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_4.Aligned.sortedByCoord.out.bam --OUTPUT RGB_RLP_lowDV_1ststrand_25C_4.md.bam --METRICS_FILE RGB_RLP_lowDV_1ststrand_25C_4.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:04:58.568 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 07:04:58 GMT 2026] MarkDuplicates --INPUT RGB_RLP_lowDV_1ststrand_25C_4.Aligned.sortedByCoord.out.bam --OUTPUT RGB_RLP_lowDV_1ststrand_25C_4.md.bam --METRICS_FILE RGB_RLP_lowDV_1ststrand_25C_4.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 07:04:58 GMT 2026] Executing as ?@nf-09054ea69f59653fad86b88fafbb33f1-1f494-gnxdt 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 07:04:58 MarkDuplicates Start of doWork freeMemory: 105493680; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-04 07:04:58 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-04 07:04:58 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-04 07:05:02 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:3,412,022
INFO 2026-06-04 07:05:02 MarkDuplicates Tracking 685 as yet unmatched pairs. 0 records in RAM.
INFO 2026-06-04 07:05:05 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 2s. Last read position: chr1:11,972,968
INFO 2026-06-04 07:05:05 MarkDuplicates Tracking 1464 as yet unmatched pairs. 109 records in RAM.
INFO 2026-06-04 07:05:06 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: chr1:19,739,838
INFO 2026-06-04 07:05:06 MarkDuplicates Tracking 1955 as yet unmatched pairs. 22 records in RAM.
INFO 2026-06-04 07:05:08 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: chr1:24,354,423
INFO 2026-06-04 07:05:08 MarkDuplicates Tracking 2532 as yet unmatched pairs. 23 records in RAM.
INFO 2026-06-04 07:05:10 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 2s. Last read position: chr1:30,966,143
INFO 2026-06-04 07:05:10 MarkDuplicates Tracking 3254 as yet unmatched pairs. 119 records in RAM.
INFO 2026-06-04 07:05:12 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: chr1:36,286,597
INFO 2026-06-04 07:05:12 MarkDuplicates Tracking 3862 as yet unmatched pairs. 116 records in RAM.
INFO 2026-06-04 07:05:14 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: chr1:43,578,900
INFO 2026-06-04 07:05:14 MarkDuplicates Tracking 4667 as yet unmatched pairs. 323 records in RAM.
INFO 2026-06-04 07:05:16 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr1:54,243,234
INFO 2026-06-04 07:05:16 MarkDuplicates Tracking 5080 as yet unmatched pairs. 121 records in RAM.
INFO 2026-06-04 07:05:17 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: chr1:92,323,817
INFO 2026-06-04 07:05:17 MarkDuplicates Tracking 5515 as yet unmatched pairs. 34 records in RAM.
INFO 2026-06-04 07:05:19 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: chr1:113,683,402
INFO 2026-06-04 07:05:19 MarkDuplicates Tracking 6078 as yet unmatched pairs. 46 records in RAM.
INFO 2026-06-04 07:05:21 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 2s. Last read position: chr1:120,793,245
INFO 2026-06-04 07:05:21 MarkDuplicates Tracking 6590 as yet unmatched pairs. 74 records in RAM.
INFO 2026-06-04 07:05:23 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 1s. Last read position: chr1:148,576,409
INFO 2026-06-04 07:05:23 MarkDuplicates Tracking 6802 as yet unmatched pairs. 18 records in RAM.
INFO 2026-06-04 07:05:25 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: chr1:150,796,683
INFO 2026-06-04 07:05:25 MarkDuplicates Tracking 7328 as yet unmatched pairs. 202 records in RAM.
INFO 2026-06-04 07:05:26 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 1s. Last read position: chr1:153,457,805
INFO 2026-06-04 07:05:26 MarkDuplicates Tracking 8703 as yet unmatched pairs. 1132 records in RAM.
INFO 2026-06-04 07:05:27 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 1s. Last read position: chr1:154,966,182
INFO 2026-06-04 07:05:27 MarkDuplicates Tracking 8348 as yet unmatched pairs. 234 records in RAM.
INFO 2026-06-04 07:05:29 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 1s. Last read position: chr1:155,933,725
INFO 2026-06-04 07:05:29 MarkDuplicates Tracking 8717 as yet unmatched pairs. 60 records in RAM.
INFO 2026-06-04 07:05:30 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 1s. Last read position: chr1:159,927,309
INFO 2026-06-04 07:05:30 MarkDuplicates Tracking 9358 as yet unmatched pairs. 107 records in RAM.
INFO 2026-06-04 07:05:31 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 1s. Last read position: chr1:170,552,302
INFO 2026-06-04 07:05:31 MarkDuplicates Tracking 9857 as yet unmatched pairs. 47 records in RAM.
INFO 2026-06-04 07:05:33 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 1s. Last read position: chr1:186,308,750
INFO 2026-06-04 07:05:33 MarkDuplicates Tracking 10329 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-04 07:05:34 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 1s. Last read position: chr1:203,828,328
INFO 2026-06-04 07:05:34 MarkDuplicates Tracking 11048 as yet unmatched pairs. 196 records in RAM.
INFO 2026-06-04 07:05:36 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 1s. Last read position: chr1:220,253,999
INFO 2026-06-04 07:05:36 MarkDuplicates Tracking 11535 as yet unmatched pairs. 156 records in RAM.
INFO 2026-06-04 07:05:37 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 1s. Last read position: chr1:228,408,398
INFO 2026-06-04 07:05:37 MarkDuplicates Tracking 12070 as yet unmatched pairs. 35 records in RAM.
INFO 2026-06-04 07:05:38 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 1s. Last read position: chr1:247,156,679
INFO 2026-06-04 07:05:38 MarkDuplicates Tracking 12758 as yet unmatched pairs. 141 records in RAM.
INFO 2026-06-04 07:05:41 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 2s. Last read position: chr2:24,918,898
INFO 2026-06-04 07:05:41 MarkDuplicates Tracking 13205 as yet unmatched pairs. 13095 records in RAM.
INFO 2026-06-04 07:05:43 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,265
INFO 2026-06-04 07:05:43 MarkDuplicates Tracking 92787 as yet unmatched pairs. 8370 records in RAM.
INFO 2026-06-04 07:05:44 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 1s. Last read position: chr2:48,581,735
INFO 2026-06-04 07:05:44 MarkDuplicates Tracking 107015 as yet unmatched pairs. 7176 records in RAM.
INFO 2026-06-04 07:05:45 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 1s. Last read position: chr2:71,570,640
INFO 2026-06-04 07:05:45 MarkDuplicates Tracking 106488 as yet unmatched pairs. 6644 records in RAM.
INFO 2026-06-04 07:05:47 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 1s. Last read position: chr2:95,279,933
INFO 2026-06-04 07:05:47 MarkDuplicates Tracking 106145 as yet unmatched pairs. 6298 records in RAM.
INFO 2026-06-04 07:05:48 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 1s. Last read position: chr2:108,765,319
INFO 2026-06-04 07:05:48 MarkDuplicates Tracking 105743 as yet unmatched pairs. 5894 records in RAM.
INFO 2026-06-04 07:05:50 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 1s. Last read position: chr2:128,268,484
INFO 2026-06-04 07:05:50 MarkDuplicates Tracking 105097 as yet unmatched pairs. 5238 records in RAM.
INFO 2026-06-04 07:05:51 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 1s. Last read position: chr2:169,878,525
INFO 2026-06-04 07:05:51 MarkDuplicates Tracking 104584 as yet unmatched pairs. 4722 records in RAM.
INFO 2026-06-04 07:05:53 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 1s. Last read position: chr2:188,996,130
INFO 2026-06-04 07:05:53 MarkDuplicates Tracking 104660 as yet unmatched pairs. 4796 records in RAM.
INFO 2026-06-04 07:05:54 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 1s. Last read position: chr2:200,981,265
INFO 2026-06-04 07:05:54 MarkDuplicates Tracking 103464 as yet unmatched pairs. 3593 records in RAM.
INFO 2026-06-04 07:05:55 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 1s. Last read position: chr2:215,371,969
INFO 2026-06-04 07:05:55 MarkDuplicates Tracking 106486 as yet unmatched pairs. 6613 records in RAM.
INFO 2026-06-04 07:05:57 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 1s. Last read position: chr2:215,384,108
INFO 2026-06-04 07:05:57 MarkDuplicates Tracking 105099 as yet unmatched pairs. 5226 records in RAM.
INFO 2026-06-04 07:05:58 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 1s. Last read position: chr2:215,409,707
INFO 2026-06-04 07:05:58 MarkDuplicates Tracking 103391 as yet unmatched pairs. 3517 records in RAM.
INFO 2026-06-04 07:06:00 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 1s. Last read position: chr2:216,420,462
INFO 2026-06-04 07:06:00 MarkDuplicates Tracking 101538 as yet unmatched pairs. 1659 records in RAM.
INFO 2026-06-04 07:06:01 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 1s. Last read position: chr2:226,797,155
INFO 2026-06-04 07:06:01 MarkDuplicates Tracking 101057 as yet unmatched pairs. 1174 records in RAM.
INFO 2026-06-04 07:06:03 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 1s. Last read position: chr2:237,396,746
INFO 2026-06-04 07:06:03 MarkDuplicates Tracking 100531 as yet unmatched pairs. 628 records in RAM.
INFO 2026-06-04 07:06:04 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 1s. Last read position: chr3:10,125,649
INFO 2026-06-04 07:06:04 MarkDuplicates Tracking 99791 as yet unmatched pairs. 5062 records in RAM.
INFO 2026-06-04 07:06:06 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 1s. Last read position: chr3:37,319,110
INFO 2026-06-04 07:06:06 MarkDuplicates Tracking 99248 as yet unmatched pairs. 4503 records in RAM.
INFO 2026-06-04 07:06:07 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 1s. Last read position: chr3:47,916,762
INFO 2026-06-04 07:06:07 MarkDuplicates Tracking 98832 as yet unmatched pairs. 4079 records in RAM.
INFO 2026-06-04 07:06:09 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 1s. Last read position: chr3:51,441,720
INFO 2026-06-04 07:06:09 MarkDuplicates Tracking 98087 as yet unmatched pairs. 3330 records in RAM.
INFO 2026-06-04 07:06:11 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 1s. Last read position: chr3:78,661,093
INFO 2026-06-04 07:06:11 MarkDuplicates Tracking 97481 as yet unmatched pairs. 2717 records in RAM.
INFO 2026-06-04 07:06:13 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 2s. Last read position: chr3:121,698,837
INFO 2026-06-04 07:06:13 MarkDuplicates Tracking 97048 as yet unmatched pairs. 2277 records in RAM.
INFO 2026-06-04 07:06:15 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 1s. Last read position: chr3:130,980,645
INFO 2026-06-04 07:06:15 MarkDuplicates Tracking 96491 as yet unmatched pairs. 1707 records in RAM.
INFO 2026-06-04 07:06:16 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 1s. Last read position: chr3:157,148,384
INFO 2026-06-04 07:06:16 MarkDuplicates Tracking 95983 as yet unmatched pairs. 1193 records in RAM.
INFO 2026-06-04 07:06:18 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 1s. Last read position: chr3:184,572,715
INFO 2026-06-04 07:06:18 MarkDuplicates Tracking 95386 as yet unmatched pairs. 594 records in RAM.
INFO 2026-06-04 07:06:19 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 1s. Last read position: chr3:196,064,409
INFO 2026-06-04 07:06:19 MarkDuplicates Tracking 94976 as yet unmatched pairs. 181 records in RAM.
INFO 2026-06-04 07:06:20 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 1s. Last read position: chr4:6,302,268
INFO 2026-06-04 07:06:20 MarkDuplicates Tracking 94306 as yet unmatched pairs. 2247 records in RAM.
INFO 2026-06-04 07:06:22 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 1s. Last read position: chr4:48,557,568
INFO 2026-06-04 07:06:22 MarkDuplicates Tracking 93802 as yet unmatched pairs. 1740 records in RAM.
INFO 2026-06-04 07:06:23 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 1s. Last read position: chr4:82,857,090
INFO 2026-06-04 07:06:23 MarkDuplicates Tracking 93347 as yet unmatched pairs. 1282 records in RAM.
INFO 2026-06-04 07:06:25 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 1s. Last read position: chr4:122,271,066
INFO 2026-06-04 07:06:25 MarkDuplicates Tracking 92757 as yet unmatched pairs. 684 records in RAM.
INFO 2026-06-04 07:06:26 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 1s. Last read position: chr4:169,106,960
INFO 2026-06-04 07:06:26 MarkDuplicates Tracking 92259 as yet unmatched pairs. 182 records in RAM.
INFO 2026-06-04 07:06:27 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 1s. Last read position: chr5:14,462,915
INFO 2026-06-04 07:06:27 MarkDuplicates Tracking 91984 as yet unmatched pairs. 4409 records in RAM.
INFO 2026-06-04 07:06:29 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 1s. Last read position: chr5:55,969,721
INFO 2026-06-04 07:06:29 MarkDuplicates Tracking 91625 as yet unmatched pairs. 4035 records in RAM.
INFO 2026-06-04 07:06:30 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 1s. Last read position: chr5:83,541,483
INFO 2026-06-04 07:06:30 MarkDuplicates Tracking 90807 as yet unmatched pairs. 3217 records in RAM.
INFO 2026-06-04 07:06:32 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 1s. Last read position: chr5:134,560,819
INFO 2026-06-04 07:06:32 MarkDuplicates Tracking 90160 as yet unmatched pairs. 2569 records in RAM.
INFO 2026-06-04 07:06:33 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 1s. Last read position: chr5:141,394,790
INFO 2026-06-04 07:06:33 MarkDuplicates Tracking 89736 as yet unmatched pairs. 2121 records in RAM.
INFO 2026-06-04 07:06:35 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 2s. Last read position: chr5:150,404,680
INFO 2026-06-04 07:06:35 MarkDuplicates Tracking 92590 as yet unmatched pairs. 4955 records in RAM.
INFO 2026-06-04 07:06:37 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 2s. Last read position: chr5:163,518,266
INFO 2026-06-04 07:06:37 MarkDuplicates Tracking 88632 as yet unmatched pairs. 996 records in RAM.
INFO 2026-06-04 07:06:39 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 1s. Last read position: chr5:178,231,468
INFO 2026-06-04 07:06:39 MarkDuplicates Tracking 88040 as yet unmatched pairs. 403 records in RAM.
INFO 2026-06-04 07:06:40 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 1s. Last read position: chr6:7,229,163
INFO 2026-06-04 07:06:40 MarkDuplicates Tracking 87866 as yet unmatched pairs. 5762 records in RAM.
INFO 2026-06-04 07:06:42 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 1s. Last read position: chr6:26,413,053
INFO 2026-06-04 07:06:42 MarkDuplicates Tracking 86991 as yet unmatched pairs. 4883 records in RAM.
INFO 2026-06-04 07:06:43 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 1s. Last read position: chr6:31,354,212
INFO 2026-06-04 07:06:43 MarkDuplicates Tracking 87672 as yet unmatched pairs. 5564 records in RAM.
INFO 2026-06-04 07:06:44 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 1s. Last read position: chr6:31,983,344
INFO 2026-06-04 07:06:44 MarkDuplicates Tracking 85999 as yet unmatched pairs. 3891 records in RAM.
INFO 2026-06-04 07:06:46 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 1s. Last read position: chr6:33,275,804
INFO 2026-06-04 07:06:46 MarkDuplicates Tracking 85852 as yet unmatched pairs. 3744 records in RAM.
INFO 2026-06-04 07:06:48 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 1s. Last read position: chr6:41,649,650
INFO 2026-06-04 07:06:48 MarkDuplicates Tracking 84989 as yet unmatched pairs. 2864 records in RAM.
INFO 2026-06-04 07:06:49 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 1s. Last read position: chr6:53,269,160
INFO 2026-06-04 07:06:49 MarkDuplicates Tracking 84459 as yet unmatched pairs. 2333 records in RAM.
INFO 2026-06-04 07:06:50 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 1s. Last read position: chr6:98,917,482
INFO 2026-06-04 07:06:50 MarkDuplicates Tracking 83700 as yet unmatched pairs. 1568 records in RAM.
INFO 2026-06-04 07:06:52 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 1s. Last read position: chr6:135,192,412
INFO 2026-06-04 07:06:52 MarkDuplicates Tracking 83396 as yet unmatched pairs. 1259 records in RAM.
INFO 2026-06-04 07:06:53 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 1s. Last read position: chr6:156,778,143
INFO 2026-06-04 07:06:53 MarkDuplicates Tracking 82720 as yet unmatched pairs. 578 records in RAM.
INFO 2026-06-04 07:06:55 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 1s. Last read position: chr7:842,018
INFO 2026-06-04 07:06:55 MarkDuplicates Tracking 82204 as yet unmatched pairs. 5325 records in RAM.
INFO 2026-06-04 07:06:56 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 1s. Last read position: chr7:6,153,996
INFO 2026-06-04 07:06:56 MarkDuplicates Tracking 81484 as yet unmatched pairs. 4604 records in RAM.
INFO 2026-06-04 07:06:57 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 1s. Last read position: chr7:44,104,612
INFO 2026-06-04 07:06:57 MarkDuplicates Tracking 81179 as yet unmatched pairs. 4295 records in RAM.
INFO 2026-06-04 07:07:00 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 2s. Last read position: chr7:66,948,628
INFO 2026-06-04 07:07:00 MarkDuplicates Tracking 80479 as yet unmatched pairs. 3594 records in RAM.
INFO 2026-06-04 07:07:01 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 1s. Last read position: chr7:75,423,157
INFO 2026-06-04 07:07:01 MarkDuplicates Tracking 80124 as yet unmatched pairs. 3239 records in RAM.
INFO 2026-06-04 07:07:03 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 1s. Last read position: chr7:94,409,789
INFO 2026-06-04 07:07:03 MarkDuplicates Tracking 80028 as yet unmatched pairs. 3142 records in RAM.
INFO 2026-06-04 07:07:04 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 1s. Last read position: chr7:100,153,474
INFO 2026-06-04 07:07:04 MarkDuplicates Tracking 79081 as yet unmatched pairs. 2195 records in RAM.
INFO 2026-06-04 07:07:06 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 1s. Last read position: chr7:101,000,311
INFO 2026-06-04 07:07:06 MarkDuplicates Tracking 78619 as yet unmatched pairs. 1732 records in RAM.
INFO 2026-06-04 07:07:07 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 1s. Last read position: chr7:107,975,388
INFO 2026-06-04 07:07:07 MarkDuplicates Tracking 78276 as yet unmatched pairs. 1389 records in RAM.
INFO 2026-06-04 07:07:08 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 1s. Last read position: chr7:138,460,645
INFO 2026-06-04 07:07:08 MarkDuplicates Tracking 77917 as yet unmatched pairs. 1026 records in RAM.
INFO 2026-06-04 07:07:09 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 1s. Last read position: chr7:150,470,838
INFO 2026-06-04 07:07:09 MarkDuplicates Tracking 77258 as yet unmatched pairs. 365 records in RAM.
INFO 2026-06-04 07:07:11 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 1s. Last read position: chr8:18,011,775
INFO 2026-06-04 07:07:11 MarkDuplicates Tracking 76767 as yet unmatched pairs. 5274 records in RAM.
INFO 2026-06-04 07:07:13 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 1s. Last read position: chr8:37,841,270
INFO 2026-06-04 07:07:13 MarkDuplicates Tracking 76178 as yet unmatched pairs. 4685 records in RAM.
INFO 2026-06-04 07:07:14 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 1s. Last read position: chr8:43,013,062
INFO 2026-06-04 07:07:14 MarkDuplicates Tracking 75637 as yet unmatched pairs. 4143 records in RAM.
INFO 2026-06-04 07:07:15 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 1s. Last read position: chr8:69,658,530
INFO 2026-06-04 07:07:15 MarkDuplicates Tracking 75104 as yet unmatched pairs. 3609 records in RAM.
INFO 2026-06-04 07:07:17 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 1s. Last read position: chr8:100,721,517
INFO 2026-06-04 07:07:17 MarkDuplicates Tracking 75179 as yet unmatched pairs. 3684 records in RAM.
INFO 2026-06-04 07:07:18 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 1s. Last read position: chr8:124,475,182
INFO 2026-06-04 07:07:18 MarkDuplicates Tracking 74116 as yet unmatched pairs. 2615 records in RAM.
INFO 2026-06-04 07:07:20 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 1s. Last read position: chr8:143,809,619
INFO 2026-06-04 07:07:20 MarkDuplicates Tracking 73509 as yet unmatched pairs. 2004 records in RAM.
INFO 2026-06-04 07:07:21 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 1s. Last read position: chr8:143,860,621
INFO 2026-06-04 07:07:21 MarkDuplicates Tracking 74319 as yet unmatched pairs. 2814 records in RAM.
INFO 2026-06-04 07:07:22 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr8:143,862,996
INFO 2026-06-04 07:07:22 MarkDuplicates Tracking 74642 as yet unmatched pairs. 3137 records in RAM.
INFO 2026-06-04 07:07:23 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 1s. Last read position: chr8:143,865,503
INFO 2026-06-04 07:07:23 MarkDuplicates Tracking 72553 as yet unmatched pairs. 1048 records in RAM.
INFO 2026-06-04 07:07:25 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 1s. Last read position: chr8:143,927,682
INFO 2026-06-04 07:07:25 MarkDuplicates Tracking 72270 as yet unmatched pairs. 757 records in RAM.
INFO 2026-06-04 07:07:26 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 1s. Last read position: chr9:6,007,455
INFO 2026-06-04 07:07:26 MarkDuplicates Tracking 71438 as yet unmatched pairs. 3756 records in RAM.
INFO 2026-06-04 07:07:28 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 1s. Last read position: chr9:35,736,263
INFO 2026-06-04 07:07:28 MarkDuplicates Tracking 70999 as yet unmatched pairs. 3315 records in RAM.
INFO 2026-06-04 07:07:29 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 1s. Last read position: chr9:93,268,626
INFO 2026-06-04 07:07:29 MarkDuplicates Tracking 70438 as yet unmatched pairs. 2744 records in RAM.
INFO 2026-06-04 07:07:31 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 1s. Last read position: chr9:114,309,355
INFO 2026-06-04 07:07:31 MarkDuplicates Tracking 69897 as yet unmatched pairs. 2201 records in RAM.
INFO 2026-06-04 07:07:33 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 1s. Last read position: chr9:128,153,284
INFO 2026-06-04 07:07:33 MarkDuplicates Tracking 69286 as yet unmatched pairs. 1587 records in RAM.
INFO 2026-06-04 07:07:35 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 1s. Last read position: chr9:131,629,242
INFO 2026-06-04 07:07:35 MarkDuplicates Tracking 68812 as yet unmatched pairs. 1111 records in RAM.
INFO 2026-06-04 07:07:37 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 2s. Last read position: chr9:136,806,157
INFO 2026-06-04 07:07:37 MarkDuplicates Tracking 68119 as yet unmatched pairs. 418 records in RAM.
INFO 2026-06-04 07:07:39 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 1s. Last read position: chr10:8,058,612
INFO 2026-06-04 07:07:39 MarkDuplicates Tracking 67845 as yet unmatched pairs. 3643 records in RAM.
INFO 2026-06-04 07:07:40 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 1s. Last read position: chr10:32,511,393
INFO 2026-06-04 07:07:40 MarkDuplicates Tracking 66960 as yet unmatched pairs. 2758 records in RAM.
INFO 2026-06-04 07:07:42 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 1s. Last read position: chr10:50,097,709
INFO 2026-06-04 07:07:42 MarkDuplicates Tracking 66577 as yet unmatched pairs. 2372 records in RAM.
INFO 2026-06-04 07:07:43 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 1s. Last read position: chr10:74,136,710
INFO 2026-06-04 07:07:43 MarkDuplicates Tracking 66039 as yet unmatched pairs. 1829 records in RAM.
INFO 2026-06-04 07:07:45 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 1s. Last read position: chr10:93,374,940
INFO 2026-06-04 07:07:45 MarkDuplicates Tracking 65620 as yet unmatched pairs. 1400 records in RAM.
INFO 2026-06-04 07:07:47 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 1s. Last read position: chr10:103,602,563
INFO 2026-06-04 07:07:47 MarkDuplicates Tracking 65092 as yet unmatched pairs. 870 records in RAM.
INFO 2026-06-04 07:07:48 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 1s. Last read position: chr10:125,740,598
INFO 2026-06-04 07:07:48 MarkDuplicates Tracking 64493 as yet unmatched pairs. 268 records in RAM.
INFO 2026-06-04 07:07:49 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 1s. Last read position: chr11:702,941
INFO 2026-06-04 07:07:49 MarkDuplicates Tracking 63884 as yet unmatched pairs. 6335 records in RAM.
INFO 2026-06-04 07:07:51 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 1s. Last read position: chr11:2,884,957
INFO 2026-06-04 07:07:51 MarkDuplicates Tracking 63425 as yet unmatched pairs. 5876 records in RAM.
INFO 2026-06-04 07:07:53 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 1s. Last read position: chr11:16,974,713
INFO 2026-06-04 07:07:53 MarkDuplicates Tracking 62917 as yet unmatched pairs. 5367 records in RAM.
INFO 2026-06-04 07:07:54 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 1s. Last read position: chr11:46,429,003
INFO 2026-06-04 07:07:54 MarkDuplicates Tracking 62314 as yet unmatched pairs. 4761 records in RAM.
INFO 2026-06-04 07:07:56 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 2s. Last read position: chr11:61,367,959
INFO 2026-06-04 07:07:56 MarkDuplicates Tracking 61821 as yet unmatched pairs. 4268 records in RAM.
INFO 2026-06-04 07:07:58 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 1s. Last read position: chr11:62,800,394
INFO 2026-06-04 07:07:58 MarkDuplicates Tracking 61266 as yet unmatched pairs. 3708 records in RAM.
INFO 2026-06-04 07:08:00 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 1s. Last read position: chr11:65,546,533
INFO 2026-06-04 07:08:00 MarkDuplicates Tracking 60921 as yet unmatched pairs. 3358 records in RAM.
INFO 2026-06-04 07:08:01 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 1s. Last read position: chr11:66,701,144
INFO 2026-06-04 07:08:01 MarkDuplicates Tracking 59969 as yet unmatched pairs. 2406 records in RAM.
INFO 2026-06-04 07:08:03 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 1s. Last read position: chr11:71,538,138
INFO 2026-06-04 07:08:03 MarkDuplicates Tracking 59357 as yet unmatched pairs. 1792 records in RAM.
INFO 2026-06-04 07:08:04 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 1s. Last read position: chr11:77,922,442
INFO 2026-06-04 07:08:04 MarkDuplicates Tracking 58777 as yet unmatched pairs. 1210 records in RAM.
INFO 2026-06-04 07:08:05 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 1s. Last read position: chr11:118,339,101
INFO 2026-06-04 07:08:05 MarkDuplicates Tracking 58163 as yet unmatched pairs. 594 records in RAM.
INFO 2026-06-04 07:08:07 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 1s. Last read position: chr11:134,243,158
INFO 2026-06-04 07:08:07 MarkDuplicates Tracking 57588 as yet unmatched pairs. 19 records in RAM.
INFO 2026-06-04 07:08:09 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 1s. Last read position: chr12:6,936,738
INFO 2026-06-04 07:08:09 MarkDuplicates Tracking 57126 as yet unmatched pairs. 5080 records in RAM.
INFO 2026-06-04 07:08:10 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 1s. Last read position: chr12:20,496,377
INFO 2026-06-04 07:08:10 MarkDuplicates Tracking 56536 as yet unmatched pairs. 4488 records in RAM.
INFO 2026-06-04 07:08:12 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 1s. Last read position: chr12:47,798,898
INFO 2026-06-04 07:08:12 MarkDuplicates Tracking 56574 as yet unmatched pairs. 4524 records in RAM.
INFO 2026-06-04 07:08:13 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 1s. Last read position: chr12:51,357,401
INFO 2026-06-04 07:08:13 MarkDuplicates Tracking 55579 as yet unmatched pairs. 3527 records in RAM.
INFO 2026-06-04 07:08:15 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 2s. Last read position: chr12:54,516,962
INFO 2026-06-04 07:08:15 MarkDuplicates Tracking 54983 as yet unmatched pairs. 2931 records in RAM.
INFO 2026-06-04 07:08:17 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 1s. Last read position: chr12:57,156,859
INFO 2026-06-04 07:08:17 MarkDuplicates Tracking 54551 as yet unmatched pairs. 2496 records in RAM.
INFO 2026-06-04 07:08:18 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 1s. Last read position: chr12:76,031,358
INFO 2026-06-04 07:08:18 MarkDuplicates Tracking 53929 as yet unmatched pairs. 1873 records in RAM.
INFO 2026-06-04 07:08:20 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 1s. Last read position: chr12:109,241,199
INFO 2026-06-04 07:08:20 MarkDuplicates Tracking 53422 as yet unmatched pairs. 1364 records in RAM.
INFO 2026-06-04 07:08:22 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 2s. Last read position: chr12:120,496,415
INFO 2026-06-04 07:08:22 MarkDuplicates Tracking 52955 as yet unmatched pairs. 889 records in RAM.
INFO 2026-06-04 07:08:23 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 1s. Last read position: chr12:131,991,424
INFO 2026-06-04 07:08:23 MarkDuplicates Tracking 52348 as yet unmatched pairs. 282 records in RAM.
INFO 2026-06-04 07:08:25 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 1s. Last read position: chr13:31,148,460
INFO 2026-06-04 07:08:25 MarkDuplicates Tracking 51864 as yet unmatched pairs. 1737 records in RAM.
INFO 2026-06-04 07:08:27 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 1s. Last read position: chr13:80,336,874
INFO 2026-06-04 07:08:27 MarkDuplicates Tracking 51251 as yet unmatched pairs. 1108 records in RAM.
INFO 2026-06-04 07:08:29 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 2s. Last read position: chr13:112,860,300
INFO 2026-06-04 07:08:29 MarkDuplicates Tracking 50675 as yet unmatched pairs. 530 records in RAM.
INFO 2026-06-04 07:08:31 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 1s. Last read position: chr14:21,492,829
INFO 2026-06-04 07:08:31 MarkDuplicates Tracking 49992 as yet unmatched pairs. 3306 records in RAM.
INFO 2026-06-04 07:08:32 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 1s. Last read position: chr14:35,308,984
INFO 2026-06-04 07:08:32 MarkDuplicates Tracking 49561 as yet unmatched pairs. 2875 records in RAM.
INFO 2026-06-04 07:08:34 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 1s. Last read position: chr14:61,725,959
INFO 2026-06-04 07:08:34 MarkDuplicates Tracking 48908 as yet unmatched pairs. 2218 records in RAM.
INFO 2026-06-04 07:08:35 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 1s. Last read position: chr14:74,817,194
INFO 2026-06-04 07:08:35 MarkDuplicates Tracking 48328 as yet unmatched pairs. 1638 records in RAM.
INFO 2026-06-04 07:08:36 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 1s. Last read position: chr14:99,502,348
INFO 2026-06-04 07:08:36 MarkDuplicates Tracking 47763 as yet unmatched pairs. 1069 records in RAM.
INFO 2026-06-04 07:08:38 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 1s. Last read position: chr14:104,943,256
INFO 2026-06-04 07:08:38 MarkDuplicates Tracking 47414 as yet unmatched pairs. 719 records in RAM.
INFO 2026-06-04 07:08:39 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 1s. Last read position: chr15:28,186,699
INFO 2026-06-04 07:08:39 MarkDuplicates Tracking 46644 as yet unmatched pairs. 2673 records in RAM.
INFO 2026-06-04 07:08:41 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 1s. Last read position: chr15:42,152,672
INFO 2026-06-04 07:08:41 MarkDuplicates Tracking 46128 as yet unmatched pairs. 2156 records in RAM.
INFO 2026-06-04 07:08:42 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 1s. Last read position: chr15:57,234,043
INFO 2026-06-04 07:08:42 MarkDuplicates Tracking 46334 as yet unmatched pairs. 2360 records in RAM.
INFO 2026-06-04 07:08:44 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 1s. Last read position: chr15:72,202,563
INFO 2026-06-04 07:08:44 MarkDuplicates Tracking 45279 as yet unmatched pairs. 1303 records in RAM.
INFO 2026-06-04 07:08:45 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 1s. Last read position: chr15:83,018,179
INFO 2026-06-04 07:08:45 MarkDuplicates Tracking 44658 as yet unmatched pairs. 681 records in RAM.
INFO 2026-06-04 07:08:47 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 1s. Last read position: chr15:101,384,398
INFO 2026-06-04 07:08:47 MarkDuplicates Tracking 44004 as yet unmatched pairs. 27 records in RAM.
INFO 2026-06-04 07:08:48 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 1s. Last read position: chr16:1,772,366
INFO 2026-06-04 07:08:48 MarkDuplicates Tracking 43375 as yet unmatched pairs. 5686 records in RAM.
INFO 2026-06-04 07:08:49 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 1s. Last read position: chr16:2,765,851
INFO 2026-06-04 07:08:49 MarkDuplicates Tracking 42841 as yet unmatched pairs. 5152 records in RAM.
INFO 2026-06-04 07:08:51 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 1s. Last read position: chr16:5,082,623
INFO 2026-06-04 07:08:51 MarkDuplicates Tracking 42040 as yet unmatched pairs. 4347 records in RAM.
INFO 2026-06-04 07:08:52 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 1s. Last read position: chr16:15,630,400
INFO 2026-06-04 07:08:52 MarkDuplicates Tracking 41678 as yet unmatched pairs. 3985 records in RAM.
INFO 2026-06-04 07:08:54 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 1s. Last read position: chr16:18,380,617
INFO 2026-06-04 07:08:54 MarkDuplicates Tracking 41639 as yet unmatched pairs. 3946 records in RAM.
INFO 2026-06-04 07:08:55 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 1s. Last read position: chr16:21,851,845
INFO 2026-06-04 07:08:55 MarkDuplicates Tracking 41131 as yet unmatched pairs. 3438 records in RAM.
INFO 2026-06-04 07:08:56 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 1s. Last read position: chr16:28,726,743
INFO 2026-06-04 07:08:56 MarkDuplicates Tracking 40769 as yet unmatched pairs. 3076 records in RAM.
INFO 2026-06-04 07:08:58 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 1s. Last read position: chr16:30,067,254
INFO 2026-06-04 07:08:58 MarkDuplicates Tracking 40544 as yet unmatched pairs. 2851 records in RAM.
INFO 2026-06-04 07:09:00 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 1s. Last read position: chr16:31,132,436
INFO 2026-06-04 07:09:00 MarkDuplicates Tracking 39834 as yet unmatched pairs. 2140 records in RAM.
INFO 2026-06-04 07:09:01 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 1s. Last read position: chr16:57,154,243
INFO 2026-06-04 07:09:01 MarkDuplicates Tracking 39319 as yet unmatched pairs. 1623 records in RAM.
INFO 2026-06-04 07:09:03 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 1s. Last read position: chr16:70,481,409
INFO 2026-06-04 07:09:03 MarkDuplicates Tracking 38661 as yet unmatched pairs. 962 records in RAM.
INFO 2026-06-04 07:09:05 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 1s. Last read position: chr16:88,433,009
INFO 2026-06-04 07:09:05 MarkDuplicates Tracking 38153 as yet unmatched pairs. 453 records in RAM.
INFO 2026-06-04 07:09:06 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 1s. Last read position: chr17:1,736,038
INFO 2026-06-04 07:09:06 MarkDuplicates Tracking 37489 as yet unmatched pairs. 11159 records in RAM.
INFO 2026-06-04 07:09:08 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 1s. Last read position: chr17:7,258,883
INFO 2026-06-04 07:09:08 MarkDuplicates Tracking 36903 as yet unmatched pairs. 10573 records in RAM.
INFO 2026-06-04 07:09:10 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 1s. Last read position: chr17:15,545,762
INFO 2026-06-04 07:09:10 MarkDuplicates Tracking 36373 as yet unmatched pairs. 10042 records in RAM.
INFO 2026-06-04 07:09:11 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 1s. Last read position: chr17:28,715,656
INFO 2026-06-04 07:09:11 MarkDuplicates Tracking 35999 as yet unmatched pairs. 9668 records in RAM.
INFO 2026-06-04 07:09:12 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 1s. Last read position: chr17:36,538,333
INFO 2026-06-04 07:09:12 MarkDuplicates Tracking 35323 as yet unmatched pairs. 8991 records in RAM.
INFO 2026-06-04 07:09:14 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 1s. Last read position: chr17:40,126,210
INFO 2026-06-04 07:09:14 MarkDuplicates Tracking 34855 as yet unmatched pairs. 8523 records in RAM.
INFO 2026-06-04 07:09:15 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 1s. Last read position: chr17:43,013,544
INFO 2026-06-04 07:09:15 MarkDuplicates Tracking 34172 as yet unmatched pairs. 7839 records in RAM.
INFO 2026-06-04 07:09:17 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 1s. Last read position: chr17:48,543,004
INFO 2026-06-04 07:09:17 MarkDuplicates Tracking 33644 as yet unmatched pairs. 7311 records in RAM.
INFO 2026-06-04 07:09:18 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 1s. Last read position: chr17:50,187,068
INFO 2026-06-04 07:09:18 MarkDuplicates Tracking 40937 as yet unmatched pairs. 14604 records in RAM.
INFO 2026-06-04 07:09:20 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 1s. Last read position: chr17:50,189,225
INFO 2026-06-04 07:09:20 MarkDuplicates Tracking 38585 as yet unmatched pairs. 12251 records in RAM.
INFO 2026-06-04 07:09:21 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 1s. Last read position: chr17:50,190,829
INFO 2026-06-04 07:09:21 MarkDuplicates Tracking 35737 as yet unmatched pairs. 9403 records in RAM.
INFO 2026-06-04 07:09:23 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 1s. Last read position: chr17:50,193,974
INFO 2026-06-04 07:09:23 MarkDuplicates Tracking 43082 as yet unmatched pairs. 16747 records in RAM.
INFO 2026-06-04 07:09:25 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 1s. Last read position: chr17:50,195,563
INFO 2026-06-04 07:09:25 MarkDuplicates Tracking 39999 as yet unmatched pairs. 13664 records in RAM.
INFO 2026-06-04 07:09:26 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr17:50,197,057
INFO 2026-06-04 07:09:26 MarkDuplicates Tracking 46173 as yet unmatched pairs. 19837 records in RAM.
INFO 2026-06-04 07:09:28 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr17:50,369,997
INFO 2026-06-04 07:09:28 MarkDuplicates Tracking 29335 as yet unmatched pairs. 2999 records in RAM.
INFO 2026-06-04 07:09:29 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 1s. Last read position: chr17:63,704,123
INFO 2026-06-04 07:09:29 MarkDuplicates Tracking 28711 as yet unmatched pairs. 2375 records in RAM.
INFO 2026-06-04 07:09:31 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 1s. Last read position: chr17:75,588,753
INFO 2026-06-04 07:09:31 MarkDuplicates Tracking 28138 as yet unmatched pairs. 1802 records in RAM.
INFO 2026-06-04 07:09:32 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 1s. Last read position: chr17:80,138,252
INFO 2026-06-04 07:09:32 MarkDuplicates Tracking 27451 as yet unmatched pairs. 1115 records in RAM.
INFO 2026-06-04 07:09:34 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 1s. Last read position: chr17:81,860,361
INFO 2026-06-04 07:09:34 MarkDuplicates Tracking 27055 as yet unmatched pairs. 719 records in RAM.
INFO 2026-06-04 07:09:37 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 2s. Last read position: chr18:11,851,766
INFO 2026-06-04 07:09:37 MarkDuplicates Tracking 26247 as yet unmatched pairs. 1063 records in RAM.
INFO 2026-06-04 07:09:38 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 1s. Last read position: chr18:49,984,787
INFO 2026-06-04 07:09:38 MarkDuplicates Tracking 25626 as yet unmatched pairs. 441 records in RAM.
INFO 2026-06-04 07:09:40 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 2s. Last read position: chr19:871,602
INFO 2026-06-04 07:09:40 MarkDuplicates Tracking 25051 as yet unmatched pairs. 10605 records in RAM.
INFO 2026-06-04 07:09:42 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 1s. Last read position: chr19:2,271,432
INFO 2026-06-04 07:09:42 MarkDuplicates Tracking 24631 as yet unmatched pairs. 10184 records in RAM.
INFO 2026-06-04 07:09:44 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 1s. Last read position: chr19:5,590,375
INFO 2026-06-04 07:09:44 MarkDuplicates Tracking 23653 as yet unmatched pairs. 9205 records in RAM.
INFO 2026-06-04 07:09:45 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 1s. Last read position: chr19:8,117,552
INFO 2026-06-04 07:09:45 MarkDuplicates Tracking 23030 as yet unmatched pairs. 8580 records in RAM.
INFO 2026-06-04 07:09:47 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 1s. Last read position: chr19:11,024,409
INFO 2026-06-04 07:09:47 MarkDuplicates Tracking 22376 as yet unmatched pairs. 7925 records in RAM.
INFO 2026-06-04 07:09:48 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 1s. Last read position: chr19:13,983,528
INFO 2026-06-04 07:09:48 MarkDuplicates Tracking 21790 as yet unmatched pairs. 7339 records in RAM.
INFO 2026-06-04 07:09:50 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 1s. Last read position: chr19:15,272,987
INFO 2026-06-04 07:09:50 MarkDuplicates Tracking 21606 as yet unmatched pairs. 7155 records in RAM.
INFO 2026-06-04 07:09:51 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 1s. Last read position: chr19:18,281,219
INFO 2026-06-04 07:09:51 MarkDuplicates Tracking 20536 as yet unmatched pairs. 6085 records in RAM.
INFO 2026-06-04 07:09:53 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 1s. Last read position: chr19:34,221,703
INFO 2026-06-04 07:09:53 MarkDuplicates Tracking 19807 as yet unmatched pairs. 5356 records in RAM.
INFO 2026-06-04 07:09:55 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 1s. Last read position: chr19:38,611,046
INFO 2026-06-04 07:09:55 MarkDuplicates Tracking 18872 as yet unmatched pairs. 4419 records in RAM.
INFO 2026-06-04 07:09:56 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 1s. Last read position: chr19:39,979,895
INFO 2026-06-04 07:09:56 MarkDuplicates Tracking 18405 as yet unmatched pairs. 3951 records in RAM.
INFO 2026-06-04 07:09:58 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 1s. Last read position: chr19:42,249,436
INFO 2026-06-04 07:09:58 MarkDuplicates Tracking 18058 as yet unmatched pairs. 3604 records in RAM.
INFO 2026-06-04 07:09:59 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 1s. Last read position: chr19:44,914,878
INFO 2026-06-04 07:09:59 MarkDuplicates Tracking 17263 as yet unmatched pairs. 2807 records in RAM.
INFO 2026-06-04 07:10:01 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 1s. Last read position: chr19:48,474,179
INFO 2026-06-04 07:10:01 MarkDuplicates Tracking 16492 as yet unmatched pairs. 2035 records in RAM.
INFO 2026-06-04 07:10:02 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 1s. Last read position: chr19:49,933,064
INFO 2026-06-04 07:10:02 MarkDuplicates Tracking 15746 as yet unmatched pairs. 1289 records in RAM.
INFO 2026-06-04 07:10:04 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 1s. Last read position: chr19:55,386,769
INFO 2026-06-04 07:10:04 MarkDuplicates Tracking 16072 as yet unmatched pairs. 1615 records in RAM.
INFO 2026-06-04 07:10:07 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 2s. Last read position: chr19:58,549,966
INFO 2026-06-04 07:10:07 MarkDuplicates Tracking 14786 as yet unmatched pairs. 329 records in RAM.
INFO 2026-06-04 07:10:09 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr20:17,607,124
INFO 2026-06-04 07:10:09 MarkDuplicates Tracking 13905 as yet unmatched pairs. 3035 records in RAM.
INFO 2026-06-04 07:10:10 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 1s. Last read position: chr20:34,749,493
INFO 2026-06-04 07:10:10 MarkDuplicates Tracking 13388 as yet unmatched pairs. 2518 records in RAM.
INFO 2026-06-04 07:10:12 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 1s. Last read position: chr20:41,173,426
INFO 2026-06-04 07:10:12 MarkDuplicates Tracking 12843 as yet unmatched pairs. 1973 records in RAM.
INFO 2026-06-04 07:10:14 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 1s. Last read position: chr20:49,114,866
INFO 2026-06-04 07:10:14 MarkDuplicates Tracking 12286 as yet unmatched pairs. 1414 records in RAM.
INFO 2026-06-04 07:10:15 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 1s. Last read position: chr20:62,319,773
INFO 2026-06-04 07:10:15 MarkDuplicates Tracking 11812 as yet unmatched pairs. 939 records in RAM.
INFO 2026-06-04 07:10:17 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 1s. Last read position: chr20:64,273,226
INFO 2026-06-04 07:10:17 MarkDuplicates Tracking 10904 as yet unmatched pairs. 31 records in RAM.
INFO 2026-06-04 07:10:18 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 1s. Last read position: chr21:8,435,858
INFO 2026-06-04 07:10:18 MarkDuplicates Tracking 10327 as yet unmatched pairs. 1839 records in RAM.
INFO 2026-06-04 07:10:19 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 1s. Last read position: chr21:33,551,736
INFO 2026-06-04 07:10:19 MarkDuplicates Tracking 9842 as yet unmatched pairs. 1354 records in RAM.
INFO 2026-06-04 07:10:21 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:05:20s. Time for last 1,000,000: 1s. Last read position: chr21:45,405,372
INFO 2026-06-04 07:10:21 MarkDuplicates Tracking 9215 as yet unmatched pairs. 727 records in RAM.
INFO 2026-06-04 07:10:22 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 1s. Last read position: chr22:19,880,688
INFO 2026-06-04 07:10:22 MarkDuplicates Tracking 8367 as yet unmatched pairs. 2910 records in RAM.
INFO 2026-06-04 07:10:24 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 1s. Last read position: chr22:26,541,447
INFO 2026-06-04 07:10:24 MarkDuplicates Tracking 7815 as yet unmatched pairs. 2358 records in RAM.
INFO 2026-06-04 07:10:25 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 1s. Last read position: chr22:32,802,078
INFO 2026-06-04 07:10:25 MarkDuplicates Tracking 7225 as yet unmatched pairs. 1768 records in RAM.
INFO 2026-06-04 07:10:27 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 1s. Last read position: chr22:39,522,524
INFO 2026-06-04 07:10:27 MarkDuplicates Tracking 6555 as yet unmatched pairs. 1098 records in RAM.
INFO 2026-06-04 07:10:28 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 1s. Last read position: chr22:49,961,538
INFO 2026-06-04 07:10:28 MarkDuplicates Tracking 5961 as yet unmatched pairs. 504 records in RAM.
INFO 2026-06-04 07:10:30 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 1s. Last read position: chrX:12,820,791
INFO 2026-06-04 07:10:30 MarkDuplicates Tracking 5241 as yet unmatched pairs. 2909 records in RAM.
INFO 2026-06-04 07:10:31 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 1s. Last read position: chrX:47,582,459
INFO 2026-06-04 07:10:31 MarkDuplicates Tracking 4850 as yet unmatched pairs. 2517 records in RAM.
INFO 2026-06-04 07:10:33 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 1s. Last read position: chrX:54,815,321
INFO 2026-06-04 07:10:33 MarkDuplicates Tracking 4206 as yet unmatched pairs. 1873 records in RAM.
INFO 2026-06-04 07:10:35 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 2s. Last read position: chrX:100,665,307
INFO 2026-06-04 07:10:35 MarkDuplicates Tracking 3600 as yet unmatched pairs. 1266 records in RAM.
INFO 2026-06-04 07:10:36 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 1s. Last read position: chrX:139,740,993
INFO 2026-06-04 07:10:36 MarkDuplicates Tracking 3156 as yet unmatched pairs. 822 records in RAM.
INFO 2026-06-04 07:10:38 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 1s. Last read position: chrX:154,460,338
INFO 2026-06-04 07:10:38 MarkDuplicates Tracking 2566 as yet unmatched pairs. 232 records in RAM.
INFO 2026-06-04 07:10:40 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 1s. Last read position: GL000220.1:159,477
INFO 2026-06-04 07:10:40 MarkDuplicates Tracking 1457 as yet unmatched pairs. 22 records in RAM.
INFO 2026-06-04 07:10:41 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 1s. Last read position: KI270733.1:178,261
INFO 2026-06-04 07:10:41 MarkDuplicates Tracking 9 as yet unmatched pairs. 5 records in RAM.
INFO 2026-06-04 07:10:41 MarkDuplicates Read 217133344 records. 0 pairs never matched.
INFO 2026-06-04 07:10:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 36632480864; totalMemory: 61605937152; maxMemory: 63585648640
INFO 2026-06-04 07:10:51 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-04 07:10:56 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-04 07:11:11 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-04 07:11:24 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-04 07:11:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300842872; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-04 07:11:27 MarkDuplicates Marking 83239642 records as duplicates.
INFO 2026-06-04 07:11:27 MarkDuplicates Found 8709297 optical duplicate clusters.
INFO 2026-06-04 07:11:27 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-04 07:11:44 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:17s. Time for last 10,000,000: 17s. Last read position: chr1:113,683,402
INFO 2026-06-04 07:12:02 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:34s. Time for last 10,000,000: 17s. Last read position: chr1:203,828,328
INFO 2026-06-04 07:12:19 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:52s. Time for last 10,000,000: 17s. Last read position: chr2:128,268,484
INFO 2026-06-04 07:12:36 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:08s. Time for last 10,000,000: 16s. Last read position: chr3:10,125,649
INFO 2026-06-04 07:12:53 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:26s. Time for last 10,000,000: 17s. Last read position: chr4:6,302,268
INFO 2026-06-04 07:13:10 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:43s. Time for last 10,000,000: 17s. Last read position: chr5:150,404,680
INFO 2026-06-04 07:13:27 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:00s. Time for last 10,000,000: 16s. Last read position: chr6:98,917,482
INFO 2026-06-04 07:13:44 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:16s. Time for last 10,000,000: 16s. Last read position: chr7:101,000,311
INFO 2026-06-04 07:14:01 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:33s. Time for last 10,000,000: 16s. Last read position: chr8:143,809,619
INFO 2026-06-04 07:14:17 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:50s. Time for last 10,000,000: 16s. Last read position: chr9:131,629,242
INFO 2026-06-04 07:14:34 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:03:07s. Time for last 10,000,000: 16s. Last read position: chr11:2,884,957
INFO 2026-06-04 07:14:51 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:24s. Time for last 10,000,000: 17s. Last read position: chr11:134,243,158
INFO 2026-06-04 07:15:08 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:41s. Time for last 10,000,000: 16s. Last read position: chr12:131,991,424
INFO 2026-06-04 07:15:25 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:03:58s. Time for last 10,000,000: 16s. Last read position: chr15:28,186,699
INFO 2026-06-04 07:15:42 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:04:14s. Time for last 10,000,000: 16s. Last read position: chr16:18,380,617
INFO 2026-06-04 07:15:59 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:31s. Time for last 10,000,000: 16s. Last read position: chr17:15,545,762
INFO 2026-06-04 07:16:15 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:04:48s. Time for last 10,000,000: 16s. Last read position: chr17:50,195,563
INFO 2026-06-04 07:16:33 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:05:06s. Time for last 10,000,000: 17s. Last read position: chr19:2,271,432
INFO 2026-06-04 07:16:51 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:05:24s. Time for last 10,000,000: 17s. Last read position: chr19:42,249,436
INFO 2026-06-04 07:17:08 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:05:41s. Time for last 10,000,000: 17s. Last read position: chr20:62,319,773
INFO 2026-06-04 07:17:25 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:05:58s. Time for last 10,000,000: 16s. Last read position: chrX:12,820,791
INFO 2026-06-04 07:17:41 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-04 07:17:41 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-04 07:17:41 MarkDuplicates Getting Memory Stats.
INFO 2026-06-04 07:17:41 MarkDuplicates Before output close freeMemory: 201873080; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-04 07:17:41 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-04 07:17:41 MarkDuplicates After output close freeMemory: 104309824; totalMemory: 134217728; maxMemory: 63585648640
[Thu Jun 04 07:17:41 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 12.72 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory