-04 07:08:53 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 1s. Last read position: chr14:96,313,129
INFO 2026-06-04 07:08:53 MarkDuplicates Tracking 46355 as yet unmatched pairs. 1061 records in RAM.
INFO 2026-06-04 07:08:55 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 1s. Last read position: chr14:104,939,262
INFO 2026-06-04 07:08:55 MarkDuplicates Tracking 45789 as yet unmatched pairs. 493 records in RAM.
INFO 2026-06-04 07:08:56 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 1s. Last read position: chr15:24,978,245
INFO 2026-06-04 07:08:56 MarkDuplicates Tracking 45310 as yet unmatched pairs. 2658 records in RAM.
INFO 2026-06-04 07:08:57 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 1s. Last read position: chr15:41,766,858
INFO 2026-06-04 07:08:57 MarkDuplicates Tracking 44795 as yet unmatched pairs. 2140 records in RAM.
INFO 2026-06-04 07:08:59 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 1s. Last read position: chr15:56,391,351
INFO 2026-06-04 07:08:59 MarkDuplicates Tracking 44300 as yet unmatched pairs. 1643 records in RAM.
INFO 2026-06-04 07:09:00 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 1s. Last read position: chr15:71,215,269
INFO 2026-06-04 07:09:00 MarkDuplicates Tracking 43771 as yet unmatched pairs. 1114 records in RAM.
INFO 2026-06-04 07:09:02 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 1s. Last read position: chr15:82,434,224
INFO 2026-06-04 07:09:02 MarkDuplicates Tracking 43172 as yet unmatched pairs. 512 records in RAM.
INFO 2026-06-04 07:09:04 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 2s. Last read position: chr15:100,612,174
INFO 2026-06-04 07:09:04 MarkDuplicates Tracking 42706 as yet unmatched pairs. 39 records in RAM.
INFO 2026-06-04 07:09:06 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 1s. Last read position: chr16:1,760,521
INFO 2026-06-04 07:09:06 MarkDuplicates Tracking 42145 as yet unmatched pairs. 5665 records in RAM.
INFO 2026-06-04 07:09:08 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 1s. Last read position: chr16:2,764,330
INFO 2026-06-04 07:09:08 MarkDuplicates Tracking 41737 as yet unmatched pairs. 5257 records in RAM.
INFO 2026-06-04 07:09:09 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 1s. Last read position: chr16:4,884,297
INFO 2026-06-04 07:09:09 MarkDuplicates Tracking 40875 as yet unmatched pairs. 4395 records in RAM.
INFO 2026-06-04 07:09:11 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 1s. Last read position: chr16:15,363,938
INFO 2026-06-04 07:09:11 MarkDuplicates Tracking 40542 as yet unmatched pairs. 4062 records in RAM.
INFO 2026-06-04 07:09:12 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 1s. Last read position: chr16:18,364,545
INFO 2026-06-04 07:09:12 MarkDuplicates Tracking 40415 as yet unmatched pairs. 3933 records in RAM.
INFO 2026-06-04 07:09:13 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 1s. Last read position: chr16:21,837,562
INFO 2026-06-04 07:09:13 MarkDuplicates Tracking 40235 as yet unmatched pairs. 3749 records in RAM.
INFO 2026-06-04 07:09:15 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 1s. Last read position: chr16:28,605,903
INFO 2026-06-04 07:09:15 MarkDuplicates Tracking 39643 as yet unmatched pairs. 3152 records in RAM.
INFO 2026-06-04 07:09:17 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 2s. Last read position: chr16:29,987,351
INFO 2026-06-04 07:09:17 MarkDuplicates Tracking 39198 as yet unmatched pairs. 2699 records in RAM.
INFO 2026-06-04 07:09:19 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 2s. Last read position: chr16:31,080,653
INFO 2026-06-04 07:09:19 MarkDuplicates Tracking 38669 as yet unmatched pairs. 2170 records in RAM.
INFO 2026-06-04 07:09:21 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 1s. Last read position: chr16:57,025,709
INFO 2026-06-04 07:09:21 MarkDuplicates Tracking 38140 as yet unmatched pairs. 1639 records in RAM.
INFO 2026-06-04 07:09:23 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 2s. Last read position: chr16:70,268,317
INFO 2026-06-04 07:09:23 MarkDuplicates Tracking 37518 as yet unmatched pairs. 1017 records in RAM.
INFO 2026-06-04 07:09:25 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 1s. Last read position: chr16:88,428,353
INFO 2026-06-04 07:09:25 MarkDuplicates Tracking 37012 as yet unmatched pairs. 511 records in RAM.
INFO 2026-06-04 07:09:26 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 1s. Last read position: chr17:1,681,652
INFO 2026-06-04 07:09:26 MarkDuplicates Tracking 36371 as yet unmatched pairs. 10988 records in RAM.
INFO 2026-06-04 07:09:28 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 1s. Last read position: chr17:7,240,835
INFO 2026-06-04 07:09:28 MarkDuplicates Tracking 35965 as yet unmatched pairs. 10582 records in RAM.
INFO 2026-06-04 07:09:29 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 1s. Last read position: chr17:13,011,687
INFO 2026-06-04 07:09:29 MarkDuplicates Tracking 35212 as yet unmatched pairs. 9829 records in RAM.
INFO 2026-06-04 07:09:31 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr17:28,695,507
INFO 2026-06-04 07:09:31 MarkDuplicates Tracking 34721 as yet unmatched pairs. 9337 records in RAM.
INFO 2026-06-04 07:09:32 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr17:36,386,595
INFO 2026-06-04 07:09:32 MarkDuplicates Tracking 34175 as yet unmatched pairs. 8791 records in RAM.
INFO 2026-06-04 07:09:34 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 1s. Last read position: chr17:40,053,586
INFO 2026-06-04 07:09:34 MarkDuplicates Tracking 33654 as yet unmatched pairs. 8270 records in RAM.
INFO 2026-06-04 07:09:36 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 1s. Last read position: chr17:42,852,224
INFO 2026-06-04 07:09:36 MarkDuplicates Tracking 33031 as yet unmatched pairs. 7647 records in RAM.
INFO 2026-06-04 07:09:37 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 1s. Last read position: chr17:48,051,452
INFO 2026-06-04 07:09:37 MarkDuplicates Tracking 32572 as yet unmatched pairs. 7187 records in RAM.
INFO 2026-06-04 07:09:39 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 1s. Last read position: chr17:50,187,032
INFO 2026-06-04 07:09:39 MarkDuplicates Tracking 42338 as yet unmatched pairs. 16953 records in RAM.
INFO 2026-06-04 07:09:41 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 2s. Last read position: chr17:50,189,181
INFO 2026-06-04 07:09:41 MarkDuplicates Tracking 39437 as yet unmatched pairs. 14052 records in RAM.
INFO 2026-06-04 07:09:42 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 1s. Last read position: chr17:50,190,552
INFO 2026-06-04 07:09:42 MarkDuplicates Tracking 37896 as yet unmatched pairs. 12511 records in RAM.
INFO 2026-06-04 07:09:44 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 1s. Last read position: chr17:50,193,961
INFO 2026-06-04 07:09:44 MarkDuplicates Tracking 40989 as yet unmatched pairs. 15594 records in RAM.
INFO 2026-06-04 07:09:46 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 1s. Last read position: chr17:50,195,468
INFO 2026-06-04 07:09:46 MarkDuplicates Tracking 37725 as yet unmatched pairs. 12330 records in RAM.
INFO 2026-06-04 07:09:49 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 2s. Last read position: chr17:50,197,046
INFO 2026-06-04 07:09:49 MarkDuplicates Tracking 45025 as yet unmatched pairs. 19630 records in RAM.
INFO 2026-06-04 07:09:51 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 2s. Last read position: chr17:50,346,161
INFO 2026-06-04 07:09:51 MarkDuplicates Tracking 28259 as yet unmatched pairs. 2861 records in RAM.
INFO 2026-06-04 07:09:53 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 1s. Last read position: chr17:63,550,649
INFO 2026-06-04 07:09:53 MarkDuplicates Tracking 27721 as yet unmatched pairs. 2323 records in RAM.
INFO 2026-06-04 07:09:54 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 1s. Last read position: chr17:75,569,322
INFO 2026-06-04 07:09:54 MarkDuplicates Tracking 27154 as yet unmatched pairs. 1750 records in RAM.
INFO 2026-06-04 07:09:56 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 1s. Last read position: chr17:80,110,958
INFO 2026-06-04 07:09:56 MarkDuplicates Tracking 26582 as yet unmatched pairs. 1177 records in RAM.
INFO 2026-06-04 07:09:57 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 1s. Last read position: chr17:81,847,305
INFO 2026-06-04 07:09:57 MarkDuplicates Tracking 26107 as yet unmatched pairs. 702 records in RAM.
INFO 2026-06-04 07:09:59 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 1s. Last read position: chr18:9,954,097
INFO 2026-06-04 07:09:59 MarkDuplicates Tracking 25393 as yet unmatched pairs. 1100 records in RAM.
INFO 2026-06-04 07:10:02 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 2s. Last read position: chr18:49,797,517
INFO 2026-06-04 07:10:02 MarkDuplicates Tracking 24850 as yet unmatched pairs. 553 records in RAM.
INFO 2026-06-04 07:10:03 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 1s. Last read position: chr19:808,706
INFO 2026-06-04 07:10:03 MarkDuplicates Tracking 24307 as yet unmatched pairs. 10605 records in RAM.
INFO 2026-06-04 07:10:05 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 1s. Last read position: chr19:2,244,596
INFO 2026-06-04 07:10:05 MarkDuplicates Tracking 23565 as yet unmatched pairs. 9863 records in RAM.
INFO 2026-06-04 07:10:06 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 1s. Last read position: chr19:5,245,923
INFO 2026-06-04 07:10:06 MarkDuplicates Tracking 22798 as yet unmatched pairs. 9096 records in RAM.
INFO 2026-06-04 07:10:08 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 1s. Last read position: chr19:7,963,397
INFO 2026-06-04 07:10:08 MarkDuplicates Tracking 22048 as yet unmatched pairs. 8346 records in RAM.
INFO 2026-06-04 07:10:10 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 1s. Last read position: chr19:10,987,680
INFO 2026-06-04 07:10:10 MarkDuplicates Tracking 21534 as yet unmatched pairs. 7830 records in RAM.
INFO 2026-06-04 07:10:12 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 1s. Last read position: chr19:13,929,415
INFO 2026-06-04 07:10:12 MarkDuplicates Tracking 20795 as yet unmatched pairs. 7090 records in RAM.
INFO 2026-06-04 07:10:13 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr19:15,267,439
INFO 2026-06-04 07:10:13 MarkDuplicates Tracking 20780 as yet unmatched pairs. 7075 records in RAM.
INFO 2026-06-04 07:10:16 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 2s. Last read position: chr19:18,280,480
INFO 2026-06-04 07:10:16 MarkDuplicates Tracking 19791 as yet unmatched pairs. 6085 records in RAM.
INFO 2026-06-04 07:10:17 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 1s. Last read position: chr19:33,796,977
INFO 2026-06-04 07:10:17 MarkDuplicates Tracking 18880 as yet unmatched pairs. 5174 records in RAM.
INFO 2026-06-04 07:10:19 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 1s. Last read position: chr19:38,383,312
INFO 2026-06-04 07:10:19 MarkDuplicates Tracking 18074 as yet unmatched pairs. 4368 records in RAM.
INFO 2026-06-04 07:10:20 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 1s. Last read position: chr19:39,927,414
INFO 2026-06-04 07:10:20 MarkDuplicates Tracking 17487 as yet unmatched pairs. 3781 records in RAM.
INFO 2026-06-04 07:10:22 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 1s. Last read position: chr19:42,242,238
INFO 2026-06-04 07:10:22 MarkDuplicates Tracking 16882 as yet unmatched pairs. 3174 records in RAM.
INFO 2026-06-04 07:10:23 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 1s. Last read position: chr19:44,908,902
INFO 2026-06-04 07:10:23 MarkDuplicates Tracking 16464 as yet unmatched pairs. 2753 records in RAM.
INFO 2026-06-04 07:10:25 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 1s. Last read position: chr19:48,390,467
INFO 2026-06-04 07:10:25 MarkDuplicates Tracking 15695 as yet unmatched pairs. 1984 records in RAM.
INFO 2026-06-04 07:10:27 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 1s. Last read position: chr19:49,908,896
INFO 2026-06-04 07:10:27 MarkDuplicates Tracking 14996 as yet unmatched pairs. 1284 records in RAM.
INFO 2026-06-04 07:10:28 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 1s. Last read position: chr19:55,386,385
INFO 2026-06-04 07:10:28 MarkDuplicates Tracking 14745 as yet unmatched pairs. 1031 records in RAM.
INFO 2026-06-04 07:10:30 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 1s. Last read position: chr19:58,549,013
INFO 2026-06-04 07:10:30 MarkDuplicates Tracking 13946 as yet unmatched pairs. 232 records in RAM.
INFO 2026-06-04 07:10:32 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 2s. Last read position: chr20:16,429,891
INFO 2026-06-04 07:10:32 MarkDuplicates Tracking 13157 as yet unmatched pairs. 3049 records in RAM.
INFO 2026-06-04 07:10:34 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 1s. Last read position: chr20:34,740,925
INFO 2026-06-04 07:10:34 MarkDuplicates Tracking 12684 as yet unmatched pairs. 2573 records in RAM.
INFO 2026-06-04 07:10:35 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 1s. Last read position: chr20:41,165,050
INFO 2026-06-04 07:10:35 MarkDuplicates Tracking 11996 as yet unmatched pairs. 1885 records in RAM.
INFO 2026-06-04 07:10:37 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 1s. Last read position: chr20:49,046,404
INFO 2026-06-04 07:10:37 MarkDuplicates Tracking 11488 as yet unmatched pairs. 1377 records in RAM.
INFO 2026-06-04 07:10:39 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 1s. Last read position: chr20:62,314,675
INFO 2026-06-04 07:10:39 MarkDuplicates Tracking 10919 as yet unmatched pairs. 806 records in RAM.
INFO 2026-06-04 07:10:40 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 1s. Last read position: chr20:64,032,905
INFO 2026-06-04 07:10:40 MarkDuplicates Tracking 10216 as yet unmatched pairs. 103 records in RAM.
INFO 2026-06-04 07:10:41 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 1s. Last read position: chr21:8,441,943
INFO 2026-06-04 07:10:41 MarkDuplicates Tracking 9685 as yet unmatched pairs. 1720 records in RAM.
INFO 2026-06-04 07:10:43 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 1s. Last read position: chr21:34,095,678
INFO 2026-06-04 07:10:43 MarkDuplicates Tracking 9069 as yet unmatched pairs. 1104 records in RAM.
INFO 2026-06-04 07:10:44 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 1s. Last read position: chr21:45,494,896
INFO 2026-06-04 07:10:44 MarkDuplicates Tracking 8641 as yet unmatched pairs. 676 records in RAM.
INFO 2026-06-04 07:10:46 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 1s. Last read position: chr22:20,425,983
INFO 2026-06-04 07:10:46 MarkDuplicates Tracking 7858 as yet unmatched pairs. 2861 records in RAM.
INFO 2026-06-04 07:10:48 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:05:43s. Time for last 1,000,000: 1s. Last read position: chr22:28,796,074
INFO 2026-06-04 07:10:48 MarkDuplicates Tracking 7796 as yet unmatched pairs. 2799 records in RAM.
INFO 2026-06-04 07:10:49 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 1s. Last read position: chr22:36,227,547
INFO 2026-06-04 07:10:49 MarkDuplicates Tracking 6630 as yet unmatched pairs. 1633 records in RAM.
INFO 2026-06-04 07:10:53 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 3s. Last read position: chr22:40,830,934
INFO 2026-06-04 07:10:53 MarkDuplicates Tracking 6090 as yet unmatched pairs. 1092 records in RAM.
INFO 2026-06-04 07:10:54 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 1s. Last read position: chr22:50,277,634
INFO 2026-06-04 07:10:54 MarkDuplicates Tracking 5429 as yet unmatched pairs. 431 records in RAM.
INFO 2026-06-04 07:10:56 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 1s. Last read position: chrX:16,786,579
INFO 2026-06-04 07:10:56 MarkDuplicates Tracking 4725 as yet unmatched pairs. 2712 records in RAM.
INFO 2026-06-04 07:10:57 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 1s. Last read position: chrX:48,576,538
INFO 2026-06-04 07:10:57 MarkDuplicates Tracking 4239 as yet unmatched pairs. 2221 records in RAM.
INFO 2026-06-04 07:10:59 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 1s. Last read position: chrX:57,909,689
INFO 2026-06-04 07:10:59 MarkDuplicates Tracking 3665 as yet unmatched pairs. 1647 records in RAM.
INFO 2026-06-04 07:11:02 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 2s. Last read position: chrX:101,656,430
INFO 2026-06-04 07:11:02 MarkDuplicates Tracking 3207 as yet unmatched pairs. 1188 records in RAM.
INFO 2026-06-04 07:11:03 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 1s. Last read position: chrX:149,525,763
INFO 2026-06-04 07:11:03 MarkDuplicates Tracking 2696 as yet unmatched pairs. 677 records in RAM.
INFO 2026-06-04 07:11:05 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 1s. Last read position: chrX:154,535,271
INFO 2026-06-04 07:11:05 MarkDuplicates Tracking 2104 as yet unmatched pairs. 85 records in RAM.
INFO 2026-06-04 07:11:06 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 1s. Last read position: KI270711.1:12,875
INFO 2026-06-04 07:11:06 MarkDuplicates Tracking 1267 as yet unmatched pairs. 44 records in RAM.
INFO 2026-06-04 07:11:07 MarkDuplicates Read 216823383 records. 0 pairs never matched.
INFO 2026-06-04 07:11:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 38512529584; totalMemory: 63518539776; maxMemory: 63585648640
INFO 2026-06-04 07:11:17 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-04 07:11:23 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-04 07:11:48 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-04 07:12:04 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-04 07:12:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300840880; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-04 07:12:07 MarkDuplicates Marking 82373058 records as duplicates.
INFO 2026-06-04 07:12:07 MarkDuplicates Found 7065129 optical duplicate clusters.
INFO 2026-06-04 07:12:07 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-04 07:12:26 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:19s. Time for last 10,000,000: 19s. Last read position: chr1:113,672,680
INFO 2026-06-04 07:12:44 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:37s. Time for last 10,000,000: 18s. Last read position: chr1:203,348,002
INFO 2026-06-04 07:13:02 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:55s. Time for last 10,000,000: 18s. Last read position: chr2:127,636,556
INFO 2026-06-04 07:13:22 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:14s. Time for last 10,000,000: 19s. Last read position: chr3:9,834,738
INFO 2026-06-04 07:13:41 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:34s. Time for last 10,000,000: 19s. Last read position: chr4:3,439,454
INFO 2026-06-04 07:14:00 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:53s. Time for last 10,000,000: 19s. Last read position: chr5:150,402,564
INFO 2026-06-04 07:14:18 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:11s. Time for last 10,000,000: 18s. Last read position: chr6:89,338,240
INFO 2026-06-04 07:14:37 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:30s. Time for last 10,000,000: 18s. Last read position: chr7:100,998,997
INFO 2026-06-04 07:14:55 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:48s. Time for last 10,000,000: 18s. Last read position: chr8:143,738,087
INFO 2026-06-04 07:15:13 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:03:06s. Time for last 10,000,000: 17s. Last read position: chr9:131,487,166
INFO 2026-06-04 07:15:31 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:03:24s. Time for last 10,000,000: 18s. Last read position: chr11:2,138,069
INFO 2026-06-04 07:15:49 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:42s. Time for last 10,000,000: 18s. Last read position: chr11:130,196,413
INFO 2026-06-04 07:16:08 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:04:01s. Time for last 10,000,000: 18s. Last read position: chr12:131,909,779
INFO 2026-06-04 07:16:26 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:04:19s. Time for last 10,000,000: 18s. Last read position: chr15:24,978,245
INFO 2026-06-04 07:16:45 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:04:38s. Time for last 10,000,000: 18s. Last read position: chr16:18,364,545
INFO 2026-06-04 07:17:03 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:56s. Time for last 10,000,000: 18s. Last read position: chr17:13,011,687
INFO 2026-06-04 07:17:21 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:05:14s. Time for last 10,000,000: 18s. Last read position: chr17:50,195,468
INFO 2026-06-04 07:17:40 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:05:32s. Time for last 10,000,000: 18s. Last read position: chr19:2,244,596
INFO 2026-06-04 07:17:58 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:05:51s. Time for last 10,000,000: 18s. Last read position: chr19:42,242,238
INFO 2026-06-04 07:18:17 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:06:10s. Time for last 10,000,000: 18s. Last read position: chr20:62,314,675
INFO 2026-06-04 07:18:35 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:06:28s. Time for last 10,000,000: 18s. Last read position: chrX:16,786,579
INFO 2026-06-04 07:18:50 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-04 07:18:50 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-04 07:18:50 MarkDuplicates Getting Memory Stats.
INFO 2026-06-04 07:18:51 MarkDuplicates Before output close freeMemory: 201908656; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-04 07:18:51 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-04 07:18:51 MarkDuplicates After output close freeMemory: 104310280; totalMemory: 134217728; maxMemory: 63585648640
[Thu Jun 04 07:18:51 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 13.80 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory