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 BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_1.md.bam --METRICS_FILE BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
08:19:33.639 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Jun 08 08:19:33 GMT 2026] MarkDuplicates --INPUT BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_1.md.bam --METRICS_FILE BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_1.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 08:19:33 GMT 2026] Executing as ?@nf-d729ed13623bf75c7e3cc50d07b5b530-06f4d-f54tc on Linux 6.12.88 amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0
INFO 2026-06-08 08:19:33 MarkDuplicates Start of doWork freeMemory: 105494696; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 08:19:33 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 08:19:33 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 08:19:38 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:2,189,653
INFO 2026-06-08 08:19:38 MarkDuplicates Tracking 2548 as yet unmatched pairs. 42 records in RAM.
INFO 2026-06-08 08:19:41 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: chr1:10,129,407
INFO 2026-06-08 08:19:41 MarkDuplicates Tracking 5253 as yet unmatched pairs. 42 records in RAM.
INFO 2026-06-08 08:19:43 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: chr1:15,933,889
INFO 2026-06-08 08:19:43 MarkDuplicates Tracking 7452 as yet unmatched pairs. 15 records in RAM.
INFO 2026-06-08 08:19:46 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 2s. Last read position: chr1:20,654,696
INFO 2026-06-08 08:19:46 MarkDuplicates Tracking 9862 as yet unmatched pairs. 151 records in RAM.
INFO 2026-06-08 08:19:49 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 3s. Last read position: chr1:22,647,379
INFO 2026-06-08 08:19:49 MarkDuplicates Tracking 12701 as yet unmatched pairs. 616 records in RAM.
INFO 2026-06-08 08:19:51 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr1:26,474,110
INFO 2026-06-08 08:19:51 MarkDuplicates Tracking 14289 as yet unmatched pairs. 83 records in RAM.
INFO 2026-06-08 08:19:53 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: chr1:30,964,674
INFO 2026-06-08 08:19:53 MarkDuplicates Tracking 16610 as yet unmatched pairs. 26 records in RAM.
INFO 2026-06-08 08:19:56 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 2s. Last read position: chr1:35,187,973
INFO 2026-06-08 08:19:56 MarkDuplicates Tracking 19082 as yet unmatched pairs. 20 records in RAM.
INFO 2026-06-08 08:19:59 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 2s. Last read position: chr1:39,379,331
INFO 2026-06-08 08:19:59 MarkDuplicates Tracking 21571 as yet unmatched pairs. 103 records in RAM.
INFO 2026-06-08 08:20:01 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 2s. Last read position: chr1:43,591,378
INFO 2026-06-08 08:20:01 MarkDuplicates Tracking 23783 as yet unmatched pairs. 67 records in RAM.
INFO 2026-06-08 08:20:04 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 2s. Last read position: chr1:47,334,014
INFO 2026-06-08 08:20:04 MarkDuplicates Tracking 26145 as yet unmatched pairs. 65 records in RAM.
INFO 2026-06-08 08:20:06 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 2s. Last read position: chr1:61,769,306
INFO 2026-06-08 08:20:06 MarkDuplicates Tracking 28448 as yet unmatched pairs. 77 records in RAM.
INFO 2026-06-08 08:20:08 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 2s. Last read position: chr1:88,684,615
INFO 2026-06-08 08:20:08 MarkDuplicates Tracking 30507 as yet unmatched pairs. 55 records in RAM.
INFO 2026-06-08 08:20:11 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 2s. Last read position: chr1:102,940,351
INFO 2026-06-08 08:20:11 MarkDuplicates Tracking 32683 as yet unmatched pairs. 151 records in RAM.
INFO 2026-06-08 08:20:14 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 2s. Last read position: chr1:111,131,494
INFO 2026-06-08 08:20:14 MarkDuplicates Tracking 34864 as yet unmatched pairs. 57 records in RAM.
INFO 2026-06-08 08:20:16 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 2s. Last read position: chr1:116,388,706
INFO 2026-06-08 08:20:16 MarkDuplicates Tracking 37150 as yet unmatched pairs. 138 records in RAM.
INFO 2026-06-08 08:20:18 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 1s. Last read position: chr1:119,925,800
INFO 2026-06-08 08:20:18 MarkDuplicates Tracking 39890 as yet unmatched pairs. 478 records in RAM.
INFO 2026-06-08 08:20:20 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 2s. Last read position: chr1:120,557,148
INFO 2026-06-08 08:20:20 MarkDuplicates Tracking 41555 as yet unmatched pairs. 145 records in RAM.
INFO 2026-06-08 08:20:21 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 1s. Last read position: chr1:145,995,225
INFO 2026-06-08 08:20:21 MarkDuplicates Tracking 43043 as yet unmatched pairs. 347 records in RAM.
INFO 2026-06-08 08:20:24 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 2s. Last read position: chr1:147,624,040
INFO 2026-06-08 08:20:24 MarkDuplicates Tracking 43713 as yet unmatched pairs. 107 records in RAM.
INFO 2026-06-08 08:20:25 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 1s. Last read position: chr1:149,005,003
INFO 2026-06-08 08:20:25 MarkDuplicates Tracking 44687 as yet unmatched pairs. 92 records in RAM.
INFO 2026-06-08 08:20:27 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 1s. Last read position: chr1:149,886,465
INFO 2026-06-08 08:20:27 MarkDuplicates Tracking 45834 as yet unmatched pairs. 228 records in RAM.
INFO 2026-06-08 08:20:29 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 1s. Last read position: chr1:150,764,657
INFO 2026-06-08 08:20:29 MarkDuplicates Tracking 47922 as yet unmatched pairs. 75 records in RAM.
INFO 2026-06-08 08:20:31 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 2s. Last read position: chr1:151,529,491
INFO 2026-06-08 08:20:31 MarkDuplicates Tracking 50195 as yet unmatched pairs. 20 records in RAM.
INFO 2026-06-08 08:20:33 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 1s. Last read position: chr1:153,982,731
INFO 2026-06-08 08:20:33 MarkDuplicates Tracking 52813 as yet unmatched pairs. 208 records in RAM.
INFO 2026-06-08 08:20:35 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 2s. Last read position: chr1:154,597,946
INFO 2026-06-08 08:20:35 MarkDuplicates Tracking 54897 as yet unmatched pairs. 236 records in RAM.
INFO 2026-06-08 08:20:38 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 2s. Last read position: chr1:155,187,360
INFO 2026-06-08 08:20:38 MarkDuplicates Tracking 59417 as yet unmatched pairs. 2395 records in RAM.
INFO 2026-06-08 08:20:40 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 2s. Last read position: chr1:155,318,204
INFO 2026-06-08 08:20:40 MarkDuplicates Tracking 58889 as yet unmatched pairs. 63 records in RAM.
INFO 2026-06-08 08:20:43 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 2s. Last read position: chr1:156,051,243
INFO 2026-06-08 08:20:43 MarkDuplicates Tracking 61031 as yet unmatched pairs. 79 records in RAM.
INFO 2026-06-08 08:20:45 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 1s. Last read position: chr1:156,669,730
INFO 2026-06-08 08:20:45 MarkDuplicates Tracking 63412 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 08:20:47 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 2s. Last read position: chr1:160,325,591
INFO 2026-06-08 08:20:47 MarkDuplicates Tracking 65817 as yet unmatched pairs. 178 records in RAM.
INFO 2026-06-08 08:20:49 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 1s. Last read position: chr1:161,542,608
INFO 2026-06-08 08:20:49 MarkDuplicates Tracking 69574 as yet unmatched pairs. 1590 records in RAM.
INFO 2026-06-08 08:20:52 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 2s. Last read position: chr1:165,728,056
INFO 2026-06-08 08:20:52 MarkDuplicates Tracking 70009 as yet unmatched pairs. 83 records in RAM.
INFO 2026-06-08 08:20:54 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 2s. Last read position: chr1:171,532,437
INFO 2026-06-08 08:20:54 MarkDuplicates Tracking 72465 as yet unmatched pairs. 93 records in RAM.
INFO 2026-06-08 08:20:56 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 2s. Last read position: chr1:179,335,603
INFO 2026-06-08 08:20:56 MarkDuplicates Tracking 74605 as yet unmatched pairs. 66 records in RAM.
INFO 2026-06-08 08:20:58 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 1s. Last read position: chr1:183,132,399
INFO 2026-06-08 08:20:58 MarkDuplicates Tracking 76860 as yet unmatched pairs. 50 records in RAM.
INFO 2026-06-08 08:21:00 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 2s. Last read position: chr1:186,360,334
INFO 2026-06-08 08:21:00 MarkDuplicates Tracking 79081 as yet unmatched pairs. 298 records in RAM.
INFO 2026-06-08 08:21:03 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 2s. Last read position: chr1:201,988,903
INFO 2026-06-08 08:21:03 MarkDuplicates Tracking 80972 as yet unmatched pairs. 60 records in RAM.
INFO 2026-06-08 08:21:05 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 1s. Last read position: chr1:204,410,623
INFO 2026-06-08 08:21:05 MarkDuplicates Tracking 83039 as yet unmatched pairs. 48 records in RAM.
INFO 2026-06-08 08:21:08 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 2s. Last read position: chr1:208,210,376
INFO 2026-06-08 08:21:08 MarkDuplicates Tracking 85045 as yet unmatched pairs. 6 records in RAM.
INFO 2026-06-08 08:21:09 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 1s. Last read position: chr1:215,620,201
INFO 2026-06-08 08:21:09 MarkDuplicates Tracking 87657 as yet unmatched pairs. 383 records in RAM.
INFO 2026-06-08 08:21:12 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 2s. Last read position: chr1:223,752,002
INFO 2026-06-08 08:21:12 MarkDuplicates Tracking 89579 as yet unmatched pairs. 144 records in RAM.
INFO 2026-06-08 08:21:14 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 2s. Last read position: chr1:226,381,081
INFO 2026-06-08 08:21:14 MarkDuplicates Tracking 91563 as yet unmatched pairs. 133 records in RAM.
INFO 2026-06-08 08:21:16 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 1s. Last read position: chr1:229,432,085
INFO 2026-06-08 08:21:16 MarkDuplicates Tracking 94278 as yet unmatched pairs. 181 records in RAM.
INFO 2026-06-08 08:21:18 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 1s. Last read position: chr1:235,729,615
INFO 2026-06-08 08:21:18 MarkDuplicates Tracking 96694 as yet unmatched pairs. 44 records in RAM.
INFO 2026-06-08 08:21:20 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 2s. Last read position: chr1:245,156,471
INFO 2026-06-08 08:21:20 MarkDuplicates Tracking 98874 as yet unmatched pairs. 44 records in RAM.
INFO 2026-06-08 08:21:24 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 3s. Last read position: chr2:10,423,021
INFO 2026-06-08 08:21:24 MarkDuplicates Tracking 101059 as yet unmatched pairs. 100875 records in RAM.
INFO 2026-06-08 08:21:26 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 2s. Last read position: chr2:25,628,365
INFO 2026-06-08 08:21:26 MarkDuplicates Tracking 103338 as yet unmatched pairs. 103147 records in RAM.
INFO 2026-06-08 08:21:28 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 1s. Last read position: chr2:32,224,685
INFO 2026-06-08 08:21:28 MarkDuplicates Tracking 105586 as yet unmatched pairs. 105395 records in RAM.
INFO 2026-06-08 08:21:30 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,264
INFO 2026-06-08 08:21:30 MarkDuplicates Tracking 375876 as yet unmatched pairs. 99542 records in RAM.
INFO 2026-06-08 08:21:33 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,406
INFO 2026-06-08 08:21:33 MarkDuplicates Tracking 867163 as yet unmatched pairs. 88393 records in RAM.
INFO 2026-06-08 08:21:35 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,443
INFO 2026-06-08 08:21:35 MarkDuplicates Tracking 916105 as yet unmatched pairs. 87357 records in RAM.
INFO 2026-06-08 08:21:37 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 2s. Last read position: chr2:43,901,382
INFO 2026-06-08 08:21:37 MarkDuplicates Tracking 916680 as yet unmatched pairs. 84925 records in RAM.
INFO 2026-06-08 08:21:39 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 2s. Last read position: chr2:55,317,213
INFO 2026-06-08 08:21:39 MarkDuplicates Tracking 914369 as yet unmatched pairs. 82611 records in RAM.
INFO 2026-06-08 08:21:41 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 2s. Last read position: chr2:69,013,593
INFO 2026-06-08 08:21:41 MarkDuplicates Tracking 912286 as yet unmatched pairs. 80525 records in RAM.
INFO 2026-06-08 08:21:43 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 2s. Last read position: chr2:74,462,954
INFO 2026-06-08 08:21:43 MarkDuplicates Tracking 909986 as yet unmatched pairs. 78222 records in RAM.
INFO 2026-06-08 08:21:45 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 1s. Last read position: chr2:87,788,728
INFO 2026-06-08 08:21:45 MarkDuplicates Tracking 907733 as yet unmatched pairs. 75965 records in RAM.
INFO 2026-06-08 08:21:47 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 1s. Last read position: chr2:97,507,036
INFO 2026-06-08 08:21:47 MarkDuplicates Tracking 905818 as yet unmatched pairs. 74049 records in RAM.
INFO 2026-06-08 08:21:49 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 1s. Last read position: chr2:106,098,764
INFO 2026-06-08 08:21:49 MarkDuplicates Tracking 903568 as yet unmatched pairs. 71790 records in RAM.
INFO 2026-06-08 08:21:52 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 2s. Last read position: chr2:110,533,490
INFO 2026-06-08 08:21:52 MarkDuplicates Tracking 902102 as yet unmatched pairs. 70320 records in RAM.
INFO 2026-06-08 08:21:54 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 2s. Last read position: chr2:119,367,026
INFO 2026-06-08 08:21:54 MarkDuplicates Tracking 900717 as yet unmatched pairs. 68931 records in RAM.
INFO 2026-06-08 08:21:56 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 1s. Last read position: chr2:131,501,207
INFO 2026-06-08 08:21:56 MarkDuplicates Tracking 898586 as yet unmatched pairs. 66796 records in RAM.
INFO 2026-06-08 08:21:58 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr2:151,494,201
INFO 2026-06-08 08:21:58 MarkDuplicates Tracking 896607 as yet unmatched pairs. 64812 records in RAM.
INFO 2026-06-08 08:22:00 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 1s. Last read position: chr2:151,666,096
INFO 2026-06-08 08:22:00 MarkDuplicates Tracking 894683 as yet unmatched pairs. 62886 records in RAM.
INFO 2026-06-08 08:22:01 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 1s. Last read position: chr2:167,242,680
INFO 2026-06-08 08:22:01 MarkDuplicates Tracking 892466 as yet unmatched pairs. 60657 records in RAM.
INFO 2026-06-08 08:22:03 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 1s. Last read position: chr2:175,937,369
INFO 2026-06-08 08:22:03 MarkDuplicates Tracking 890330 as yet unmatched pairs. 58520 records in RAM.
INFO 2026-06-08 08:22:05 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 1s. Last read position: chr2:178,544,217
INFO 2026-06-08 08:22:05 MarkDuplicates Tracking 888329 as yet unmatched pairs. 56518 records in RAM.
INFO 2026-06-08 08:22:07 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 1s. Last read position: chr2:178,567,610
INFO 2026-06-08 08:22:07 MarkDuplicates Tracking 886545 as yet unmatched pairs. 54725 records in RAM.
INFO 2026-06-08 08:22:10 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 2s. Last read position: chr2:178,590,010
INFO 2026-06-08 08:22:10 MarkDuplicates Tracking 884186 as yet unmatched pairs. 52366 records in RAM.
INFO 2026-06-08 08:22:12 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 2s. Last read position: chr2:178,618,265
INFO 2026-06-08 08:22:12 MarkDuplicates Tracking 882070 as yet unmatched pairs. 50247 records in RAM.
INFO 2026-06-08 08:22:14 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 2s. Last read position: chr2:178,681,436
INFO 2026-06-08 08:22:14 MarkDuplicates Tracking 880284 as yet unmatched pairs. 48461 records in RAM.
INFO 2026-06-08 08:22:17 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 2s. Last read position: chr2:178,732,440
INFO 2026-06-08 08:22:17 MarkDuplicates Tracking 877903 as yet unmatched pairs. 46079 records in RAM.
INFO 2026-06-08 08:22:19 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 2s. Last read position: chr2:181,896,024
INFO 2026-06-08 08:22:19 MarkDuplicates Tracking 875623 as yet unmatched pairs. 43799 records in RAM.
INFO 2026-06-08 08:22:21 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 2s. Last read position: chr2:188,994,312
INFO 2026-06-08 08:22:21 MarkDuplicates Tracking 873554 as yet unmatched pairs. 41730 records in RAM.
INFO 2026-06-08 08:22:23 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 1s. Last read position: chr2:189,009,161
INFO 2026-06-08 08:22:23 MarkDuplicates Tracking 871136 as yet unmatched pairs. 39308 records in RAM.
INFO 2026-06-08 08:22:25 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 1s. Last read position: chr2:191,008,964
INFO 2026-06-08 08:22:25 MarkDuplicates Tracking 868259 as yet unmatched pairs. 36425 records in RAM.
INFO 2026-06-08 08:22:26 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 1s. Last read position: chr2:203,391,046
INFO 2026-06-08 08:22:26 MarkDuplicates Tracking 865868 as yet unmatched pairs. 34031 records in RAM.
INFO 2026-06-08 08:22:28 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 1s. Last read position: chr2:215,361,591
INFO 2026-06-08 08:22:28 MarkDuplicates Tracking 868561 as yet unmatched pairs. 36714 records in RAM.
INFO 2026-06-08 08:22:30 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 1s. Last read position: chr2:215,371,942
INFO 2026-06-08 08:22:30 MarkDuplicates Tracking 864027 as yet unmatched pairs. 32179 records in RAM.
INFO 2026-06-08 08:22:32 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 1s. Last read position: chr2:215,375,249
INFO 2026-06-08 08:22:32 MarkDuplicates Tracking 862444 as yet unmatched pairs. 30580 records in RAM.
INFO 2026-06-08 08:22:34 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 1s. Last read position: chr2:215,379,191
INFO 2026-06-08 08:22:34 MarkDuplicates Tracking 862021 as yet unmatched pairs. 30157 records in RAM.
INFO 2026-06-08 08:22:36 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 2s. Last read position: chr2:215,384,963
INFO 2026-06-08 08:22:36 MarkDuplicates Tracking 857260 as yet unmatched pairs. 25394 records in RAM.
INFO 2026-06-08 08:22:39 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 2s. Last read position: chr2:215,394,699
INFO 2026-06-08 08:22:39 MarkDuplicates Tracking 858557 as yet unmatched pairs. 26690 records in RAM.
INFO 2026-06-08 08:22:41 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 2s. Last read position: chr2:215,406,416
INFO 2026-06-08 08:22:41 MarkDuplicates Tracking 852940 as yet unmatched pairs. 21073 records in RAM.
INFO 2026-06-08 08:22:43 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 2s. Last read position: chr2:215,409,991
INFO 2026-06-08 08:22:43 MarkDuplicates Tracking 851673 as yet unmatched pairs. 19806 records in RAM.
INFO 2026-06-08 08:22:45 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 2s. Last read position: chr2:215,423,483
INFO 2026-06-08 08:22:45 MarkDuplicates Tracking 850465 as yet unmatched pairs. 18595 records in RAM.
INFO 2026-06-08 08:22:47 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 1s. Last read position: chr2:215,433,376
INFO 2026-06-08 08:22:47 MarkDuplicates Tracking 847162 as yet unmatched pairs. 15292 records in RAM.
INFO 2026-06-08 08:22:49 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 1s. Last read position: chr2:218,650,325
INFO 2026-06-08 08:22:49 MarkDuplicates Tracking 841935 as yet unmatched pairs. 10064 records in RAM.
INFO 2026-06-08 08:22:51 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 1s. Last read position: chr2:227,534,907
INFO 2026-06-08 08:22:51 MarkDuplicates Tracking 839508 as yet unmatched pairs. 7618 records in RAM.
INFO 2026-06-08 08:22:53 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 2s. Last read position: chr2:233,551,412
INFO 2026-06-08 08:22:53 MarkDuplicates Tracking 837439 as yet unmatched pairs. 5546 records in RAM.
INFO 2026-06-08 08:22:55 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 2s. Last read position: chr2:237,396,727
INFO 2026-06-08 08:22:55 MarkDuplicates Tracking 835141 as yet unmatched pairs. 3247 records in RAM.
INFO 2026-06-08 08:22:57 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 1s. Last read position: chr2:241,262,824
INFO 2026-06-08 08:22:57 MarkDuplicates Tracking 832691 as yet unmatched pairs. 797 records in RAM.
INFO 2026-06-08 08:22:59 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 2s. Last read position: chr3:10,142,932
INFO 2026-06-08 08:22:59 MarkDuplicates Tracking 830219 as yet unmatched pairs. 47600 records in RAM.
INFO 2026-06-08 08:23:01 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 1s. Last read position: chr3:16,260,809
INFO 2026-06-08 08:23:01 MarkDuplicates Tracking 827823 as yet unmatched pairs. 45202 records in RAM.
INFO 2026-06-08 08:23:03 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 1s. Last read position: chr3:37,275,654
INFO 2026-06-08 08:23:03 MarkDuplicates Tracking 825571 as yet unmatched pairs. 42947 records in RAM.
INFO 2026-06-08 08:23:05 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 2s. Last read position: chr3:42,639,129
INFO 2026-06-08 08:23:05 MarkDuplicates Tracking 823467 as yet unmatched pairs. 40843 records in RAM.
INFO 2026-06-08 08:23:07 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 1s. Last read position: chr3:47,745,983
INFO 2026-06-08 08:23:07 MarkDuplicates Tracking 821043 as yet unmatched pairs. 38417 records in RAM.
INFO 2026-06-08 08:23:09 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 2s. Last read position: chr3:49,028,479
INFO 2026-06-08 08:23:09 MarkDuplicates Tracking 818823 as yet unmatched pairs. 36197 records in RAM.
INFO 2026-06-08 08:23:11 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 1s. Last read position: chr3:49,810,033
INFO 2026-06-08 08:23:11 MarkDuplicates Tracking 816396 as yet unmatched pairs. 33768 records in RAM.
INFO 2026-06-08 08:23:12 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 1s. Last read position: chr3:52,471,835
INFO 2026-06-08 08:23:12 MarkDuplicates Tracking 814077 as yet unmatched pairs. 31447 records in RAM.
INFO 2026-06-08 08:23:15 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 2s. Last read position: chr3:57,575,589
INFO 2026-06-08 08:23:15 MarkDuplicates Tracking 811874 as yet unmatched pairs. 29241 records in RAM.
INFO 2026-06-08 08:23:18 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 3s. Last read position: chr3:69,104,490
INFO 2026-06-08 08:23:18 MarkDuplicates Tracking 809234 as yet unmatched pairs. 26598 records in RAM.
INFO 2026-06-08 08:23:20 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 1s. Last read position: chr3:101,576,476
INFO 2026-06-08 08:23:20 MarkDuplicates Tracking 807221 as yet unmatched pairs. 24583 records in RAM.
INFO 2026-06-08 08:23:22 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 2s. Last read position: chr3:113,781,055
INFO 2026-06-08 08:23:22 MarkDuplicates Tracking 805150 as yet unmatched pairs. 22510 records in RAM.
INFO 2026-06-08 08:23:24 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 2s. Last read position: chr3:122,701,524
INFO 2026-06-08 08:23:24 MarkDuplicates Tracking 802955 as yet unmatched pairs. 20305 records in RAM.
INFO 2026-06-08 08:23:26 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 1s. Last read position: chr3:128,797,942
INFO 2026-06-08 08:23:26 MarkDuplicates Tracking 800713 as yet unmatched pairs. 18055 records in RAM.
INFO 2026-06-08 08:23:28 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 1s. Last read position: chr3:132,467,194
INFO 2026-06-08 08:23:28 MarkDuplicates Tracking 798143 as yet unmatched pairs. 15468 records in RAM.
INFO 2026-06-08 08:23:30 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 1s. Last read position: chr3:142,332,990
INFO 2026-06-08 08:23:30 MarkDuplicates Tracking 795910 as yet unmatched pairs. 13229 records in RAM.
INFO 2026-06-08 08:23:32 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 2s. Last read position: chr3:156,704,985
INFO 2026-06-08 08:23:32 MarkDuplicates Tracking 793706 as yet unmatched pairs. 11016 records in RAM.
INFO 2026-06-08 08:23:34 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 2s. Last read position: chr3:172,764,457
INFO 2026-06-08 08:23:34 MarkDuplicates Tracking 791511 as yet unmatched pairs. 8819 records in RAM.
INFO 2026-06-08 08:23:36 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 1s. Last read position: chr3:184,181,735
INFO 2026-06-08 08:23:36 MarkDuplicates Tracking 789310 as yet unmatched pairs. 6617 records in RAM.
INFO 2026-06-08 08:23:38 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 1s. Last read position: chr3:185,473,077
INFO 2026-06-08 08:23:38 MarkDuplicates Tracking 786710 as yet unmatched pairs. 4014 records in RAM.
INFO 2026-06-08 08:23:40 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 1s. Last read position: chr3:195,726,505
INFO 2026-06-08 08:23:40 MarkDuplicates Tracking 784529 as yet unmatched pairs. 1828 records in RAM.
INFO 2026-06-08 08:23:42 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 2s. Last read position: chr4:932,499
INFO 2026-06-08 08:23:42 MarkDuplicates Tracking 782300 as yet unmatched pairs. 24538 records in RAM.
INFO 2026-06-08 08:23:44 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 1s. Last read position: chr4:2,930,927
INFO 2026-06-08 08:23:44 MarkDuplicates Tracking 779925 as yet unmatched pairs. 22161 records in RAM.
INFO 2026-06-08 08:23:46 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 1s. Last read position: chr4:10,100,295
INFO 2026-06-08 08:23:46 MarkDuplicates Tracking 777098 as yet unmatched pairs. 19317 records in RAM.
INFO 2026-06-08 08:23:48 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 2s. Last read position: chr4:39,552,086
INFO 2026-06-08 08:23:48 MarkDuplicates Tracking 775150 as yet unmatched pairs. 17366 records in RAM.
INFO 2026-06-08 08:23:50 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 1s. Last read position: chr4:57,033,248
INFO 2026-06-08 08:23:50 MarkDuplicates Tracking 772931 as yet unmatched pairs. 15137 records in RAM.
INFO 2026-06-08 08:23:51 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 1s. Last read position: chr4:77,161,668
INFO 2026-06-08 08:23:51 MarkDuplicates Tracking 770709 as yet unmatched pairs. 12913 records in RAM.
INFO 2026-06-08 08:23:53 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 1s. Last read position: chr4:88,008,064
INFO 2026-06-08 08:23:53 MarkDuplicates Tracking 768335 as yet unmatched pairs. 10537 records in RAM.
INFO 2026-06-08 08:23:55 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 1s. Last read position: chr4:118,513,764
INFO 2026-06-08 08:23:55 MarkDuplicates Tracking 766216 as yet unmatched pairs. 8417 records in RAM.
INFO 2026-06-08 08:23:57 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 1s. Last read position: chr4:140,622,621
INFO 2026-06-08 08:23:57 MarkDuplicates Tracking 764593 as yet unmatched pairs. 6789 records in RAM.
INFO 2026-06-08 08:23:59 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 1s. Last read position: chr4:151,102,968
INFO 2026-06-08 08:23:59 MarkDuplicates Tracking 762166 as yet unmatched pairs. 4360 records in RAM.
INFO 2026-06-08 08:24:00 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 1s. Last read position: chr4:163,528,958
INFO 2026-06-08 08:24:00 MarkDuplicates Tracking 759841 as yet unmatched pairs. 2033 records in RAM.
INFO 2026-06-08 08:24:03 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 2s. Last read position: chr5:254,440
INFO 2026-06-08 08:24:03 MarkDuplicates Tracking 757748 as yet unmatched pairs. 51908 records in RAM.
INFO 2026-06-08 08:24:05 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 1s. Last read position: chr5:14,293,020
INFO 2026-06-08 08:24:05 MarkDuplicates Tracking 755638 as yet unmatched pairs. 49793 records in RAM.
INFO 2026-06-08 08:24:07 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 2s. Last read position: chr5:31,526,600
INFO 2026-06-08 08:24:07 MarkDuplicates Tracking 752962 as yet unmatched pairs. 47117 records in RAM.
INFO 2026-06-08 08:24:10 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 2s. Last read position: chr5:39,206,059
INFO 2026-06-08 08:24:10 MarkDuplicates Tracking 750876 as yet unmatched pairs. 45025 records in RAM.
INFO 2026-06-08 08:24:12 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 2s. Last read position: chr5:56,881,599
INFO 2026-06-08 08:24:12 MarkDuplicates Tracking 748915 as yet unmatched pairs. 43063 records in RAM.
INFO 2026-06-08 08:24:14 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 2s. Last read position: chr5:69,420,484
INFO 2026-06-08 08:24:14 MarkDuplicates Tracking 746788 as yet unmatched pairs. 40927 records in RAM.
INFO 2026-06-08 08:24:16 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 1s. Last read position: chr5:71,035,683
INFO 2026-06-08 08:24:16 MarkDuplicates Tracking 747205 as yet unmatched pairs. 41331 records in RAM.
INFO 2026-06-08 08:24:18 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 1s. Last read position: chr5:76,716,318
INFO 2026-06-08 08:24:18 MarkDuplicates Tracking 744133 as yet unmatched pairs. 38257 records in RAM.
INFO 2026-06-08 08:24:19 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 1s. Last read position: chr5:83,541,503
INFO 2026-06-08 08:24:19 MarkDuplicates Tracking 742078 as yet unmatched pairs. 36201 records in RAM.
INFO 2026-06-08 08:24:21 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 1s. Last read position: chr5:98,903,878
INFO 2026-06-08 08:24:21 MarkDuplicates Tracking 740157 as yet unmatched pairs. 34272 records in RAM.
INFO 2026-06-08 08:24:23 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 1s. Last read position: chr5:123,418,497
INFO 2026-06-08 08:24:23 MarkDuplicates Tracking 737933 as yet unmatched pairs. 32039 records in RAM.
INFO 2026-06-08 08:24:25 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 1s. Last read position: chr5:134,200,406
INFO 2026-06-08 08:24:25 MarkDuplicates Tracking 735941 as yet unmatched pairs. 30045 records in RAM.
INFO 2026-06-08 08:24:27 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 1s. Last read position: chr5:135,571,191
INFO 2026-06-08 08:24:27 MarkDuplicates Tracking 739010 as yet unmatched pairs. 33113 records in RAM.
INFO 2026-06-08 08:24:29 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 1s. Last read position: chr5:135,880,050
INFO 2026-06-08 08:24:29 MarkDuplicates Tracking 731082 as yet unmatched pairs. 25180 records in RAM.
INFO 2026-06-08 08:24:31 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 1s. Last read position: chr5:139,623,412
INFO 2026-06-08 08:24:31 MarkDuplicates Tracking 728842 as yet unmatched pairs. 22940 records in RAM.
INFO 2026-06-08 08:24:32 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 1s. Last read position: chr5:141,524,143
INFO 2026-06-08 08:24:32 MarkDuplicates Tracking 726340 as yet unmatched pairs. 20377 records in RAM.
INFO 2026-06-08 08:24:34 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 1s. Last read position: chr5:149,978,278
INFO 2026-06-08 08:24:34 MarkDuplicates Tracking 724217 as yet unmatched pairs. 18252 records in RAM.
INFO 2026-06-08 08:24:36 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 1s. Last read position: chr5:150,402,225
INFO 2026-06-08 08:24:36 MarkDuplicates Tracking 733009 as yet unmatched pairs. 27044 records in RAM.
INFO 2026-06-08 08:24:38 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 1s. Last read position: chr5:150,405,152
INFO 2026-06-08 08:24:38 MarkDuplicates Tracking 724137 as yet unmatched pairs. 18171 records in RAM.
INFO 2026-06-08 08:24:39 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 1s. Last read position: chr5:151,108,479
INFO 2026-06-08 08:24:39 MarkDuplicates Tracking 716926 as yet unmatched pairs. 10959 records in RAM.
INFO 2026-06-08 08:24:42 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 2s. Last read position: chr5:159,203,622
INFO 2026-06-08 08:24:42 MarkDuplicates Tracking 714519 as yet unmatched pairs. 8551 records in RAM.
INFO 2026-06-08 08:24:44 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 1s. Last read position: chr5:172,924,011
INFO 2026-06-08 08:24:44 MarkDuplicates Tracking 712897 as yet unmatched pairs. 6929 records in RAM.
INFO 2026-06-08 08:24:46 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 2s. Last read position: chr5:177,515,811
INFO 2026-06-08 08:24:46 MarkDuplicates Tracking 710348 as yet unmatched pairs. 4380 records in RAM.
INFO 2026-06-08 08:24:48 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 2s. Last read position: chr5:179,822,999
INFO 2026-06-08 08:24:48 MarkDuplicates Tracking 708616 as yet unmatched pairs. 2646 records in RAM.
INFO 2026-06-08 08:24:51 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 2s. Last read position: chr6:2,115,847
INFO 2026-06-08 08:24:51 MarkDuplicates Tracking 705936 as yet unmatched pairs. 44488 records in RAM.
INFO 2026-06-08 08:24:53 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 1s. Last read position: chr6:10,751,190
INFO 2026-06-08 08:24:53 MarkDuplicates Tracking 703918 as yet unmatched pairs. 42463 records in RAM.
INFO 2026-06-08 08:24:55 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 1s. Last read position: chr6:25,966,741
INFO 2026-06-08 08:24:55 MarkDuplicates Tracking 701363 as yet unmatched pairs. 39898 records in RAM.
INFO 2026-06-08 08:24:56 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 1s. Last read position: chr6:29,942,558
INFO 2026-06-08 08:24:56 MarkDuplicates Tracking 700021 as yet unmatched pairs. 38555 records in RAM.
INFO 2026-06-08 08:24:58 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 1s. Last read position: chr6:31,179,643
INFO 2026-06-08 08:24:58 MarkDuplicates Tracking 697078 as yet unmatched pairs. 35611 records in RAM.
INFO 2026-06-08 08:25:00 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 2s. Last read position: chr6:31,664,063
INFO 2026-06-08 08:25:00 MarkDuplicates Tracking 694934 as yet unmatched pairs. 33467 records in RAM.
INFO 2026-06-08 08:25:01 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 1s. Last read position: chr6:31,828,309
INFO 2026-06-08 08:25:01 MarkDuplicates Tracking 693979 as yet unmatched pairs. 32511 records in RAM.
INFO 2026-06-08 08:25:03 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 1s. Last read position: chr6:31,993,933
INFO 2026-06-08 08:25:03 MarkDuplicates Tracking 691842 as yet unmatched pairs. 30374 records in RAM.
INFO 2026-06-08 08:25:05 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 1s. Last read position: chr6:32,179,896
INFO 2026-06-08 08:25:05 MarkDuplicates Tracking 689904 as yet unmatched pairs. 28435 records in RAM.
INFO 2026-06-08 08:25:07 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 1s. Last read position: chr6:33,080,765
INFO 2026-06-08 08:25:07 MarkDuplicates Tracking 687830 as yet unmatched pairs. 26359 records in RAM.
INFO 2026-06-08 08:25:09 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 1s. Last read position: chr6:34,137,583
INFO 2026-06-08 08:25:09 MarkDuplicates Tracking 685306 as yet unmatched pairs. 23829 records in RAM.
INFO 2026-06-08 08:25:11 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 1s. Last read position: chr6:41,587,740
INFO 2026-06-08 08:25:11 MarkDuplicates Tracking 683019 as yet unmatched pairs. 21541 records in RAM.
INFO 2026-06-08 08:25:12 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 1s. Last read position: chr6:44,232,414
INFO 2026-06-08 08:25:12 MarkDuplicates Tracking 680711 as yet unmatched pairs. 19233 records in RAM.
INFO 2026-06-08 08:25:14 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 1s. Last read position: chr6:56,616,161
INFO 2026-06-08 08:25:14 MarkDuplicates Tracking 678406 as yet unmatched pairs. 16915 records in RAM.
INFO 2026-06-08 08:25:16 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 1s. Last read position: chr6:75,183,384
INFO 2026-06-08 08:25:16 MarkDuplicates Tracking 676405 as yet unmatched pairs. 14912 records in RAM.
INFO 2026-06-08 08:25:18 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 2s. Last read position: chr6:89,865,975
INFO 2026-06-08 08:25:18 MarkDuplicates Tracking 673871 as yet unmatched pairs. 12373 records in RAM.
INFO 2026-06-08 08:25:20 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 1s. Last read position: chr6:116,436,006
INFO 2026-06-08 08:25:20 MarkDuplicates Tracking 671576 as yet unmatched pairs. 10075 records in RAM.
INFO 2026-06-08 08:25:22 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 1s. Last read position: chr6:137,266,905
INFO 2026-06-08 08:25:22 MarkDuplicates Tracking 669429 as yet unmatched pairs. 7927 records in RAM.
INFO 2026-06-08 08:25:24 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 2s. Last read position: chr6:151,808,035
INFO 2026-06-08 08:25:24 MarkDuplicates Tracking 668052 as yet unmatched pairs. 6548 records in RAM.
INFO 2026-06-08 08:25:26 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 2s. Last read position: chr6:157,936,009
INFO 2026-06-08 08:25:26 MarkDuplicates Tracking 664698 as yet unmatched pairs. 3190 records in RAM.
INFO 2026-06-08 08:25:28 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 2s. Last read position: chr6:166,999,470
INFO 2026-06-08 08:25:28 MarkDuplicates Tracking 662447 as yet unmatched pairs. 938 records in RAM.
INFO 2026-06-08 08:25:31 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 2s. Last read position: chr7:2,647,236
INFO 2026-06-08 08:25:31 MarkDuplicates Tracking 660038 as yet unmatched pairs. 43396 records in RAM.
INFO 2026-06-08 08:25:33 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 1s. Last read position: chr7:5,528,157
INFO 2026-06-08 08:25:33 MarkDuplicates Tracking 658245 as yet unmatched pairs. 41603 records in RAM.
INFO 2026-06-08 08:25:35 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 1s. Last read position: chr7:7,594,978
INFO 2026-06-08 08:25:35 MarkDuplicates Tracking 654971 as yet unmatched pairs. 38324 records in RAM.
INFO 2026-06-08 08:25:37 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 1s. Last read position: chr7:27,769,824
INFO 2026-06-08 08:25:37 MarkDuplicates Tracking 652861 as yet unmatched pairs. 36212 records in RAM.
INFO 2026-06-08 08:25:39 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 2s. Last read position: chr7:44,007,364
INFO 2026-06-08 08:25:39 MarkDuplicates Tracking 650500 as yet unmatched pairs. 33851 records in RAM.
INFO 2026-06-08 08:25:42 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 2s. Last read position: chr7:48,094,814
INFO 2026-06-08 08:25:42 MarkDuplicates Tracking 648177 as yet unmatched pairs. 31527 records in RAM.
INFO 2026-06-08 08:25:44 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 1s. Last read position: chr7:72,971,527
INFO 2026-06-08 08:25:44 MarkDuplicates Tracking 646365 as yet unmatched pairs. 29715 records in RAM.
INFO 2026-06-08 08:25:45 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 1s. Last read position: chr7:75,197,980
INFO 2026-06-08 08:25:45 MarkDuplicates Tracking 645003 as yet unmatched pairs. 28353 records in RAM.
INFO 2026-06-08 08:25:47 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 1s. Last read position: chr7:76,304,130
INFO 2026-06-08 08:25:47 MarkDuplicates Tracking 643064 as yet unmatched pairs. 26414 records in RAM.
INFO 2026-06-08 08:25:49 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 2s. Last read position: chr7:92,002,108
INFO 2026-06-08 08:25:49 MarkDuplicates Tracking 641107 as yet unmatched pairs. 24456 records in RAM.
INFO 2026-06-08 08:25:51 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:06:16s. Time for last 1,000,000: 2s. Last read position: chr7:94,401,599
INFO 2026-06-08 08:25:51 MarkDuplicates Tracking 641390 as yet unmatched pairs. 24737 records in RAM.
INFO 2026-06-08 08:25:54 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 2s. Last read position: chr7:94,422,980
INFO 2026-06-08 08:25:54 MarkDuplicates Tracking 637010 as yet unmatched pairs. 20357 records in RAM.
INFO 2026-06-08 08:25:56 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 1s. Last read position: chr7:99,012,182
INFO 2026-06-08 08:25:56 MarkDuplicates Tracking 634194 as yet unmatched pairs. 17536 records in RAM.
INFO 2026-06-08 08:25:58 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 1s. Last read position: chr7:100,478,087
INFO 2026-06-08 08:25:58 MarkDuplicates Tracking 631991 as yet unmatched pairs. 15332 records in RAM.
INFO 2026-06-08 08:26:00 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 1s. Last read position: chr7:102,510,228
INFO 2026-06-08 08:26:00 MarkDuplicates Tracking 630104 as yet unmatched pairs. 13442 records in RAM.
INFO 2026-06-08 08:26:01 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 1s. Last read position: chr7:105,133,022
INFO 2026-06-08 08:26:01 MarkDuplicates Tracking 628885 as yet unmatched pairs. 12222 records in RAM.
INFO 2026-06-08 08:26:03 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 1s. Last read position: chr7:127,589,082
INFO 2026-06-08 08:26:03 MarkDuplicates Tracking 626791 as yet unmatched pairs. 10119 records in RAM.
INFO 2026-06-08 08:26:06 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:06:30s. Time for last 1,000,000: 2s. Last read position: chr7:133,275,038
INFO 2026-06-08 08:26:06 MarkDuplicates Tracking 624343 as yet unmatched pairs. 7670 records in RAM.
INFO 2026-06-08 08:26:08 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 2s. Last read position: chr7:140,702,970
INFO 2026-06-08 08:26:08 MarkDuplicates Tracking 622636 as yet unmatched pairs. 5954 records in RAM.
INFO 2026-06-08 08:26:09 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 1s. Last read position: chr7:144,372,380
INFO 2026-06-08 08:26:09 MarkDuplicates Tracking 620436 as yet unmatched pairs. 3752 records in RAM.
INFO 2026-06-08 08:26:11 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 1s. Last read position: chr7:152,176,295
INFO 2026-06-08 08:26:11 MarkDuplicates Tracking 618021 as yet unmatched pairs. 1333 records in RAM.
INFO 2026-06-08 08:26:13 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 2s. Last read position: chr8:11,847,802
INFO 2026-06-08 08:26:13 MarkDuplicates Tracking 616292 as yet unmatched pairs. 34527 records in RAM.
INFO 2026-06-08 08:26:15 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 1s. Last read position: chr8:22,614,179
INFO 2026-06-08 08:26:15 MarkDuplicates Tracking 613623 as yet unmatched pairs. 31857 records in RAM.
INFO 2026-06-08 08:26:17 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 1s. Last read position: chr8:37,872,879
INFO 2026-06-08 08:26:17 MarkDuplicates Tracking 611068 as yet unmatched pairs. 29301 records in RAM.
INFO 2026-06-08 08:26:19 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 1s. Last read position: chr8:41,941,301
INFO 2026-06-08 08:26:19 MarkDuplicates Tracking 609018 as yet unmatched pairs. 27249 records in RAM.
INFO 2026-06-08 08:26:21 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 1s. Last read position: chr8:52,656,963
INFO 2026-06-08 08:26:21 MarkDuplicates Tracking 606509 as yet unmatched pairs. 24728 records in RAM.
INFO 2026-06-08 08:26:23 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:06:47s. Time for last 1,000,000: 1s. Last read position: chr8:69,627,777
INFO 2026-06-08 08:26:23 MarkDuplicates Tracking 604571 as yet unmatched pairs. 22787 records in RAM.
INFO 2026-06-08 08:26:25 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 1s. Last read position: chr8:85,438,903
INFO 2026-06-08 08:26:25 MarkDuplicates Tracking 602631 as yet unmatched pairs. 20841 records in RAM.
INFO 2026-06-08 08:26:27 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 2s. Last read position: chr8:99,501,795
INFO 2026-06-08 08:26:27 MarkDuplicates Tracking 600314 as yet unmatched pairs. 18523 records in RAM.
INFO 2026-06-08 08:26:29 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 2s. Last read position: chr8:102,838,844
INFO 2026-06-08 08:26:29 MarkDuplicates Tracking 598226 as yet unmatched pairs. 16435 records in RAM.
INFO 2026-06-08 08:26:31 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 2s. Last read position: chr8:115,619,353
INFO 2026-06-08 08:26:31 MarkDuplicates Tracking 595889 as yet unmatched pairs. 14098 records in RAM.
INFO 2026-06-08 08:26:33 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 1s. Last read position: chr8:127,736,151
INFO 2026-06-08 08:26:33 MarkDuplicates Tracking 593604 as yet unmatched pairs. 11813 records in RAM.
INFO 2026-06-08 08:26:35 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:07:00s. Time for last 1,000,000: 1s. Last read position: chr8:143,560,609
INFO 2026-06-08 08:26:35 MarkDuplicates Tracking 591257 as yet unmatched pairs. 9464 records in RAM.
INFO 2026-06-08 08:26:37 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 1s. Last read position: chr8:143,859,756
INFO 2026-06-08 08:26:37 MarkDuplicates Tracking 589267 as yet unmatched pairs. 7474 records in RAM.
INFO 2026-06-08 08:26:38 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:07:03s. Time for last 1,000,000: 1s. Last read position: chr8:143,863,818
INFO 2026-06-08 08:26:38 MarkDuplicates Tracking 588434 as yet unmatched pairs. 6641 records in RAM.
INFO 2026-06-08 08:26:40 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:07:04s. Time for last 1,000,000: 1s. Last read position: chr8:143,919,393
INFO 2026-06-08 08:26:40 MarkDuplicates Tracking 587464 as yet unmatched pairs. 5671 records in RAM.
INFO 2026-06-08 08:26:41 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 1s. Last read position: chr8:144,241,005
INFO 2026-06-08 08:26:41 MarkDuplicates Tracking 584034 as yet unmatched pairs. 2241 records in RAM.
INFO 2026-06-08 08:26:44 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 2s. Last read position: chr9:2,073,272
INFO 2026-06-08 08:26:44 MarkDuplicates Tracking 581423 as yet unmatched pairs. 30778 records in RAM.
INFO 2026-06-08 08:26:46 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:07:11s. Time for last 1,000,000: 2s. Last read position: chr9:25,678,240
INFO 2026-06-08 08:26:46 MarkDuplicates Tracking 579222 as yet unmatched pairs. 28571 records in RAM.
INFO 2026-06-08 08:26:48 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 1s. Last read position: chr9:35,609,251
INFO 2026-06-08 08:26:48 MarkDuplicates Tracking 576981 as yet unmatched pairs. 26328 records in RAM.
INFO 2026-06-08 08:26:50 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:07:15s. Time for last 1,000,000: 2s. Last read position: chr9:68,483,877
INFO 2026-06-08 08:26:50 MarkDuplicates Tracking 575074 as yet unmatched pairs. 24405 records in RAM.
INFO 2026-06-08 08:26:52 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:07:17s. Time for last 1,000,000: 1s. Last read position: chr9:89,002,138
INFO 2026-06-08 08:26:52 MarkDuplicates Tracking 573054 as yet unmatched pairs. 22384 records in RAM.
INFO 2026-06-08 08:26:54 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:07:18s. Time for last 1,000,000: 1s. Last read position: chr9:97,482,990
INFO 2026-06-08 08:26:54 MarkDuplicates Tracking 570793 as yet unmatched pairs. 20112 records in RAM.
INFO 2026-06-08 08:26:56 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:07:20s. Time for last 1,000,000: 1s. Last read position: chr9:111,661,677
INFO 2026-06-08 08:26:56 MarkDuplicates Tracking 568684 as yet unmatched pairs. 18002 records in RAM.
INFO 2026-06-08 08:26:58 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:07:22s. Time for last 1,000,000: 1s. Last read position: chr9:120,913,534
INFO 2026-06-08 08:26:58 MarkDuplicates Tracking 566304 as yet unmatched pairs. 15621 records in RAM.
INFO 2026-06-08 08:26:59 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:07:24s. Time for last 1,000,000: 1s. Last read position: chr9:125,349,389
INFO 2026-06-08 08:26:59 MarkDuplicates Tracking 563973 as yet unmatched pairs. 13285 records in RAM.
INFO 2026-06-08 08:27:01 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:07:26s. Time for last 1,000,000: 1s. Last read position: chr9:128,583,252
INFO 2026-06-08 08:27:01 MarkDuplicates Tracking 561510 as yet unmatched pairs. 10819 records in RAM.
INFO 2026-06-08 08:27:03 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:07:28s. Time for last 1,000,000: 1s. Last read position: chr9:131,144,578
INFO 2026-06-08 08:27:03 MarkDuplicates Tracking 559117 as yet unmatched pairs. 8424 records in RAM.
INFO 2026-06-08 08:27:05 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:07:30s. Time for last 1,000,000: 1s. Last read position: chr9:134,050,487
INFO 2026-06-08 08:27:05 MarkDuplicates Tracking 556931 as yet unmatched pairs. 6238 records in RAM.
INFO 2026-06-08 08:27:07 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:07:31s. Time for last 1,000,000: 1s. Last read position: chr9:136,496,324
INFO 2026-06-08 08:27:07 MarkDuplicates Tracking 554125 as yet unmatched pairs. 3425 records in RAM.
INFO 2026-06-08 08:27:09 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:07:33s. Time for last 1,000,000: 1s. Last read position: chr9:137,436,888
INFO 2026-06-08 08:27:09 MarkDuplicates Tracking 551420 as yet unmatched pairs. 716 records in RAM.
INFO 2026-06-08 08:27:11 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:07:35s. Time for last 1,000,000: 2s. Last read position: chr10:7,769,245
INFO 2026-06-08 08:27:11 MarkDuplicates Tracking 549131 as yet unmatched pairs. 28724 records in RAM.
INFO 2026-06-08 08:27:13 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:07:37s. Time for last 1,000,000: 1s. Last read position: chr10:21,741,893
INFO 2026-06-08 08:27:13 MarkDuplicates Tracking 546900 as yet unmatched pairs. 26492 records in RAM.
INFO 2026-06-08 08:27:15 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:07:39s. Time for last 1,000,000: 1s. Last read position: chr10:32,018,332
INFO 2026-06-08 08:27:15 MarkDuplicates Tracking 545681 as yet unmatched pairs. 25267 records in RAM.
INFO 2026-06-08 08:27:17 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:07:42s. Time for last 1,000,000: 2s. Last read position: chr10:43,102,388
INFO 2026-06-08 08:27:17 MarkDuplicates Tracking 543407 as yet unmatched pairs. 22993 records in RAM.
INFO 2026-06-08 08:27:20 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:07:44s. Time for last 1,000,000: 2s. Last read position: chr10:44,378,606
INFO 2026-06-08 08:27:20 MarkDuplicates Tracking 540086 as yet unmatched pairs. 19672 records in RAM.
INFO 2026-06-08 08:27:22 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:07:46s. Time for last 1,000,000: 1s. Last read position: chr10:58,196,144
INFO 2026-06-08 08:27:22 MarkDuplicates Tracking 538355 as yet unmatched pairs. 17939 records in RAM.
INFO 2026-06-08 08:27:24 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:07:48s. Time for last 1,000,000: 1s. Last read position: chr10:71,751,687
INFO 2026-06-08 08:27:24 MarkDuplicates Tracking 536182 as yet unmatched pairs. 15764 records in RAM.
INFO 2026-06-08 08:27:25 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:07:50s. Time for last 1,000,000: 1s. Last read position: chr10:77,869,156
INFO 2026-06-08 08:27:25 MarkDuplicates Tracking 533906 as yet unmatched pairs. 13487 records in RAM.
INFO 2026-06-08 08:27:27 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:07:52s. Time for last 1,000,000: 1s. Last read position: chr10:87,931,059
INFO 2026-06-08 08:27:27 MarkDuplicates Tracking 531997 as yet unmatched pairs. 11578 records in RAM.
INFO 2026-06-08 08:27:29 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:07:53s. Time for last 1,000,000: 1s. Last read position: chr10:96,159,863
INFO 2026-06-08 08:27:29 MarkDuplicates Tracking 529767 as yet unmatched pairs. 9348 records in RAM.
INFO 2026-06-08 08:27:31 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:07:55s. Time for last 1,000,000: 1s. Last read position: chr10:102,139,688
INFO 2026-06-08 08:27:31 MarkDuplicates Tracking 527392 as yet unmatched pairs. 6972 records in RAM.
INFO 2026-06-08 08:27:33 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:07:57s. Time for last 1,000,000: 1s. Last read position: chr10:113,898,109
INFO 2026-06-08 08:27:33 MarkDuplicates Tracking 525113 as yet unmatched pairs. 4693 records in RAM.
INFO 2026-06-08 08:27:35 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:07:59s. Time for last 1,000,000: 1s. Last read position: chr10:121,841,103
INFO 2026-06-08 08:27:35 MarkDuplicates Tracking 522826 as yet unmatched pairs. 2400 records in RAM.
INFO 2026-06-08 08:27:36 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:08:01s. Time for last 1,000,000: 1s. Last read position: chr10:133,395,712
INFO 2026-06-08 08:27:36 MarkDuplicates Tracking 520731 as yet unmatched pairs. 301 records in RAM.
INFO 2026-06-08 08:27:39 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:08:03s. Time for last 1,000,000: 2s. Last read position: chr11:320,664
INFO 2026-06-08 08:27:39 MarkDuplicates Tracking 519555 as yet unmatched pairs. 58498 records in RAM.
INFO 2026-06-08 08:27:41 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 2s. Last read position: chr11:1,251,541
INFO 2026-06-08 08:27:41 MarkDuplicates Tracking 515669 as yet unmatched pairs. 54609 records in RAM.
INFO 2026-06-08 08:27:43 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:08:07s. Time for last 1,000,000: 1s. Last read position: chr11:6,401,574
INFO 2026-06-08 08:27:43 MarkDuplicates Tracking 513095 as yet unmatched pairs. 52032 records in RAM.
INFO 2026-06-08 08:27:45 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:08:09s. Time for last 1,000,000: 2s. Last read position: chr11:10,797,759
INFO 2026-06-08 08:27:45 MarkDuplicates Tracking 511311 as yet unmatched pairs. 50248 records in RAM.
INFO 2026-06-08 08:27:47 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:08:11s. Time for last 1,000,000: 1s. Last read position: chr11:18,403,771
INFO 2026-06-08 08:27:47 MarkDuplicates Tracking 509034 as yet unmatched pairs. 47970 records in RAM.
INFO 2026-06-08 08:27:49 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:08:14s. Time for last 1,000,000: 2s. Last read position: chr11:35,663,218
INFO 2026-06-08 08:27:49 MarkDuplicates Tracking 506541 as yet unmatched pairs. 45477 records in RAM.
INFO 2026-06-08 08:27:52 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 2s. Last read position: chr11:47,275,149
INFO 2026-06-08 08:27:52 MarkDuplicates Tracking 504479 as yet unmatched pairs. 43415 records in RAM.
INFO 2026-06-08 08:27:54 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:08:18s. Time for last 1,000,000: 2s. Last read position: chr11:57,803,732
INFO 2026-06-08 08:27:54 MarkDuplicates Tracking 502272 as yet unmatched pairs. 41203 records in RAM.
INFO 2026-06-08 08:27:56 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:08:20s. Time for last 1,000,000: 2s. Last read position: chr11:61,964,998
INFO 2026-06-08 08:27:56 MarkDuplicates Tracking 500603 as yet unmatched pairs. 39526 records in RAM.
INFO 2026-06-08 08:27:58 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:08:22s. Time for last 1,000,000: 1s. Last read position: chr11:62,519,273
INFO 2026-06-08 08:27:58 MarkDuplicates Tracking 498077 as yet unmatched pairs. 36999 records in RAM.
INFO 2026-06-08 08:28:00 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:08:24s. Time for last 1,000,000: 2s. Last read position: chr11:62,527,642
INFO 2026-06-08 08:28:00 MarkDuplicates Tracking 496476 as yet unmatched pairs. 35398 records in RAM.
INFO 2026-06-08 08:28:02 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:08:26s. Time for last 1,000,000: 2s. Last read position: chr11:62,570,992
INFO 2026-06-08 08:28:02 MarkDuplicates Tracking 493753 as yet unmatched pairs. 32675 records in RAM.
INFO 2026-06-08 08:28:04 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:08:28s. Time for last 1,000,000: 2s. Last read position: chr11:64,234,816
INFO 2026-06-08 08:28:04 MarkDuplicates Tracking 491374 as yet unmatched pairs. 30285 records in RAM.
INFO 2026-06-08 08:28:06 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:08:30s. Time for last 1,000,000: 2s. Last read position: chr11:65,501,699
INFO 2026-06-08 08:28:06 MarkDuplicates Tracking 488652 as yet unmatched pairs. 27553 records in RAM.
INFO 2026-06-08 08:28:08 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 2s. Last read position: chr11:66,063,056
INFO 2026-06-08 08:28:08 MarkDuplicates Tracking 486137 as yet unmatched pairs. 25032 records in RAM.
INFO 2026-06-08 08:28:10 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 1s. Last read position: chr11:67,995,685
INFO 2026-06-08 08:28:10 MarkDuplicates Tracking 483486 as yet unmatched pairs. 22381 records in RAM.
INFO 2026-06-08 08:28:12 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:08:36s. Time for last 1,000,000: 1s. Last read position: chr11:70,798,454
INFO 2026-06-08 08:28:12 MarkDuplicates Tracking 481179 as yet unmatched pairs. 20071 records in RAM.
INFO 2026-06-08 08:28:13 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:08:38s. Time for last 1,000,000: 1s. Last read position: chr11:72,757,829
INFO 2026-06-08 08:28:13 MarkDuplicates Tracking 479026 as yet unmatched pairs. 17918 records in RAM.
INFO 2026-06-08 08:29:24 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:09:48s. Time for last 1,000,000: 70s. Last read position: chr11:75,400,757
INFO 2026-06-08 08:29:24 MarkDuplicates Tracking 477035 as yet unmatched pairs. 15926 records in RAM.
INFO 2026-06-08 08:29:26 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:09:50s. Time for last 1,000,000: 2s. Last read position: chr11:76,796,424
INFO 2026-06-08 08:29:26 MarkDuplicates Tracking 474274 as yet unmatched pairs. 13165 records in RAM.
INFO 2026-06-08 08:29:28 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:09:53s. Time for last 1,000,000: 2s. Last read position: chr11:78,104,361
INFO 2026-06-08 08:29:28 MarkDuplicates Tracking 472996 as yet unmatched pairs. 11887 records in RAM.
INFO 2026-06-08 08:29:31 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:09:55s. Time for last 1,000,000: 2s. Last read position: chr11:86,807,958
INFO 2026-06-08 08:29:31 MarkDuplicates Tracking 469806 as yet unmatched pairs. 8697 records in RAM.
INFO 2026-06-08 08:29:32 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:09:57s. Time for last 1,000,000: 1s. Last read position: chr11:111,703,313
INFO 2026-06-08 08:29:32 MarkDuplicates Tracking 467555 as yet unmatched pairs. 6445 records in RAM.
INFO 2026-06-08 08:29:34 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 1s. Last read position: chr11:118,897,627
INFO 2026-06-08 08:29:34 MarkDuplicates Tracking 465775 as yet unmatched pairs. 4663 records in RAM.
INFO 2026-06-08 08:29:36 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:10:00s. Time for last 1,000,000: 1s. Last read position: chr11:123,061,139
INFO 2026-06-08 08:29:36 MarkDuplicates Tracking 464010 as yet unmatched pairs. 2896 records in RAM.
INFO 2026-06-08 08:29:39 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:10:03s. Time for last 1,000,000: 2s. Last read position: chr12:354,078
INFO 2026-06-08 08:29:39 MarkDuplicates Tracking 461002 as yet unmatched pairs. 65544 records in RAM.
INFO 2026-06-08 08:29:41 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 2s. Last read position: chr12:6,022,753
INFO 2026-06-08 08:29:41 MarkDuplicates Tracking 458617 as yet unmatched pairs. 63157 records in RAM.
INFO 2026-06-08 08:29:43 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:10:08s. Time for last 1,000,000: 1s. Last read position: chr12:6,769,653
INFO 2026-06-08 08:29:43 MarkDuplicates Tracking 456469 as yet unmatched pairs. 61000 records in RAM.
INFO 2026-06-08 08:29:45 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:10:10s. Time for last 1,000,000: 1s. Last read position: chr12:9,077,799
INFO 2026-06-08 08:29:45 MarkDuplicates Tracking 454262 as yet unmatched pairs. 58793 records in RAM.
INFO 2026-06-08 08:29:47 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:10:11s. Time for last 1,000,000: 1s. Last read position: chr12:14,503,828
INFO 2026-06-08 08:29:47 MarkDuplicates Tracking 452101 as yet unmatched pairs. 56630 records in RAM.
INFO 2026-06-08 08:29:49 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:10:13s. Time for last 1,000,000: 1s. Last read position: chr12:29,370,159
INFO 2026-06-08 08:29:49 MarkDuplicates Tracking 450040 as yet unmatched pairs. 54566 records in RAM.
INFO 2026-06-08 08:29:51 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:10:16s. Time for last 1,000,000: 2s. Last read position: chr12:40,458,759
INFO 2026-06-08 08:29:51 MarkDuplicates Tracking 448204 as yet unmatched pairs. 52730 records in RAM.
INFO 2026-06-08 08:29:53 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:10:18s. Time for last 1,000,000: 1s. Last read position: chr12:40,485,140
INFO 2026-06-08 08:29:53 MarkDuplicates Tracking 446423 as yet unmatched pairs. 50949 records in RAM.
INFO 2026-06-08 08:29:55 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:10:19s. Time for last 1,000,000: 1s. Last read position: chr12:40,487,879
INFO 2026-06-08 08:29:55 MarkDuplicates Tracking 446191 as yet unmatched pairs. 50716 records in RAM.
INFO 2026-06-08 08:29:57 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:10:21s. Time for last 1,000,000: 1s. Last read position: chr12:40,500,194
INFO 2026-06-08 08:29:57 MarkDuplicates Tracking 441060 as yet unmatched pairs. 45585 records in RAM.
INFO 2026-06-08 08:29:59 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:10:23s. Time for last 1,000,000: 1s. Last read position: chr12:40,542,283
INFO 2026-06-08 08:29:59 MarkDuplicates Tracking 439794 as yet unmatched pairs. 44319 records in RAM.
INFO 2026-06-08 08:30:01 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:10:25s. Time for last 1,000,000: 2s. Last read position: chr12:46,201,124
INFO 2026-06-08 08:30:01 MarkDuplicates Tracking 437247 as yet unmatched pairs. 41761 records in RAM.
INFO 2026-06-08 08:30:03 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:10:27s. Time for last 1,000,000: 1s. Last read position: chr12:49,043,970
INFO 2026-06-08 08:30:03 MarkDuplicates Tracking 434604 as yet unmatched pairs. 39118 records in RAM.
INFO 2026-06-08 08:30:05 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:10:29s. Time for last 1,000,000: 2s. Last read position: chr12:49,755,739
INFO 2026-06-08 08:30:05 MarkDuplicates Tracking 432935 as yet unmatched pairs. 37449 records in RAM.
INFO 2026-06-08 08:30:07 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:10:32s. Time for last 1,000,000: 2s. Last read position: chr12:52,949,367
INFO 2026-06-08 08:30:07 MarkDuplicates Tracking 430567 as yet unmatched pairs. 35081 records in RAM.
INFO 2026-06-08 08:30:09 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:10:34s. Time for last 1,000,000: 1s. Last read position: chr12:54,182,425
INFO 2026-06-08 08:30:09 MarkDuplicates Tracking 428493 as yet unmatched pairs. 33007 records in RAM.
INFO 2026-06-08 08:30:11 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:10:36s. Time for last 1,000,000: 1s. Last read position: chr12:56,099,668
INFO 2026-06-08 08:30:11 MarkDuplicates Tracking 426481 as yet unmatched pairs. 30994 records in RAM.
INFO 2026-06-08 08:30:13 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:10:38s. Time for last 1,000,000: 1s. Last read position: chr12:56,469,400
INFO 2026-06-08 08:30:13 MarkDuplicates Tracking 423914 as yet unmatched pairs. 28423 records in RAM.
INFO 2026-06-08 08:30:15 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:10:40s. Time for last 1,000,000: 2s. Last read position: chr12:57,099,995
INFO 2026-06-08 08:30:15 MarkDuplicates Tracking 422491 as yet unmatched pairs. 27000 records in RAM.
INFO 2026-06-08 08:30:19 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:10:43s. Time for last 1,000,000: 3s. Last read position: chr12:57,515,241
INFO 2026-06-08 08:30:19 MarkDuplicates Tracking 419459 as yet unmatched pairs. 23968 records in RAM.
INFO 2026-06-08 08:30:21 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:10:45s. Time for last 1,000,000: 1s. Last read position: chr12:66,153,359
INFO 2026-06-08 08:30:21 MarkDuplicates Tracking 417539 as yet unmatched pairs. 22048 records in RAM.
INFO 2026-06-08 08:30:23 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:10:47s. Time for last 1,000,000: 2s. Last read position: chr12:79,845,374
INFO 2026-06-08 08:30:23 MarkDuplicates Tracking 415182 as yet unmatched pairs. 19679 records in RAM.
INFO 2026-06-08 08:30:25 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:10:49s. Time for last 1,000,000: 2s. Last read position: chr12:98,531,812
INFO 2026-06-08 08:30:25 MarkDuplicates Tracking 413056 as yet unmatched pairs. 17551 records in RAM.
INFO 2026-06-08 08:30:28 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:10:52s. Time for last 1,000,000: 2s. Last read position: chr12:103,938,348
INFO 2026-06-08 08:30:28 MarkDuplicates Tracking 410667 as yet unmatched pairs. 15162 records in RAM.
INFO 2026-06-08 08:30:30 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:10:54s. Time for last 1,000,000: 1s. Last read position: chr12:110,327,984
INFO 2026-06-08 08:30:30 MarkDuplicates Tracking 408821 as yet unmatched pairs. 13315 records in RAM.
INFO 2026-06-08 08:30:32 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:10:56s. Time for last 1,000,000: 1s. Last read position: chr12:112,505,849
INFO 2026-06-08 08:30:32 MarkDuplicates Tracking 406062 as yet unmatched pairs. 10556 records in RAM.
INFO 2026-06-08 08:30:34 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 1s. Last read position: chr12:118,199,178
INFO 2026-06-08 08:30:34 MarkDuplicates Tracking 403657 as yet unmatched pairs. 8141 records in RAM.
INFO 2026-06-08 08:30:36 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:11:00s. Time for last 1,000,000: 2s. Last read position: chr12:121,641,577
INFO 2026-06-08 08:30:36 MarkDuplicates Tracking 401436 as yet unmatched pairs. 5920 records in RAM.
INFO 2026-06-08 08:30:38 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:11:02s. Time for last 1,000,000: 2s. Last read position: chr12:124,012,776
INFO 2026-06-08 08:30:38 MarkDuplicates Tracking 399196 as yet unmatched pairs. 3674 records in RAM.
INFO 2026-06-08 08:30:40 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:11:04s. Time for last 1,000,000: 1s. Last read position: chr12:132,053,575
INFO 2026-06-08 08:30:40 MarkDuplicates Tracking 396934 as yet unmatched pairs. 1410 records in RAM.
INFO 2026-06-08 08:30:42 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:11:06s. Time for last 1,000,000: 1s. Last read position: chr13:23,340,427
INFO 2026-06-08 08:30:42 MarkDuplicates Tracking 394659 as yet unmatched pairs. 10110 records in RAM.
INFO 2026-06-08 08:30:44 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:11:08s. Time for last 1,000,000: 1s. Last read position: chr13:37,579,978
INFO 2026-06-08 08:30:44 MarkDuplicates Tracking 392756 as yet unmatched pairs. 8203 records in RAM.
INFO 2026-06-08 08:30:46 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:11:10s. Time for last 1,000,000: 1s. Last read position: chr13:48,463,771
INFO 2026-06-08 08:30:46 MarkDuplicates Tracking 390368 as yet unmatched pairs. 5814 records in RAM.
INFO 2026-06-08 08:30:48 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:11:12s. Time for last 1,000,000: 2s. Last read position: chr13:95,787,029
INFO 2026-06-08 08:30:48 MarkDuplicates Tracking 388235 as yet unmatched pairs. 3677 records in RAM.
INFO 2026-06-08 08:30:50 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:11:14s. Time for last 1,000,000: 1s. Last read position: chr13:110,879,958
INFO 2026-06-08 08:30:50 MarkDuplicates Tracking 385839 as yet unmatched pairs. 1280 records in RAM.
INFO 2026-06-08 08:30:52 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:11:16s. Time for last 1,000,000: 2s. Last read position: chr14:21,230,997
INFO 2026-06-08 08:30:52 MarkDuplicates Tracking 383789 as yet unmatched pairs. 30747 records in RAM.
INFO 2026-06-08 08:30:54 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:11:18s. Time for last 1,000,000: 1s. Last read position: chr14:23,359,615
INFO 2026-06-08 08:30:54 MarkDuplicates Tracking 381111 as yet unmatched pairs. 28066 records in RAM.
INFO 2026-06-08 08:30:56 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:11:20s. Time for last 1,000,000: 2s. Last read position: chr14:24,374,430
INFO 2026-06-08 08:30:56 MarkDuplicates Tracking 378722 as yet unmatched pairs. 25674 records in RAM.
INFO 2026-06-08 08:30:58 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:11:22s. Time for last 1,000,000: 2s. Last read position: chr14:37,591,577
INFO 2026-06-08 08:30:58 MarkDuplicates Tracking 376534 as yet unmatched pairs. 23483 records in RAM.
INFO 2026-06-08 08:31:00 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:11:25s. Time for last 1,000,000: 2s. Last read position: chr14:50,770,412
INFO 2026-06-08 08:31:00 MarkDuplicates Tracking 374397 as yet unmatched pairs. 21344 records in RAM.
INFO 2026-06-08 08:31:02 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:11:27s. Time for last 1,000,000: 1s. Last read position: chr14:59,498,798
INFO 2026-06-08 08:31:02 MarkDuplicates Tracking 372212 as yet unmatched pairs. 19157 records in RAM.
INFO 2026-06-08 08:31:04 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:11:28s. Time for last 1,000,000: 1s. Last read position: chr14:65,733,335
INFO 2026-06-08 08:31:04 MarkDuplicates Tracking 370568 as yet unmatched pairs. 17511 records in RAM.
INFO 2026-06-08 08:31:06 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:11:30s. Time for last 1,000,000: 1s. Last read position: chr14:73,076,334
INFO 2026-06-08 08:31:06 MarkDuplicates Tracking 367858 as yet unmatched pairs. 14795 records in RAM.
INFO 2026-06-08 08:31:08 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:11:32s. Time for last 1,000,000: 2s. Last read position: chr14:75,965,689
INFO 2026-06-08 08:31:08 MarkDuplicates Tracking 365452 as yet unmatched pairs. 12388 records in RAM.
INFO 2026-06-08 08:31:10 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:11:34s. Time for last 1,000,000: 1s. Last read position: chr14:91,999,315
INFO 2026-06-08 08:31:10 MarkDuplicates Tracking 363261 as yet unmatched pairs. 10196 records in RAM.
INFO 2026-06-08 08:31:12 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:11:36s. Time for last 1,000,000: 1s. Last read position: chr14:95,535,141
INFO 2026-06-08 08:31:12 MarkDuplicates Tracking 360814 as yet unmatched pairs. 7747 records in RAM.
INFO 2026-06-08 08:31:14 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:11:39s. Time for last 1,000,000: 2s. Last read position: chr14:101,988,747
INFO 2026-06-08 08:31:14 MarkDuplicates Tracking 358657 as yet unmatched pairs. 5574 records in RAM.
INFO 2026-06-08 08:31:16 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:11:41s. Time for last 1,000,000: 2s. Last read position: chr14:103,685,639
INFO 2026-06-08 08:31:16 MarkDuplicates Tracking 356352 as yet unmatched pairs. 3267 records in RAM.
INFO 2026-06-08 08:31:18 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:11:43s. Time for last 1,000,000: 1s. Last read position: chr14:105,624,625
INFO 2026-06-08 08:31:18 MarkDuplicates Tracking 353764 as yet unmatched pairs. 677 records in RAM.
INFO 2026-06-08 08:31:20 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:11:45s. Time for last 1,000,000: 1s. Last read position: chr15:28,116,787
INFO 2026-06-08 08:31:20 MarkDuplicates Tracking 352073 as yet unmatched pairs. 22056 records in RAM.
INFO 2026-06-08 08:31:22 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:11:46s. Time for last 1,000,000: 1s. Last read position: chr15:38,299,472
INFO 2026-06-08 08:31:22 MarkDuplicates Tracking 350228 as yet unmatched pairs. 20206 records in RAM.
INFO 2026-06-08 08:31:24 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:11:48s. Time for last 1,000,000: 1s. Last read position: chr15:41,669,790
INFO 2026-06-08 08:31:24 MarkDuplicates Tracking 348132 as yet unmatched pairs. 18108 records in RAM.
INFO 2026-06-08 08:31:26 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:11:50s. Time for last 1,000,000: 1s. Last read position: chr15:43,768,539
INFO 2026-06-08 08:31:26 MarkDuplicates Tracking 346061 as yet unmatched pairs. 16037 records in RAM.
INFO 2026-06-08 08:31:29 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:11:53s. Time for last 1,000,000: 2s. Last read position: chr15:48,878,302
INFO 2026-06-08 08:31:29 MarkDuplicates Tracking 343555 as yet unmatched pairs. 13528 records in RAM.
INFO 2026-06-08 08:31:31 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:11:55s. Time for last 1,000,000: 1s. Last read position: chr15:58,772,006
INFO 2026-06-08 08:31:31 MarkDuplicates Tracking 341474 as yet unmatched pairs. 11444 records in RAM.
INFO 2026-06-08 08:31:32 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:11:57s. Time for last 1,000,000: 1s. Last read position: chr15:64,870,532
INFO 2026-06-08 08:31:32 MarkDuplicates Tracking 339213 as yet unmatched pairs. 9182 records in RAM.
INFO 2026-06-08 08:31:34 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:11:59s. Time for last 1,000,000: 1s. Last read position: chr15:72,209,708
INFO 2026-06-08 08:31:34 MarkDuplicates Tracking 336885 as yet unmatched pairs. 6853 records in RAM.
INFO 2026-06-08 08:31:36 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:12:01s. Time for last 1,000,000: 1s. Last read position: chr15:76,947,480
INFO 2026-06-08 08:31:36 MarkDuplicates Tracking 334553 as yet unmatched pairs. 4519 records in RAM.
INFO 2026-06-08 08:31:38 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:12:03s. Time for last 1,000,000: 2s. Last read position: chr15:85,743,799
INFO 2026-06-08 08:31:38 MarkDuplicates Tracking 332467 as yet unmatched pairs. 2426 records in RAM.
INFO 2026-06-08 08:31:40 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:12:05s. Time for last 1,000,000: 2s. Last read position: chr15:101,177,544
INFO 2026-06-08 08:31:40 MarkDuplicates Tracking 330319 as yet unmatched pairs. 267 records in RAM.
INFO 2026-06-08 08:31:43 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:12:07s. Time for last 1,000,000: 2s. Last read position: chr16:671,977
INFO 2026-06-08 08:31:43 MarkDuplicates Tracking 327928 as yet unmatched pairs. 49526 records in RAM.
INFO 2026-06-08 08:31:45 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:12:09s. Time for last 1,000,000: 1s. Last read position: chr16:1,525,987
INFO 2026-06-08 08:31:45 MarkDuplicates Tracking 324925 as yet unmatched pairs. 46522 records in RAM.
INFO 2026-06-08 08:31:47 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:12:11s. Time for last 1,000,000: 1s. Last read position: chr16:2,106,110
INFO 2026-06-08 08:31:47 MarkDuplicates Tracking 322144 as yet unmatched pairs. 43740 records in RAM.
INFO 2026-06-08 08:31:49 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:12:13s. Time for last 1,000,000: 1s. Last read position: chr16:2,762,138
INFO 2026-06-08 08:31:49 MarkDuplicates Tracking 319853 as yet unmatched pairs. 41448 records in RAM.
INFO 2026-06-08 08:31:51 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:12:15s. Time for last 1,000,000: 2s. Last read position: chr16:3,289,539
INFO 2026-06-08 08:31:51 MarkDuplicates Tracking 317432 as yet unmatched pairs. 39026 records in RAM.
INFO 2026-06-08 08:31:53 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:12:17s. Time for last 1,000,000: 1s. Last read position: chr16:4,812,225
INFO 2026-06-08 08:31:53 MarkDuplicates Tracking 315031 as yet unmatched pairs. 36625 records in RAM.
INFO 2026-06-08 08:31:55 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:12:19s. Time for last 1,000,000: 1s. Last read position: chr16:11,927,805
INFO 2026-06-08 08:31:55 MarkDuplicates Tracking 313013 as yet unmatched pairs. 34607 records in RAM.
INFO 2026-06-08 08:31:56 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:12:21s. Time for last 1,000,000: 1s. Last read position: chr16:14,926,140
INFO 2026-06-08 08:31:56 MarkDuplicates Tracking 311577 as yet unmatched pairs. 33171 records in RAM.
INFO 2026-06-08 08:31:58 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:12:22s. Time for last 1,000,000: 1s. Last read position: chr16:15,687,377
INFO 2026-06-08 08:31:58 MarkDuplicates Tracking 310283 as yet unmatched pairs. 31877 records in RAM.
INFO 2026-06-08 08:31:59 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:12:24s. Time for last 1,000,000: 1s. Last read position: chr16:16,357,565
INFO 2026-06-08 08:31:59 MarkDuplicates Tracking 309943 as yet unmatched pairs. 31537 records in RAM.
INFO 2026-06-08 08:32:01 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:12:26s. Time for last 1,000,000: 1s. Last read position: chr16:18,351,456
INFO 2026-06-08 08:32:01 MarkDuplicates Tracking 309069 as yet unmatched pairs. 30662 records in RAM.
INFO 2026-06-08 08:32:03 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:12:27s. Time for last 1,000,000: 1s. Last read position: chr16:18,797,952
INFO 2026-06-08 08:32:03 MarkDuplicates Tracking 308253 as yet unmatched pairs. 29846 records in RAM.
INFO 2026-06-08 08:32:05 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:12:29s. Time for last 1,000,000: 1s. Last read position: chr16:21,404,727
INFO 2026-06-08 08:32:05 MarkDuplicates Tracking 306199 as yet unmatched pairs. 27791 records in RAM.
INFO 2026-06-08 08:32:07 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:12:31s. Time for last 1,000,000: 2s. Last read position: chr16:21,843,706
INFO 2026-06-08 08:32:07 MarkDuplicates Tracking 305184 as yet unmatched pairs. 26776 records in RAM.
INFO 2026-06-08 08:32:08 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:12:33s. Time for last 1,000,000: 1s. Last read position: chr16:22,534,336
INFO 2026-06-08 08:32:08 MarkDuplicates Tracking 304493 as yet unmatched pairs. 26085 records in RAM.
INFO 2026-06-08 08:32:10 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:12:35s. Time for last 1,000,000: 1s. Last read position: chr16:28,106,412
INFO 2026-06-08 08:32:10 MarkDuplicates Tracking 302721 as yet unmatched pairs. 24313 records in RAM.
INFO 2026-06-08 08:32:12 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:12:36s. Time for last 1,000,000: 1s. Last read position: chr16:28,981,538
INFO 2026-06-08 08:32:12 MarkDuplicates Tracking 300747 as yet unmatched pairs. 22336 records in RAM.
INFO 2026-06-08 08:32:13 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:12:38s. Time for last 1,000,000: 1s. Last read position: chr16:29,545,362
INFO 2026-06-08 08:32:13 MarkDuplicates Tracking 300342 as yet unmatched pairs. 21931 records in RAM.
INFO 2026-06-08 08:32:15 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:12:40s. Time for last 1,000,000: 1s. Last read position: chr16:30,186,854
INFO 2026-06-08 08:32:15 MarkDuplicates Tracking 297798 as yet unmatched pairs. 19387 records in RAM.
INFO 2026-06-08 08:32:17 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:12:41s. Time for last 1,000,000: 1s. Last read position: chr16:30,660,293
INFO 2026-06-08 08:32:17 MarkDuplicates Tracking 296202 as yet unmatched pairs. 17791 records in RAM.
INFO 2026-06-08 08:32:19 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:12:43s. Time for last 1,000,000: 1s. Last read position: chr16:31,182,525
INFO 2026-06-08 08:32:19 MarkDuplicates Tracking 294428 as yet unmatched pairs. 16017 records in RAM.
INFO 2026-06-08 08:32:21 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:12:45s. Time for last 1,000,000: 1s. Last read position: chr16:50,291,750
INFO 2026-06-08 08:32:21 MarkDuplicates Tracking 291609 as yet unmatched pairs. 13196 records in RAM.
INFO 2026-06-08 08:32:23 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:12:48s. Time for last 1,000,000: 2s. Last read position: chr16:57,650,303
INFO 2026-06-08 08:32:23 MarkDuplicates Tracking 289385 as yet unmatched pairs. 10970 records in RAM.
INFO 2026-06-08 08:32:25 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:12:49s. Time for last 1,000,000: 1s. Last read position: chr16:67,908,735
INFO 2026-06-08 08:32:25 MarkDuplicates Tracking 286891 as yet unmatched pairs. 8476 records in RAM.
INFO 2026-06-08 08:32:27 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:12:51s. Time for last 1,000,000: 1s. Last read position: chr16:70,677,808
INFO 2026-06-08 08:32:27 MarkDuplicates Tracking 284676 as yet unmatched pairs. 6242 records in RAM.
INFO 2026-06-08 08:32:29 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:12:53s. Time for last 1,000,000: 1s. Last read position: chr16:84,179,185
INFO 2026-06-08 08:32:29 MarkDuplicates Tracking 282484 as yet unmatched pairs. 4050 records in RAM.
INFO 2026-06-08 08:32:30 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:12:55s. Time for last 1,000,000: 1s. Last read position: chr16:88,858,780
INFO 2026-06-08 08:32:30 MarkDuplicates Tracking 279913 as yet unmatched pairs. 1476 records in RAM.
INFO 2026-06-08 08:32:33 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:12:58s. Time for last 1,000,000: 2s. Last read position: chr17:1,643,825
INFO 2026-06-08 08:32:33 MarkDuplicates Tracking 277314 as yet unmatched pairs. 110495 records in RAM.
INFO 2026-06-08 08:32:35 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:13:00s. Time for last 1,000,000: 1s. Last read position: chr17:4,833,581
INFO 2026-06-08 08:32:35 MarkDuplicates Tracking 274829 as yet unmatched pairs. 108009 records in RAM.
INFO 2026-06-08 08:32:37 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:13:02s. Time for last 1,000,000: 1s. Last read position: chr17:7,384,596
INFO 2026-06-08 08:32:37 MarkDuplicates Tracking 272310 as yet unmatched pairs. 105489 records in RAM.
INFO 2026-06-08 08:32:39 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:13:03s. Time for last 1,000,000: 1s. Last read position: chr17:8,228,128
INFO 2026-06-08 08:32:39 MarkDuplicates Tracking 270382 as yet unmatched pairs. 103555 records in RAM.
INFO 2026-06-08 08:32:41 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:13:05s. Time for last 1,000,000: 1s. Last read position: chr17:16,382,058
INFO 2026-06-08 08:32:41 MarkDuplicates Tracking 268573 as yet unmatched pairs. 101746 records in RAM.
INFO 2026-06-08 08:32:43 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:13:07s. Time for last 1,000,000: 1s. Last read position: chr17:21,198,325
INFO 2026-06-08 08:32:43 MarkDuplicates Tracking 265782 as yet unmatched pairs. 98955 records in RAM.
INFO 2026-06-08 08:32:45 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:13:10s. Time for last 1,000,000: 2s. Last read position: chr17:29,482,274
INFO 2026-06-08 08:32:45 MarkDuplicates Tracking 263814 as yet unmatched pairs. 96986 records in RAM.
INFO 2026-06-08 08:32:47 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:13:12s. Time for last 1,000,000: 2s. Last read position: chr17:32,360,654
INFO 2026-06-08 08:32:47 MarkDuplicates Tracking 261472 as yet unmatched pairs. 94643 records in RAM.
INFO 2026-06-08 08:32:49 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:13:14s. Time for last 1,000,000: 1s. Last read position: chr17:36,578,138
INFO 2026-06-08 08:32:49 MarkDuplicates Tracking 259509 as yet unmatched pairs. 92679 records in RAM.
INFO 2026-06-08 08:32:51 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:13:15s. Time for last 1,000,000: 1s. Last read position: chr17:38,780,515
INFO 2026-06-08 08:32:51 MarkDuplicates Tracking 257716 as yet unmatched pairs. 90885 records in RAM.
INFO 2026-06-08 08:32:53 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:13:17s. Time for last 1,000,000: 1s. Last read position: chr17:39,706,873
INFO 2026-06-08 08:32:53 MarkDuplicates Tracking 256383 as yet unmatched pairs. 89550 records in RAM.
INFO 2026-06-08 08:32:55 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:13:19s. Time for last 1,000,000: 1s. Last read position: chr17:39,716,537
INFO 2026-06-08 08:32:55 MarkDuplicates Tracking 256680 as yet unmatched pairs. 89847 records in RAM.
INFO 2026-06-08 08:32:57 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:13:21s. Time for last 1,000,000: 1s. Last read position: chr17:39,727,380
INFO 2026-06-08 08:32:57 MarkDuplicates Tracking 251592 as yet unmatched pairs. 84759 records in RAM.
INFO 2026-06-08 08:32:59 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:13:23s. Time for last 1,000,000: 1s. Last read position: chr17:40,416,004
INFO 2026-06-08 08:32:59 MarkDuplicates Tracking 248491 as yet unmatched pairs. 81658 records in RAM.
INFO 2026-06-08 08:33:00 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:13:25s. Time for last 1,000,000: 1s. Last read position: chr17:41,819,596
INFO 2026-06-08 08:33:00 MarkDuplicates Tracking 245718 as yet unmatched pairs. 78885 records in RAM.
INFO 2026-06-08 08:33:03 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:13:27s. Time for last 1,000,000: 2s. Last read position: chr17:42,565,689
INFO 2026-06-08 08:33:03 MarkDuplicates Tracking 243296 as yet unmatched pairs. 76463 records in RAM.
INFO 2026-06-08 08:33:05 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:13:30s. Time for last 1,000,000: 2s. Last read position: chr17:44,189,337
INFO 2026-06-08 08:33:05 MarkDuplicates Tracking 241092 as yet unmatched pairs. 74259 records in RAM.
INFO 2026-06-08 08:33:07 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:13:32s. Time for last 1,000,000: 2s. Last read position: chr17:45,983,439
INFO 2026-06-08 08:33:07 MarkDuplicates Tracking 238640 as yet unmatched pairs. 71807 records in RAM.
INFO 2026-06-08 08:33:09 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:13:33s. Time for last 1,000,000: 1s. Last read position: chr17:47,976,795
INFO 2026-06-08 08:33:09 MarkDuplicates Tracking 237184 as yet unmatched pairs. 70350 records in RAM.
INFO 2026-06-08 08:33:11 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:13:35s. Time for last 1,000,000: 1s. Last read position: chr17:50,185,505
INFO 2026-06-08 08:33:11 MarkDuplicates Tracking 238606 as yet unmatched pairs. 71772 records in RAM.
INFO 2026-06-08 08:33:13 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:13:37s. Time for last 1,000,000: 1s. Last read position: chr17:50,186,683
INFO 2026-06-08 08:33:13 MarkDuplicates Tracking 234729 as yet unmatched pairs. 67895 records in RAM.
INFO 2026-06-08 08:33:15 MarkDuplicates Read 368,000,000 records. Elapsed time: 00:13:39s. Time for last 1,000,000: 1s. Last read position: chr17:50,187,077
INFO 2026-06-08 08:33:15 MarkDuplicates Tracking 240064 as yet unmatched pairs. 73223 records in RAM.
INFO 2026-06-08 08:33:17 MarkDuplicates Read 369,000,000 records. Elapsed time: 00:13:41s. Time for last 1,000,000: 1s. Last read position: chr17:50,188,102
INFO 2026-06-08 08:33:17 MarkDuplicates Tracking 240663 as yet unmatched pairs. 73822 records in RAM.
INFO 2026-06-08 08:33:19 MarkDuplicates Read 370,000,000 records. Elapsed time: 00:13:43s. Time for last 1,000,000: 2s. Last read position: chr17:50,188,931
INFO 2026-06-08 08:33:19 MarkDuplicates Tracking 234466 as yet unmatched pairs. 67625 records in RAM.
INFO 2026-06-08 08:33:21 MarkDuplicates Read 371,000,000 records. Elapsed time: 00:13:45s. Time for last 1,000,000: 1s. Last read position: chr17:50,189,504
INFO 2026-06-08 08:33:21 MarkDuplicates Tracking 230895 as yet unmatched pairs. 64054 records in RAM.
INFO 2026-06-08 08:33:23 MarkDuplicates Read 372,000,000 records. Elapsed time: 00:13:47s. Time for last 1,000,000: 1s. Last read position: chr17:50,190,079
INFO 2026-06-08 08:33:23 MarkDuplicates Tracking 228950 as yet unmatched pairs. 62109 records in RAM.
INFO 2026-06-08 08:33:25 MarkDuplicates Read 373,000,000 records. Elapsed time: 00:13:49s. Time for last 1,000,000: 1s. Last read position: chr17:50,191,442
INFO 2026-06-08 08:33:25 MarkDuplicates Tracking 224249 as yet unmatched pairs. 57408 records in RAM.
INFO 2026-06-08 08:33:27 MarkDuplicates Read 374,000,000 records. Elapsed time: 00:13:51s. Time for last 1,000,000: 2s. Last read position: chr17:50,192,672
INFO 2026-06-08 08:33:27 MarkDuplicates Tracking 223987 as yet unmatched pairs. 57142 records in RAM.
INFO 2026-06-08 08:33:29 MarkDuplicates Read 375,000,000 records. Elapsed time: 00:13:53s. Time for last 1,000,000: 2s. Last read position: chr17:50,194,014
INFO 2026-06-08 08:33:29 MarkDuplicates Tracking 221454 as yet unmatched pairs. 54608 records in RAM.
INFO 2026-06-08 08:33:32 MarkDuplicates Read 376,000,000 records. Elapsed time: 00:13:56s. Time for last 1,000,000: 2s. Last read position: chr17:50,194,597
INFO 2026-06-08 08:33:32 MarkDuplicates Tracking 215757 as yet unmatched pairs. 48911 records in RAM.
INFO 2026-06-08 08:33:34 MarkDuplicates Read 377,000,000 records. Elapsed time: 00:13:58s. Time for last 1,000,000: 2s. Last read position: chr17:50,195,280
INFO 2026-06-08 08:33:34 MarkDuplicates Tracking 215467 as yet unmatched pairs. 48620 records in RAM.
INFO 2026-06-08 08:33:36 MarkDuplicates Read 378,000,000 records. Elapsed time: 00:14:00s. Time for last 1,000,000: 1s. Last read position: chr17:50,196,154
INFO 2026-06-08 08:33:36 MarkDuplicates Tracking 215040 as yet unmatched pairs. 48192 records in RAM.
INFO 2026-06-08 08:33:38 MarkDuplicates Read 379,000,000 records. Elapsed time: 00:14:02s. Time for last 1,000,000: 2s. Last read position: chr17:50,196,512
INFO 2026-06-08 08:33:38 MarkDuplicates Tracking 213869 as yet unmatched pairs. 47021 records in RAM.
INFO 2026-06-08 08:33:40 MarkDuplicates Read 380,000,000 records. Elapsed time: 00:14:04s. Time for last 1,000,000: 2s. Last read position: chr17:50,197,740
INFO 2026-06-08 08:33:40 MarkDuplicates Tracking 214247 as yet unmatched pairs. 47399 records in RAM.
INFO 2026-06-08 08:33:42 MarkDuplicates Read 381,000,000 records. Elapsed time: 00:14:06s. Time for last 1,000,000: 1s. Last read position: chr17:50,199,256
INFO 2026-06-08 08:33:42 MarkDuplicates Tracking 202087 as yet unmatched pairs. 35239 records in RAM.
INFO 2026-06-08 08:33:44 MarkDuplicates Read 382,000,000 records. Elapsed time: 00:14:08s. Time for last 1,000,000: 1s. Last read position: chr17:50,199,875
INFO 2026-06-08 08:33:44 MarkDuplicates Tracking 196605 as yet unmatched pairs. 29757 records in RAM.
INFO 2026-06-08 08:33:45 MarkDuplicates Read 383,000,000 records. Elapsed time: 00:14:10s. Time for last 1,000,000: 1s. Last read position: chr17:51,168,255
INFO 2026-06-08 08:33:45 MarkDuplicates Tracking 193400 as yet unmatched pairs. 26551 records in RAM.
INFO 2026-06-08 08:33:47 MarkDuplicates Read 384,000,000 records. Elapsed time: 00:14:12s. Time for last 1,000,000: 2s. Last read position: chr17:59,683,092
INFO 2026-06-08 08:33:47 MarkDuplicates Tracking 190479 as yet unmatched pairs. 23628 records in RAM.
INFO 2026-06-08 08:33:50 MarkDuplicates Read 385,000,000 records. Elapsed time: 00:14:14s. Time for last 1,000,000: 2s. Last read position: chr17:63,194,013
INFO 2026-06-08 08:33:50 MarkDuplicates Tracking 188359 as yet unmatched pairs. 21507 records in RAM.
INFO 2026-06-08 08:33:52 MarkDuplicates Read 386,000,000 records. Elapsed time: 00:14:16s. Time for last 1,000,000: 2s. Last read position: chr17:64,571,798
INFO 2026-06-08 08:33:52 MarkDuplicates Tracking 185754 as yet unmatched pairs. 18899 records in RAM.
INFO 2026-06-08 08:33:54 MarkDuplicates Read 387,000,000 records. Elapsed time: 00:14:19s. Time for last 1,000,000: 2s. Last read position: chr17:68,515,407
INFO 2026-06-08 08:33:54 MarkDuplicates Tracking 184949 as yet unmatched pairs. 18094 records in RAM.
INFO 2026-06-08 08:33:56 MarkDuplicates Read 388,000,000 records. Elapsed time: 00:14:21s. Time for last 1,000,000: 2s. Last read position: chr17:74,775,636
INFO 2026-06-08 08:33:56 MarkDuplicates Tracking 181358 as yet unmatched pairs. 14502 records in RAM.
INFO 2026-06-08 08:33:58 MarkDuplicates Read 389,000,000 records. Elapsed time: 00:14:23s. Time for last 1,000,000: 1s. Last read position: chr17:75,896,746
INFO 2026-06-08 08:33:58 MarkDuplicates Tracking 178798 as yet unmatched pairs. 11942 records in RAM.
INFO 2026-06-08 08:34:00 MarkDuplicates Read 390,000,000 records. Elapsed time: 00:14:25s. Time for last 1,000,000: 1s. Last read position: chr17:78,870,897
INFO 2026-06-08 08:34:00 MarkDuplicates Tracking 176580 as yet unmatched pairs. 9723 records in RAM.
INFO 2026-06-08 08:34:03 MarkDuplicates Read 391,000,000 records. Elapsed time: 00:14:27s. Time for last 1,000,000: 2s. Last read position: chr17:80,343,150
INFO 2026-06-08 08:34:03 MarkDuplicates Tracking 174138 as yet unmatched pairs. 7278 records in RAM.
INFO 2026-06-08 08:34:05 MarkDuplicates Read 392,000,000 records. Elapsed time: 00:14:29s. Time for last 1,000,000: 2s. Last read position: chr17:81,559,361
INFO 2026-06-08 08:34:05 MarkDuplicates Tracking 171659 as yet unmatched pairs. 4799 records in RAM.
INFO 2026-06-08 08:34:07 MarkDuplicates Read 393,000,000 records. Elapsed time: 00:14:31s. Time for last 1,000,000: 1s. Last read position: chr17:82,084,618
INFO 2026-06-08 08:34:07 MarkDuplicates Tracking 168902 as yet unmatched pairs. 2042 records in RAM.
INFO 2026-06-08 08:34:09 MarkDuplicates Read 394,000,000 records. Elapsed time: 00:14:33s. Time for last 1,000,000: 1s. Last read position: chr18:3,253,264
INFO 2026-06-08 08:34:09 MarkDuplicates Tracking 166388 as yet unmatched pairs. 8001 records in RAM.
INFO 2026-06-08 08:34:11 MarkDuplicates Read 395,000,000 records. Elapsed time: 00:14:35s. Time for last 1,000,000: 1s. Last read position: chr18:23,466,187
INFO 2026-06-08 08:34:11 MarkDuplicates Tracking 164250 as yet unmatched pairs. 5862 records in RAM.
INFO 2026-06-08 08:34:12 MarkDuplicates Read 396,000,000 records. Elapsed time: 00:14:37s. Time for last 1,000,000: 1s. Last read position: chr18:46,228,695
INFO 2026-06-08 08:34:12 MarkDuplicates Tracking 162238 as yet unmatched pairs. 3850 records in RAM.
INFO 2026-06-08 08:34:15 MarkDuplicates Read 397,000,000 records. Elapsed time: 00:14:39s. Time for last 1,000,000: 2s. Last read position: chr18:62,275,456
INFO 2026-06-08 08:34:15 MarkDuplicates Tracking 160191 as yet unmatched pairs. 1802 records in RAM.
INFO 2026-06-08 08:34:17 MarkDuplicates Read 398,000,000 records. Elapsed time: 00:14:42s. Time for last 1,000,000: 2s. Last read position: chr19:890,979
INFO 2026-06-08 08:34:17 MarkDuplicates Tracking 157634 as yet unmatched pairs. 63348 records in RAM.
INFO 2026-06-08 08:34:19 MarkDuplicates Read 399,000,000 records. Elapsed time: 00:14:44s. Time for last 1,000,000: 1s. Last read position: chr19:2,127,191
INFO 2026-06-08 08:34:19 MarkDuplicates Tracking 154939 as yet unmatched pairs. 60652 records in RAM.
INFO 2026-06-08 08:34:21 MarkDuplicates Read 400,000,000 records. Elapsed time: 00:14:46s. Time for last 1,000,000: 1s. Last read position: chr19:4,719,851
INFO 2026-06-08 08:34:21 MarkDuplicates Tracking 152084 as yet unmatched pairs. 57795 records in RAM.
INFO 2026-06-08 08:34:23 MarkDuplicates Read 401,000,000 records. Elapsed time: 00:14:48s. Time for last 1,000,000: 1s. Last read position: chr19:7,459,853
INFO 2026-06-08 08:34:23 MarkDuplicates Tracking 149543 as yet unmatched pairs. 55252 records in RAM.
INFO 2026-06-08 08:34:25 MarkDuplicates Read 402,000,000 records. Elapsed time: 00:14:50s. Time for last 1,000,000: 2s. Last read position: chr19:10,114,287
INFO 2026-06-08 08:34:25 MarkDuplicates Tracking 147013 as yet unmatched pairs. 52721 records in RAM.
INFO 2026-06-08 08:34:28 MarkDuplicates Read 403,000,000 records. Elapsed time: 00:14:53s. Time for last 1,000,000: 2s. Last read position: chr19:11,345,388
INFO 2026-06-08 08:34:28 MarkDuplicates Tracking 144813 as yet unmatched pairs. 50521 records in RAM.
INFO 2026-06-08 08:34:30 MarkDuplicates Read 404,000,000 records. Elapsed time: 00:14:55s. Time for last 1,000,000: 2s. Last read position: chr19:13,081,702
INFO 2026-06-08 08:34:30 MarkDuplicates Tracking 142121 as yet unmatched pairs. 47824 records in RAM.
INFO 2026-06-08 08:34:32 MarkDuplicates Read 405,000,000 records. Elapsed time: 00:14:57s. Time for last 1,000,000: 1s. Last read position: chr19:15,178,000
INFO 2026-06-08 08:34:32 MarkDuplicates Tracking 139578 as yet unmatched pairs. 45280 records in RAM.
INFO 2026-06-08 08:34:34 MarkDuplicates Read 406,000,000 records. Elapsed time: 00:14:59s. Time for last 1,000,000: 1s. Last read position: chr19:16,841,945
INFO 2026-06-08 08:34:34 MarkDuplicates Tracking 137031 as yet unmatched pairs. 42733 records in RAM.
INFO 2026-06-08 08:34:37 MarkDuplicates Read 407,000,000 records. Elapsed time: 00:15:01s. Time for last 1,000,000: 2s. Last read position: chr19:18,419,637
INFO 2026-06-08 08:34:37 MarkDuplicates Tracking 134330 as yet unmatched pairs. 40031 records in RAM.
INFO 2026-06-08 08:34:39 MarkDuplicates Read 408,000,000 records. Elapsed time: 00:15:03s. Time for last 1,000,000: 1s. Last read position: chr19:23,374,687
INFO 2026-06-08 08:34:39 MarkDuplicates Tracking 131563 as yet unmatched pairs. 37264 records in RAM.
INFO 2026-06-08 08:34:41 MarkDuplicates Read 409,000,000 records. Elapsed time: 00:15:05s. Time for last 1,000,000: 1s. Last read position: chr19:35,547,386
INFO 2026-06-08 08:34:41 MarkDuplicates Tracking 128897 as yet unmatched pairs. 34595 records in RAM.
INFO 2026-06-08 08:34:42 MarkDuplicates Read 410,000,000 records. Elapsed time: 00:15:07s. Time for last 1,000,000: 1s. Last read position: chr19:38,417,083
INFO 2026-06-08 08:34:42 MarkDuplicates Tracking 126448 as yet unmatched pairs. 32146 records in RAM.
INFO 2026-06-08 08:34:44 MarkDuplicates Read 411,000,000 records. Elapsed time: 00:15:09s. Time for last 1,000,000: 1s. Last read position: chr19:39,875,534
INFO 2026-06-08 08:34:44 MarkDuplicates Tracking 124212 as yet unmatched pairs. 29910 records in RAM.
INFO 2026-06-08 08:34:46 MarkDuplicates Read 412,000,000 records. Elapsed time: 00:15:10s. Time for last 1,000,000: 1s. Last read position: chr19:40,255,198
INFO 2026-06-08 08:34:46 MarkDuplicates Tracking 122137 as yet unmatched pairs. 27835 records in RAM.
INFO 2026-06-08 08:34:49 MarkDuplicates Read 413,000,000 records. Elapsed time: 00:15:13s. Time for last 1,000,000: 2s. Last read position: chr19:41,762,196
INFO 2026-06-08 08:34:49 MarkDuplicates Tracking 119964 as yet unmatched pairs. 25662 records in RAM.
INFO 2026-06-08 08:34:51 MarkDuplicates Read 414,000,000 records. Elapsed time: 00:15:15s. Time for last 1,000,000: 1s. Last read position: chr19:43,552,174
INFO 2026-06-08 08:34:51 MarkDuplicates Tracking 116991 as yet unmatched pairs. 22679 records in RAM.
INFO 2026-06-08 08:34:53 MarkDuplicates Read 415,000,000 records. Elapsed time: 00:15:17s. Time for last 1,000,000: 1s. Last read position: chr19:45,263,326
INFO 2026-06-08 08:34:53 MarkDuplicates Tracking 114162 as yet unmatched pairs. 19850 records in RAM.
INFO 2026-06-08 08:34:55 MarkDuplicates Read 416,000,000 records. Elapsed time: 00:15:19s. Time for last 1,000,000: 1s. Last read position: chr19:46,787,871
INFO 2026-06-08 08:34:55 MarkDuplicates Tracking 111407 as yet unmatched pairs. 17094 records in RAM.
INFO 2026-06-08 08:34:56 MarkDuplicates Read 417,000,000 records. Elapsed time: 00:15:21s. Time for last 1,000,000: 1s. Last read position: chr19:48,615,386
INFO 2026-06-08 08:34:56 MarkDuplicates Tracking 109226 as yet unmatched pairs. 14913 records in RAM.
INFO 2026-06-08 08:34:58 MarkDuplicates Read 418,000,000 records. Elapsed time: 00:15:23s. Time for last 1,000,000: 1s. Last read position: chr19:49,525,476
INFO 2026-06-08 08:34:58 MarkDuplicates Tracking 106658 as yet unmatched pairs. 12345 records in RAM.
INFO 2026-06-08 08:35:00 MarkDuplicates Read 419,000,000 records. Elapsed time: 00:15:24s. Time for last 1,000,000: 1s. Last read position: chr19:50,480,899
INFO 2026-06-08 08:35:00 MarkDuplicates Tracking 103951 as yet unmatched pairs. 9638 records in RAM.
INFO 2026-06-08 08:35:02 MarkDuplicates Read 420,000,000 records. Elapsed time: 00:15:26s. Time for last 1,000,000: 2s. Last read position: chr19:54,206,385
INFO 2026-06-08 08:35:02 MarkDuplicates Tracking 102127 as yet unmatched pairs. 7814 records in RAM.
INFO 2026-06-08 08:35:04 MarkDuplicates Read 421,000,000 records. Elapsed time: 00:15:28s. Time for last 1,000,000: 2s. Last read position: chr19:55,386,582
INFO 2026-06-08 08:35:04 MarkDuplicates Tracking 99802 as yet unmatched pairs. 5489 records in RAM.
INFO 2026-06-08 08:35:06 MarkDuplicates Read 422,000,000 records. Elapsed time: 00:15:31s. Time for last 1,000,000: 2s. Last read position: chr19:57,808,591
INFO 2026-06-08 08:35:06 MarkDuplicates Tracking 97020 as yet unmatched pairs. 2707 records in RAM.
INFO 2026-06-08 08:35:08 MarkDuplicates Read 423,000,000 records. Elapsed time: 00:15:32s. Time for last 1,000,000: 1s. Last read position: chr19:58,548,861
INFO 2026-06-08 08:35:08 MarkDuplicates Tracking 94918 as yet unmatched pairs. 605 records in RAM.
INFO 2026-06-08 08:35:10 MarkDuplicates Read 424,000,000 records. Elapsed time: 00:15:34s. Time for last 1,000,000: 2s. Last read position: chr20:3,691,362
INFO 2026-06-08 08:35:10 MarkDuplicates Tracking 92496 as yet unmatched pairs. 22196 records in RAM.
INFO 2026-06-08 08:35:12 MarkDuplicates Read 425,000,000 records. Elapsed time: 00:15:36s. Time for last 1,000,000: 1s. Last read position: chr20:17,643,036
INFO 2026-06-08 08:35:12 MarkDuplicates Tracking 90198 as yet unmatched pairs. 19898 records in RAM.
INFO 2026-06-08 08:35:15 MarkDuplicates Read 426,000,000 records. Elapsed time: 00:15:39s. Time for last 1,000,000: 2s. Last read position: chr20:25,676,737
INFO 2026-06-08 08:35:15 MarkDuplicates Tracking 87955 as yet unmatched pairs. 17655 records in RAM.
INFO 2026-06-08 08:35:17 MarkDuplicates Read 427,000,000 records. Elapsed time: 00:15:41s. Time for last 1,000,000: 2s. Last read position: chr20:35,003,506
INFO 2026-06-08 08:35:17 MarkDuplicates Tracking 85703 as yet unmatched pairs. 15402 records in RAM.
INFO 2026-06-08 08:35:19 MarkDuplicates Read 428,000,000 records. Elapsed time: 00:15:44s. Time for last 1,000,000: 2s. Last read position: chr20:37,737,392
INFO 2026-06-08 08:35:19 MarkDuplicates Tracking 83370 as yet unmatched pairs. 13069 records in RAM.
INFO 2026-06-08 08:35:21 MarkDuplicates Read 429,000,000 records. Elapsed time: 00:15:46s. Time for last 1,000,000: 2s. Last read position: chr20:44,943,107
INFO 2026-06-08 08:35:21 MarkDuplicates Tracking 81095 as yet unmatched pairs. 10793 records in RAM.
INFO 2026-06-08 08:35:23 MarkDuplicates Read 430,000,000 records. Elapsed time: 00:15:48s. Time for last 1,000,000: 2s. Last read position: chr20:49,084,074
INFO 2026-06-08 08:35:23 MarkDuplicates Tracking 78748 as yet unmatched pairs. 8446 records in RAM.
INFO 2026-06-08 08:35:26 MarkDuplicates Read 431,000,000 records. Elapsed time: 00:15:50s. Time for last 1,000,000: 2s. Last read position: chr20:58,434,646
INFO 2026-06-08 08:35:26 MarkDuplicates Tracking 76268 as yet unmatched pairs. 5964 records in RAM.
INFO 2026-06-08 08:35:28 MarkDuplicates Read 432,000,000 records. Elapsed time: 00:15:52s. Time for last 1,000,000: 1s. Last read position: chr20:62,353,152
INFO 2026-06-08 08:35:28 MarkDuplicates Tracking 73571 as yet unmatched pairs. 3266 records in RAM.
INFO 2026-06-08 08:35:31 MarkDuplicates Read 433,000,000 records. Elapsed time: 00:15:55s. Time for last 1,000,000: 3s. Last read position: chr20:63,865,344
INFO 2026-06-08 08:35:31 MarkDuplicates Tracking 70909 as yet unmatched pairs. 604 records in RAM.
INFO 2026-06-08 08:35:33 MarkDuplicates Read 434,000,000 records. Elapsed time: 00:15:57s. Time for last 1,000,000: 1s. Last read position: chr21:8,252,339
INFO 2026-06-08 08:35:33 MarkDuplicates Tracking 69371 as yet unmatched pairs. 12588 records in RAM.
INFO 2026-06-08 08:35:34 MarkDuplicates Read 435,000,000 records. Elapsed time: 00:15:59s. Time for last 1,000,000: 1s. Last read position: chr21:8,441,953
INFO 2026-06-08 08:35:34 MarkDuplicates Tracking 68479 as yet unmatched pairs. 11687 records in RAM.
INFO 2026-06-08 08:35:36 MarkDuplicates Read 436,000,000 records. Elapsed time: 00:16:00s. Time for last 1,000,000: 1s. Last read position: chr21:26,966,159
INFO 2026-06-08 08:35:36 MarkDuplicates Tracking 66606 as yet unmatched pairs. 9814 records in RAM.
INFO 2026-06-08 08:35:39 MarkDuplicates Read 437,000,000 records. Elapsed time: 00:16:03s. Time for last 1,000,000: 2s. Last read position: chr21:36,245,205
INFO 2026-06-08 08:35:39 MarkDuplicates Tracking 64330 as yet unmatched pairs. 7538 records in RAM.
INFO 2026-06-08 08:35:42 MarkDuplicates Read 438,000,000 records. Elapsed time: 00:16:06s. Time for last 1,000,000: 3s. Last read position: chr21:42,313,504
INFO 2026-06-08 08:35:42 MarkDuplicates Tracking 63776 as yet unmatched pairs. 6984 records in RAM.
INFO 2026-06-08 08:35:44 MarkDuplicates Read 439,000,000 records. Elapsed time: 00:16:08s. Time for last 1,000,000: 2s. Last read position: chr21:45,510,192
INFO 2026-06-08 08:35:44 MarkDuplicates Tracking 59791 as yet unmatched pairs. 2998 records in RAM.
INFO 2026-06-08 08:35:46 MarkDuplicates Read 440,000,000 records. Elapsed time: 00:16:10s. Time for last 1,000,000: 2s. Last read position: chr21:46,430,586
INFO 2026-06-08 08:35:46 MarkDuplicates Tracking 57067 as yet unmatched pairs. 274 records in RAM.
INFO 2026-06-08 08:35:48 MarkDuplicates Read 441,000,000 records. Elapsed time: 00:16:13s. Time for last 1,000,000: 2s. Last read position: chr22:20,668,081
INFO 2026-06-08 08:35:48 MarkDuplicates Tracking 54583 as yet unmatched pairs. 24095 records in RAM.
INFO 2026-06-08 08:35:50 MarkDuplicates Read 442,000,000 records. Elapsed time: 00:16:14s. Time for last 1,000,000: 1s. Last read position: chr22:23,782,425
INFO 2026-06-08 08:35:50 MarkDuplicates Tracking 52912 as yet unmatched pairs. 22424 records in RAM.
INFO 2026-06-08 08:35:52 MarkDuplicates Read 443,000,000 records. Elapsed time: 00:16:16s. Time for last 1,000,000: 1s. Last read position: chr22:28,795,706
INFO 2026-06-08 08:35:52 MarkDuplicates Tracking 53164 as yet unmatched pairs. 22676 records in RAM.
INFO 2026-06-08 08:35:54 MarkDuplicates Read 444,000,000 records. Elapsed time: 00:16:18s. Time for last 1,000,000: 1s. Last read position: chr22:30,340,308
INFO 2026-06-08 08:35:54 MarkDuplicates Tracking 47211 as yet unmatched pairs. 16723 records in RAM.
INFO 2026-06-08 08:35:56 MarkDuplicates Read 445,000,000 records. Elapsed time: 00:16:20s. Time for last 1,000,000: 1s. Last read position: chr22:36,141,453
INFO 2026-06-08 08:35:56 MarkDuplicates Tracking 44745 as yet unmatched pairs. 14257 records in RAM.
INFO 2026-06-08 08:35:58 MarkDuplicates Read 446,000,000 records. Elapsed time: 00:16:22s. Time for last 1,000,000: 2s. Last read position: chr22:37,299,255
INFO 2026-06-08 08:35:58 MarkDuplicates Tracking 42247 as yet unmatched pairs. 11759 records in RAM.
INFO 2026-06-08 08:36:00 MarkDuplicates Read 447,000,000 records. Elapsed time: 00:16:24s. Time for last 1,000,000: 1s. Last read position: chr22:38,501,274
INFO 2026-06-08 08:36:00 MarkDuplicates Tracking 40062 as yet unmatched pairs. 9573 records in RAM.
INFO 2026-06-08 08:36:01 MarkDuplicates Read 448,000,000 records. Elapsed time: 00:16:26s. Time for last 1,000,000: 1s. Last read position: chr22:41,160,616
INFO 2026-06-08 08:36:01 MarkDuplicates Tracking 37387 as yet unmatched pairs. 6898 records in RAM.
INFO 2026-06-08 08:36:03 MarkDuplicates Read 449,000,000 records. Elapsed time: 00:16:28s. Time for last 1,000,000: 1s. Last read position: chr22:45,563,034
INFO 2026-06-08 08:36:03 MarkDuplicates Tracking 35056 as yet unmatched pairs. 4566 records in RAM.
INFO 2026-06-08 08:36:05 MarkDuplicates Read 450,000,000 records. Elapsed time: 00:16:30s. Time for last 1,000,000: 1s. Last read position: chr22:50,284,132
INFO 2026-06-08 08:36:05 MarkDuplicates Tracking 32352 as yet unmatched pairs. 1862 records in RAM.
INFO 2026-06-08 08:36:08 MarkDuplicates Read 451,000,000 records. Elapsed time: 00:16:32s. Time for last 1,000,000: 2s. Last read position: chrX:3,317,503
INFO 2026-06-08 08:36:08 MarkDuplicates Tracking 29525 as yet unmatched pairs. 24041 records in RAM.
INFO 2026-06-08 08:36:09 MarkDuplicates Read 452,000,000 records. Elapsed time: 00:16:34s. Time for last 1,000,000: 1s. Last read position: chrX:17,103,738
INFO 2026-06-08 08:36:09 MarkDuplicates Tracking 27702 as yet unmatched pairs. 22218 records in RAM.
INFO 2026-06-08 08:36:12 MarkDuplicates Read 453,000,000 records. Elapsed time: 00:16:36s. Time for last 1,000,000: 2s. Last read position: chrX:40,597,542
INFO 2026-06-08 08:36:12 MarkDuplicates Tracking 25303 as yet unmatched pairs. 19800 records in RAM.
INFO 2026-06-08 08:36:14 MarkDuplicates Read 454,000,000 records. Elapsed time: 00:16:39s. Time for last 1,000,000: 2s. Last read position: chrX:47,585,239
INFO 2026-06-08 08:36:14 MarkDuplicates Tracking 23099 as yet unmatched pairs. 17594 records in RAM.
INFO 2026-06-08 08:36:18 MarkDuplicates Read 455,000,000 records. Elapsed time: 00:16:43s. Time for last 1,000,000: 3s. Last read position: chrX:53,380,102
INFO 2026-06-08 08:36:18 MarkDuplicates Tracking 20594 as yet unmatched pairs. 15089 records in RAM.
INFO 2026-06-08 08:36:22 MarkDuplicates Read 456,000,000 records. Elapsed time: 00:16:46s. Time for last 1,000,000: 3s. Last read position: chrX:65,739,748
INFO 2026-06-08 08:36:22 MarkDuplicates Tracking 18330 as yet unmatched pairs. 12825 records in RAM.
INFO 2026-06-08 08:36:24 MarkDuplicates Read 457,000,000 records. Elapsed time: 00:16:48s. Time for last 1,000,000: 2s. Last read position: chrX:74,592,632
INFO 2026-06-08 08:36:24 MarkDuplicates Tracking 16214 as yet unmatched pairs. 10709 records in RAM.
INFO 2026-06-08 08:36:26 MarkDuplicates Read 458,000,000 records. Elapsed time: 00:16:50s. Time for last 1,000,000: 1s. Last read position: chrX:101,391,464
INFO 2026-06-08 08:36:26 MarkDuplicates Tracking 14329 as yet unmatched pairs. 8824 records in RAM.
INFO 2026-06-08 08:36:28 MarkDuplicates Read 459,000,000 records. Elapsed time: 00:16:52s. Time for last 1,000,000: 1s. Last read position: chrX:118,396,969
INFO 2026-06-08 08:36:28 MarkDuplicates Tracking 12198 as yet unmatched pairs. 6693 records in RAM.
INFO 2026-06-08 08:36:30 MarkDuplicates Read 460,000,000 records. Elapsed time: 00:16:54s. Time for last 1,000,000: 2s. Last read position: chrX:136,499,603
INFO 2026-06-08 08:36:30 MarkDuplicates Tracking 9937 as yet unmatched pairs. 4432 records in RAM.
INFO 2026-06-08 08:36:33 MarkDuplicates Read 461,000,000 records. Elapsed time: 00:16:58s. Time for last 1,000,000: 3s. Last read position: chrX:154,032,333
INFO 2026-06-08 08:36:33 MarkDuplicates Tracking 7758 as yet unmatched pairs. 2251 records in RAM.
INFO 2026-06-08 08:36:35 MarkDuplicates Read 462,000,000 records. Elapsed time: 00:17:00s. Time for last 1,000,000: 1s. Last read position: chrX:156,025,017
INFO 2026-06-08 08:36:35 MarkDuplicates Tracking 5514 as yet unmatched pairs. 7 records in RAM.
INFO 2026-06-08 08:36:37 MarkDuplicates Read 463,000,000 records. Elapsed time: 00:17:01s. Time for last 1,000,000: 1s. Last read position: GL000220.1:158,222
INFO 2026-06-08 08:36:37 MarkDuplicates Tracking 3836 as yet unmatched pairs. 75 records in RAM.
INFO 2026-06-08 08:36:38 MarkDuplicates Read 464,000,000 records. Elapsed time: 00:17:02s. Time for last 1,000,000: 1s. Last read position: KI270733.1:133,596
INFO 2026-06-08 08:36:38 MarkDuplicates Tracking 587 as yet unmatched pairs. 535 records in RAM.
INFO 2026-06-08 08:36:39 MarkDuplicates Read 464885229 records. 0 pairs never matched.
INFO 2026-06-08 08:37:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 39933197240; totalMemory: 57042534400; maxMemory: 63585648640
INFO 2026-06-08 08:37:50 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:38:12 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:38:35 OpticalDuplicateFinder Large duplicate set. size = 2216
INFO 2026-06-08 08:38:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,753
INFO 2026-06-08 08:38:35 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,739
INFO 2026-06-08 08:38:35 OpticalDuplicateFinder Large duplicate set. size = 1039
INFO 2026-06-08 08:38:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:26,281
INFO 2026-06-08 08:38:35 OpticalDuplicateFinder Large duplicate set. size = 1051
INFO 2026-06-08 08:38:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,550
INFO 2026-06-08 08:38:35 OpticalDuplicateFinder Large duplicate set. size = 1247
INFO 2026-06-08 08:38:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-19,467
INFO 2026-06-08 08:38:35 OpticalDuplicateFinder Large duplicate set. size = 1181
INFO 2026-06-08 08:38:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,930
INFO 2026-06-08 08:38:35 OpticalDuplicateFinder Large duplicate set. size = 1060
INFO 2026-06-08 08:38:35 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:7,415
INFO 2026-06-08 08:38:36 OpticalDuplicateFinder Large duplicate set. size = 1039
INFO 2026-06-08 08:38:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:1,162
INFO 2026-06-08 08:38:36 OpticalDuplicateFinder Large duplicate set. size = 1054
INFO 2026-06-08 08:38:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,694
INFO 2026-06-08 08:38:37 OpticalDuplicateFinder Large duplicate set. size = 1051
INFO 2026-06-08 08:38:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,713
INFO 2026-06-08 08:38:42 OpticalDuplicateFinder Large duplicate set. size = 1182
INFO 2026-06-08 08:38:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,322
INFO 2026-06-08 08:38:42 OpticalDuplicateFinder Large duplicate set. size = 1203
INFO 2026-06-08 08:38:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,691
INFO 2026-06-08 08:38:42 OpticalDuplicateFinder Large duplicate set. size = 1855
INFO 2026-06-08 08:38:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-14,791
INFO 2026-06-08 08:38:42 OpticalDuplicateFinder Large duplicate set. size = 1063
INFO 2026-06-08 08:38:42 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,767
INFO 2026-06-08 08:39:06 OpticalDuplicateFinder Large duplicate set. size = 1486
INFO 2026-06-08 08:39:06 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,234
INFO 2026-06-08 08:39:06 OpticalDuplicateFinder Large duplicate set. size = 1165
INFO 2026-06-08 08:39:06 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,098
INFO 2026-06-08 08:39:06 OpticalDuplicateFinder Large duplicate set. size = 1390
INFO 2026-06-08 08:39:06 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:10,215
INFO 2026-06-08 08:39:06 OpticalDuplicateFinder Large duplicate set. size = 1030
INFO 2026-06-08 08:39:06 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,996
INFO 2026-06-08 08:39:06 OpticalDuplicateFinder Large duplicate set. size = 1342
INFO 2026-06-08 08:39:06 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,025
INFO 2026-06-08 08:39:06 OpticalDuplicateFinder Large duplicate set. size = 1022
INFO 2026-06-08 08:39:06 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-14,605
INFO 2026-06-08 08:39:07 OpticalDuplicateFinder Large duplicate set. size = 1178
INFO 2026-06-08 08:39:07 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,291
INFO 2026-06-08 08:39:07 OpticalDuplicateFinder Large duplicate set. size = 1447
INFO 2026-06-08 08:39:07 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,703
INFO 2026-06-08 08:39:07 OpticalDuplicateFinder Large duplicate set. size = 1356
INFO 2026-06-08 08:39:07 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,956
INFO 2026-06-08 08:39:07 OpticalDuplicateFinder Large duplicate set. size = 1001
INFO 2026-06-08 08:39:07 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,034
INFO 2026-06-08 08:39:07 OpticalDuplicateFinder Large duplicate set. size = 1045
INFO 2026-06-08 08:39:07 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:6,081
INFO 2026-06-08 08:39:07 OpticalDuplicateFinder Large duplicate set. size = 1055
INFO 2026-06-08 08:39:07 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:5,369
INFO 2026-06-08 08:39:07 OpticalDuplicateFinder Large duplicate set. size = 1090
INFO 2026-06-08 08:39:07 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-27,346
INFO 2026-06-08 08:39:07 OpticalDuplicateFinder Large duplicate set. size = 1544
INFO 2026-06-08 08:39:07 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,158
INFO 2026-06-08 08:39:07 OpticalDuplicateFinder Large duplicate set. size = 1083
INFO 2026-06-08 08:39:07 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,558
INFO 2026-06-08 08:39:07 OpticalDuplicateFinder Large duplicate set. size = 1313
INFO 2026-06-08 08:39:07 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,190
INFO 2026-06-08 08:39:07 OpticalDuplicateFinder Large duplicate set. size = 1149
INFO 2026-06-08 08:39:07 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-27,516
INFO 2026-06-08 08:39:07 OpticalDuplicateFinder Large duplicate set. size = 1040
INFO 2026-06-08 08:39:07 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,153
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder Large duplicate set. size = 1007
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-25,405
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder Large duplicate set. size = 1021
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,087
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder Large duplicate set. size = 1136
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,172
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder Large duplicate set. size = 1992
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,744
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder Large duplicate set. size = 1432
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,800
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder Large duplicate set. size = 1075
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:4,778
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder Large duplicate set. size = 1338
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,793
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder Large duplicate set. size = 1568
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,066
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder Large duplicate set. size = 1180
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,866
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder Large duplicate set. size = 1249
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:26,993
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder Large duplicate set. size = 1547
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,099
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder Large duplicate set. size = 1009
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:14,413
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder Large duplicate set. size = 2490
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,756
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:25,610
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder Large duplicate set. size = 1221
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,383
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder Large duplicate set. size = 1780
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:8,030
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder Large duplicate set. size = 2093
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,789
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:17,067
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder Large duplicate set. size = 1597
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,982
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder Large duplicate set. size = 1845
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,552
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder Large duplicate set. size = 1692
INFO 2026-06-08 08:39:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,465
INFO 2026-06-08 08:39:09 OpticalDuplicateFinder Large duplicate set. size = 1500
INFO 2026-06-08 08:39:09 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,836
INFO 2026-06-08 08:39:09 OpticalDuplicateFinder Large duplicate set. size = 1819
INFO 2026-06-08 08:39:09 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,225
INFO 2026-06-08 08:39:37 MarkDuplicates Traversing fragment information and detecting duplicates.
WARNING 2026-06-08 08:39:38 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
INFO 2026-06-08 08:40:42 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:40:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 204603720; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:40:43 MarkDuplicates Marking 276121682 records as duplicates.
INFO 2026-06-08 08:40:43 MarkDuplicates Found 7380414 optical duplicate clusters.
INFO 2026-06-08 08:40:43 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 08:41:01 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:18s. Time for last 10,000,000: 18s. Last read position: chr1:43,591,378
INFO 2026-06-08 08:41:19 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:36s. Time for last 10,000,000: 17s. Last read position: chr1:147,624,040
INFO 2026-06-08 08:41:37 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:54s. Time for last 10,000,000: 17s. Last read position: chr1:156,669,730
INFO 2026-06-08 08:41:56 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:13s. Time for last 10,000,000: 18s. Last read position: chr1:208,210,376
INFO 2026-06-08 08:42:14 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:31s. Time for last 10,000,000: 18s. Last read position: chr2:32,916,264
INFO 2026-06-08 08:42:32 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:49s. Time for last 10,000,000: 18s. Last read position: chr2:110,533,490
INFO 2026-06-08 08:42:50 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:07s. Time for last 10,000,000: 18s. Last read position: chr2:178,618,265
INFO 2026-06-08 08:43:09 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:25s. Time for last 10,000,000: 18s. Last read position: chr2:215,375,249
INFO 2026-06-08 08:43:27 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:43s. Time for last 10,000,000: 17s. Last read position: chr2:233,551,412
INFO 2026-06-08 08:43:45 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:03:02s. Time for last 10,000,000: 18s. Last read position: chr3:52,471,835
INFO 2026-06-08 08:44:04 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:03:20s. Time for last 10,000,000: 18s. Last read position: chr3:172,764,457
INFO 2026-06-08 08:44:22 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:39s. Time for last 10,000,000: 18s. Last read position: chr4:88,008,064
INFO 2026-06-08 08:44:40 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:57s. Time for last 10,000,000: 18s. Last read position: chr5:69,420,484
INFO 2026-06-08 08:44:58 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:04:15s. Time for last 10,000,000: 18s. Last read position: chr5:141,524,143
INFO 2026-06-08 08:45:16 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:04:33s. Time for last 10,000,000: 17s. Last read position: chr6:10,751,190
INFO 2026-06-08 08:45:34 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:50s. Time for last 10,000,000: 17s. Last read position: chr6:41,587,740
INFO 2026-06-08 08:45:52 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:05:08s. Time for last 10,000,000: 17s. Last read position: chr7:2,647,236
INFO 2026-06-08 08:46:09 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:05:26s. Time for last 10,000,000: 17s. Last read position: chr7:94,401,599
INFO 2026-06-08 08:46:27 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:05:44s. Time for last 10,000,000: 17s. Last read position: chr7:152,176,295
INFO 2026-06-08 08:46:45 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:06:02s. Time for last 10,000,000: 17s. Last read position: chr8:115,619,353
INFO 2026-06-08 08:47:03 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:06:20s. Time for last 10,000,000: 17s. Last read position: chr9:68,483,877
INFO 2026-06-08 08:47:21 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:06:38s. Time for last 10,000,000: 17s. Last read position: chr9:137,436,888
INFO 2026-06-08 08:47:39 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:06:56s. Time for last 10,000,000: 17s. Last read position: chr10:96,159,863
INFO 2026-06-08 08:47:57 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:07:14s. Time for last 10,000,000: 17s. Last read position: chr11:35,663,218
INFO 2026-06-08 08:48:15 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:07:32s. Time for last 10,000,000: 18s. Last read position: chr11:67,995,685
INFO 2026-06-08 08:48:33 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:07:50s. Time for last 10,000,000: 17s. Last read position: chr12:354,078
INFO 2026-06-08 08:48:51 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:08:08s. Time for last 10,000,000: 17s. Last read position: chr12:40,542,283
INFO 2026-06-08 08:49:09 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:08:25s. Time for last 10,000,000: 17s. Last read position: chr12:66,153,359
INFO 2026-06-08 08:49:32 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:08:49s. Time for last 10,000,000: 23s. Last read position: chr13:23,340,427
INFO 2026-06-08 08:49:55 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:09:12s. Time for last 10,000,000: 22s. Last read position: chr14:59,498,798
INFO 2026-06-08 08:50:16 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:09:32s. Time for last 10,000,000: 20s. Last read position: chr15:38,299,472
INFO 2026-06-08 08:50:34 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:09:51s. Time for last 10,000,000: 18s. Last read position: chr16:671,977
INFO 2026-06-08 08:50:53 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:10:10s. Time for last 10,000,000: 18s. Last read position: chr16:18,351,456
INFO 2026-06-08 08:51:12 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:10:28s. Time for last 10,000,000: 18s. Last read position: chr16:31,182,525
INFO 2026-06-08 08:51:30 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:10:47s. Time for last 10,000,000: 18s. Last read position: chr17:8,228,128
INFO 2026-06-08 08:51:48 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:11:05s. Time for last 10,000,000: 18s. Last read position: chr17:40,416,004
INFO 2026-06-08 08:52:13 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:11:29s. Time for last 10,000,000: 24s. Last read position: chr17:50,188,931
INFO 2026-06-08 08:52:35 MarkDuplicates Written 380,000,000 records. Elapsed time: 00:11:52s. Time for last 10,000,000: 22s. Last read position: chr17:50,197,740
INFO 2026-06-08 08:52:53 MarkDuplicates Written 390,000,000 records. Elapsed time: 00:12:10s. Time for last 10,000,000: 17s. Last read position: chr17:78,870,897
INFO 2026-06-08 08:53:12 MarkDuplicates Written 400,000,000 records. Elapsed time: 00:12:29s. Time for last 10,000,000: 19s. Last read position: chr19:4,719,851
INFO 2026-06-08 08:53:32 MarkDuplicates Written 410,000,000 records. Elapsed time: 00:12:48s. Time for last 10,000,000: 19s. Last read position: chr19:38,417,083
INFO 2026-06-08 08:53:51 MarkDuplicates Written 420,000,000 records. Elapsed time: 00:13:08s. Time for last 10,000,000: 19s. Last read position: chr19:54,206,385
INFO 2026-06-08 08:54:09 MarkDuplicates Written 430,000,000 records. Elapsed time: 00:13:26s. Time for last 10,000,000: 18s. Last read position: chr20:49,084,074
INFO 2026-06-08 08:54:27 MarkDuplicates Written 440,000,000 records. Elapsed time: 00:13:44s. Time for last 10,000,000: 17s. Last read position: chr21:46,430,586
INFO 2026-06-08 08:54:46 MarkDuplicates Written 450,000,000 records. Elapsed time: 00:14:02s. Time for last 10,000,000: 18s. Last read position: chr22:50,284,132
INFO 2026-06-08 08:55:07 MarkDuplicates Written 460,000,000 records. Elapsed time: 00:14:24s. Time for last 10,000,000: 21s. Last read position: chrX:136,499,603
INFO 2026-06-08 08:55:25 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:55:25 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:55:25 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:55:25 MarkDuplicates Before output close freeMemory: 204548688; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:55:25 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:55:25 MarkDuplicates After output close freeMemory: 104802688; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 08:55:25 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 35.87 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory