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 dna_s776.Aligned.sortedByCoord.out.bam --OUTPUT dna_s776.md.bam --METRICS_FILE dna_s776.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:38:48.044 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Jun 08 07:38:48 GMT 2026] MarkDuplicates --INPUT dna_s776.Aligned.sortedByCoord.out.bam --OUTPUT dna_s776.md.bam --METRICS_FILE dna_s776.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 07:38:48 GMT 2026] Executing as ?@nf-7574870dc61c8da6f6b89e3a13bd3e7c-1644c-dbhdx on Linux 6.12.88 amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0
INFO 2026-06-08 07:38:48 MarkDuplicates Start of doWork freeMemory: 105829304; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:38:48 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:38:48 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:38:56 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 5s. Last read position: chr1:7,835,886
INFO 2026-06-08 07:38:56 MarkDuplicates Tracking 2630 as yet unmatched pairs. 215 records in RAM.
INFO 2026-06-08 07:39:00 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 4s. Last read position: chr1:13,281,585
INFO 2026-06-08 07:39:00 MarkDuplicates Tracking 5559 as yet unmatched pairs. 792 records in RAM.
INFO 2026-06-08 07:39:06 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 6s. Last read position: chr1:17,222,364
INFO 2026-06-08 07:39:06 MarkDuplicates Tracking 7412 as yet unmatched pairs. 474 records in RAM.
INFO 2026-06-08 07:39:11 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 4s. Last read position: chr1:26,346,611
INFO 2026-06-08 07:39:11 MarkDuplicates Tracking 10353 as yet unmatched pairs. 611 records in RAM.
INFO 2026-06-08 07:39:14 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 3s. Last read position: chr1:36,179,660
INFO 2026-06-08 07:39:14 MarkDuplicates Tracking 13506 as yet unmatched pairs. 744 records in RAM.
INFO 2026-06-08 07:39:18 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 4s. Last read position: chr1:44,139,454
INFO 2026-06-08 07:39:18 MarkDuplicates Tracking 16682 as yet unmatched pairs. 1197 records in RAM.
INFO 2026-06-08 07:39:22 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 3s. Last read position: chr1:54,722,772
INFO 2026-06-08 07:39:22 MarkDuplicates Tracking 19369 as yet unmatched pairs. 919 records in RAM.
INFO 2026-06-08 07:39:26 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 4s. Last read position: chr1:77,955,191
INFO 2026-06-08 07:39:26 MarkDuplicates Tracking 24130 as yet unmatched pairs. 1207 records in RAM.
INFO 2026-06-08 07:39:29 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 3s. Last read position: chr1:103,691,314
INFO 2026-06-08 07:39:29 MarkDuplicates Tracking 28560 as yet unmatched pairs. 1167 records in RAM.
INFO 2026-06-08 07:39:33 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 3s. Last read position: chr1:117,144,262
INFO 2026-06-08 07:39:33 MarkDuplicates Tracking 32625 as yet unmatched pairs. 2049 records in RAM.
INFO 2026-06-08 07:39:37 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 3s. Last read position: chr1:145,867,237
INFO 2026-06-08 07:39:37 MarkDuplicates Tracking 34643 as yet unmatched pairs. 1055 records in RAM.
INFO 2026-06-08 07:39:40 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 3s. Last read position: chr1:151,401,996
INFO 2026-06-08 07:39:40 MarkDuplicates Tracking 36552 as yet unmatched pairs. 943 records in RAM.
INFO 2026-06-08 07:39:44 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 3s. Last read position: chr1:156,158,517
INFO 2026-06-08 07:39:44 MarkDuplicates Tracking 38746 as yet unmatched pairs. 950 records in RAM.
INFO 2026-06-08 07:39:48 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 3s. Last read position: chr1:161,548,555
INFO 2026-06-08 07:39:48 MarkDuplicates Tracking 41313 as yet unmatched pairs. 1029 records in RAM.
INFO 2026-06-08 07:39:51 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 3s. Last read position: chr1:179,107,843
INFO 2026-06-08 07:39:51 MarkDuplicates Tracking 45647 as yet unmatched pairs. 1674 records in RAM.
INFO 2026-06-08 07:39:55 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 3s. Last read position: chr1:201,899,783
INFO 2026-06-08 07:39:55 MarkDuplicates Tracking 48905 as yet unmatched pairs. 795 records in RAM.
INFO 2026-06-08 07:39:58 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 3s. Last read position: chr1:206,415,906
INFO 2026-06-08 07:39:58 MarkDuplicates Tracking 51140 as yet unmatched pairs. 553 records in RAM.
INFO 2026-06-08 07:40:02 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 3s. Last read position: chr1:226,065,739
INFO 2026-06-08 07:40:02 MarkDuplicates Tracking 56130 as yet unmatched pairs. 1586 records in RAM.
INFO 2026-06-08 07:40:05 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 3s. Last read position: chr1:241,513,604
INFO 2026-06-08 07:40:05 MarkDuplicates Tracking 58242 as yet unmatched pairs. 237 records in RAM.
INFO 2026-06-08 07:40:08 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 3s. Last read position: chr2:11,634,321
INFO 2026-06-08 07:40:08 MarkDuplicates Tracking 61734 as yet unmatched pairs. 17214 records in RAM.
INFO 2026-06-08 07:40:12 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 3s. Last read position: chr2:27,137,968
INFO 2026-06-08 07:40:12 MarkDuplicates Tracking 65226 as yet unmatched pairs. 18006 records in RAM.
INFO 2026-06-08 07:40:16 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 3s. Last read position: chr2:32,916,406
INFO 2026-06-08 07:40:16 MarkDuplicates Tracking 171148 as yet unmatched pairs. 12988 records in RAM.
INFO 2026-06-08 07:40:20 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 3s. Last read position: chr2:47,799,256
INFO 2026-06-08 07:40:20 MarkDuplicates Tracking 183005 as yet unmatched pairs. 12369 records in RAM.
INFO 2026-06-08 07:40:24 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 4s. Last read position: chr2:70,275,641
INFO 2026-06-08 07:40:24 MarkDuplicates Tracking 184762 as yet unmatched pairs. 10864 records in RAM.
INFO 2026-06-08 07:40:28 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 3s. Last read position: chr2:86,990,944
INFO 2026-06-08 07:40:28 MarkDuplicates Tracking 186332 as yet unmatched pairs. 9978 records in RAM.
INFO 2026-06-08 07:40:30 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 2s. Last read position: chr2:97,734,242
INFO 2026-06-08 07:40:30 MarkDuplicates Tracking 187674 as yet unmatched pairs. 9443 records in RAM.
INFO 2026-06-08 07:40:33 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 2s. Last read position: chr2:109,838,988
INFO 2026-06-08 07:40:33 MarkDuplicates Tracking 189037 as yet unmatched pairs. 8669 records in RAM.
INFO 2026-06-08 07:40:35 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 2s. Last read position: chr2:113,470,993
INFO 2026-06-08 07:40:35 MarkDuplicates Tracking 189675 as yet unmatched pairs. 7958 records in RAM.
INFO 2026-06-08 07:40:38 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 2s. Last read position: chr2:135,812,320
INFO 2026-06-08 07:40:38 MarkDuplicates Tracking 191675 as yet unmatched pairs. 6960 records in RAM.
INFO 2026-06-08 07:40:42 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 3s. Last read position: chr2:165,138,063
INFO 2026-06-08 07:40:42 MarkDuplicates Tracking 194305 as yet unmatched pairs. 5962 records in RAM.
INFO 2026-06-08 07:40:45 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 3s. Last read position: chr2:178,591,342
INFO 2026-06-08 07:40:45 MarkDuplicates Tracking 195925 as yet unmatched pairs. 5066 records in RAM.
INFO 2026-06-08 07:40:50 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 4s. Last read position: chr2:197,398,056
INFO 2026-06-08 07:40:50 MarkDuplicates Tracking 197933 as yet unmatched pairs. 4178 records in RAM.
INFO 2026-06-08 07:40:53 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 3s. Last read position: chr2:214,781,162
INFO 2026-06-08 07:40:53 MarkDuplicates Tracking 200070 as yet unmatched pairs. 3488 records in RAM.
INFO 2026-06-08 07:40:57 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 3s. Last read position: chr2:224,500,348
INFO 2026-06-08 07:40:57 MarkDuplicates Tracking 200711 as yet unmatched pairs. 2031 records in RAM.
INFO 2026-06-08 07:41:01 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 4s. Last read position: chr2:239,050,050
INFO 2026-06-08 07:41:01 MarkDuplicates Tracking 203144 as yet unmatched pairs. 1951 records in RAM.
INFO 2026-06-08 07:41:05 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 3s. Last read position: chr3:10,088,788
INFO 2026-06-08 07:41:05 MarkDuplicates Tracking 203345 as yet unmatched pairs. 14539 records in RAM.
INFO 2026-06-08 07:41:08 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 3s. Last read position: chr3:12,366,031
INFO 2026-06-08 07:41:08 MarkDuplicates Tracking 204473 as yet unmatched pairs. 13900 records in RAM.
INFO 2026-06-08 07:41:11 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 3s. Last read position: chr3:32,106,586
INFO 2026-06-08 07:41:11 MarkDuplicates Tracking 205438 as yet unmatched pairs. 12032 records in RAM.
INFO 2026-06-08 07:41:15 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 3s. Last read position: chr3:45,967,891
INFO 2026-06-08 07:41:15 MarkDuplicates Tracking 206702 as yet unmatched pairs. 11030 records in RAM.
INFO 2026-06-08 07:41:19 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 3s. Last read position: chr3:49,910,824
INFO 2026-06-08 07:41:19 MarkDuplicates Tracking 207138 as yet unmatched pairs. 10003 records in RAM.
INFO 2026-06-08 07:41:21 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 2s. Last read position: chr3:58,645,622
INFO 2026-06-08 07:41:21 MarkDuplicates Tracking 207812 as yet unmatched pairs. 8981 records in RAM.
INFO 2026-06-08 07:41:25 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 3s. Last read position: chr3:93,892,974
INFO 2026-06-08 07:41:25 MarkDuplicates Tracking 210307 as yet unmatched pairs. 7504 records in RAM.
INFO 2026-06-08 07:41:28 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 3s. Last read position: chr3:121,488,857
INFO 2026-06-08 07:41:28 MarkDuplicates Tracking 212929 as yet unmatched pairs. 6580 records in RAM.
INFO 2026-06-08 07:41:32 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 3s. Last read position: chr3:133,523,709
INFO 2026-06-08 07:41:32 MarkDuplicates Tracking 213367 as yet unmatched pairs. 4957 records in RAM.
INFO 2026-06-08 07:41:36 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 4s. Last read position: chr3:154,276,199
INFO 2026-06-08 07:41:36 MarkDuplicates Tracking 214746 as yet unmatched pairs. 3523 records in RAM.
INFO 2026-06-08 07:41:39 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 3s. Last read position: chr3:182,942,485
INFO 2026-06-08 07:41:39 MarkDuplicates Tracking 217315 as yet unmatched pairs. 2532 records in RAM.
INFO 2026-06-08 07:41:43 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 3s. Last read position: chr3:189,886,331
INFO 2026-06-08 07:41:43 MarkDuplicates Tracking 217603 as yet unmatched pairs. 993 records in RAM.
INFO 2026-06-08 07:41:46 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 3s. Last read position: chr4:1,945,558
INFO 2026-06-08 07:41:46 MarkDuplicates Tracking 219192 as yet unmatched pairs. 12781 records in RAM.
INFO 2026-06-08 07:41:50 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 3s. Last read position: chr4:9,272,384
INFO 2026-06-08 07:41:50 MarkDuplicates Tracking 218413 as yet unmatched pairs. 10577 records in RAM.
INFO 2026-06-08 07:41:54 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 4s. Last read position: chr4:41,745,008
INFO 2026-06-08 07:41:54 MarkDuplicates Tracking 221700 as yet unmatched pairs. 10258 records in RAM.
INFO 2026-06-08 07:41:57 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 3s. Last read position: chr4:67,490,154
INFO 2026-06-08 07:41:57 MarkDuplicates Tracking 221954 as yet unmatched pairs. 7432 records in RAM.
INFO 2026-06-08 07:42:00 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 2s. Last read position: chr4:87,893,785
INFO 2026-06-08 07:42:00 MarkDuplicates Tracking 223298 as yet unmatched pairs. 6135 records in RAM.
INFO 2026-06-08 07:42:03 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 2s. Last read position: chr4:118,810,057
INFO 2026-06-08 07:42:03 MarkDuplicates Tracking 224912 as yet unmatched pairs. 4252 records in RAM.
INFO 2026-06-08 07:42:06 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 2s. Last read position: chr4:152,322,737
INFO 2026-06-08 07:42:06 MarkDuplicates Tracking 227413 as yet unmatched pairs. 3080 records in RAM.
INFO 2026-06-08 07:42:09 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 2s. Last read position: chr4:186,665,270
INFO 2026-06-08 07:42:09 MarkDuplicates Tracking 228273 as yet unmatched pairs. 232 records in RAM.
INFO 2026-06-08 07:42:12 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 3s. Last read position: chr5:28,465,430
INFO 2026-06-08 07:42:12 MarkDuplicates Tracking 229680 as yet unmatched pairs. 12708 records in RAM.
INFO 2026-06-08 07:42:17 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 4s. Last read position: chr5:55,491,069
INFO 2026-06-08 07:42:17 MarkDuplicates Tracking 231127 as yet unmatched pairs. 11081 records in RAM.
INFO 2026-06-08 07:42:20 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 3s. Last read position: chr5:74,750,311
INFO 2026-06-08 07:42:20 MarkDuplicates Tracking 232003 as yet unmatched pairs. 9664 records in RAM.
INFO 2026-06-08 07:42:24 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 3s. Last read position: chr5:109,378,470
INFO 2026-06-08 07:42:24 MarkDuplicates Tracking 233464 as yet unmatched pairs. 7764 records in RAM.
INFO 2026-06-08 07:42:27 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 3s. Last read position: chr5:132,644,294
INFO 2026-06-08 07:42:27 MarkDuplicates Tracking 235573 as yet unmatched pairs. 7246 records in RAM.
INFO 2026-06-08 07:42:31 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 3s. Last read position: chr5:141,636,466
INFO 2026-06-08 07:42:31 MarkDuplicates Tracking 234146 as yet unmatched pairs. 4295 records in RAM.
INFO 2026-06-08 07:42:34 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 3s. Last read position: chr5:154,903,011
INFO 2026-06-08 07:42:34 MarkDuplicates Tracking 234410 as yet unmatched pairs. 2694 records in RAM.
INFO 2026-06-08 07:42:38 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 3s. Last read position: chr5:177,295,027
INFO 2026-06-08 07:42:38 MarkDuplicates Tracking 235815 as yet unmatched pairs. 1586 records in RAM.
INFO 2026-06-08 07:42:42 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 4s. Last read position: chr6:7,576,967
INFO 2026-06-08 07:42:42 MarkDuplicates Tracking 235400 as yet unmatched pairs. 18028 records in RAM.
INFO 2026-06-08 07:42:46 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 3s. Last read position: chr6:29,723,413
INFO 2026-06-08 07:42:46 MarkDuplicates Tracking 236756 as yet unmatched pairs. 17009 records in RAM.
INFO 2026-06-08 07:42:49 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 3s. Last read position: chr6:32,033,960
INFO 2026-06-08 07:42:49 MarkDuplicates Tracking 235900 as yet unmatched pairs. 15285 records in RAM.
INFO 2026-06-08 07:42:54 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 4s. Last read position: chr6:35,795,666
INFO 2026-06-08 07:42:54 MarkDuplicates Tracking 235505 as yet unmatched pairs. 13870 records in RAM.
INFO 2026-06-08 07:42:56 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 2s. Last read position: chr6:44,258,912
INFO 2026-06-08 07:42:56 MarkDuplicates Tracking 236571 as yet unmatched pairs. 13545 records in RAM.
INFO 2026-06-08 07:42:59 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 2s. Last read position: chr6:76,900,194
INFO 2026-06-08 07:42:59 MarkDuplicates Tracking 236284 as yet unmatched pairs. 10276 records in RAM.
INFO 2026-06-08 07:43:03 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 3s. Last read position: chr6:106,552,130
INFO 2026-06-08 07:43:03 MarkDuplicates Tracking 236946 as yet unmatched pairs. 8118 records in RAM.
INFO 2026-06-08 07:43:07 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 3s. Last read position: chr6:123,223,863
INFO 2026-06-08 07:43:07 MarkDuplicates Tracking 237010 as yet unmatched pairs. 6170 records in RAM.
INFO 2026-06-08 07:43:10 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 3s. Last read position: chr6:137,204,516
INFO 2026-06-08 07:43:10 MarkDuplicates Tracking 237249 as yet unmatched pairs. 4445 records in RAM.
INFO 2026-06-08 07:43:13 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 3s. Last read position: chr6:152,141,119
INFO 2026-06-08 07:43:13 MarkDuplicates Tracking 236945 as yet unmatched pairs. 2212 records in RAM.
INFO 2026-06-08 07:43:17 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 3s. Last read position: chr6:164,724,825
INFO 2026-06-08 07:43:17 MarkDuplicates Tracking 236974 as yet unmatched pairs. 427 records in RAM.
INFO 2026-06-08 07:43:20 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 3s. Last read position: chr7:6,737,281
INFO 2026-06-08 07:43:20 MarkDuplicates Tracking 237541 as yet unmatched pairs. 19741 records in RAM.
INFO 2026-06-08 07:43:25 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 4s. Last read position: chr7:17,850,969
INFO 2026-06-08 07:43:25 MarkDuplicates Tracking 236795 as yet unmatched pairs. 17342 records in RAM.
INFO 2026-06-08 07:43:28 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 3s. Last read position: chr7:44,258,665
INFO 2026-06-08 07:43:28 MarkDuplicates Tracking 236924 as yet unmatched pairs. 15120 records in RAM.
INFO 2026-06-08 07:43:31 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 3s. Last read position: chr7:55,201,816
INFO 2026-06-08 07:43:31 MarkDuplicates Tracking 237496 as yet unmatched pairs. 14246 records in RAM.
INFO 2026-06-08 07:43:34 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 3s. Last read position: chr7:74,236,973
INFO 2026-06-08 07:43:34 MarkDuplicates Tracking 236683 as yet unmatched pairs. 11746 records in RAM.
INFO 2026-06-08 07:43:37 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 2s. Last read position: chr7:86,765,149
INFO 2026-06-08 07:43:37 MarkDuplicates Tracking 237316 as yet unmatched pairs. 11085 records in RAM.
INFO 2026-06-08 07:43:41 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 4s. Last read position: chr7:100,554,091
INFO 2026-06-08 07:43:41 MarkDuplicates Tracking 236615 as yet unmatched pairs. 8686 records in RAM.
INFO 2026-06-08 07:43:46 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 4s. Last read position: chr7:102,602,341
INFO 2026-06-08 07:43:46 MarkDuplicates Tracking 236176 as yet unmatched pairs. 7556 records in RAM.
INFO 2026-06-08 07:43:49 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 3s. Last read position: chr7:122,697,982
INFO 2026-06-08 07:43:49 MarkDuplicates Tracking 236214 as yet unmatched pairs. 5570 records in RAM.
INFO 2026-06-08 07:43:52 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 3s. Last read position: chr7:140,719,612
INFO 2026-06-08 07:43:52 MarkDuplicates Tracking 236463 as yet unmatched pairs. 3873 records in RAM.
INFO 2026-06-08 07:43:55 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 2s. Last read position: chr7:149,722,478
INFO 2026-06-08 07:43:55 MarkDuplicates Tracking 235731 as yet unmatched pairs. 1848 records in RAM.
INFO 2026-06-08 07:43:59 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 3s. Last read position: chr8:3,201,636
INFO 2026-06-08 07:43:59 MarkDuplicates Tracking 235112 as yet unmatched pairs. 18467 records in RAM.
INFO 2026-06-08 07:44:02 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 2s. Last read position: chr8:11,826,097
INFO 2026-06-08 07:44:02 MarkDuplicates Tracking 234999 as yet unmatched pairs. 17520 records in RAM.
INFO 2026-06-08 07:44:05 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 3s. Last read position: chr8:31,076,208
INFO 2026-06-08 07:44:05 MarkDuplicates Tracking 234795 as yet unmatched pairs. 15535 records in RAM.
INFO 2026-06-08 07:44:09 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 3s. Last read position: chr8:32,705,684
INFO 2026-06-08 07:44:09 MarkDuplicates Tracking 234802 as yet unmatched pairs. 14434 records in RAM.
INFO 2026-06-08 07:44:13 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 3s. Last read position: chr8:38,274,850
INFO 2026-06-08 07:44:13 MarkDuplicates Tracking 234373 as yet unmatched pairs. 12822 records in RAM.
INFO 2026-06-08 07:44:17 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 3s. Last read position: chr8:42,395,001
INFO 2026-06-08 07:44:17 MarkDuplicates Tracking 232903 as yet unmatched pairs. 10345 records in RAM.
INFO 2026-06-08 07:44:20 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 3s. Last read position: chr8:70,736,613
INFO 2026-06-08 07:44:20 MarkDuplicates Tracking 232458 as yet unmatched pairs. 7641 records in RAM.
INFO 2026-06-08 07:44:24 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 3s. Last read position: chr8:102,280,461
INFO 2026-06-08 07:44:24 MarkDuplicates Tracking 232363 as yet unmatched pairs. 4996 records in RAM.
INFO 2026-06-08 07:44:27 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 3s. Last read position: chr8:134,012,918
INFO 2026-06-08 07:44:27 MarkDuplicates Tracking 231909 as yet unmatched pairs. 2005 records in RAM.
INFO 2026-06-08 07:44:30 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 3s. Last read position: chr8:144,512,256
INFO 2026-06-08 07:44:30 MarkDuplicates Tracking 232210 as yet unmatched pairs. 1316 records in RAM.
INFO 2026-06-08 07:44:34 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:05:43s. Time for last 1,000,000: 3s. Last read position: chr9:13,889,539
INFO 2026-06-08 07:44:34 MarkDuplicates Tracking 230485 as yet unmatched pairs. 18623 records in RAM.
INFO 2026-06-08 07:44:38 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 3s. Last read position: chr9:34,835,327
INFO 2026-06-08 07:44:38 MarkDuplicates Tracking 229939 as yet unmatched pairs. 16354 records in RAM.
INFO 2026-06-08 07:44:41 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 3s. Last read position: chr9:42,187,420
INFO 2026-06-08 07:44:41 MarkDuplicates Tracking 229676 as yet unmatched pairs. 15119 records in RAM.
INFO 2026-06-08 07:44:43 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 2s. Last read position: chr9:65,698,515
INFO 2026-06-08 07:44:43 MarkDuplicates Tracking 228944 as yet unmatched pairs. 13792 records in RAM.
INFO 2026-06-08 07:44:46 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 3s. Last read position: chr9:83,973,031
INFO 2026-06-08 07:44:46 MarkDuplicates Tracking 228527 as yet unmatched pairs. 11981 records in RAM.
INFO 2026-06-08 07:44:51 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 4s. Last read position: chr9:84,916,476
INFO 2026-06-08 07:44:51 MarkDuplicates Tracking 228420 as yet unmatched pairs. 10991 records in RAM.
INFO 2026-06-08 07:44:55 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 3s. Last read position: chr9:95,449,860
INFO 2026-06-08 07:44:55 MarkDuplicates Tracking 227044 as yet unmatched pairs. 8296 records in RAM.
INFO 2026-06-08 07:44:58 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 3s. Last read position: chr9:113,507,594
INFO 2026-06-08 07:44:58 MarkDuplicates Tracking 226132 as yet unmatched pairs. 5839 records in RAM.
INFO 2026-06-08 07:45:01 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 3s. Last read position: chr9:128,820,541
INFO 2026-06-08 07:45:01 MarkDuplicates Tracking 225120 as yet unmatched pairs. 3499 records in RAM.
INFO 2026-06-08 07:45:05 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 3s. Last read position: chr9:134,437,807
INFO 2026-06-08 07:45:05 MarkDuplicates Tracking 225504 as yet unmatched pairs. 3032 records in RAM.
INFO 2026-06-08 07:45:08 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 3s. Last read position: chr9:138,319,932
INFO 2026-06-08 07:45:08 MarkDuplicates Tracking 223198 as yet unmatched pairs. 0 records in RAM.
INFO 2026-06-08 07:45:11 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 3s. Last read position: chr10:27,186,442
INFO 2026-06-08 07:45:11 MarkDuplicates Tracking 222367 as yet unmatched pairs. 15826 records in RAM.
INFO 2026-06-08 07:45:15 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 3s. Last read position: chr10:45,788,799
INFO 2026-06-08 07:45:15 MarkDuplicates Tracking 221450 as yet unmatched pairs. 13436 records in RAM.
INFO 2026-06-08 07:45:18 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 3s. Last read position: chr10:68,401,707
INFO 2026-06-08 07:45:18 MarkDuplicates Tracking 220614 as yet unmatched pairs. 11026 records in RAM.
INFO 2026-06-08 07:45:22 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:06:31s. Time for last 1,000,000: 4s. Last read position: chr10:86,472,178
INFO 2026-06-08 07:45:22 MarkDuplicates Tracking 219532 as yet unmatched pairs. 8640 records in RAM.
INFO 2026-06-08 07:45:25 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 3s. Last read position: chr10:96,187,831
INFO 2026-06-08 07:45:25 MarkDuplicates Tracking 218469 as yet unmatched pairs. 6455 records in RAM.
INFO 2026-06-08 07:45:29 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 3s. Last read position: chr10:106,776,589
INFO 2026-06-08 07:45:29 MarkDuplicates Tracking 217519 as yet unmatched pairs. 4451 records in RAM.
INFO 2026-06-08 07:45:32 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 3s. Last read position: chr10:121,585,777
INFO 2026-06-08 07:45:32 MarkDuplicates Tracking 217190 as yet unmatched pairs. 2840 records in RAM.
INFO 2026-06-08 07:45:36 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 3s. Last read position: chr11:555,318
INFO 2026-06-08 07:45:36 MarkDuplicates Tracking 215221 as yet unmatched pairs. 22498 records in RAM.
INFO 2026-06-08 07:45:40 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 3s. Last read position: chr11:5,641,283
INFO 2026-06-08 07:45:40 MarkDuplicates Tracking 214055 as yet unmatched pairs. 20731 records in RAM.
INFO 2026-06-08 07:45:43 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 3s. Last read position: chr11:19,351,034
INFO 2026-06-08 07:45:43 MarkDuplicates Tracking 212846 as yet unmatched pairs. 18505 records in RAM.
INFO 2026-06-08 07:45:47 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 3s. Last read position: chr11:47,679,961
INFO 2026-06-08 07:45:47 MarkDuplicates Tracking 211593 as yet unmatched pairs. 15657 records in RAM.
INFO 2026-06-08 07:45:50 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:07:00s. Time for last 1,000,000: 3s. Last read position: chr11:62,611,531
INFO 2026-06-08 07:45:50 MarkDuplicates Tracking 210565 as yet unmatched pairs. 13684 records in RAM.
INFO 2026-06-08 07:45:54 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:07:03s. Time for last 1,000,000: 3s. Last read position: chr11:66,526,688
INFO 2026-06-08 07:45:54 MarkDuplicates Tracking 209575 as yet unmatched pairs. 12041 records in RAM.
INFO 2026-06-08 07:45:58 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:07:07s. Time for last 1,000,000: 3s. Last read position: chr11:75,071,463
INFO 2026-06-08 07:45:58 MarkDuplicates Tracking 208267 as yet unmatched pairs. 9941 records in RAM.
INFO 2026-06-08 07:46:02 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:07:11s. Time for last 1,000,000: 4s. Last read position: chr11:95,836,228
INFO 2026-06-08 07:46:02 MarkDuplicates Tracking 207002 as yet unmatched pairs. 7291 records in RAM.
INFO 2026-06-08 07:46:06 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:07:15s. Time for last 1,000,000: 3s. Last read position: chr11:112,118,863
INFO 2026-06-08 07:46:06 MarkDuplicates Tracking 205562 as yet unmatched pairs. 4569 records in RAM.
INFO 2026-06-08 07:46:09 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:07:19s. Time for last 1,000,000: 3s. Last read position: chr11:120,125,678
INFO 2026-06-08 07:46:09 MarkDuplicates Tracking 204309 as yet unmatched pairs. 2415 records in RAM.
INFO 2026-06-08 07:46:13 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:07:22s. Time for last 1,000,000: 3s. Last read position: chr12:556,865
INFO 2026-06-08 07:46:13 MarkDuplicates Tracking 202800 as yet unmatched pairs. 26320 records in RAM.
INFO 2026-06-08 07:46:18 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 4s. Last read position: chr12:9,298,810
INFO 2026-06-08 07:46:18 MarkDuplicates Tracking 201462 as yet unmatched pairs. 24182 records in RAM.
INFO 2026-06-08 07:46:21 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:07:30s. Time for last 1,000,000: 2s. Last read position: chr12:11,815,822
INFO 2026-06-08 07:46:21 MarkDuplicates Tracking 201197 as yet unmatched pairs. 23246 records in RAM.
INFO 2026-06-08 07:46:24 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:07:33s. Time for last 1,000,000: 3s. Last read position: chr12:15,911,308
INFO 2026-06-08 07:46:24 MarkDuplicates Tracking 198863 as yet unmatched pairs. 20274 records in RAM.
INFO 2026-06-08 07:46:28 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:07:37s. Time for last 1,000,000: 4s. Last read position: chr12:44,683,578
INFO 2026-06-08 07:46:28 MarkDuplicates Tracking 196926 as yet unmatched pairs. 16809 records in RAM.
INFO 2026-06-08 07:46:33 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:07:42s. Time for last 1,000,000: 4s. Last read position: chr12:50,461,165
INFO 2026-06-08 07:46:33 MarkDuplicates Tracking 195666 as yet unmatched pairs. 14912 records in RAM.
INFO 2026-06-08 07:46:36 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:07:45s. Time for last 1,000,000: 3s. Last read position: chr12:56,142,192
INFO 2026-06-08 07:46:36 MarkDuplicates Tracking 194358 as yet unmatched pairs. 12967 records in RAM.
INFO 2026-06-08 07:46:40 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:07:49s. Time for last 1,000,000: 4s. Last read position: chr12:68,553,326
INFO 2026-06-08 07:46:40 MarkDuplicates Tracking 192860 as yet unmatched pairs. 10624 records in RAM.
INFO 2026-06-08 07:46:44 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:07:53s. Time for last 1,000,000: 4s. Last read position: chr12:98,543,991
INFO 2026-06-08 07:46:44 MarkDuplicates Tracking 190580 as yet unmatched pairs. 6834 records in RAM.
INFO 2026-06-08 07:46:48 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:07:58s. Time for last 1,000,000: 4s. Last read position: chr12:112,313,082
INFO 2026-06-08 07:46:48 MarkDuplicates Tracking 189261 as yet unmatched pairs. 4393 records in RAM.
INFO 2026-06-08 07:46:52 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:08:01s. Time for last 1,000,000: 3s. Last read position: chr12:122,363,945
INFO 2026-06-08 07:46:52 MarkDuplicates Tracking 187590 as yet unmatched pairs. 1953 records in RAM.
INFO 2026-06-08 07:46:56 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 3s. Last read position: chr13:21,176,881
INFO 2026-06-08 07:46:56 MarkDuplicates Tracking 186059 as yet unmatched pairs. 12119 records in RAM.
INFO 2026-06-08 07:46:59 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:08:08s. Time for last 1,000,000: 3s. Last read position: chr13:37,105,052
INFO 2026-06-08 07:46:59 MarkDuplicates Tracking 184167 as yet unmatched pairs. 9232 records in RAM.
INFO 2026-06-08 07:47:04 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:08:13s. Time for last 1,000,000: 4s. Last read position: chr13:72,755,997
INFO 2026-06-08 07:47:04 MarkDuplicates Tracking 182189 as yet unmatched pairs. 5679 records in RAM.
INFO 2026-06-08 07:47:07 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 3s. Last read position: chr13:109,823,270
INFO 2026-06-08 07:47:07 MarkDuplicates Tracking 178959 as yet unmatched pairs. 788 records in RAM.
INFO 2026-06-08 07:47:11 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:08:20s. Time for last 1,000,000: 3s. Last read position: chr14:23,522,264
INFO 2026-06-08 07:47:11 MarkDuplicates Tracking 177420 as yet unmatched pairs. 13102 records in RAM.
INFO 2026-06-08 07:47:14 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 3s. Last read position: chr14:50,445,050
INFO 2026-06-08 07:47:14 MarkDuplicates Tracking 174894 as yet unmatched pairs. 9425 records in RAM.
INFO 2026-06-08 07:47:18 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:08:27s. Time for last 1,000,000: 4s. Last read position: chr14:73,492,353
INFO 2026-06-08 07:47:18 MarkDuplicates Tracking 172553 as yet unmatched pairs. 5950 records in RAM.
INFO 2026-06-08 07:47:21 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:08:30s. Time for last 1,000,000: 3s. Last read position: chr14:95,099,705
INFO 2026-06-08 07:47:21 MarkDuplicates Tracking 170544 as yet unmatched pairs. 2885 records in RAM.
INFO 2026-06-08 07:47:25 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 3s. Last read position: chr15:20,533,586
INFO 2026-06-08 07:47:25 MarkDuplicates Tracking 168328 as yet unmatched pairs. 22299 records in RAM.
INFO 2026-06-08 07:47:28 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:08:38s. Time for last 1,000,000: 3s. Last read position: chr15:30,947,125
INFO 2026-06-08 07:47:28 MarkDuplicates Tracking 167191 as yet unmatched pairs. 20760 records in RAM.
INFO 2026-06-08 07:47:31 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 2s. Last read position: chr15:41,736,168
INFO 2026-06-08 07:47:31 MarkDuplicates Tracking 165628 as yet unmatched pairs. 18589 records in RAM.
INFO 2026-06-08 07:47:35 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:08:44s. Time for last 1,000,000: 3s. Last read position: chr15:49,488,010
INFO 2026-06-08 07:47:35 MarkDuplicates Tracking 164445 as yet unmatched pairs. 16900 records in RAM.
INFO 2026-06-08 07:47:37 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:08:47s. Time for last 1,000,000: 2s. Last read position: chr15:67,416,387
INFO 2026-06-08 07:47:37 MarkDuplicates Tracking 161329 as yet unmatched pairs. 12880 records in RAM.
INFO 2026-06-08 07:47:40 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 2s. Last read position: chr15:81,343,897
INFO 2026-06-08 07:47:40 MarkDuplicates Tracking 159534 as yet unmatched pairs. 10412 records in RAM.
INFO 2026-06-08 07:47:45 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 4s. Last read position: chr15:87,974,083
INFO 2026-06-08 07:47:45 MarkDuplicates Tracking 159190 as yet unmatched pairs. 9575 records in RAM.
INFO 2026-06-08 07:47:48 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:08:57s. Time for last 1,000,000: 3s. Last read position: chr15:88,046,014
INFO 2026-06-08 07:47:48 MarkDuplicates Tracking 157052 as yet unmatched pairs. 7046 records in RAM.
INFO 2026-06-08 07:47:52 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:09:01s. Time for last 1,000,000: 3s. Last read position: chr15:88,114,738
INFO 2026-06-08 07:47:52 MarkDuplicates Tracking 155017 as yet unmatched pairs. 4609 records in RAM.
INFO 2026-06-08 07:47:55 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:09:04s. Time for last 1,000,000: 3s. Last read position: chr15:92,900,917
INFO 2026-06-08 07:47:55 MarkDuplicates Tracking 152671 as yet unmatched pairs. 1839 records in RAM.
INFO 2026-06-08 07:47:59 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 3s. Last read position: chr16:1,497,121
INFO 2026-06-08 07:47:59 MarkDuplicates Tracking 150689 as yet unmatched pairs. 20572 records in RAM.
INFO 2026-06-08 07:48:01 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:09:10s. Time for last 1,000,000: 2s. Last read position: chr16:3,564,135
INFO 2026-06-08 07:48:01 MarkDuplicates Tracking 148948 as yet unmatched pairs. 18595 records in RAM.
INFO 2026-06-08 07:48:05 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 3s. Last read position: chr16:14,918,041
INFO 2026-06-08 07:48:05 MarkDuplicates Tracking 147039 as yet unmatched pairs. 16156 records in RAM.
INFO 2026-06-08 07:48:08 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:09:17s. Time for last 1,000,000: 3s. Last read position: chr16:21,839,390
INFO 2026-06-08 07:48:08 MarkDuplicates Tracking 145537 as yet unmatched pairs. 14318 records in RAM.
INFO 2026-06-08 07:48:11 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 3s. Last read position: chr16:29,993,184
INFO 2026-06-08 07:48:11 MarkDuplicates Tracking 144113 as yet unmatched pairs. 12486 records in RAM.
INFO 2026-06-08 07:48:14 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:09:23s. Time for last 1,000,000: 3s. Last read position: chr16:47,122,592
INFO 2026-06-08 07:48:14 MarkDuplicates Tracking 142229 as yet unmatched pairs. 10018 records in RAM.
INFO 2026-06-08 07:48:17 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:09:26s. Time for last 1,000,000: 2s. Last read position: chr16:67,100,394
INFO 2026-06-08 07:48:17 MarkDuplicates Tracking 140264 as yet unmatched pairs. 7366 records in RAM.
INFO 2026-06-08 07:48:20 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:09:30s. Time for last 1,000,000: 3s. Last read position: chr16:72,787,190
INFO 2026-06-08 07:48:20 MarkDuplicates Tracking 138144 as yet unmatched pairs. 4862 records in RAM.
INFO 2026-06-08 07:48:24 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:09:33s. Time for last 1,000,000: 3s. Last read position: chr16:88,712,024
INFO 2026-06-08 07:48:24 MarkDuplicates Tracking 135355 as yet unmatched pairs. 1439 records in RAM.
INFO 2026-06-08 07:48:28 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 3s. Last read position: chr17:2,058,773
INFO 2026-06-08 07:48:28 MarkDuplicates Tracking 133584 as yet unmatched pairs. 28691 records in RAM.
INFO 2026-06-08 07:48:31 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:09:40s. Time for last 1,000,000: 3s. Last read position: chr17:7,674,456
INFO 2026-06-08 07:48:31 MarkDuplicates Tracking 131841 as yet unmatched pairs. 26670 records in RAM.
INFO 2026-06-08 07:48:35 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 3s. Last read position: chr17:16,032,403
INFO 2026-06-08 07:48:35 MarkDuplicates Tracking 129911 as yet unmatched pairs. 24354 records in RAM.
INFO 2026-06-08 07:48:38 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:09:47s. Time for last 1,000,000: 3s. Last read position: chr17:27,601,867
INFO 2026-06-08 07:48:38 MarkDuplicates Tracking 127464 as yet unmatched pairs. 21555 records in RAM.
INFO 2026-06-08 07:48:41 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:09:50s. Time for last 1,000,000: 3s. Last read position: chr17:35,119,443
INFO 2026-06-08 07:48:41 MarkDuplicates Tracking 126177 as yet unmatched pairs. 19875 records in RAM.
INFO 2026-06-08 07:48:45 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:09:54s. Time for last 1,000,000: 4s. Last read position: chr17:39,909,579
INFO 2026-06-08 07:48:45 MarkDuplicates Tracking 123640 as yet unmatched pairs. 17049 records in RAM.
INFO 2026-06-08 07:48:49 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:09:58s. Time for last 1,000,000: 3s. Last read position: chr17:41,976,760
INFO 2026-06-08 07:48:49 MarkDuplicates Tracking 121771 as yet unmatched pairs. 14906 records in RAM.
INFO 2026-06-08 07:48:52 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:10:01s. Time for last 1,000,000: 3s. Last read position: chr17:43,542,207
INFO 2026-06-08 07:48:52 MarkDuplicates Tracking 120777 as yet unmatched pairs. 13627 records in RAM.
INFO 2026-06-08 07:48:55 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:10:05s. Time for last 1,000,000: 3s. Last read position: chr17:48,592,122
INFO 2026-06-08 07:48:55 MarkDuplicates Tracking 118111 as yet unmatched pairs. 10674 records in RAM.
INFO 2026-06-08 07:48:59 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:10:08s. Time for last 1,000,000: 3s. Last read position: chr17:59,893,790
INFO 2026-06-08 07:48:59 MarkDuplicates Tracking 116553 as yet unmatched pairs. 8643 records in RAM.
INFO 2026-06-08 07:49:02 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:10:11s. Time for last 1,000,000: 3s. Last read position: chr17:67,874,810
INFO 2026-06-08 07:49:02 MarkDuplicates Tracking 113418 as yet unmatched pairs. 5149 records in RAM.
INFO 2026-06-08 07:49:05 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:10:14s. Time for last 1,000,000: 3s. Last read position: chr17:76,469,907
INFO 2026-06-08 07:49:05 MarkDuplicates Tracking 111171 as yet unmatched pairs. 2502 records in RAM.
INFO 2026-06-08 07:49:09 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:10:18s. Time for last 1,000,000: 3s. Last read position: chr17:82,961,267
INFO 2026-06-08 07:49:09 MarkDuplicates Tracking 109023 as yet unmatched pairs. 58 records in RAM.
INFO 2026-06-08 07:49:12 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:10:21s. Time for last 1,000,000: 3s. Last read position: chr18:31,966,968
INFO 2026-06-08 07:49:12 MarkDuplicates Tracking 105375 as yet unmatched pairs. 8123 records in RAM.
INFO 2026-06-08 07:49:16 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:10:25s. Time for last 1,000,000: 3s. Last read position: chr18:48,619,482
INFO 2026-06-08 07:49:16 MarkDuplicates Tracking 102358 as yet unmatched pairs. 4598 records in RAM.
INFO 2026-06-08 07:49:20 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:10:29s. Time for last 1,000,000: 3s. Last read position: chr18:80,197,019
INFO 2026-06-08 07:49:20 MarkDuplicates Tracking 98473 as yet unmatched pairs. 12 records in RAM.
INFO 2026-06-08 07:49:23 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:10:33s. Time for last 1,000,000: 3s. Last read position: chr19:3,573,300
INFO 2026-06-08 07:49:23 MarkDuplicates Tracking 96410 as yet unmatched pairs. 22784 records in RAM.
INFO 2026-06-08 07:49:27 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:10:36s. Time for last 1,000,000: 3s. Last read position: chr19:7,631,704
INFO 2026-06-08 07:49:27 MarkDuplicates Tracking 94149 as yet unmatched pairs. 20345 records in RAM.
INFO 2026-06-08 07:49:30 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:10:39s. Time for last 1,000,000: 3s. Last read position: chr19:10,565,686
INFO 2026-06-08 07:49:30 MarkDuplicates Tracking 92120 as yet unmatched pairs. 18131 records in RAM.
INFO 2026-06-08 07:49:34 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:10:43s. Time for last 1,000,000: 3s. Last read position: chr19:15,022,664
INFO 2026-06-08 07:49:34 MarkDuplicates Tracking 89947 as yet unmatched pairs. 15775 records in RAM.
INFO 2026-06-08 07:49:37 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 3s. Last read position: chr19:18,832,220
INFO 2026-06-08 07:49:37 MarkDuplicates Tracking 87922 as yet unmatched pairs. 13567 records in RAM.
INFO 2026-06-08 07:49:39 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:10:48s. Time for last 1,000,000: 2s. Last read position: chr19:36,140,973
INFO 2026-06-08 07:49:39 MarkDuplicates Tracking 85244 as yet unmatched pairs. 10564 records in RAM.
INFO 2026-06-08 07:49:42 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:10:51s. Time for last 1,000,000: 2s. Last read position: chr19:41,332,146
INFO 2026-06-08 07:49:42 MarkDuplicates Tracking 83256 as yet unmatched pairs. 8357 records in RAM.
INFO 2026-06-08 07:49:45 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:10:54s. Time for last 1,000,000: 3s. Last read position: chr19:45,891,037
INFO 2026-06-08 07:49:45 MarkDuplicates Tracking 80899 as yet unmatched pairs. 5828 records in RAM.
INFO 2026-06-08 07:49:49 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 3s. Last read position: chr19:50,406,562
INFO 2026-06-08 07:49:49 MarkDuplicates Tracking 78907 as yet unmatched pairs. 3650 records in RAM.
INFO 2026-06-08 07:49:52 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:11:01s. Time for last 1,000,000: 3s. Last read position: chr19:55,642,180
INFO 2026-06-08 07:49:52 MarkDuplicates Tracking 76508 as yet unmatched pairs. 1066 records in RAM.
INFO 2026-06-08 07:49:55 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:11:04s. Time for last 1,000,000: 3s. Last read position: chr20:10,412,640
INFO 2026-06-08 07:49:55 MarkDuplicates Tracking 73945 as yet unmatched pairs. 12962 records in RAM.
INFO 2026-06-08 07:49:59 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:11:08s. Time for last 1,000,000: 3s. Last read position: chr20:32,943,625
INFO 2026-06-08 07:49:59 MarkDuplicates Tracking 70057 as yet unmatched pairs. 8752 records in RAM.
INFO 2026-06-08 07:50:03 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:11:12s. Time for last 1,000,000: 3s. Last read position: chr20:42,470,232
INFO 2026-06-08 07:50:03 MarkDuplicates Tracking 67278 as yet unmatched pairs. 5766 records in RAM.
INFO 2026-06-08 07:50:06 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:11:15s. Time for last 1,000,000: 3s. Last read position: chr20:57,172,971
INFO 2026-06-08 07:50:06 MarkDuplicates Tracking 64114 as yet unmatched pairs. 2330 records in RAM.
INFO 2026-06-08 07:50:09 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:11:19s. Time for last 1,000,000: 3s. Last read position: chr21:5,037,141
INFO 2026-06-08 07:50:09 MarkDuplicates Tracking 62549 as yet unmatched pairs. 10166 records in RAM.
INFO 2026-06-08 07:50:11 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:11:21s. Time for last 1,000,000: 2s. Last read position: chr21:26,929,803
INFO 2026-06-08 07:50:11 MarkDuplicates Tracking 58842 as yet unmatched pairs. 6152 records in RAM.
INFO 2026-06-08 07:50:14 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:11:23s. Time for last 1,000,000: 2s. Last read position: chr21:41,494,394
INFO 2026-06-08 07:50:14 MarkDuplicates Tracking 56175 as yet unmatched pairs. 3226 records in RAM.
INFO 2026-06-08 07:50:17 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:11:26s. Time for last 1,000,000: 3s. Last read position: chr21:46,301,984
INFO 2026-06-08 07:50:17 MarkDuplicates Tracking 53506 as yet unmatched pairs. 432 records in RAM.
INFO 2026-06-08 07:50:21 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:11:30s. Time for last 1,000,000: 3s. Last read position: chr22:20,564,251
INFO 2026-06-08 07:50:21 MarkDuplicates Tracking 51232 as yet unmatched pairs. 12508 records in RAM.
INFO 2026-06-08 07:50:24 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:11:33s. Time for last 1,000,000: 3s. Last read position: chr22:23,181,117
INFO 2026-06-08 07:50:24 MarkDuplicates Tracking 50533 as yet unmatched pairs. 11708 records in RAM.
INFO 2026-06-08 07:50:27 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:11:36s. Time for last 1,000,000: 3s. Last read position: chr22:24,188,330
INFO 2026-06-08 07:50:27 MarkDuplicates Tracking 47676 as yet unmatched pairs. 8736 records in RAM.
INFO 2026-06-08 07:50:30 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:11:39s. Time for last 1,000,000: 2s. Last read position: chr22:30,462,153
INFO 2026-06-08 07:50:30 MarkDuplicates Tracking 45057 as yet unmatched pairs. 5989 records in RAM.
INFO 2026-06-08 07:50:33 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:11:42s. Time for last 1,000,000: 3s. Last read position: chr22:39,968,038
INFO 2026-06-08 07:50:33 MarkDuplicates Tracking 42388 as yet unmatched pairs. 3189 records in RAM.
INFO 2026-06-08 07:50:36 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:11:45s. Time for last 1,000,000: 2s. Last read position: chr22:50,523,133
INFO 2026-06-08 07:50:36 MarkDuplicates Tracking 39684 as yet unmatched pairs. 373 records in RAM.
INFO 2026-06-08 07:50:40 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:11:49s. Time for last 1,000,000: 4s. Last read position: chrX:20,125,802
INFO 2026-06-08 07:50:40 MarkDuplicates Tracking 36646 as yet unmatched pairs. 31458 records in RAM.
INFO 2026-06-08 07:50:44 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:11:53s. Time for last 1,000,000: 3s. Last read position: chrX:45,070,039
INFO 2026-06-08 07:50:44 MarkDuplicates Tracking 32087 as yet unmatched pairs. 26872 records in RAM.
INFO 2026-06-08 07:50:47 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:11:56s. Time for last 1,000,000: 3s. Last read position: chrX:50,311,389
INFO 2026-06-08 07:50:47 MarkDuplicates Tracking 29370 as yet unmatched pairs. 24145 records in RAM.
INFO 2026-06-08 07:50:50 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:11:59s. Time for last 1,000,000: 3s. Last read position: chrX:65,529,731
INFO 2026-06-08 07:50:50 MarkDuplicates Tracking 26386 as yet unmatched pairs. 21143 records in RAM.
INFO 2026-06-08 07:50:54 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:12:03s. Time for last 1,000,000: 3s. Last read position: chrX:71,240,196
INFO 2026-06-08 07:50:54 MarkDuplicates Tracking 24303 as yet unmatched pairs. 19032 records in RAM.
INFO 2026-06-08 07:50:57 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:12:06s. Time for last 1,000,000: 3s. Last read position: chrX:91,878,390
INFO 2026-06-08 07:50:57 MarkDuplicates Tracking 19885 as yet unmatched pairs. 14574 records in RAM.
INFO 2026-06-08 07:51:00 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:12:09s. Time for last 1,000,000: 2s. Last read position: chrX:112,899,698
INFO 2026-06-08 07:51:00 MarkDuplicates Tracking 15395 as yet unmatched pairs. 10046 records in RAM.
INFO 2026-06-08 07:51:02 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:12:11s. Time for last 1,000,000: 2s. Last read position: chrX:130,384,922
INFO 2026-06-08 07:51:02 MarkDuplicates Tracking 11725 as yet unmatched pairs. 6351 records in RAM.
INFO 2026-06-08 07:51:05 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:12:14s. Time for last 1,000,000: 2s. Last read position: chrX:149,930,766
INFO 2026-06-08 07:51:05 MarkDuplicates Tracking 8254 as yet unmatched pairs. 2858 records in RAM.
INFO 2026-06-08 07:51:08 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:12:17s. Time for last 1,000,000: 3s. Last read position: chrX:154,823,635
INFO 2026-06-08 07:51:08 MarkDuplicates Tracking 5899 as yet unmatched pairs. 487 records in RAM.
INFO 2026-06-08 07:51:11 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:12:20s. Time for last 1,000,000: 3s. Last read position: KI270728.1:1,454,402
INFO 2026-06-08 07:51:11 MarkDuplicates Tracking 1697 as yet unmatched pairs. 173 records in RAM.
INFO 2026-06-08 07:51:13 MarkDuplicates Read 212721094 records. 0 pairs never matched.
INFO 2026-06-08 07:51:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 37999333048; totalMemory: 62847451136; maxMemory: 63585648640
INFO 2026-06-08 07:51:43 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 07:52:00 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 07:52:38 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 07:53:01 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 07:53:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300901928; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-08 07:53:03 MarkDuplicates Marking 34018042 records as duplicates.
INFO 2026-06-08 07:53:03 MarkDuplicates Found 7847335 optical duplicate clusters.
INFO 2026-06-08 07:53:03 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 07:53:42 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:38s. Time for last 10,000,000: 38s. Last read position: chr1:117,144,262
INFO 2026-06-08 07:54:18 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:01:15s. Time for last 10,000,000: 36s. Last read position: chr2:11,634,321
INFO 2026-06-08 07:54:55 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:51s. Time for last 10,000,000: 36s. Last read position: chr2:165,138,063
INFO 2026-06-08 07:55:29 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:02:26s. Time for last 10,000,000: 34s. Last read position: chr3:49,910,824
INFO 2026-06-08 07:56:05 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:03:01s. Time for last 10,000,000: 35s. Last read position: chr4:41,745,008
INFO 2026-06-08 07:56:40 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:03:37s. Time for last 10,000,000: 35s. Last read position: chr5:132,644,294
INFO 2026-06-08 07:57:15 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:04:12s. Time for last 10,000,000: 34s. Last read position: chr6:106,552,130
INFO 2026-06-08 07:57:48 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:04:45s. Time for last 10,000,000: 33s. Last read position: chr7:86,765,149
INFO 2026-06-08 07:58:22 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:05:19s. Time for last 10,000,000: 33s. Last read position: chr8:38,274,850
INFO 2026-06-08 07:58:56 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:05:52s. Time for last 10,000,000: 33s. Last read position: chr9:83,973,031
INFO 2026-06-08 07:59:30 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:06:26s. Time for last 10,000,000: 33s. Last read position: chr10:86,472,178
INFO 2026-06-08 08:00:04 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:07:00s. Time for last 10,000,000: 33s. Last read position: chr11:75,071,463
INFO 2026-06-08 08:00:38 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:07:34s. Time for last 10,000,000: 34s. Last read position: chr12:56,142,192
INFO 2026-06-08 08:01:12 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:08:09s. Time for last 10,000,000: 34s. Last read position: chr14:50,445,050
INFO 2026-06-08 08:01:47 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:08:43s. Time for last 10,000,000: 34s. Last read position: chr15:88,046,014
INFO 2026-06-08 08:02:20 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:09:16s. Time for last 10,000,000: 33s. Last read position: chr16:72,787,190
INFO 2026-06-08 08:02:52 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:09:49s. Time for last 10,000,000: 32s. Last read position: chr17:48,592,122
INFO 2026-06-08 08:03:25 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:10:21s. Time for last 10,000,000: 32s. Last read position: chr19:10,565,686
INFO 2026-06-08 08:03:58 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:10:54s. Time for last 10,000,000: 32s. Last read position: chr20:42,470,232
INFO 2026-06-08 08:04:30 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:11:26s. Time for last 10,000,000: 31s. Last read position: chr22:39,968,038
INFO 2026-06-08 08:05:02 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:11:59s. Time for last 10,000,000: 32s. Last read position: chrX:149,930,766
INFO 2026-06-08 08:05:19 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:05:19 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:05:19 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:05:20 MarkDuplicates Before output close freeMemory: 202065208; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:05:20 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:05:20 MarkDuplicates After output close freeMemory: 104373064; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 08:05:20 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 26.53 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory