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 tih_rna_sample_00576_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00576_B23MVV7LT4_1.md.bam --METRICS_FILE tih_rna_sample_00576_B23MVV7LT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
08:16:18.963 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 08:16:18 GMT 2026] MarkDuplicates --INPUT tih_rna_sample_00576_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00576_B23MVV7LT4_1.md.bam --METRICS_FILE tih_rna_sample_00576_B23MVV7LT4_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 08:16:18 GMT 2026] Executing as ?@nf-94787b9ca6b5645f1d5da38d1058352c-67454-42fkn 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 08:16:19 MarkDuplicates Start of doWork freeMemory: 105828392; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 08:16:19 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 08:16:19 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 08:16:23 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:1,482,289
INFO 2026-06-08 08:16:23 MarkDuplicates Tracking 2914 as yet unmatched pairs. 134 records in RAM.
INFO 2026-06-08 08:16:27 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 3s. Last read position: chr1:7,970,950
INFO 2026-06-08 08:16:27 MarkDuplicates Tracking 5767 as yet unmatched pairs. 251 records in RAM.
INFO 2026-06-08 08:16:30 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 3s. Last read position: chr1:12,022,153
INFO 2026-06-08 08:16:30 MarkDuplicates Tracking 8223 as yet unmatched pairs. 123 records in RAM.
INFO 2026-06-08 08:16:32 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 2s. Last read position: chr1:17,409,184
INFO 2026-06-08 08:16:32 MarkDuplicates Tracking 10782 as yet unmatched pairs. 327 records in RAM.
INFO 2026-06-08 08:16:35 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: chr1:21,846,131
INFO 2026-06-08 08:16:35 MarkDuplicates Tracking 13149 as yet unmatched pairs. 214 records in RAM.
INFO 2026-06-08 08:16:37 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 2s. Last read position: chr1:24,666,865
INFO 2026-06-08 08:16:37 MarkDuplicates Tracking 15482 as yet unmatched pairs. 126 records in RAM.
INFO 2026-06-08 08:16:39 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 2s. Last read position: chr1:27,666,410
INFO 2026-06-08 08:16:39 MarkDuplicates Tracking 20252 as yet unmatched pairs. 2413 records in RAM.
INFO 2026-06-08 08:16:42 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 2s. Last read position: chr1:31,908,835
INFO 2026-06-08 08:16:42 MarkDuplicates Tracking 21000 as yet unmatched pairs. 513 records in RAM.
INFO 2026-06-08 08:16:45 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 2s. Last read position: chr1:35,435,034
INFO 2026-06-08 08:16:45 MarkDuplicates Tracking 23175 as yet unmatched pairs. 175 records in RAM.
INFO 2026-06-08 08:16:47 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 2s. Last read position: chr1:39,422,483
INFO 2026-06-08 08:16:47 MarkDuplicates Tracking 25531 as yet unmatched pairs. 87 records in RAM.
INFO 2026-06-08 08:16:50 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 2s. Last read position: chr1:43,603,344
INFO 2026-06-08 08:16:50 MarkDuplicates Tracking 28036 as yet unmatched pairs. 122 records in RAM.
INFO 2026-06-08 08:16:52 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 1s. Last read position: chr1:48,089,462
INFO 2026-06-08 08:16:52 MarkDuplicates Tracking 30475 as yet unmatched pairs. 9 records in RAM.
INFO 2026-06-08 08:16:54 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 2s. Last read position: chr1:61,082,707
INFO 2026-06-08 08:16:54 MarkDuplicates Tracking 33304 as yet unmatched pairs. 355 records in RAM.
INFO 2026-06-08 08:16:57 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 3s. Last read position: chr1:78,655,374
INFO 2026-06-08 08:16:57 MarkDuplicates Tracking 35627 as yet unmatched pairs. 313 records in RAM.
INFO 2026-06-08 08:16:59 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 2s. Last read position: chr1:99,910,756
INFO 2026-06-08 08:16:59 MarkDuplicates Tracking 37707 as yet unmatched pairs. 200 records in RAM.
INFO 2026-06-08 08:17:01 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 2s. Last read position: chr1:110,603,476
INFO 2026-06-08 08:17:01 MarkDuplicates Tracking 40022 as yet unmatched pairs. 14 records in RAM.
INFO 2026-06-08 08:17:04 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 2s. Last read position: chr1:116,754,938
INFO 2026-06-08 08:17:04 MarkDuplicates Tracking 42270 as yet unmatched pairs. 45 records in RAM.
INFO 2026-06-08 08:17:06 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 1s. Last read position: chr1:120,453,879
INFO 2026-06-08 08:17:06 MarkDuplicates Tracking 44632 as yet unmatched pairs. 105 records in RAM.
INFO 2026-06-08 08:17:08 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 1s. Last read position: chr1:146,135,337
INFO 2026-06-08 08:17:08 MarkDuplicates Tracking 46028 as yet unmatched pairs. 282 records in RAM.
INFO 2026-06-08 08:17:10 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 2s. Last read position: chr1:148,590,885
INFO 2026-06-08 08:17:10 MarkDuplicates Tracking 46971 as yet unmatched pairs. 108 records in RAM.
INFO 2026-06-08 08:17:12 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 1s. Last read position: chr1:149,926,699
INFO 2026-06-08 08:17:12 MarkDuplicates Tracking 48404 as yet unmatched pairs. 204 records in RAM.
INFO 2026-06-08 08:17:14 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 1s. Last read position: chr1:151,198,980
INFO 2026-06-08 08:17:14 MarkDuplicates Tracking 50883 as yet unmatched pairs. 248 records in RAM.
INFO 2026-06-08 08:17:16 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 2s. Last read position: chr1:153,631,758
INFO 2026-06-08 08:17:16 MarkDuplicates Tracking 53205 as yet unmatched pairs. 40 records in RAM.
INFO 2026-06-08 08:17:19 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 2s. Last read position: chr1:154,207,480
INFO 2026-06-08 08:17:19 MarkDuplicates Tracking 56062 as yet unmatched pairs. 565 records in RAM.
INFO 2026-06-08 08:17:21 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 2s. Last read position: chr1:155,058,049
INFO 2026-06-08 08:17:21 MarkDuplicates Tracking 58171 as yet unmatched pairs. 257 records in RAM.
INFO 2026-06-08 08:17:23 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 1s. Last read position: chr1:155,747,306
INFO 2026-06-08 08:17:23 MarkDuplicates Tracking 60369 as yet unmatched pairs. 132 records in RAM.
INFO 2026-06-08 08:17:26 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 2s. Last read position: chr1:156,592,122
INFO 2026-06-08 08:17:26 MarkDuplicates Tracking 62962 as yet unmatched pairs. 166 records in RAM.
INFO 2026-06-08 08:17:28 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 2s. Last read position: chr1:159,920,367
INFO 2026-06-08 08:17:28 MarkDuplicates Tracking 65435 as yet unmatched pairs. 400 records in RAM.
INFO 2026-06-08 08:17:31 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 2s. Last read position: chr1:161,542,739
INFO 2026-06-08 08:17:31 MarkDuplicates Tracking 69182 as yet unmatched pairs. 1753 records in RAM.
INFO 2026-06-08 08:17:32 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 1s. Last read position: chr1:171,515,835
INFO 2026-06-08 08:17:32 MarkDuplicates Tracking 70059 as yet unmatched pairs. 330 records in RAM.
INFO 2026-06-08 08:17:34 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 1s. Last read position: chr1:178,906,789
INFO 2026-06-08 08:17:34 MarkDuplicates Tracking 72368 as yet unmatched pairs. 437 records in RAM.
INFO 2026-06-08 08:17:36 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 1s. Last read position: chr1:186,318,737
INFO 2026-06-08 08:17:36 MarkDuplicates Tracking 75389 as yet unmatched pairs. 870 records in RAM.
INFO 2026-06-08 08:17:38 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 2s. Last read position: chr1:201,468,566
INFO 2026-06-08 08:17:38 MarkDuplicates Tracking 76792 as yet unmatched pairs. 117 records in RAM.
INFO 2026-06-08 08:17:40 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 2s. Last read position: chr1:204,410,139
INFO 2026-06-08 08:17:40 MarkDuplicates Tracking 79172 as yet unmatched pairs. 176 records in RAM.
INFO 2026-06-08 08:17:42 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 1s. Last read position: chr1:211,313,472
INFO 2026-06-08 08:17:42 MarkDuplicates Tracking 81600 as yet unmatched pairs. 366 records in RAM.
INFO 2026-06-08 08:17:44 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 2s. Last read position: chr1:222,724,145
INFO 2026-06-08 08:17:44 MarkDuplicates Tracking 83694 as yet unmatched pairs. 166 records in RAM.
INFO 2026-06-08 08:17:46 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 1s. Last read position: chr1:226,152,342
INFO 2026-06-08 08:17:46 MarkDuplicates Tracking 86088 as yet unmatched pairs. 308 records in RAM.
INFO 2026-06-08 08:17:48 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 1s. Last read position: chr1:231,336,240
INFO 2026-06-08 08:17:48 MarkDuplicates Tracking 88599 as yet unmatched pairs. 106 records in RAM.
INFO 2026-06-08 08:17:50 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 1s. Last read position: chr1:240,144,855
INFO 2026-06-08 08:17:50 MarkDuplicates Tracking 91125 as yet unmatched pairs. 10 records in RAM.
INFO 2026-06-08 08:17:53 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 3s. Last read position: chr2:3,192,452
INFO 2026-06-08 08:17:53 MarkDuplicates Tracking 93552 as yet unmatched pairs. 93207 records in RAM.
INFO 2026-06-08 08:17:56 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 3s. Last read position: chr2:20,203,131
INFO 2026-06-08 08:17:56 MarkDuplicates Tracking 96342 as yet unmatched pairs. 95986 records in RAM.
INFO 2026-06-08 08:17:59 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 2s. Last read position: chr2:27,337,942
INFO 2026-06-08 08:17:59 MarkDuplicates Tracking 98701 as yet unmatched pairs. 98342 records in RAM.
INFO 2026-06-08 08:18:01 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,258
INFO 2026-06-08 08:18:01 MarkDuplicates Tracking 136810 as yet unmatched pairs. 97634 records in RAM.
INFO 2026-06-08 08:18:04 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,264
INFO 2026-06-08 08:18:04 MarkDuplicates Tracking 703940 as yet unmatched pairs. 60700 records in RAM.
INFO 2026-06-08 08:18:05 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,406
INFO 2026-06-08 08:18:05 MarkDuplicates Tracking 813719 as yet unmatched pairs. 53444 records in RAM.
INFO 2026-06-08 08:18:07 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 1s. Last read position: chr2:41,157,335
INFO 2026-06-08 08:18:07 MarkDuplicates Tracking 861353 as yet unmatched pairs. 49127 records in RAM.
INFO 2026-06-08 08:18:09 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 1s. Last read position: chr2:54,629,492
INFO 2026-06-08 08:18:09 MarkDuplicates Tracking 858998 as yet unmatched pairs. 46763 records in RAM.
INFO 2026-06-08 08:18:11 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 2s. Last read position: chr2:65,072,258
INFO 2026-06-08 08:18:11 MarkDuplicates Tracking 856688 as yet unmatched pairs. 44451 records in RAM.
INFO 2026-06-08 08:18:13 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 1s. Last read position: chr2:74,048,146
INFO 2026-06-08 08:18:13 MarkDuplicates Tracking 854175 as yet unmatched pairs. 41937 records in RAM.
INFO 2026-06-08 08:18:15 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 1s. Last read position: chr2:86,529,222
INFO 2026-06-08 08:18:15 MarkDuplicates Tracking 851865 as yet unmatched pairs. 39612 records in RAM.
INFO 2026-06-08 08:18:17 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 2s. Last read position: chr2:97,158,114
INFO 2026-06-08 08:18:17 MarkDuplicates Tracking 849684 as yet unmatched pairs. 37427 records in RAM.
INFO 2026-06-08 08:18:19 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 1s. Last read position: chr2:108,766,204
INFO 2026-06-08 08:18:19 MarkDuplicates Tracking 847719 as yet unmatched pairs. 35453 records in RAM.
INFO 2026-06-08 08:18:21 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 1s. Last read position: chr2:119,955,171
INFO 2026-06-08 08:18:21 MarkDuplicates Tracking 845828 as yet unmatched pairs. 33557 records in RAM.
INFO 2026-06-08 08:18:22 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 1s. Last read position: chr2:135,788,427
INFO 2026-06-08 08:18:22 MarkDuplicates Tracking 843694 as yet unmatched pairs. 31406 records in RAM.
INFO 2026-06-08 08:18:24 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 1s. Last read position: chr2:161,308,499
INFO 2026-06-08 08:18:24 MarkDuplicates Tracking 841333 as yet unmatched pairs. 29033 records in RAM.
INFO 2026-06-08 08:18:27 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 2s. Last read position: chr2:177,219,142
INFO 2026-06-08 08:18:27 MarkDuplicates Tracking 839285 as yet unmatched pairs. 26974 records in RAM.
INFO 2026-06-08 08:18:29 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 2s. Last read position: chr2:188,998,707
INFO 2026-06-08 08:18:29 MarkDuplicates Tracking 837295 as yet unmatched pairs. 24975 records in RAM.
INFO 2026-06-08 08:18:32 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 2s. Last read position: chr2:196,769,864
INFO 2026-06-08 08:18:32 MarkDuplicates Tracking 834369 as yet unmatched pairs. 22046 records in RAM.
INFO 2026-06-08 08:18:34 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 2s. Last read position: chr2:207,575,385
INFO 2026-06-08 08:18:34 MarkDuplicates Tracking 832266 as yet unmatched pairs. 19923 records in RAM.
INFO 2026-06-08 08:18:36 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 2s. Last read position: chr2:215,370,395
INFO 2026-06-08 08:18:36 MarkDuplicates Tracking 835060 as yet unmatched pairs. 22704 records in RAM.
INFO 2026-06-08 08:18:38 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 2s. Last read position: chr2:215,384,892
INFO 2026-06-08 08:18:38 MarkDuplicates Tracking 830720 as yet unmatched pairs. 18364 records in RAM.
INFO 2026-06-08 08:18:40 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 1s. Last read position: chr2:215,414,859
INFO 2026-06-08 08:18:40 MarkDuplicates Tracking 827049 as yet unmatched pairs. 14688 records in RAM.
INFO 2026-06-08 08:18:42 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr2:217,809,822
INFO 2026-06-08 08:18:42 MarkDuplicates Tracking 823117 as yet unmatched pairs. 10754 records in RAM.
INFO 2026-06-08 08:18:44 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 1s. Last read position: chr2:219,565,461
INFO 2026-06-08 08:18:44 MarkDuplicates Tracking 820627 as yet unmatched pairs. 8256 records in RAM.
INFO 2026-06-08 08:18:46 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 2s. Last read position: chr2:231,278,437
INFO 2026-06-08 08:18:46 MarkDuplicates Tracking 818099 as yet unmatched pairs. 5716 records in RAM.
INFO 2026-06-08 08:18:48 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 1s. Last read position: chr2:237,379,131
INFO 2026-06-08 08:18:48 MarkDuplicates Tracking 815715 as yet unmatched pairs. 3320 records in RAM.
INFO 2026-06-08 08:18:50 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 2s. Last read position: chr2:241,434,999
INFO 2026-06-08 08:18:50 MarkDuplicates Tracking 812826 as yet unmatched pairs. 407 records in RAM.
INFO 2026-06-08 08:18:53 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 2s. Last read position: chr3:10,278,348
INFO 2026-06-08 08:18:53 MarkDuplicates Tracking 810547 as yet unmatched pairs. 38340 records in RAM.
INFO 2026-06-08 08:18:55 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 2s. Last read position: chr3:25,606,054
INFO 2026-06-08 08:18:55 MarkDuplicates Tracking 808155 as yet unmatched pairs. 35933 records in RAM.
INFO 2026-06-08 08:18:57 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 1s. Last read position: chr3:39,102,710
INFO 2026-06-08 08:18:57 MarkDuplicates Tracking 805747 as yet unmatched pairs. 33497 records in RAM.
INFO 2026-06-08 08:18:58 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 1s. Last read position: chr3:47,057,183
INFO 2026-06-08 08:18:58 MarkDuplicates Tracking 803261 as yet unmatched pairs. 31001 records in RAM.
INFO 2026-06-08 08:19:00 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 1s. Last read position: chr3:49,001,573
INFO 2026-06-08 08:19:00 MarkDuplicates Tracking 800599 as yet unmatched pairs. 28336 records in RAM.
INFO 2026-06-08 08:19:02 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 1s. Last read position: chr3:49,813,088
INFO 2026-06-08 08:19:02 MarkDuplicates Tracking 798075 as yet unmatched pairs. 25806 records in RAM.
INFO 2026-06-08 08:19:04 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 2s. Last read position: chr3:52,504,786
INFO 2026-06-08 08:19:04 MarkDuplicates Tracking 795530 as yet unmatched pairs. 23258 records in RAM.
INFO 2026-06-08 08:19:06 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 1s. Last read position: chr3:58,125,675
INFO 2026-06-08 08:19:06 MarkDuplicates Tracking 793187 as yet unmatched pairs. 20912 records in RAM.
INFO 2026-06-08 08:19:08 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 1s. Last read position: chr3:99,848,394
INFO 2026-06-08 08:19:08 MarkDuplicates Tracking 790874 as yet unmatched pairs. 18582 records in RAM.
INFO 2026-06-08 08:19:10 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 1s. Last read position: chr3:120,335,869
INFO 2026-06-08 08:19:10 MarkDuplicates Tracking 788582 as yet unmatched pairs. 16290 records in RAM.
INFO 2026-06-08 08:19:12 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 2s. Last read position: chr3:125,107,701
INFO 2026-06-08 08:19:12 MarkDuplicates Tracking 786244 as yet unmatched pairs. 13946 records in RAM.
INFO 2026-06-08 08:19:14 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 1s. Last read position: chr3:129,606,147
INFO 2026-06-08 08:19:14 MarkDuplicates Tracking 783793 as yet unmatched pairs. 11488 records in RAM.
INFO 2026-06-08 08:19:16 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 1s. Last read position: chr3:146,528,792
INFO 2026-06-08 08:19:16 MarkDuplicates Tracking 781977 as yet unmatched pairs. 9657 records in RAM.
INFO 2026-06-08 08:19:18 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 1s. Last read position: chr3:170,360,403
INFO 2026-06-08 08:19:18 MarkDuplicates Tracking 779226 as yet unmatched pairs. 6883 records in RAM.
INFO 2026-06-08 08:19:20 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 2s. Last read position: chr3:184,193,799
INFO 2026-06-08 08:19:20 MarkDuplicates Tracking 776593 as yet unmatched pairs. 4241 records in RAM.
INFO 2026-06-08 08:19:22 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 2s. Last read position: chr3:195,568,887
INFO 2026-06-08 08:19:22 MarkDuplicates Tracking 777697 as yet unmatched pairs. 5332 records in RAM.
INFO 2026-06-08 08:19:26 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 3s. Last read position: chr4:673,370
INFO 2026-06-08 08:19:26 MarkDuplicates Tracking 772195 as yet unmatched pairs. 22787 records in RAM.
INFO 2026-06-08 08:19:28 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 2s. Last read position: chr4:3,105,359
INFO 2026-06-08 08:19:28 MarkDuplicates Tracking 769470 as yet unmatched pairs. 20054 records in RAM.
INFO 2026-06-08 08:19:30 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 2s. Last read position: chr4:15,644,523
INFO 2026-06-08 08:19:30 MarkDuplicates Tracking 766764 as yet unmatched pairs. 17327 records in RAM.
INFO 2026-06-08 08:19:32 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 2s. Last read position: chr4:40,808,757
INFO 2026-06-08 08:19:32 MarkDuplicates Tracking 764556 as yet unmatched pairs. 15089 records in RAM.
INFO 2026-06-08 08:19:34 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 2s. Last read position: chr4:56,994,466
INFO 2026-06-08 08:19:34 MarkDuplicates Tracking 762281 as yet unmatched pairs. 12791 records in RAM.
INFO 2026-06-08 08:19:36 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 1s. Last read position: chr4:82,460,015
INFO 2026-06-08 08:19:36 MarkDuplicates Tracking 759861 as yet unmatched pairs. 10358 records in RAM.
INFO 2026-06-08 08:19:38 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 2s. Last read position: chr4:102,722,932
INFO 2026-06-08 08:19:38 MarkDuplicates Tracking 757533 as yet unmatched pairs. 8027 records in RAM.
INFO 2026-06-08 08:19:40 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 1s. Last read position: chr4:122,349,962
INFO 2026-06-08 08:19:40 MarkDuplicates Tracking 755369 as yet unmatched pairs. 5847 records in RAM.
INFO 2026-06-08 08:19:42 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: chr4:150,198,052
INFO 2026-06-08 08:19:42 MarkDuplicates Tracking 752947 as yet unmatched pairs. 3411 records in RAM.
INFO 2026-06-08 08:19:44 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 1s. Last read position: chr4:169,010,013
INFO 2026-06-08 08:19:44 MarkDuplicates Tracking 750837 as yet unmatched pairs. 1270 records in RAM.
INFO 2026-06-08 08:19:47 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 3s. Last read position: chr5:6,714,000
INFO 2026-06-08 08:19:47 MarkDuplicates Tracking 748248 as yet unmatched pairs. 44168 records in RAM.
INFO 2026-06-08 08:19:49 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 2s. Last read position: chr5:31,511,069
INFO 2026-06-08 08:19:49 MarkDuplicates Tracking 745785 as yet unmatched pairs. 41678 records in RAM.
INFO 2026-06-08 08:19:51 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 1s. Last read position: chr5:42,801,144
INFO 2026-06-08 08:19:51 MarkDuplicates Tracking 745645 as yet unmatched pairs. 41527 records in RAM.
INFO 2026-06-08 08:19:53 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 1s. Last read position: chr5:66,596,607
INFO 2026-06-08 08:19:53 MarkDuplicates Tracking 741578 as yet unmatched pairs. 37446 records in RAM.
INFO 2026-06-08 08:19:55 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 1s. Last read position: chr5:73,502,488
INFO 2026-06-08 08:19:55 MarkDuplicates Tracking 740508 as yet unmatched pairs. 36357 records in RAM.
INFO 2026-06-08 08:19:57 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 1s. Last read position: chr5:80,436,973
INFO 2026-06-08 08:19:57 MarkDuplicates Tracking 737601 as yet unmatched pairs. 33445 records in RAM.
INFO 2026-06-08 08:19:59 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 2s. Last read position: chr5:97,026,616
INFO 2026-06-08 08:19:59 MarkDuplicates Tracking 735385 as yet unmatched pairs. 31215 records in RAM.
INFO 2026-06-08 08:20:01 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 2s. Last read position: chr5:126,608,429
INFO 2026-06-08 08:20:01 MarkDuplicates Tracking 733005 as yet unmatched pairs. 28829 records in RAM.
INFO 2026-06-08 08:20:03 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 1s. Last read position: chr5:134,718,072
INFO 2026-06-08 08:20:03 MarkDuplicates Tracking 730658 as yet unmatched pairs. 26459 records in RAM.
INFO 2026-06-08 08:20:06 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 2s. Last read position: chr5:139,389,780
INFO 2026-06-08 08:20:06 MarkDuplicates Tracking 728662 as yet unmatched pairs. 24454 records in RAM.
INFO 2026-06-08 08:20:08 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 2s. Last read position: chr5:141,863,175
INFO 2026-06-08 08:20:08 MarkDuplicates Tracking 725712 as yet unmatched pairs. 21481 records in RAM.
INFO 2026-06-08 08:20:10 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 2s. Last read position: chr5:150,131,979
INFO 2026-06-08 08:20:10 MarkDuplicates Tracking 723771 as yet unmatched pairs. 19530 records in RAM.
INFO 2026-06-08 08:20:12 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 2s. Last read position: chr5:150,403,280
INFO 2026-06-08 08:20:12 MarkDuplicates Tracking 732517 as yet unmatched pairs. 28269 records in RAM.
INFO 2026-06-08 08:20:14 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 2s. Last read position: chr5:150,406,947
INFO 2026-06-08 08:20:14 MarkDuplicates Tracking 725290 as yet unmatched pairs. 21040 records in RAM.
INFO 2026-06-08 08:20:16 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 1s. Last read position: chr5:154,792,669
INFO 2026-06-08 08:20:16 MarkDuplicates Tracking 715821 as yet unmatched pairs. 11568 records in RAM.
INFO 2026-06-08 08:20:18 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 1s. Last read position: chr5:171,392,785
INFO 2026-06-08 08:20:18 MarkDuplicates Tracking 716576 as yet unmatched pairs. 12308 records in RAM.
INFO 2026-06-08 08:20:20 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 2s. Last read position: chr5:177,371,504
INFO 2026-06-08 08:20:20 MarkDuplicates Tracking 710880 as yet unmatched pairs. 6608 records in RAM.
INFO 2026-06-08 08:20:22 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 2s. Last read position: chr5:179,766,694
INFO 2026-06-08 08:20:22 MarkDuplicates Tracking 708477 as yet unmatched pairs. 4190 records in RAM.
INFO 2026-06-08 08:20:24 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 2s. Last read position: chr5:179,837,053
INFO 2026-06-08 08:20:24 MarkDuplicates Tracking 707221 as yet unmatched pairs. 2933 records in RAM.
INFO 2026-06-08 08:20:27 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 2s. Last read position: chr6:7,229,464
INFO 2026-06-08 08:20:27 MarkDuplicates Tracking 703708 as yet unmatched pairs. 41827 records in RAM.
INFO 2026-06-08 08:20:29 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 1s. Last read position: chr6:24,701,497
INFO 2026-06-08 08:20:29 MarkDuplicates Tracking 701027 as yet unmatched pairs. 39137 records in RAM.
INFO 2026-06-08 08:20:30 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 1s. Last read position: chr6:29,944,599
INFO 2026-06-08 08:20:30 MarkDuplicates Tracking 701902 as yet unmatched pairs. 40008 records in RAM.
INFO 2026-06-08 08:20:33 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 2s. Last read position: chr6:31,354,507
INFO 2026-06-08 08:20:33 MarkDuplicates Tracking 697287 as yet unmatched pairs. 35392 records in RAM.
INFO 2026-06-08 08:20:35 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 1s. Last read position: chr6:31,817,181
INFO 2026-06-08 08:20:35 MarkDuplicates Tracking 694354 as yet unmatched pairs. 32454 records in RAM.
INFO 2026-06-08 08:20:37 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 1s. Last read position: chr6:32,024,295
INFO 2026-06-08 08:20:37 MarkDuplicates Tracking 693342 as yet unmatched pairs. 31441 records in RAM.
INFO 2026-06-08 08:20:38 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 1s. Last read position: chr6:32,842,741
INFO 2026-06-08 08:20:38 MarkDuplicates Tracking 690255 as yet unmatched pairs. 28352 records in RAM.
INFO 2026-06-08 08:20:40 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 1s. Last read position: chr6:33,416,924
INFO 2026-06-08 08:20:40 MarkDuplicates Tracking 688108 as yet unmatched pairs. 26203 records in RAM.
INFO 2026-06-08 08:20:42 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 1s. Last read position: chr6:41,071,633
INFO 2026-06-08 08:20:42 MarkDuplicates Tracking 685114 as yet unmatched pairs. 23194 records in RAM.
INFO 2026-06-08 08:20:44 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 1s. Last read position: chr6:44,230,642
INFO 2026-06-08 08:20:44 MarkDuplicates Tracking 682829 as yet unmatched pairs. 20904 records in RAM.
INFO 2026-06-08 08:20:48 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 3s. Last read position: chr6:73,373,162
INFO 2026-06-08 08:20:48 MarkDuplicates Tracking 680364 as yet unmatched pairs. 18432 records in RAM.
INFO 2026-06-08 08:20:50 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 2s. Last read position: chr6:87,477,401
INFO 2026-06-08 08:20:50 MarkDuplicates Tracking 678257 as yet unmatched pairs. 16319 records in RAM.
INFO 2026-06-08 08:20:52 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 2s. Last read position: chr6:111,374,624
INFO 2026-06-08 08:20:52 MarkDuplicates Tracking 675940 as yet unmatched pairs. 13996 records in RAM.
INFO 2026-06-08 08:20:54 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 1s. Last read position: chr6:135,195,794
INFO 2026-06-08 08:20:54 MarkDuplicates Tracking 674074 as yet unmatched pairs. 12118 records in RAM.
INFO 2026-06-08 08:20:56 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 1s. Last read position: chr6:149,578,891
INFO 2026-06-08 08:20:56 MarkDuplicates Tracking 671252 as yet unmatched pairs. 9286 records in RAM.
INFO 2026-06-08 08:20:58 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 1s. Last read position: chr6:151,880,660
INFO 2026-06-08 08:20:58 MarkDuplicates Tracking 670151 as yet unmatched pairs. 8177 records in RAM.
INFO 2026-06-08 08:21:00 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 1s. Last read position: chr6:158,767,035
INFO 2026-06-08 08:21:00 MarkDuplicates Tracking 666760 as yet unmatched pairs. 4778 records in RAM.
INFO 2026-06-08 08:21:02 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 1s. Last read position: chr6:161,107,905
INFO 2026-06-08 08:21:02 MarkDuplicates Tracking 663558 as yet unmatched pairs. 1564 records in RAM.
INFO 2026-06-08 08:21:04 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 2s. Last read position: chr7:1,555,433
INFO 2026-06-08 08:21:04 MarkDuplicates Tracking 660905 as yet unmatched pairs. 43246 records in RAM.
INFO 2026-06-08 08:21:06 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 1s. Last read position: chr7:5,389,284
INFO 2026-06-08 08:21:06 MarkDuplicates Tracking 658264 as yet unmatched pairs. 40602 records in RAM.
INFO 2026-06-08 08:21:08 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 1s. Last read position: chr7:12,570,858
INFO 2026-06-08 08:21:08 MarkDuplicates Tracking 655337 as yet unmatched pairs. 37663 records in RAM.
INFO 2026-06-08 08:21:10 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 1s. Last read position: chr7:32,573,247
INFO 2026-06-08 08:21:10 MarkDuplicates Tracking 653080 as yet unmatched pairs. 35393 records in RAM.
INFO 2026-06-08 08:21:12 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 2s. Last read position: chr7:44,113,915
INFO 2026-06-08 08:21:12 MarkDuplicates Tracking 650911 as yet unmatched pairs. 33221 records in RAM.
INFO 2026-06-08 08:21:14 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 1s. Last read position: chr7:66,130,822
INFO 2026-06-08 08:21:14 MarkDuplicates Tracking 648441 as yet unmatched pairs. 30740 records in RAM.
INFO 2026-06-08 08:21:16 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 2s. Last read position: chr7:73,769,423
INFO 2026-06-08 08:21:16 MarkDuplicates Tracking 647706 as yet unmatched pairs. 29988 records in RAM.
INFO 2026-06-08 08:21:18 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 2s. Last read position: chr7:75,501,460
INFO 2026-06-08 08:21:18 MarkDuplicates Tracking 645192 as yet unmatched pairs. 27469 records in RAM.
INFO 2026-06-08 08:21:20 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 2s. Last read position: chr7:77,025,044
INFO 2026-06-08 08:21:20 MarkDuplicates Tracking 642569 as yet unmatched pairs. 24846 records in RAM.
INFO 2026-06-08 08:21:22 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 1s. Last read position: chr7:92,345,866
INFO 2026-06-08 08:21:22 MarkDuplicates Tracking 640538 as yet unmatched pairs. 22808 records in RAM.
INFO 2026-06-08 08:21:24 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 1s. Last read position: chr7:94,665,104
INFO 2026-06-08 08:21:24 MarkDuplicates Tracking 638671 as yet unmatched pairs. 20938 records in RAM.
INFO 2026-06-08 08:21:26 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 1s. Last read position: chr7:100,107,419
INFO 2026-06-08 08:21:26 MarkDuplicates Tracking 635720 as yet unmatched pairs. 17987 records in RAM.
INFO 2026-06-08 08:21:28 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 1s. Last read position: chr7:101,183,655
INFO 2026-06-08 08:21:28 MarkDuplicates Tracking 632911 as yet unmatched pairs. 15177 records in RAM.
INFO 2026-06-08 08:21:30 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr7:102,660,138
INFO 2026-06-08 08:21:30 MarkDuplicates Tracking 632234 as yet unmatched pairs. 14494 records in RAM.
INFO 2026-06-08 08:21:32 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 1s. Last read position: chr7:123,545,612
INFO 2026-06-08 08:21:32 MarkDuplicates Tracking 629803 as yet unmatched pairs. 12056 records in RAM.
INFO 2026-06-08 08:21:34 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 1s. Last read position: chr7:133,895,629
INFO 2026-06-08 08:21:34 MarkDuplicates Tracking 627248 as yet unmatched pairs. 9490 records in RAM.
INFO 2026-06-08 08:21:35 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 1s. Last read position: chr7:140,133,583
INFO 2026-06-08 08:21:35 MarkDuplicates Tracking 625311 as yet unmatched pairs. 7543 records in RAM.
INFO 2026-06-08 08:21:37 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 1s. Last read position: chr7:149,011,846
INFO 2026-06-08 08:21:37 MarkDuplicates Tracking 622982 as yet unmatched pairs. 5209 records in RAM.
INFO 2026-06-08 08:21:39 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 1s. Last read position: chr7:151,082,469
INFO 2026-06-08 08:21:39 MarkDuplicates Tracking 620111 as yet unmatched pairs. 2334 records in RAM.
INFO 2026-06-08 08:21:41 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 2s. Last read position: chr8:1,860,042
INFO 2026-06-08 08:21:41 MarkDuplicates Tracking 617793 as yet unmatched pairs. 50842 records in RAM.
INFO 2026-06-08 08:21:43 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 1s. Last read position: chr8:18,059,595
INFO 2026-06-08 08:21:43 MarkDuplicates Tracking 615854 as yet unmatched pairs. 48894 records in RAM.
INFO 2026-06-08 08:21:45 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 1s. Last read position: chr8:27,606,428
INFO 2026-06-08 08:21:45 MarkDuplicates Tracking 613112 as yet unmatched pairs. 46131 records in RAM.
INFO 2026-06-08 08:21:47 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 2s. Last read position: chr8:38,415,870
INFO 2026-06-08 08:21:47 MarkDuplicates Tracking 610619 as yet unmatched pairs. 43632 records in RAM.
INFO 2026-06-08 08:21:49 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 1s. Last read position: chr8:42,957,114
INFO 2026-06-08 08:21:49 MarkDuplicates Tracking 608465 as yet unmatched pairs. 41478 records in RAM.
INFO 2026-06-08 08:21:52 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 2s. Last read position: chr8:60,517,196
INFO 2026-06-08 08:21:52 MarkDuplicates Tracking 606610 as yet unmatched pairs. 39618 records in RAM.
INFO 2026-06-08 08:21:54 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 2s. Last read position: chr8:70,124,756
INFO 2026-06-08 08:21:54 MarkDuplicates Tracking 603486 as yet unmatched pairs. 36483 records in RAM.
INFO 2026-06-08 08:21:56 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 1s. Last read position: chr8:80,664,848
INFO 2026-06-08 08:21:56 MarkDuplicates Tracking 601112 as yet unmatched pairs. 34096 records in RAM.
INFO 2026-06-08 08:21:58 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 1s. Last read position: chr8:97,689,038
INFO 2026-06-08 08:21:58 MarkDuplicates Tracking 598964 as yet unmatched pairs. 31936 records in RAM.
INFO 2026-06-08 08:22:00 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 1s. Last read position: chr8:100,704,362
INFO 2026-06-08 08:22:00 MarkDuplicates Tracking 599346 as yet unmatched pairs. 32313 records in RAM.
INFO 2026-06-08 08:22:02 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 1s. Last read position: chr8:102,833,107
INFO 2026-06-08 08:22:02 MarkDuplicates Tracking 594749 as yet unmatched pairs. 27713 records in RAM.
INFO 2026-06-08 08:22:04 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:05:43s. Time for last 1,000,000: 1s. Last read position: chr8:115,619,180
INFO 2026-06-08 08:22:04 MarkDuplicates Tracking 595357 as yet unmatched pairs. 28295 records in RAM.
INFO 2026-06-08 08:22:06 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 1s. Last read position: chr8:123,346,206
INFO 2026-06-08 08:22:06 MarkDuplicates Tracking 589224 as yet unmatched pairs. 22138 records in RAM.
INFO 2026-06-08 08:22:08 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 1s. Last read position: chr8:140,311,280
INFO 2026-06-08 08:22:08 MarkDuplicates Tracking 587491 as yet unmatched pairs. 20391 records in RAM.
INFO 2026-06-08 08:22:10 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 1s. Last read position: chr8:143,559,406
INFO 2026-06-08 08:22:10 MarkDuplicates Tracking 584129 as yet unmatched pairs. 17025 records in RAM.
INFO 2026-06-08 08:22:12 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 1s. Last read position: chr8:143,811,042
INFO 2026-06-08 08:22:12 MarkDuplicates Tracking 581023 as yet unmatched pairs. 13901 records in RAM.
INFO 2026-06-08 08:22:13 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 1s. Last read position: chr8:143,861,626
INFO 2026-06-08 08:22:13 MarkDuplicates Tracking 579842 as yet unmatched pairs. 12719 records in RAM.
INFO 2026-06-08 08:22:15 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 1s. Last read position: chr8:143,866,287
INFO 2026-06-08 08:22:15 MarkDuplicates Tracking 578822 as yet unmatched pairs. 11697 records in RAM.
INFO 2026-06-08 08:22:16 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 1s. Last read position: chr8:143,923,879
INFO 2026-06-08 08:22:16 MarkDuplicates Tracking 576176 as yet unmatched pairs. 9048 records in RAM.
INFO 2026-06-08 08:22:18 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 1s. Last read position: chr8:144,079,869
INFO 2026-06-08 08:22:18 MarkDuplicates Tracking 573068 as yet unmatched pairs. 5928 records in RAM.
INFO 2026-06-08 08:22:20 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 1s. Last read position: chr8:144,400,465
INFO 2026-06-08 08:22:20 MarkDuplicates Tracking 570557 as yet unmatched pairs. 3413 records in RAM.
INFO 2026-06-08 08:22:23 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 2s. Last read position: chr9:134,979
INFO 2026-06-08 08:22:23 MarkDuplicates Tracking 567176 as yet unmatched pairs. 29840 records in RAM.
INFO 2026-06-08 08:22:25 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 2s. Last read position: chr9:19,116,167
INFO 2026-06-08 08:22:25 MarkDuplicates Tracking 564960 as yet unmatched pairs. 27615 records in RAM.
INFO 2026-06-08 08:22:27 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 1s. Last read position: chr9:35,062,019
INFO 2026-06-08 08:22:27 MarkDuplicates Tracking 562653 as yet unmatched pairs. 25307 records in RAM.
INFO 2026-06-08 08:22:29 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 1s. Last read position: chr9:69,221,135
INFO 2026-06-08 08:22:29 MarkDuplicates Tracking 560300 as yet unmatched pairs. 22943 records in RAM.
INFO 2026-06-08 08:22:31 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 1s. Last read position: chr9:92,274,445
INFO 2026-06-08 08:22:31 MarkDuplicates Tracking 557954 as yet unmatched pairs. 20597 records in RAM.
INFO 2026-06-08 08:22:33 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 1s. Last read position: chr9:104,809,495
INFO 2026-06-08 08:22:33 MarkDuplicates Tracking 555477 as yet unmatched pairs. 18112 records in RAM.
INFO 2026-06-08 08:22:35 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 1s. Last read position: chr9:114,377,218
INFO 2026-06-08 08:22:35 MarkDuplicates Tracking 553229 as yet unmatched pairs. 15863 records in RAM.
INFO 2026-06-08 08:22:37 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:06:16s. Time for last 1,000,000: 1s. Last read position: chr9:125,298,952
INFO 2026-06-08 08:22:37 MarkDuplicates Tracking 550781 as yet unmatched pairs. 13412 records in RAM.
INFO 2026-06-08 08:22:39 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 2s. Last read position: chr9:128,525,408
INFO 2026-06-08 08:22:39 MarkDuplicates Tracking 547871 as yet unmatched pairs. 10495 records in RAM.
INFO 2026-06-08 08:22:41 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 1s. Last read position: chr9:131,096,850
INFO 2026-06-08 08:22:41 MarkDuplicates Tracking 545756 as yet unmatched pairs. 8378 records in RAM.
INFO 2026-06-08 08:22:42 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 1s. Last read position: chr9:134,048,370
INFO 2026-06-08 08:22:42 MarkDuplicates Tracking 543465 as yet unmatched pairs. 6083 records in RAM.
INFO 2026-06-08 08:22:44 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 1s. Last read position: chr9:136,840,868
INFO 2026-06-08 08:22:44 MarkDuplicates Tracking 540484 as yet unmatched pairs. 3101 records in RAM.
INFO 2026-06-08 08:22:46 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 1s. Last read position: chr9:137,835,008
INFO 2026-06-08 08:22:46 MarkDuplicates Tracking 537419 as yet unmatched pairs. 32 records in RAM.
INFO 2026-06-08 08:22:48 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 1s. Last read position: chr10:12,094,260
INFO 2026-06-08 08:22:48 MarkDuplicates Tracking 535133 as yet unmatched pairs. 24414 records in RAM.
INFO 2026-06-08 08:22:51 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:06:30s. Time for last 1,000,000: 2s. Last read position: chr10:28,535,625
INFO 2026-06-08 08:22:51 MarkDuplicates Tracking 533100 as yet unmatched pairs. 22379 records in RAM.
INFO 2026-06-08 08:22:53 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 1s. Last read position: chr10:44,991,021
INFO 2026-06-08 08:22:53 MarkDuplicates Tracking 530617 as yet unmatched pairs. 19891 records in RAM.
INFO 2026-06-08 08:22:54 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 1s. Last read position: chr10:59,906,130
INFO 2026-06-08 08:22:54 MarkDuplicates Tracking 529384 as yet unmatched pairs. 18650 records in RAM.
INFO 2026-06-08 08:22:57 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 2s. Last read position: chr10:73,247,043
INFO 2026-06-08 08:22:57 MarkDuplicates Tracking 526332 as yet unmatched pairs. 15591 records in RAM.
INFO 2026-06-08 08:22:59 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 2s. Last read position: chr10:78,035,706
INFO 2026-06-08 08:22:59 MarkDuplicates Tracking 525326 as yet unmatched pairs. 14582 records in RAM.
INFO 2026-06-08 08:23:01 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 1s. Last read position: chr10:89,339,699
INFO 2026-06-08 08:23:01 MarkDuplicates Tracking 522853 as yet unmatched pairs. 12100 records in RAM.
INFO 2026-06-08 08:23:03 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 1s. Last read position: chr10:96,984,573
INFO 2026-06-08 08:23:03 MarkDuplicates Tracking 519379 as yet unmatched pairs. 8610 records in RAM.
INFO 2026-06-08 08:23:05 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:06:44s. Time for last 1,000,000: 1s. Last read position: chr10:102,358,513
INFO 2026-06-08 08:23:05 MarkDuplicates Tracking 517061 as yet unmatched pairs. 6265 records in RAM.
INFO 2026-06-08 08:23:07 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:06:46s. Time for last 1,000,000: 1s. Last read position: chr10:116,940,585
INFO 2026-06-08 08:23:07 MarkDuplicates Tracking 515306 as yet unmatched pairs. 4510 records in RAM.
INFO 2026-06-08 08:23:09 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 1s. Last read position: chr10:125,027,549
INFO 2026-06-08 08:23:09 MarkDuplicates Tracking 512275 as yet unmatched pairs. 1456 records in RAM.
INFO 2026-06-08 08:23:13 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 4s. Last read position: chr11:319,733
INFO 2026-06-08 08:23:13 MarkDuplicates Tracking 512118 as yet unmatched pairs. 65260 records in RAM.
INFO 2026-06-08 08:23:15 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 1s. Last read position: chr11:639,921
INFO 2026-06-08 08:23:15 MarkDuplicates Tracking 507018 as yet unmatched pairs. 60154 records in RAM.
INFO 2026-06-08 08:23:17 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 1s. Last read position: chr11:1,759,056
INFO 2026-06-08 08:23:17 MarkDuplicates Tracking 504926 as yet unmatched pairs. 58062 records in RAM.
INFO 2026-06-08 08:23:19 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 1s. Last read position: chr11:5,884,420
INFO 2026-06-08 08:23:19 MarkDuplicates Tracking 501876 as yet unmatched pairs. 55003 records in RAM.
INFO 2026-06-08 08:23:21 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:07:00s. Time for last 1,000,000: 2s. Last read position: chr11:9,585,282
INFO 2026-06-08 08:23:21 MarkDuplicates Tracking 499461 as yet unmatched pairs. 52582 records in RAM.
INFO 2026-06-08 08:23:23 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 1s. Last read position: chr11:18,296,959
INFO 2026-06-08 08:23:23 MarkDuplicates Tracking 497082 as yet unmatched pairs. 50203 records in RAM.
INFO 2026-06-08 08:23:25 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:07:04s. Time for last 1,000,000: 1s. Last read position: chr11:35,260,763
INFO 2026-06-08 08:23:25 MarkDuplicates Tracking 494797 as yet unmatched pairs. 47912 records in RAM.
INFO 2026-06-08 08:23:26 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 1s. Last read position: chr11:47,284,941
INFO 2026-06-08 08:23:26 MarkDuplicates Tracking 492393 as yet unmatched pairs. 45500 records in RAM.
INFO 2026-06-08 08:23:28 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 1s. Last read position: chr11:57,796,592
INFO 2026-06-08 08:23:28 MarkDuplicates Tracking 490224 as yet unmatched pairs. 43331 records in RAM.
INFO 2026-06-08 08:23:30 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 1s. Last read position: chr11:61,790,514
INFO 2026-06-08 08:23:30 MarkDuplicates Tracking 487497 as yet unmatched pairs. 40600 records in RAM.
INFO 2026-06-08 08:23:32 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:07:11s. Time for last 1,000,000: 1s. Last read position: chr11:62,525,527
INFO 2026-06-08 08:23:32 MarkDuplicates Tracking 485885 as yet unmatched pairs. 38988 records in RAM.
INFO 2026-06-08 08:23:34 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 2s. Last read position: chr11:62,629,826
INFO 2026-06-08 08:23:34 MarkDuplicates Tracking 483461 as yet unmatched pairs. 36564 records in RAM.
INFO 2026-06-08 08:23:37 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:07:16s. Time for last 1,000,000: 2s. Last read position: chr11:63,999,707
INFO 2026-06-08 08:23:37 MarkDuplicates Tracking 480686 as yet unmatched pairs. 33789 records in RAM.
INFO 2026-06-08 08:23:39 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:07:19s. Time for last 1,000,000: 2s. Last read position: chr11:65,108,364
INFO 2026-06-08 08:23:39 MarkDuplicates Tracking 478074 as yet unmatched pairs. 31176 records in RAM.
INFO 2026-06-08 08:23:41 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:07:21s. Time for last 1,000,000: 1s. Last read position: chr11:65,623,563
INFO 2026-06-08 08:23:41 MarkDuplicates Tracking 475725 as yet unmatched pairs. 28805 records in RAM.
INFO 2026-06-08 08:23:43 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:07:22s. Time for last 1,000,000: 1s. Last read position: chr11:66,468,168
INFO 2026-06-08 08:23:43 MarkDuplicates Tracking 472836 as yet unmatched pairs. 25916 records in RAM.
INFO 2026-06-08 08:23:45 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:07:24s. Time for last 1,000,000: 1s. Last read position: chr11:67,435,037
INFO 2026-06-08 08:23:45 MarkDuplicates Tracking 469867 as yet unmatched pairs. 22943 records in RAM.
INFO 2026-06-08 08:23:47 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:07:26s. Time for last 1,000,000: 1s. Last read position: chr11:69,643,090
INFO 2026-06-08 08:23:47 MarkDuplicates Tracking 469373 as yet unmatched pairs. 22449 records in RAM.
INFO 2026-06-08 08:23:49 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:07:28s. Time for last 1,000,000: 1s. Last read position: chr11:72,014,181
INFO 2026-06-08 08:23:49 MarkDuplicates Tracking 465285 as yet unmatched pairs. 18359 records in RAM.
INFO 2026-06-08 08:23:50 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:07:30s. Time for last 1,000,000: 1s. Last read position: chr11:74,370,927
INFO 2026-06-08 08:23:50 MarkDuplicates Tracking 462033 as yet unmatched pairs. 15090 records in RAM.
INFO 2026-06-08 08:23:52 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:07:32s. Time for last 1,000,000: 1s. Last read position: chr11:85,663,786
INFO 2026-06-08 08:23:52 MarkDuplicates Tracking 459871 as yet unmatched pairs. 12925 records in RAM.
INFO 2026-06-08 08:23:54 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:07:33s. Time for last 1,000,000: 1s. Last read position: chr11:102,162,388
INFO 2026-06-08 08:23:54 MarkDuplicates Tracking 457649 as yet unmatched pairs. 10692 records in RAM.
INFO 2026-06-08 08:23:56 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:07:36s. Time for last 1,000,000: 2s. Last read position: chr11:117,136,911
INFO 2026-06-08 08:23:56 MarkDuplicates Tracking 455069 as yet unmatched pairs. 8111 records in RAM.
INFO 2026-06-08 08:23:58 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:07:38s. Time for last 1,000,000: 2s. Last read position: chr11:118,901,152
INFO 2026-06-08 08:23:58 MarkDuplicates Tracking 453181 as yet unmatched pairs. 6223 records in RAM.
INFO 2026-06-08 08:24:00 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:07:40s. Time for last 1,000,000: 2s. Last read position: chr11:123,060,146
INFO 2026-06-08 08:24:00 MarkDuplicates Tracking 451700 as yet unmatched pairs. 4737 records in RAM.
INFO 2026-06-08 08:24:03 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:07:42s. Time for last 1,000,000: 2s. Last read position: chr11:130,141,541
INFO 2026-06-08 08:24:03 MarkDuplicates Tracking 448451 as yet unmatched pairs. 1476 records in RAM.
INFO 2026-06-08 08:24:06 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:07:45s. Time for last 1,000,000: 3s. Last read position: chr12:1,574,383
INFO 2026-06-08 08:24:06 MarkDuplicates Tracking 445577 as yet unmatched pairs. 54073 records in RAM.
INFO 2026-06-08 08:24:08 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:07:47s. Time for last 1,000,000: 2s. Last read position: chr12:6,587,944
INFO 2026-06-08 08:24:08 MarkDuplicates Tracking 443468 as yet unmatched pairs. 51962 records in RAM.
INFO 2026-06-08 08:24:10 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:07:49s. Time for last 1,000,000: 1s. Last read position: chr12:7,190,513
INFO 2026-06-08 08:24:10 MarkDuplicates Tracking 440872 as yet unmatched pairs. 49366 records in RAM.
INFO 2026-06-08 08:24:12 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:07:51s. Time for last 1,000,000: 1s. Last read position: chr12:13,067,229
INFO 2026-06-08 08:24:12 MarkDuplicates Tracking 438684 as yet unmatched pairs. 47170 records in RAM.
INFO 2026-06-08 08:24:14 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:07:53s. Time for last 1,000,000: 2s. Last read position: chr12:29,349,139
INFO 2026-06-08 08:24:14 MarkDuplicates Tracking 436223 as yet unmatched pairs. 44703 records in RAM.
INFO 2026-06-08 08:24:16 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:07:55s. Time for last 1,000,000: 1s. Last read position: chr12:46,209,068
INFO 2026-06-08 08:24:16 MarkDuplicates Tracking 434243 as yet unmatched pairs. 42717 records in RAM.
INFO 2026-06-08 08:24:18 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:07:57s. Time for last 1,000,000: 1s. Last read position: chr12:49,044,908
INFO 2026-06-08 08:24:18 MarkDuplicates Tracking 431519 as yet unmatched pairs. 39993 records in RAM.
INFO 2026-06-08 08:24:20 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:07:59s. Time for last 1,000,000: 1s. Last read position: chr12:50,795,928
INFO 2026-06-08 08:24:20 MarkDuplicates Tracking 429068 as yet unmatched pairs. 37542 records in RAM.
INFO 2026-06-08 08:24:21 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:08:01s. Time for last 1,000,000: 1s. Last read position: chr12:52,904,771
INFO 2026-06-08 08:24:21 MarkDuplicates Tracking 432057 as yet unmatched pairs. 40524 records in RAM.
INFO 2026-06-08 08:24:23 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:08:03s. Time for last 1,000,000: 1s. Last read position: chr12:53,297,861
INFO 2026-06-08 08:24:23 MarkDuplicates Tracking 425097 as yet unmatched pairs. 33552 records in RAM.
INFO 2026-06-08 08:24:25 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 1s. Last read position: chr12:55,725,546
INFO 2026-06-08 08:24:25 MarkDuplicates Tracking 421912 as yet unmatched pairs. 30366 records in RAM.
INFO 2026-06-08 08:24:27 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:08:07s. Time for last 1,000,000: 1s. Last read position: chr12:56,354,850
INFO 2026-06-08 08:24:27 MarkDuplicates Tracking 419645 as yet unmatched pairs. 28097 records in RAM.
INFO 2026-06-08 08:24:29 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:08:09s. Time for last 1,000,000: 1s. Last read position: chr12:57,102,372
INFO 2026-06-08 08:24:29 MarkDuplicates Tracking 418140 as yet unmatched pairs. 26588 records in RAM.
INFO 2026-06-08 08:24:31 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:08:10s. Time for last 1,000,000: 1s. Last read position: chr12:57,720,190
INFO 2026-06-08 08:24:31 MarkDuplicates Tracking 414798 as yet unmatched pairs. 23243 records in RAM.
INFO 2026-06-08 08:24:33 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:08:13s. Time for last 1,000,000: 2s. Last read position: chr12:69,597,643
INFO 2026-06-08 08:24:33 MarkDuplicates Tracking 412484 as yet unmatched pairs. 20925 records in RAM.
INFO 2026-06-08 08:24:36 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:08:15s. Time for last 1,000,000: 2s. Last read position: chr12:94,149,901
INFO 2026-06-08 08:24:36 MarkDuplicates Tracking 410301 as yet unmatched pairs. 18737 records in RAM.
INFO 2026-06-08 08:24:38 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:08:18s. Time for last 1,000,000: 2s. Last read position: chr12:103,982,838
INFO 2026-06-08 08:24:38 MarkDuplicates Tracking 407965 as yet unmatched pairs. 16395 records in RAM.
INFO 2026-06-08 08:24:40 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:08:20s. Time for last 1,000,000: 2s. Last read position: chr12:110,435,197
INFO 2026-06-08 08:24:40 MarkDuplicates Tracking 405857 as yet unmatched pairs. 14275 records in RAM.
INFO 2026-06-08 08:24:42 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:08:22s. Time for last 1,000,000: 2s. Last read position: chr12:112,919,389
INFO 2026-06-08 08:24:42 MarkDuplicates Tracking 403550 as yet unmatched pairs. 11968 records in RAM.
INFO 2026-06-08 08:24:44 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:08:24s. Time for last 1,000,000: 2s. Last read position: chr12:118,181,437
INFO 2026-06-08 08:24:44 MarkDuplicates Tracking 400817 as yet unmatched pairs. 9235 records in RAM.
INFO 2026-06-08 08:24:46 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:08:26s. Time for last 1,000,000: 1s. Last read position: chr12:121,814,575
INFO 2026-06-08 08:24:46 MarkDuplicates Tracking 398389 as yet unmatched pairs. 6802 records in RAM.
INFO 2026-06-08 08:24:48 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:08:28s. Time for last 1,000,000: 1s. Last read position: chr12:123,943,428
INFO 2026-06-08 08:24:48 MarkDuplicates Tracking 395734 as yet unmatched pairs. 4146 records in RAM.
INFO 2026-06-08 08:24:50 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:08:30s. Time for last 1,000,000: 1s. Last read position: chr12:132,104,679
INFO 2026-06-08 08:24:50 MarkDuplicates Tracking 393321 as yet unmatched pairs. 1720 records in RAM.
INFO 2026-06-08 08:24:53 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 2s. Last read position: chr13:23,341,622
INFO 2026-06-08 08:24:53 MarkDuplicates Tracking 390812 as yet unmatched pairs. 9662 records in RAM.
INFO 2026-06-08 08:24:55 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 1s. Last read position: chr13:37,582,398
INFO 2026-06-08 08:24:55 MarkDuplicates Tracking 388967 as yet unmatched pairs. 7814 records in RAM.
INFO 2026-06-08 08:24:56 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:08:36s. Time for last 1,000,000: 1s. Last read position: chr13:51,341,224
INFO 2026-06-08 08:24:56 MarkDuplicates Tracking 386364 as yet unmatched pairs. 5211 records in RAM.
INFO 2026-06-08 08:26:06 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:09:45s. Time for last 1,000,000: 69s. Last read position: chr13:99,537,740
INFO 2026-06-08 08:26:06 MarkDuplicates Tracking 384371 as yet unmatched pairs. 3211 records in RAM.
INFO 2026-06-08 08:26:08 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:09:47s. Time for last 1,000,000: 1s. Last read position: chr13:113,823,436
INFO 2026-06-08 08:26:08 MarkDuplicates Tracking 381594 as yet unmatched pairs. 432 records in RAM.
INFO 2026-06-08 08:26:09 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:09:49s. Time for last 1,000,000: 1s. Last read position: chr14:21,525,076
INFO 2026-06-08 08:26:09 MarkDuplicates Tracking 379571 as yet unmatched pairs. 24309 records in RAM.
INFO 2026-06-08 08:26:11 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:09:51s. Time for last 1,000,000: 1s. Last read position: chr14:24,145,402
INFO 2026-06-08 08:26:11 MarkDuplicates Tracking 377876 as yet unmatched pairs. 22614 records in RAM.
INFO 2026-06-08 08:26:13 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:09:52s. Time for last 1,000,000: 1s. Last read position: chr14:35,270,442
INFO 2026-06-08 08:26:13 MarkDuplicates Tracking 374670 as yet unmatched pairs. 19400 records in RAM.
INFO 2026-06-08 08:26:15 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:09:54s. Time for last 1,000,000: 1s. Last read position: chr14:54,774,977
INFO 2026-06-08 08:26:15 MarkDuplicates Tracking 372503 as yet unmatched pairs. 17230 records in RAM.
INFO 2026-06-08 08:26:17 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:09:56s. Time for last 1,000,000: 1s. Last read position: chr14:64,003,184
INFO 2026-06-08 08:26:17 MarkDuplicates Tracking 370267 as yet unmatched pairs. 14988 records in RAM.
INFO 2026-06-08 08:26:19 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 2s. Last read position: chr14:70,995,812
INFO 2026-06-08 08:26:19 MarkDuplicates Tracking 367975 as yet unmatched pairs. 12694 records in RAM.
INFO 2026-06-08 08:26:21 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:10:01s. Time for last 1,000,000: 2s. Last read position: chr14:76,773,148
INFO 2026-06-08 08:26:21 MarkDuplicates Tracking 365392 as yet unmatched pairs. 10109 records in RAM.
INFO 2026-06-08 08:26:23 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:10:03s. Time for last 1,000,000: 1s. Last read position: chr14:93,347,274
INFO 2026-06-08 08:26:23 MarkDuplicates Tracking 362984 as yet unmatched pairs. 7689 records in RAM.
INFO 2026-06-08 08:26:25 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:10:05s. Time for last 1,000,000: 1s. Last read position: chr14:101,882,196
INFO 2026-06-08 08:26:25 MarkDuplicates Tracking 360757 as yet unmatched pairs. 5457 records in RAM.
INFO 2026-06-08 08:26:27 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 1s. Last read position: chr14:103,740,222
INFO 2026-06-08 08:26:27 MarkDuplicates Tracking 358172 as yet unmatched pairs. 2869 records in RAM.
INFO 2026-06-08 08:26:29 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:10:08s. Time for last 1,000,000: 1s. Last read position: chr14:105,771,306
INFO 2026-06-08 08:26:29 MarkDuplicates Tracking 355729 as yet unmatched pairs. 426 records in RAM.
INFO 2026-06-08 08:26:31 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:10:10s. Time for last 1,000,000: 1s. Last read position: chr15:31,327,215
INFO 2026-06-08 08:26:31 MarkDuplicates Tracking 353930 as yet unmatched pairs. 21629 records in RAM.
INFO 2026-06-08 08:26:32 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 1s. Last read position: chr15:40,980,259
INFO 2026-06-08 08:26:32 MarkDuplicates Tracking 351600 as yet unmatched pairs. 19293 records in RAM.
INFO 2026-06-08 08:26:34 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:10:14s. Time for last 1,000,000: 1s. Last read position: chr15:43,746,644
INFO 2026-06-08 08:26:34 MarkDuplicates Tracking 349673 as yet unmatched pairs. 17362 records in RAM.
INFO 2026-06-08 08:26:36 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:10:15s. Time for last 1,000,000: 1s. Last read position: chr15:50,624,180
INFO 2026-06-08 08:26:36 MarkDuplicates Tracking 347071 as yet unmatched pairs. 14760 records in RAM.
INFO 2026-06-08 08:26:38 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:10:17s. Time for last 1,000,000: 1s. Last read position: chr15:61,959,477
INFO 2026-06-08 08:26:38 MarkDuplicates Tracking 344916 as yet unmatched pairs. 12603 records in RAM.
INFO 2026-06-08 08:26:40 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:10:19s. Time for last 1,000,000: 1s. Last read position: chr15:66,379,435
INFO 2026-06-08 08:26:40 MarkDuplicates Tracking 342344 as yet unmatched pairs. 10031 records in RAM.
INFO 2026-06-08 08:26:42 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:10:21s. Time for last 1,000,000: 1s. Last read position: chr15:73,998,174
INFO 2026-06-08 08:26:42 MarkDuplicates Tracking 340485 as yet unmatched pairs. 8169 records in RAM.
INFO 2026-06-08 08:26:43 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:10:23s. Time for last 1,000,000: 1s. Last read position: chr15:78,438,304
INFO 2026-06-08 08:26:43 MarkDuplicates Tracking 337401 as yet unmatched pairs. 5084 records in RAM.
INFO 2026-06-08 08:26:45 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:10:25s. Time for last 1,000,000: 1s. Last read position: chr15:89,319,338
INFO 2026-06-08 08:26:45 MarkDuplicates Tracking 335201 as yet unmatched pairs. 2883 records in RAM.
INFO 2026-06-08 08:26:47 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 1s. Last read position: chr15:101,178,317
INFO 2026-06-08 08:26:47 MarkDuplicates Tracking 332585 as yet unmatched pairs. 256 records in RAM.
INFO 2026-06-08 08:26:49 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:10:29s. Time for last 1,000,000: 2s. Last read position: chr16:583,019
INFO 2026-06-08 08:26:49 MarkDuplicates Tracking 329997 as yet unmatched pairs. 72668 records in RAM.
INFO 2026-06-08 08:26:52 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:10:31s. Time for last 1,000,000: 2s. Last read position: chr16:1,153,718
INFO 2026-06-08 08:26:52 MarkDuplicates Tracking 326974 as yet unmatched pairs. 69640 records in RAM.
INFO 2026-06-08 08:26:54 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:10:33s. Time for last 1,000,000: 1s. Last read position: chr16:1,314,045
INFO 2026-06-08 08:26:54 MarkDuplicates Tracking 324259 as yet unmatched pairs. 66919 records in RAM.
INFO 2026-06-08 08:26:56 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:10:35s. Time for last 1,000,000: 1s. Last read position: chr16:1,777,108
INFO 2026-06-08 08:26:56 MarkDuplicates Tracking 321464 as yet unmatched pairs. 64122 records in RAM.
INFO 2026-06-08 08:26:58 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:10:37s. Time for last 1,000,000: 1s. Last read position: chr16:2,114,204
INFO 2026-06-08 08:26:58 MarkDuplicates Tracking 317884 as yet unmatched pairs. 60542 records in RAM.
INFO 2026-06-08 08:27:00 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:10:39s. Time for last 1,000,000: 2s. Last read position: chr16:2,761,589
INFO 2026-06-08 08:27:00 MarkDuplicates Tracking 316378 as yet unmatched pairs. 59034 records in RAM.
INFO 2026-06-08 08:27:02 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:10:41s. Time for last 1,000,000: 1s. Last read position: chr16:2,767,534
INFO 2026-06-08 08:27:02 MarkDuplicates Tracking 314417 as yet unmatched pairs. 57073 records in RAM.
INFO 2026-06-08 08:27:04 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:10:43s. Time for last 1,000,000: 2s. Last read position: chr16:3,727,881
INFO 2026-06-08 08:27:04 MarkDuplicates Tracking 310550 as yet unmatched pairs. 53206 records in RAM.
INFO 2026-06-08 08:27:06 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:10:45s. Time for last 1,000,000: 2s. Last read position: chr16:4,805,297
INFO 2026-06-08 08:27:06 MarkDuplicates Tracking 307744 as yet unmatched pairs. 50400 records in RAM.
INFO 2026-06-08 08:27:08 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:10:47s. Time for last 1,000,000: 1s. Last read position: chr16:11,841,696
INFO 2026-06-08 08:27:08 MarkDuplicates Tracking 305344 as yet unmatched pairs. 48000 records in RAM.
INFO 2026-06-08 08:27:10 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:10:49s. Time for last 1,000,000: 1s. Last read position: chr16:14,617,629
INFO 2026-06-08 08:27:10 MarkDuplicates Tracking 303338 as yet unmatched pairs. 45993 records in RAM.
INFO 2026-06-08 08:27:11 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:10:51s. Time for last 1,000,000: 1s. Last read position: chr16:15,036,125
INFO 2026-06-08 08:27:11 MarkDuplicates Tracking 302021 as yet unmatched pairs. 44676 records in RAM.
INFO 2026-06-08 08:27:13 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:10:52s. Time for last 1,000,000: 1s. Last read position: chr16:16,320,781
INFO 2026-06-08 08:27:13 MarkDuplicates Tracking 300325 as yet unmatched pairs. 42980 records in RAM.
INFO 2026-06-08 08:27:14 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:10:54s. Time for last 1,000,000: 1s. Last read position: chr16:18,340,457
INFO 2026-06-08 08:27:14 MarkDuplicates Tracking 299731 as yet unmatched pairs. 42386 records in RAM.
INFO 2026-06-08 08:27:16 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:10:55s. Time for last 1,000,000: 1s. Last read position: chr16:18,514,372
INFO 2026-06-08 08:27:16 MarkDuplicates Tracking 298636 as yet unmatched pairs. 41291 records in RAM.
INFO 2026-06-08 08:27:18 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:10:57s. Time for last 1,000,000: 1s. Last read position: chr16:19,699,568
INFO 2026-06-08 08:27:18 MarkDuplicates Tracking 296023 as yet unmatched pairs. 38678 records in RAM.
INFO 2026-06-08 08:27:19 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:10:59s. Time for last 1,000,000: 1s. Last read position: chr16:21,405,212
INFO 2026-06-08 08:27:19 MarkDuplicates Tracking 297271 as yet unmatched pairs. 39926 records in RAM.
INFO 2026-06-08 08:27:21 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:11:00s. Time for last 1,000,000: 1s. Last read position: chr16:21,836,384
INFO 2026-06-08 08:27:21 MarkDuplicates Tracking 294017 as yet unmatched pairs. 36672 records in RAM.
INFO 2026-06-08 08:27:23 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:11:02s. Time for last 1,000,000: 1s. Last read position: chr16:22,459,446
INFO 2026-06-08 08:27:23 MarkDuplicates Tracking 293554 as yet unmatched pairs. 36208 records in RAM.
INFO 2026-06-08 08:27:24 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:11:03s. Time for last 1,000,000: 1s. Last read position: chr16:22,534,731
INFO 2026-06-08 08:27:24 MarkDuplicates Tracking 293679 as yet unmatched pairs. 36333 records in RAM.
INFO 2026-06-08 08:27:26 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:11:05s. Time for last 1,000,000: 1s. Last read position: chr16:25,240,021
INFO 2026-06-08 08:27:26 MarkDuplicates Tracking 290931 as yet unmatched pairs. 33585 records in RAM.
INFO 2026-06-08 08:27:27 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:11:07s. Time for last 1,000,000: 1s. Last read position: chr16:28,658,292
INFO 2026-06-08 08:27:27 MarkDuplicates Tracking 288702 as yet unmatched pairs. 31356 records in RAM.
INFO 2026-06-08 08:27:29 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:11:08s. Time for last 1,000,000: 1s. Last read position: chr16:29,381,891
INFO 2026-06-08 08:27:29 MarkDuplicates Tracking 287051 as yet unmatched pairs. 29705 records in RAM.
INFO 2026-06-08 08:27:31 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:11:10s. Time for last 1,000,000: 1s. Last read position: chr16:29,485,440
INFO 2026-06-08 08:27:31 MarkDuplicates Tracking 288425 as yet unmatched pairs. 31079 records in RAM.
INFO 2026-06-08 08:27:32 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:11:12s. Time for last 1,000,000: 1s. Last read position: chr16:29,971,414
INFO 2026-06-08 08:27:32 MarkDuplicates Tracking 284958 as yet unmatched pairs. 27612 records in RAM.
INFO 2026-06-08 08:27:34 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:11:13s. Time for last 1,000,000: 1s. Last read position: chr16:30,203,806
INFO 2026-06-08 08:27:34 MarkDuplicates Tracking 282867 as yet unmatched pairs. 25516 records in RAM.
INFO 2026-06-08 08:27:35 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:11:15s. Time for last 1,000,000: 1s. Last read position: chr16:30,398,588
INFO 2026-06-08 08:27:35 MarkDuplicates Tracking 281324 as yet unmatched pairs. 23973 records in RAM.
INFO 2026-06-08 08:27:38 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:11:17s. Time for last 1,000,000: 2s. Last read position: chr16:30,737,516
INFO 2026-06-08 08:27:38 MarkDuplicates Tracking 279003 as yet unmatched pairs. 21639 records in RAM.
INFO 2026-06-08 08:27:40 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:11:19s. Time for last 1,000,000: 2s. Last read position: chr16:31,188,339
INFO 2026-06-08 08:27:40 MarkDuplicates Tracking 278303 as yet unmatched pairs. 20936 records in RAM.
INFO 2026-06-08 08:27:42 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:11:21s. Time for last 1,000,000: 2s. Last read position: chr16:50,711,330
INFO 2026-06-08 08:27:42 MarkDuplicates Tracking 273933 as yet unmatched pairs. 16564 records in RAM.
INFO 2026-06-08 08:27:45 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:11:25s. Time for last 1,000,000: 3s. Last read position: chr16:57,753,119
INFO 2026-06-08 08:27:45 MarkDuplicates Tracking 271503 as yet unmatched pairs. 14132 records in RAM.
INFO 2026-06-08 08:27:47 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:11:27s. Time for last 1,000,000: 2s. Last read position: chr16:67,936,001
INFO 2026-06-08 08:27:47 MarkDuplicates Tracking 269221 as yet unmatched pairs. 11849 records in RAM.
INFO 2026-06-08 08:27:49 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:11:29s. Time for last 1,000,000: 1s. Last read position: chr16:70,474,167
INFO 2026-06-08 08:27:49 MarkDuplicates Tracking 266726 as yet unmatched pairs. 9354 records in RAM.
INFO 2026-06-08 08:27:51 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:11:30s. Time for last 1,000,000: 1s. Last read position: chr16:78,022,590
INFO 2026-06-08 08:27:51 MarkDuplicates Tracking 266573 as yet unmatched pairs. 9200 records in RAM.
INFO 2026-06-08 08:27:53 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:11:32s. Time for last 1,000,000: 1s. Last read position: chr16:85,656,647
INFO 2026-06-08 08:27:53 MarkDuplicates Tracking 261872 as yet unmatched pairs. 4496 records in RAM.
INFO 2026-06-08 08:27:55 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:11:34s. Time for last 1,000,000: 1s. Last read position: chr16:89,280,697
INFO 2026-06-08 08:27:55 MarkDuplicates Tracking 259038 as yet unmatched pairs. 1661 records in RAM.
INFO 2026-06-08 08:27:57 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:11:37s. Time for last 1,000,000: 2s. Last read position: chr17:1,479,467
INFO 2026-06-08 08:27:57 MarkDuplicates Tracking 256544 as yet unmatched pairs. 85942 records in RAM.
INFO 2026-06-08 08:27:59 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:11:38s. Time for last 1,000,000: 1s. Last read position: chr17:3,942,686
INFO 2026-06-08 08:27:59 MarkDuplicates Tracking 253939 as yet unmatched pairs. 83337 records in RAM.
INFO 2026-06-08 08:28:01 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:11:40s. Time for last 1,000,000: 1s. Last read position: chr17:6,640,230
INFO 2026-06-08 08:28:01 MarkDuplicates Tracking 251009 as yet unmatched pairs. 80407 records in RAM.
INFO 2026-06-08 08:28:03 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:11:42s. Time for last 1,000,000: 1s. Last read position: chr17:7,513,787
INFO 2026-06-08 08:28:03 MarkDuplicates Tracking 249208 as yet unmatched pairs. 78606 records in RAM.
INFO 2026-06-08 08:28:05 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:11:44s. Time for last 1,000,000: 1s. Last read position: chr17:8,480,228
INFO 2026-06-08 08:28:05 MarkDuplicates Tracking 246049 as yet unmatched pairs. 75446 records in RAM.
INFO 2026-06-08 08:28:06 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:11:46s. Time for last 1,000,000: 1s. Last read position: chr17:17,818,270
INFO 2026-06-08 08:28:06 MarkDuplicates Tracking 244116 as yet unmatched pairs. 73510 records in RAM.
INFO 2026-06-08 08:28:08 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:11:47s. Time for last 1,000,000: 1s. Last read position: chr17:28,332,200
INFO 2026-06-08 08:28:08 MarkDuplicates Tracking 241258 as yet unmatched pairs. 70652 records in RAM.
INFO 2026-06-08 08:28:11 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:11:50s. Time for last 1,000,000: 2s. Last read position: chr17:28,883,165
INFO 2026-06-08 08:28:11 MarkDuplicates Tracking 238928 as yet unmatched pairs. 68322 records in RAM.
INFO 2026-06-08 08:28:13 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:11:53s. Time for last 1,000,000: 2s. Last read position: chr17:31,232,750
INFO 2026-06-08 08:28:13 MarkDuplicates Tracking 236571 as yet unmatched pairs. 65965 records in RAM.
INFO 2026-06-08 08:28:15 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:11:55s. Time for last 1,000,000: 1s. Last read position: chr17:36,318,746
INFO 2026-06-08 08:28:15 MarkDuplicates Tracking 234114 as yet unmatched pairs. 63505 records in RAM.
INFO 2026-06-08 08:28:17 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:11:57s. Time for last 1,000,000: 1s. Last read position: chr17:38,739,556
INFO 2026-06-08 08:28:17 MarkDuplicates Tracking 232317 as yet unmatched pairs. 61693 records in RAM.
INFO 2026-06-08 08:28:19 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:11:58s. Time for last 1,000,000: 1s. Last read position: chr17:39,723,624
INFO 2026-06-08 08:28:19 MarkDuplicates Tracking 230421 as yet unmatched pairs. 59795 records in RAM.
INFO 2026-06-08 08:28:21 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:12:00s. Time for last 1,000,000: 1s. Last read position: chr17:41,523,916
INFO 2026-06-08 08:28:21 MarkDuplicates Tracking 227995 as yet unmatched pairs. 57368 records in RAM.
INFO 2026-06-08 08:28:23 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:12:02s. Time for last 1,000,000: 1s. Last read position: chr17:42,324,778
INFO 2026-06-08 08:28:23 MarkDuplicates Tracking 224603 as yet unmatched pairs. 53976 records in RAM.
INFO 2026-06-08 08:28:24 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:12:04s. Time for last 1,000,000: 1s. Last read position: chr17:43,533,321
INFO 2026-06-08 08:28:24 MarkDuplicates Tracking 223534 as yet unmatched pairs. 52907 records in RAM.
INFO 2026-06-08 08:28:26 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:12:06s. Time for last 1,000,000: 1s. Last read position: chr17:45,149,941
INFO 2026-06-08 08:28:26 MarkDuplicates Tracking 219449 as yet unmatched pairs. 48822 records in RAM.
INFO 2026-06-08 08:28:28 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:12:07s. Time for last 1,000,000: 1s. Last read position: chr17:47,973,555
INFO 2026-06-08 08:28:28 MarkDuplicates Tracking 217602 as yet unmatched pairs. 46975 records in RAM.
INFO 2026-06-08 08:28:30 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:12:09s. Time for last 1,000,000: 1s. Last read position: chr17:50,186,399
INFO 2026-06-08 08:28:30 MarkDuplicates Tracking 216775 as yet unmatched pairs. 46148 records in RAM.
INFO 2026-06-08 08:28:32 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:12:11s. Time for last 1,000,000: 1s. Last read position: chr17:50,189,464
INFO 2026-06-08 08:28:32 MarkDuplicates Tracking 217516 as yet unmatched pairs. 46887 records in RAM.
INFO 2026-06-08 08:28:34 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:12:13s. Time for last 1,000,000: 1s. Last read position: chr17:50,192,804
INFO 2026-06-08 08:28:34 MarkDuplicates Tracking 216751 as yet unmatched pairs. 46122 records in RAM.
INFO 2026-06-08 08:28:36 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:12:16s. Time for last 1,000,000: 2s. Last read position: chr17:50,195,947
INFO 2026-06-08 08:28:36 MarkDuplicates Tracking 211706 as yet unmatched pairs. 41068 records in RAM.
INFO 2026-06-08 08:28:38 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:12:18s. Time for last 1,000,000: 2s. Last read position: chr17:50,199,314
INFO 2026-06-08 08:28:38 MarkDuplicates Tracking 207593 as yet unmatched pairs. 36948 records in RAM.
INFO 2026-06-08 08:28:40 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:12:20s. Time for last 1,000,000: 1s. Last read position: chr17:57,258,301
INFO 2026-06-08 08:28:40 MarkDuplicates Tracking 201823 as yet unmatched pairs. 31178 records in RAM.
INFO 2026-06-08 08:28:42 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:12:22s. Time for last 1,000,000: 1s. Last read position: chr17:59,674,700
INFO 2026-06-08 08:28:42 MarkDuplicates Tracking 200201 as yet unmatched pairs. 29546 records in RAM.
INFO 2026-06-08 08:28:44 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:12:23s. Time for last 1,000,000: 1s. Last read position: chr17:63,589,057
INFO 2026-06-08 08:28:44 MarkDuplicates Tracking 196570 as yet unmatched pairs. 25912 records in RAM.
INFO 2026-06-08 08:28:46 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:12:25s. Time for last 1,000,000: 1s. Last read position: chr17:67,854,527
INFO 2026-06-08 08:28:46 MarkDuplicates Tracking 194622 as yet unmatched pairs. 23961 records in RAM.
INFO 2026-06-08 08:28:48 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:12:27s. Time for last 1,000,000: 1s. Last read position: chr17:74,762,065
INFO 2026-06-08 08:28:48 MarkDuplicates Tracking 192908 as yet unmatched pairs. 22247 records in RAM.
INFO 2026-06-08 08:28:50 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:12:29s. Time for last 1,000,000: 1s. Last read position: chr17:75,846,684
INFO 2026-06-08 08:28:50 MarkDuplicates Tracking 189283 as yet unmatched pairs. 18619 records in RAM.
INFO 2026-06-08 08:28:51 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:12:31s. Time for last 1,000,000: 1s. Last read position: chr17:78,170,845
INFO 2026-06-08 08:28:51 MarkDuplicates Tracking 187157 as yet unmatched pairs. 16490 records in RAM.
INFO 2026-06-08 08:28:53 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:12:33s. Time for last 1,000,000: 1s. Last read position: chr17:79,940,898
INFO 2026-06-08 08:28:53 MarkDuplicates Tracking 184163 as yet unmatched pairs. 13495 records in RAM.
INFO 2026-06-08 08:28:55 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:12:35s. Time for last 1,000,000: 2s. Last read position: chr17:80,345,013
INFO 2026-06-08 08:28:55 MarkDuplicates Tracking 182350 as yet unmatched pairs. 11682 records in RAM.
INFO 2026-06-08 08:28:58 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:12:38s. Time for last 1,000,000: 2s. Last read position: chr17:81,251,290
INFO 2026-06-08 08:28:58 MarkDuplicates Tracking 179255 as yet unmatched pairs. 8587 records in RAM.
INFO 2026-06-08 08:29:00 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:12:39s. Time for last 1,000,000: 1s. Last read position: chr17:81,859,332
INFO 2026-06-08 08:29:00 MarkDuplicates Tracking 177147 as yet unmatched pairs. 6479 records in RAM.
INFO 2026-06-08 08:29:02 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:12:41s. Time for last 1,000,000: 1s. Last read position: chr17:82,085,840
INFO 2026-06-08 08:29:02 MarkDuplicates Tracking 174321 as yet unmatched pairs. 3653 records in RAM.
INFO 2026-06-08 08:29:04 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:12:43s. Time for last 1,000,000: 1s. Last read position: chr17:83,085,174
INFO 2026-06-08 08:29:04 MarkDuplicates Tracking 170860 as yet unmatched pairs. 192 records in RAM.
INFO 2026-06-08 08:29:05 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:12:45s. Time for last 1,000,000: 1s. Last read position: chr18:25,226,890
INFO 2026-06-08 08:29:05 MarkDuplicates Tracking 168362 as yet unmatched pairs. 5013 records in RAM.
INFO 2026-06-08 08:29:07 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:12:47s. Time for last 1,000,000: 1s. Last read position: chr18:48,619,583
INFO 2026-06-08 08:29:07 MarkDuplicates Tracking 166140 as yet unmatched pairs. 2791 records in RAM.
INFO 2026-06-08 08:29:09 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:12:48s. Time for last 1,000,000: 1s. Last read position: chr18:79,710,344
INFO 2026-06-08 08:29:09 MarkDuplicates Tracking 163546 as yet unmatched pairs. 197 records in RAM.
INFO 2026-06-08 08:29:11 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:12:51s. Time for last 1,000,000: 2s. Last read position: chr19:1,105,389
INFO 2026-06-08 08:29:11 MarkDuplicates Tracking 161381 as yet unmatched pairs. 54397 records in RAM.
INFO 2026-06-08 08:29:13 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:12:53s. Time for last 1,000,000: 1s. Last read position: chr19:2,121,944
INFO 2026-06-08 08:29:13 MarkDuplicates Tracking 158224 as yet unmatched pairs. 51240 records in RAM.
INFO 2026-06-08 08:29:15 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:12:54s. Time for last 1,000,000: 1s. Last read position: chr19:4,358,892
INFO 2026-06-08 08:29:15 MarkDuplicates Tracking 154941 as yet unmatched pairs. 47957 records in RAM.
INFO 2026-06-08 08:29:17 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:12:56s. Time for last 1,000,000: 1s. Last read position: chr19:6,380,274
INFO 2026-06-08 08:29:17 MarkDuplicates Tracking 152464 as yet unmatched pairs. 45480 records in RAM.
INFO 2026-06-08 08:29:19 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:12:58s. Time for last 1,000,000: 1s. Last read position: chr19:8,255,824
INFO 2026-06-08 08:29:19 MarkDuplicates Tracking 150603 as yet unmatched pairs. 43615 records in RAM.
INFO 2026-06-08 08:29:21 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:13:00s. Time for last 1,000,000: 2s. Last read position: chr19:10,635,447
INFO 2026-06-08 08:29:21 MarkDuplicates Tracking 147189 as yet unmatched pairs. 40197 records in RAM.
INFO 2026-06-08 08:29:23 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:13:03s. Time for last 1,000,000: 2s. Last read position: chr19:12,705,715
INFO 2026-06-08 08:29:23 MarkDuplicates Tracking 144613 as yet unmatched pairs. 37621 records in RAM.
INFO 2026-06-08 08:29:26 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:13:05s. Time for last 1,000,000: 2s. Last read position: chr19:14,516,770
INFO 2026-06-08 08:29:26 MarkDuplicates Tracking 142485 as yet unmatched pairs. 35493 records in RAM.
INFO 2026-06-08 08:29:28 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:13:07s. Time for last 1,000,000: 1s. Last read position: chr19:16,523,141
INFO 2026-06-08 08:29:28 MarkDuplicates Tracking 139029 as yet unmatched pairs. 32037 records in RAM.
INFO 2026-06-08 08:29:29 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:13:09s. Time for last 1,000,000: 1s. Last read position: chr19:18,430,841
INFO 2026-06-08 08:29:29 MarkDuplicates Tracking 136280 as yet unmatched pairs. 29288 records in RAM.
INFO 2026-06-08 08:29:31 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:13:11s. Time for last 1,000,000: 1s. Last read position: chr19:29,674,514
INFO 2026-06-08 08:29:31 MarkDuplicates Tracking 133733 as yet unmatched pairs. 26735 records in RAM.
INFO 2026-06-08 08:29:33 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:13:13s. Time for last 1,000,000: 1s. Last read position: chr19:35,787,455
INFO 2026-06-08 08:29:33 MarkDuplicates Tracking 130939 as yet unmatched pairs. 23941 records in RAM.
INFO 2026-06-08 08:29:35 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:13:14s. Time for last 1,000,000: 1s. Last read position: chr19:39,377,627
INFO 2026-06-08 08:29:35 MarkDuplicates Tracking 128546 as yet unmatched pairs. 21548 records in RAM.
INFO 2026-06-08 08:29:37 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:13:16s. Time for last 1,000,000: 1s. Last read position: chr19:40,924,422
INFO 2026-06-08 08:29:37 MarkDuplicates Tracking 127877 as yet unmatched pairs. 20879 records in RAM.
INFO 2026-06-08 08:29:38 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:13:18s. Time for last 1,000,000: 1s. Last read position: chr19:43,497,227
INFO 2026-06-08 08:29:38 MarkDuplicates Tracking 123576 as yet unmatched pairs. 16575 records in RAM.
INFO 2026-06-08 08:29:40 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:13:20s. Time for last 1,000,000: 1s. Last read position: chr19:45,642,149
INFO 2026-06-08 08:29:40 MarkDuplicates Tracking 120596 as yet unmatched pairs. 13593 records in RAM.
INFO 2026-06-08 08:29:42 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:13:22s. Time for last 1,000,000: 1s. Last read position: chr19:48,195,618
INFO 2026-06-08 08:29:42 MarkDuplicates Tracking 117820 as yet unmatched pairs. 10815 records in RAM.
INFO 2026-06-08 08:29:45 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:13:24s. Time for last 1,000,000: 2s. Last read position: chr19:49,601,606
INFO 2026-06-08 08:29:45 MarkDuplicates Tracking 115377 as yet unmatched pairs. 8372 records in RAM.
INFO 2026-06-08 08:29:47 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:13:27s. Time for last 1,000,000: 2s. Last read position: chr19:52,212,782
INFO 2026-06-08 08:29:47 MarkDuplicates Tracking 112802 as yet unmatched pairs. 5797 records in RAM.
INFO 2026-06-08 08:29:49 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:13:28s. Time for last 1,000,000: 1s. Last read position: chr19:55,094,344
INFO 2026-06-08 08:29:49 MarkDuplicates Tracking 110195 as yet unmatched pairs. 3190 records in RAM.
INFO 2026-06-08 08:29:51 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:13:30s. Time for last 1,000,000: 1s. Last read position: chr19:58,393,105
INFO 2026-06-08 08:29:51 MarkDuplicates Tracking 107847 as yet unmatched pairs. 841 records in RAM.
INFO 2026-06-08 08:29:53 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:13:32s. Time for last 1,000,000: 2s. Last read position: chr20:2,838,925
INFO 2026-06-08 08:29:53 MarkDuplicates Tracking 105101 as yet unmatched pairs. 35297 records in RAM.
INFO 2026-06-08 08:29:55 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:13:34s. Time for last 1,000,000: 1s. Last read position: chr20:10,413,791
INFO 2026-06-08 08:29:55 MarkDuplicates Tracking 102564 as yet unmatched pairs. 32759 records in RAM.
INFO 2026-06-08 08:29:57 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:13:36s. Time for last 1,000,000: 1s. Last read position: chr20:24,983,983
INFO 2026-06-08 08:29:57 MarkDuplicates Tracking 100652 as yet unmatched pairs. 30841 records in RAM.
INFO 2026-06-08 08:29:59 MarkDuplicates Read 368,000,000 records. Elapsed time: 00:13:38s. Time for last 1,000,000: 1s. Last read position: chr20:33,574,175
INFO 2026-06-08 08:29:59 MarkDuplicates Tracking 98079 as yet unmatched pairs. 28267 records in RAM.
INFO 2026-06-08 08:30:00 MarkDuplicates Read 369,000,000 records. Elapsed time: 00:13:40s. Time for last 1,000,000: 1s. Last read position: chr20:35,277,806
INFO 2026-06-08 08:30:00 MarkDuplicates Tracking 96358 as yet unmatched pairs. 26546 records in RAM.
INFO 2026-06-08 08:30:02 MarkDuplicates Read 370,000,000 records. Elapsed time: 00:13:42s. Time for last 1,000,000: 1s. Last read position: chr20:36,500,198
INFO 2026-06-08 08:30:02 MarkDuplicates Tracking 93787 as yet unmatched pairs. 23975 records in RAM.
INFO 2026-06-08 08:30:05 MarkDuplicates Read 371,000,000 records. Elapsed time: 00:13:44s. Time for last 1,000,000: 2s. Last read position: chr20:38,569,910
INFO 2026-06-08 08:30:05 MarkDuplicates Tracking 90657 as yet unmatched pairs. 20845 records in RAM.
INFO 2026-06-08 08:30:07 MarkDuplicates Read 372,000,000 records. Elapsed time: 00:13:47s. Time for last 1,000,000: 2s. Last read position: chr20:44,514,003
INFO 2026-06-08 08:30:07 MarkDuplicates Tracking 88673 as yet unmatched pairs. 18861 records in RAM.
INFO 2026-06-08 08:30:09 MarkDuplicates Read 373,000,000 records. Elapsed time: 00:13:48s. Time for last 1,000,000: 1s. Last read position: chr20:45,950,277
INFO 2026-06-08 08:30:09 MarkDuplicates Tracking 85763 as yet unmatched pairs. 15950 records in RAM.
INFO 2026-06-08 08:30:11 MarkDuplicates Read 374,000,000 records. Elapsed time: 00:13:50s. Time for last 1,000,000: 1s. Last read position: chr20:49,124,441
INFO 2026-06-08 08:30:11 MarkDuplicates Tracking 83406 as yet unmatched pairs. 13593 records in RAM.
INFO 2026-06-08 08:30:13 MarkDuplicates Read 375,000,000 records. Elapsed time: 00:13:52s. Time for last 1,000,000: 1s. Last read position: chr20:51,657,037
INFO 2026-06-08 08:30:13 MarkDuplicates Tracking 81193 as yet unmatched pairs. 11380 records in RAM.
INFO 2026-06-08 08:30:14 MarkDuplicates Read 376,000,000 records. Elapsed time: 00:13:54s. Time for last 1,000,000: 1s. Last read position: chr20:58,891,838
INFO 2026-06-08 08:30:14 MarkDuplicates Tracking 79972 as yet unmatched pairs. 10158 records in RAM.
INFO 2026-06-08 08:30:16 MarkDuplicates Read 377,000,000 records. Elapsed time: 00:13:56s. Time for last 1,000,000: 1s. Last read position: chr20:62,325,455
INFO 2026-06-08 08:30:16 MarkDuplicates Tracking 75689 as yet unmatched pairs. 5875 records in RAM.
INFO 2026-06-08 08:30:18 MarkDuplicates Read 378,000,000 records. Elapsed time: 00:13:57s. Time for last 1,000,000: 1s. Last read position: chr20:63,530,865
INFO 2026-06-08 08:30:18 MarkDuplicates Tracking 72937 as yet unmatched pairs. 3123 records in RAM.
INFO 2026-06-08 08:30:20 MarkDuplicates Read 379,000,000 records. Elapsed time: 00:13:59s. Time for last 1,000,000: 1s. Last read position: chr20:64,073,824
INFO 2026-06-08 08:30:20 MarkDuplicates Tracking 69976 as yet unmatched pairs. 162 records in RAM.
INFO 2026-06-08 08:30:22 MarkDuplicates Read 380,000,000 records. Elapsed time: 00:14:02s. Time for last 1,000,000: 2s. Last read position: chr21:8,444,578
INFO 2026-06-08 08:30:22 MarkDuplicates Tracking 68743 as yet unmatched pairs. 10830 records in RAM.
INFO 2026-06-08 08:30:24 MarkDuplicates Read 381,000,000 records. Elapsed time: 00:14:04s. Time for last 1,000,000: 2s. Last read position: chr21:33,524,820
INFO 2026-06-08 08:30:24 MarkDuplicates Tracking 66528 as yet unmatched pairs. 8615 records in RAM.
INFO 2026-06-08 08:30:26 MarkDuplicates Read 382,000,000 records. Elapsed time: 00:14:06s. Time for last 1,000,000: 1s. Last read position: chr21:39,187,162
INFO 2026-06-08 08:30:26 MarkDuplicates Tracking 64192 as yet unmatched pairs. 6278 records in RAM.
INFO 2026-06-08 08:30:28 MarkDuplicates Read 383,000,000 records. Elapsed time: 00:14:07s. Time for last 1,000,000: 1s. Last read position: chr21:44,331,945
INFO 2026-06-08 08:30:28 MarkDuplicates Tracking 61511 as yet unmatched pairs. 3597 records in RAM.
INFO 2026-06-08 08:30:30 MarkDuplicates Read 384,000,000 records. Elapsed time: 00:14:09s. Time for last 1,000,000: 1s. Last read position: chr21:46,284,255
INFO 2026-06-08 08:30:30 MarkDuplicates Tracking 59180 as yet unmatched pairs. 1266 records in RAM.
INFO 2026-06-08 08:30:32 MarkDuplicates Read 385,000,000 records. Elapsed time: 00:14:11s. Time for last 1,000,000: 1s. Last read position: chr22:20,085,972
INFO 2026-06-08 08:30:32 MarkDuplicates Tracking 56453 as yet unmatched pairs. 23795 records in RAM.
INFO 2026-06-08 08:30:34 MarkDuplicates Read 386,000,000 records. Elapsed time: 00:14:13s. Time for last 1,000,000: 1s. Last read position: chr22:23,781,081
INFO 2026-06-08 08:30:34 MarkDuplicates Tracking 53741 as yet unmatched pairs. 21083 records in RAM.
INFO 2026-06-08 08:30:35 MarkDuplicates Read 387,000,000 records. Elapsed time: 00:14:15s. Time for last 1,000,000: 1s. Last read position: chr22:29,265,591
INFO 2026-06-08 08:30:35 MarkDuplicates Tracking 51118 as yet unmatched pairs. 18460 records in RAM.
INFO 2026-06-08 08:30:37 MarkDuplicates Read 388,000,000 records. Elapsed time: 00:14:17s. Time for last 1,000,000: 1s. Last read position: chr22:31,127,392
INFO 2026-06-08 08:30:37 MarkDuplicates Tracking 48718 as yet unmatched pairs. 16060 records in RAM.
INFO 2026-06-08 08:30:39 MarkDuplicates Read 389,000,000 records. Elapsed time: 00:14:19s. Time for last 1,000,000: 1s. Last read position: chr22:36,312,098
INFO 2026-06-08 08:30:39 MarkDuplicates Tracking 46235 as yet unmatched pairs. 13577 records in RAM.
INFO 2026-06-08 08:30:41 MarkDuplicates Read 390,000,000 records. Elapsed time: 00:14:21s. Time for last 1,000,000: 1s. Last read position: chr22:38,689,311
INFO 2026-06-08 08:30:41 MarkDuplicates Tracking 43353 as yet unmatched pairs. 10695 records in RAM.
INFO 2026-06-08 08:30:43 MarkDuplicates Read 391,000,000 records. Elapsed time: 00:14:23s. Time for last 1,000,000: 2s. Last read position: chr22:41,341,100
INFO 2026-06-08 08:30:43 MarkDuplicates Tracking 40965 as yet unmatched pairs. 8307 records in RAM.
INFO 2026-06-08 08:30:46 MarkDuplicates Read 392,000,000 records. Elapsed time: 00:14:25s. Time for last 1,000,000: 2s. Last read position: chr22:46,364,658
INFO 2026-06-08 08:30:46 MarkDuplicates Tracking 38764 as yet unmatched pairs. 6106 records in RAM.
INFO 2026-06-08 08:30:47 MarkDuplicates Read 393,000,000 records. Elapsed time: 00:14:27s. Time for last 1,000,000: 1s. Last read position: chr22:50,278,159
INFO 2026-06-08 08:30:47 MarkDuplicates Tracking 35668 as yet unmatched pairs. 3010 records in RAM.
INFO 2026-06-08 08:30:49 MarkDuplicates Read 394,000,000 records. Elapsed time: 00:14:29s. Time for last 1,000,000: 2s. Last read position: chrX:1,389,725
INFO 2026-06-08 08:30:49 MarkDuplicates Tracking 32725 as yet unmatched pairs. 29295 records in RAM.
INFO 2026-06-08 08:30:51 MarkDuplicates Read 395,000,000 records. Elapsed time: 00:14:30s. Time for last 1,000,000: 1s. Last read position: chrX:17,068,400
INFO 2026-06-08 08:30:51 MarkDuplicates Tracking 30330 as yet unmatched pairs. 26900 records in RAM.
INFO 2026-06-08 08:30:52 MarkDuplicates Read 396,000,000 records. Elapsed time: 00:14:32s. Time for last 1,000,000: 1s. Last read position: chrX:41,184,550
INFO 2026-06-08 08:30:52 MarkDuplicates Tracking 27967 as yet unmatched pairs. 24534 records in RAM.
INFO 2026-06-08 08:30:54 MarkDuplicates Read 397,000,000 records. Elapsed time: 00:14:34s. Time for last 1,000,000: 1s. Last read position: chrX:46,607,179
INFO 2026-06-08 08:30:54 MarkDuplicates Tracking 25713 as yet unmatched pairs. 22280 records in RAM.
INFO 2026-06-08 08:30:56 MarkDuplicates Read 398,000,000 records. Elapsed time: 00:14:35s. Time for last 1,000,000: 1s. Last read position: chrX:49,031,419
INFO 2026-06-08 08:30:56 MarkDuplicates Tracking 22999 as yet unmatched pairs. 19566 records in RAM.
INFO 2026-06-08 08:30:58 MarkDuplicates Read 399,000,000 records. Elapsed time: 00:14:37s. Time for last 1,000,000: 1s. Last read position: chrX:53,414,820
INFO 2026-06-08 08:30:58 MarkDuplicates Tracking 20869 as yet unmatched pairs. 17436 records in RAM.
INFO 2026-06-08 08:30:59 MarkDuplicates Read 400,000,000 records. Elapsed time: 00:14:39s. Time for last 1,000,000: 1s. Last read position: chrX:56,564,665
INFO 2026-06-08 08:30:59 MarkDuplicates Tracking 18314 as yet unmatched pairs. 14881 records in RAM.
INFO 2026-06-08 08:31:01 MarkDuplicates Read 401,000,000 records. Elapsed time: 00:14:41s. Time for last 1,000,000: 1s. Last read position: chrX:71,556,771
INFO 2026-06-08 08:31:01 MarkDuplicates Tracking 16296 as yet unmatched pairs. 12863 records in RAM.
INFO 2026-06-08 08:31:04 MarkDuplicates Read 402,000,000 records. Elapsed time: 00:14:43s. Time for last 1,000,000: 2s. Last read position: chrX:80,744,083
INFO 2026-06-08 08:31:04 MarkDuplicates Tracking 13719 as yet unmatched pairs. 10286 records in RAM.
INFO 2026-06-08 08:31:06 MarkDuplicates Read 403,000,000 records. Elapsed time: 00:14:45s. Time for last 1,000,000: 1s. Last read position: chrX:119,786,721
INFO 2026-06-08 08:31:06 MarkDuplicates Tracking 11446 as yet unmatched pairs. 8013 records in RAM.
INFO 2026-06-08 08:31:07 MarkDuplicates Read 404,000,000 records. Elapsed time: 00:14:47s. Time for last 1,000,000: 1s. Last read position: chrX:136,877,946
INFO 2026-06-08 08:31:07 MarkDuplicates Tracking 9513 as yet unmatched pairs. 6079 records in RAM.
INFO 2026-06-08 08:31:09 MarkDuplicates Read 405,000,000 records. Elapsed time: 00:14:48s. Time for last 1,000,000: 1s. Last read position: chrX:153,786,127
INFO 2026-06-08 08:31:09 MarkDuplicates Tracking 7235 as yet unmatched pairs. 3800 records in RAM.
INFO 2026-06-08 08:31:11 MarkDuplicates Read 406,000,000 records. Elapsed time: 00:14:50s. Time for last 1,000,000: 1s. Last read position: chrX:154,466,740
INFO 2026-06-08 08:31:11 MarkDuplicates Tracking 4720 as yet unmatched pairs. 1284 records in RAM.
INFO 2026-06-08 08:31:12 MarkDuplicates Read 407,000,000 records. Elapsed time: 00:14:52s. Time for last 1,000,000: 1s. Last read position: GL000220.1:158,133
INFO 2026-06-08 08:31:12 MarkDuplicates Tracking 2138 as yet unmatched pairs. 40 records in RAM.
INFO 2026-06-08 08:31:13 MarkDuplicates Read 407860903 records. 0 pairs never matched.
INFO 2026-06-08 08:32:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 36110451360; totalMemory: 51573161984; maxMemory: 63585648640
INFO 2026-06-08 08:32:04 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:32:22 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:32:41 OpticalDuplicateFinder Large duplicate set. size = 1629
INFO 2026-06-08 08:32:41 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-27,120
INFO 2026-06-08 08:33:05 MarkDuplicates Traversing fragment information and detecting duplicates.
WARNING 2026-06-08 08:33:05 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
INFO 2026-06-08 08:33:54 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:34:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 35523010952; totalMemory: 51472498688; maxMemory: 63585648640
INFO 2026-06-08 08:34:03 MarkDuplicates Marking 197259764 records as duplicates.
INFO 2026-06-08 08:34:03 MarkDuplicates Found 14689274 optical duplicate clusters.
INFO 2026-06-08 08:34:03 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 08:34:20 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:17s. Time for last 10,000,000: 17s. Last read position: chr1:39,422,483
INFO 2026-06-08 08:34:37 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:34s. Time for last 10,000,000: 16s. Last read position: chr1:148,590,885
INFO 2026-06-08 08:34:53 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:50s. Time for last 10,000,000: 16s. Last read position: chr1:171,515,835
INFO 2026-06-08 08:35:10 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:07s. Time for last 10,000,000: 16s. Last read position: chr2:3,192,452
INFO 2026-06-08 08:35:26 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:23s. Time for last 10,000,000: 15s. Last read position: chr2:86,529,222
INFO 2026-06-08 08:35:43 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:40s. Time for last 10,000,000: 17s. Last read position: chr2:215,370,395
INFO 2026-06-08 08:35:59 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:01:56s. Time for last 10,000,000: 16s. Last read position: chr3:39,102,710
INFO 2026-06-08 08:36:16 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:13s. Time for last 10,000,000: 17s. Last read position: chr3:146,528,792
INFO 2026-06-08 08:36:33 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:30s. Time for last 10,000,000: 16s. Last read position: chr4:102,722,932
INFO 2026-06-08 08:36:50 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:46s. Time for last 10,000,000: 16s. Last read position: chr5:97,026,616
INFO 2026-06-08 08:37:07 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:03:03s. Time for last 10,000,000: 16s. Last read position: chr5:177,371,504
INFO 2026-06-08 08:37:23 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:19s. Time for last 10,000,000: 16s. Last read position: chr6:33,416,924
INFO 2026-06-08 08:37:39 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:36s. Time for last 10,000,000: 16s. Last read position: chr6:161,107,905
INFO 2026-06-08 08:37:55 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:03:52s. Time for last 10,000,000: 16s. Last read position: chr7:92,345,866
INFO 2026-06-08 08:38:12 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:04:09s. Time for last 10,000,000: 16s. Last read position: chr8:1,860,042
INFO 2026-06-08 08:38:29 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:25s. Time for last 10,000,000: 16s. Last read position: chr8:102,833,107
INFO 2026-06-08 08:38:45 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:04:42s. Time for last 10,000,000: 16s. Last read position: chr8:144,400,465
INFO 2026-06-08 08:39:01 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:04:58s. Time for last 10,000,000: 16s. Last read position: chr9:131,096,850
INFO 2026-06-08 08:39:18 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:05:15s. Time for last 10,000,000: 16s. Last read position: chr10:89,339,699
INFO 2026-06-08 08:39:35 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:05:32s. Time for last 10,000,000: 16s. Last read position: chr11:18,296,959
INFO 2026-06-08 08:39:51 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:05:48s. Time for last 10,000,000: 16s. Last read position: chr11:66,468,168
INFO 2026-06-08 08:40:08 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:06:05s. Time for last 10,000,000: 16s. Last read position: chr11:130,141,541
INFO 2026-06-08 08:40:25 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:06:22s. Time for last 10,000,000: 17s. Last read position: chr12:53,297,861
INFO 2026-06-08 08:40:42 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:06:39s. Time for last 10,000,000: 16s. Last read position: chr12:118,181,437
INFO 2026-06-08 08:40:58 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:06:55s. Time for last 10,000,000: 16s. Last read position: chr14:24,145,402
INFO 2026-06-08 08:41:15 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:07:12s. Time for last 10,000,000: 16s. Last read position: chr15:31,327,215
INFO 2026-06-08 08:41:32 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:07:29s. Time for last 10,000,000: 16s. Last read position: chr16:583,019
INFO 2026-06-08 08:41:48 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:07:45s. Time for last 10,000,000: 16s. Last read position: chr16:14,617,629
INFO 2026-06-08 08:42:05 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:08:01s. Time for last 10,000,000: 16s. Last read position: chr16:25,240,021
INFO 2026-06-08 08:42:21 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:08:18s. Time for last 10,000,000: 16s. Last read position: chr16:57,753,119
INFO 2026-06-08 08:42:38 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:08:35s. Time for last 10,000,000: 16s. Last read position: chr17:8,480,228
INFO 2026-06-08 08:42:55 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:08:52s. Time for last 10,000,000: 16s. Last read position: chr17:43,533,321
INFO 2026-06-08 08:43:11 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:09:08s. Time for last 10,000,000: 16s. Last read position: chr17:63,589,057
INFO 2026-06-08 08:43:27 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:09:24s. Time for last 10,000,000: 16s. Last read position: chr17:83,085,174
INFO 2026-06-08 08:43:43 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:09:40s. Time for last 10,000,000: 16s. Last read position: chr19:12,705,715
INFO 2026-06-08 08:43:59 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:09:56s. Time for last 10,000,000: 15s. Last read position: chr19:48,195,618
INFO 2026-06-08 08:44:15 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:10:12s. Time for last 10,000,000: 16s. Last read position: chr20:36,500,198
INFO 2026-06-08 08:44:31 MarkDuplicates Written 380,000,000 records. Elapsed time: 00:10:28s. Time for last 10,000,000: 15s. Last read position: chr21:8,444,578
INFO 2026-06-08 08:44:47 MarkDuplicates Written 390,000,000 records. Elapsed time: 00:10:44s. Time for last 10,000,000: 16s. Last read position: chr22:38,689,311
INFO 2026-06-08 08:45:03 MarkDuplicates Written 400,000,000 records. Elapsed time: 00:11:00s. Time for last 10,000,000: 15s. Last read position: chrX:56,564,665
INFO 2026-06-08 08:45:21 MarkDuplicates Written 410,000,000 records. Elapsed time: 00:11:18s. Time for last 10,000,000: 17s. Last read position: */*
INFO 2026-06-08 08:45:22 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:45:22 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:45:22 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:45:22 MarkDuplicates Before output close freeMemory: 203188664; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:45:22 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:45:22 MarkDuplicates After output close freeMemory: 104872888; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 08:45:22 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 29.05 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory