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 659_bCu-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam --OUTPUT 659_bCu-T1-TRNA-1_A23MVY2LT4_2.md.bam --METRICS_FILE 659_bCu-T1-TRNA-1_A23MVY2LT4_2.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:59:02.682 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 07:59:02 GMT 2026] MarkDuplicates --INPUT 659_bCu-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam --OUTPUT 659_bCu-T1-TRNA-1_A23MVY2LT4_2.md.bam --METRICS_FILE 659_bCu-T1-TRNA-1_A23MVY2LT4_2.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 07:59:02 GMT 2026] Executing as ?@nf-063711e9136d43bfa4c7e14b644165d2-604b3-m4mxj 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 07:59:02 MarkDuplicates Start of doWork freeMemory: 105828040; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:59:02 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:59:02 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:59:07 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:8,863,331
INFO 2026-06-08 07:59:07 MarkDuplicates Tracking 3519 as yet unmatched pairs. 370 records in RAM.
INFO 2026-06-08 07:59:11 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 4s. Last read position: chr1:20,652,969
INFO 2026-06-08 07:59:11 MarkDuplicates Tracking 6124 as yet unmatched pairs. 42 records in RAM.
INFO 2026-06-08 07:59:14 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 3s. Last read position: chr1:25,618,290
INFO 2026-06-08 07:59:14 MarkDuplicates Tracking 8990 as yet unmatched pairs. 75 records in RAM.
INFO 2026-06-08 07:59:18 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 3s. Last read position: chr1:35,010,473
INFO 2026-06-08 07:59:18 MarkDuplicates Tracking 12030 as yet unmatched pairs. 29 records in RAM.
INFO 2026-06-08 07:59:21 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr1:44,645,018
INFO 2026-06-08 07:59:21 MarkDuplicates Tracking 14565 as yet unmatched pairs. 87 records in RAM.
INFO 2026-06-08 07:59:25 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 3s. Last read position: chr1:97,573,852
INFO 2026-06-08 07:59:25 MarkDuplicates Tracking 17286 as yet unmatched pairs. 23 records in RAM.
INFO 2026-06-08 07:59:28 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 3s. Last read position: chr1:119,969,670
INFO 2026-06-08 07:59:28 MarkDuplicates Tracking 20694 as yet unmatched pairs. 875 records in RAM.
INFO 2026-06-08 07:59:31 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 2s. Last read position: chr1:145,961,358
INFO 2026-06-08 07:59:31 MarkDuplicates Tracking 21182 as yet unmatched pairs. 64 records in RAM.
INFO 2026-06-08 07:59:34 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 3s. Last read position: chr1:147,619,730
INFO 2026-06-08 07:59:34 MarkDuplicates Tracking 21955 as yet unmatched pairs. 48 records in RAM.
INFO 2026-06-08 07:59:37 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 3s. Last read position: chr1:149,064,458
INFO 2026-06-08 07:59:37 MarkDuplicates Tracking 22858 as yet unmatched pairs. 144 records in RAM.
INFO 2026-06-08 07:59:40 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 2s. Last read position: chr1:150,511,508
INFO 2026-06-08 07:59:40 MarkDuplicates Tracking 24415 as yet unmatched pairs. 174 records in RAM.
INFO 2026-06-08 07:59:43 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 3s. Last read position: chr1:152,216,423
INFO 2026-06-08 07:59:43 MarkDuplicates Tracking 27487 as yet unmatched pairs. 836 records in RAM.
INFO 2026-06-08 07:59:46 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 3s. Last read position: chr1:154,172,083
INFO 2026-06-08 07:59:46 MarkDuplicates Tracking 29356 as yet unmatched pairs. 536 records in RAM.
INFO 2026-06-08 07:59:49 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 2s. Last read position: chr1:155,261,668
INFO 2026-06-08 07:59:49 MarkDuplicates Tracking 31665 as yet unmatched pairs. 236 records in RAM.
INFO 2026-06-08 07:59:51 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 2s. Last read position: chr1:156,134,857
INFO 2026-06-08 07:59:51 MarkDuplicates Tracking 37506 as yet unmatched pairs. 3134 records in RAM.
INFO 2026-06-08 07:59:53 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 2s. Last read position: chr1:156,671,314
INFO 2026-06-08 07:59:53 MarkDuplicates Tracking 37485 as yet unmatched pairs. 284 records in RAM.
INFO 2026-06-08 07:59:56 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 2s. Last read position: chr1:161,509,823
INFO 2026-06-08 07:59:56 MarkDuplicates Tracking 40510 as yet unmatched pairs. 308 records in RAM.
INFO 2026-06-08 07:59:57 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 1s. Last read position: chr1:180,190,459
INFO 2026-06-08 07:59:57 MarkDuplicates Tracking 42668 as yet unmatched pairs. 209 records in RAM.
INFO 2026-06-08 08:00:00 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 2s. Last read position: chr1:201,197,286
INFO 2026-06-08 08:00:00 MarkDuplicates Tracking 46895 as yet unmatched pairs. 1463 records in RAM.
INFO 2026-06-08 08:00:03 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 3s. Last read position: chr1:201,212,815
INFO 2026-06-08 08:00:03 MarkDuplicates Tracking 48664 as yet unmatched pairs. 678 records in RAM.
INFO 2026-06-08 08:00:06 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 2s. Last read position: chr1:203,044,076
INFO 2026-06-08 08:00:06 MarkDuplicates Tracking 50974 as yet unmatched pairs. 135 records in RAM.
INFO 2026-06-08 08:00:08 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 2s. Last read position: chr1:208,060,743
INFO 2026-06-08 08:00:08 MarkDuplicates Tracking 53914 as yet unmatched pairs. 228 records in RAM.
INFO 2026-06-08 08:00:11 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 2s. Last read position: chr1:225,921,208
INFO 2026-06-08 08:00:11 MarkDuplicates Tracking 56466 as yet unmatched pairs. 82 records in RAM.
INFO 2026-06-08 08:00:13 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 2s. Last read position: chr1:236,829,188
INFO 2026-06-08 08:00:13 MarkDuplicates Tracking 60282 as yet unmatched pairs. 35 records in RAM.
INFO 2026-06-08 08:00:17 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 3s. Last read position: chr2:27,078,988
INFO 2026-06-08 08:00:17 MarkDuplicates Tracking 63373 as yet unmatched pairs. 63307 records in RAM.
INFO 2026-06-08 08:00:20 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 2s. Last read position: chr2:29,220,805
INFO 2026-06-08 08:00:20 MarkDuplicates Tracking 71879 as yet unmatched pairs. 71800 records in RAM.
INFO 2026-06-08 08:00:23 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,264
INFO 2026-06-08 08:00:23 MarkDuplicates Tracking 134079 as yet unmatched pairs. 62658 records in RAM.
INFO 2026-06-08 08:00:26 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 3s. Last read position: chr2:32,916,406
INFO 2026-06-08 08:00:26 MarkDuplicates Tracking 545081 as yet unmatched pairs. 37374 records in RAM.
INFO 2026-06-08 08:00:29 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 3s. Last read position: chr2:37,211,986
INFO 2026-06-08 08:00:29 MarkDuplicates Tracking 576514 as yet unmatched pairs. 33625 records in RAM.
INFO 2026-06-08 08:00:33 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 3s. Last read position: chr2:55,049,755
INFO 2026-06-08 08:00:33 MarkDuplicates Tracking 575215 as yet unmatched pairs. 32314 records in RAM.
INFO 2026-06-08 08:00:36 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 2s. Last read position: chr2:71,349,073
INFO 2026-06-08 08:00:36 MarkDuplicates Tracking 570963 as yet unmatched pairs. 28062 records in RAM.
INFO 2026-06-08 08:00:38 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 2s. Last read position: chr2:85,327,328
INFO 2026-06-08 08:00:38 MarkDuplicates Tracking 568380 as yet unmatched pairs. 25478 records in RAM.
INFO 2026-06-08 08:00:41 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 2s. Last read position: chr2:105,361,234
INFO 2026-06-08 08:00:41 MarkDuplicates Tracking 565947 as yet unmatched pairs. 23041 records in RAM.
INFO 2026-06-08 08:00:43 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 2s. Last read position: chr2:156,367,986
INFO 2026-06-08 08:00:43 MarkDuplicates Tracking 563551 as yet unmatched pairs. 20641 records in RAM.
INFO 2026-06-08 08:00:46 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 2s. Last read position: chr2:189,008,078
INFO 2026-06-08 08:00:46 MarkDuplicates Tracking 561338 as yet unmatched pairs. 18427 records in RAM.
INFO 2026-06-08 08:00:50 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 3s. Last read position: chr2:202,377,574
INFO 2026-06-08 08:00:50 MarkDuplicates Tracking 557585 as yet unmatched pairs. 14674 records in RAM.
INFO 2026-06-08 08:00:52 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 2s. Last read position: chr2:215,370,412
INFO 2026-06-08 08:00:52 MarkDuplicates Tracking 558325 as yet unmatched pairs. 15413 records in RAM.
INFO 2026-06-08 08:00:55 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 2s. Last read position: chr2:215,404,545
INFO 2026-06-08 08:00:55 MarkDuplicates Tracking 553974 as yet unmatched pairs. 11061 records in RAM.
INFO 2026-06-08 08:00:57 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 2s. Last read position: chr2:215,433,324
INFO 2026-06-08 08:00:57 MarkDuplicates Tracking 554024 as yet unmatched pairs. 11111 records in RAM.
INFO 2026-06-08 08:00:59 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 2s. Last read position: chr2:219,176,224
INFO 2026-06-08 08:00:59 MarkDuplicates Tracking 547934 as yet unmatched pairs. 5019 records in RAM.
INFO 2026-06-08 08:01:02 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 2s. Last read position: chr2:237,353,377
INFO 2026-06-08 08:01:02 MarkDuplicates Tracking 545885 as yet unmatched pairs. 2967 records in RAM.
INFO 2026-06-08 08:01:05 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 3s. Last read position: chr3:9,843,470
INFO 2026-06-08 08:01:05 MarkDuplicates Tracking 541960 as yet unmatched pairs. 30252 records in RAM.
INFO 2026-06-08 08:01:08 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 2s. Last read position: chr3:37,452,386
INFO 2026-06-08 08:01:08 MarkDuplicates Tracking 539125 as yet unmatched pairs. 27372 records in RAM.
INFO 2026-06-08 08:01:11 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 2s. Last read position: chr3:47,408,251
INFO 2026-06-08 08:01:11 MarkDuplicates Tracking 535614 as yet unmatched pairs. 23861 records in RAM.
INFO 2026-06-08 08:01:14 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 2s. Last read position: chr3:48,682,015
INFO 2026-06-08 08:01:14 MarkDuplicates Tracking 532572 as yet unmatched pairs. 20819 records in RAM.
INFO 2026-06-08 08:01:18 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 3s. Last read position: chr3:50,367,646
INFO 2026-06-08 08:01:18 MarkDuplicates Tracking 529439 as yet unmatched pairs. 17684 records in RAM.
INFO 2026-06-08 08:01:21 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 3s. Last read position: chr3:58,008,771
INFO 2026-06-08 08:01:21 MarkDuplicates Tracking 526990 as yet unmatched pairs. 15232 records in RAM.
INFO 2026-06-08 08:01:25 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 3s. Last read position: chr3:105,776,404
INFO 2026-06-08 08:01:25 MarkDuplicates Tracking 523932 as yet unmatched pairs. 12172 records in RAM.
INFO 2026-06-08 08:01:28 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 3s. Last read position: chr3:123,700,632
INFO 2026-06-08 08:01:28 MarkDuplicates Tracking 523888 as yet unmatched pairs. 12128 records in RAM.
INFO 2026-06-08 08:01:31 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 3s. Last read position: chr3:129,569,857
INFO 2026-06-08 08:01:31 MarkDuplicates Tracking 518498 as yet unmatched pairs. 6737 records in RAM.
INFO 2026-06-08 08:01:34 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 2s. Last read position: chr3:168,024,956
INFO 2026-06-08 08:01:34 MarkDuplicates Tracking 515607 as yet unmatched pairs. 3844 records in RAM.
INFO 2026-06-08 08:01:37 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 2s. Last read position: chr3:188,609,842
INFO 2026-06-08 08:01:37 MarkDuplicates Tracking 513863 as yet unmatched pairs. 2096 records in RAM.
INFO 2026-06-08 08:01:40 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 3s. Last read position: chr4:1,728,233
INFO 2026-06-08 08:01:40 MarkDuplicates Tracking 510144 as yet unmatched pairs. 12175 records in RAM.
INFO 2026-06-08 08:01:42 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 1s. Last read position: chr4:7,855,543
INFO 2026-06-08 08:01:42 MarkDuplicates Tracking 507561 as yet unmatched pairs. 9591 records in RAM.
INFO 2026-06-08 08:01:45 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 3s. Last read position: chr4:56,307,634
INFO 2026-06-08 08:01:45 MarkDuplicates Tracking 504168 as yet unmatched pairs. 6195 records in RAM.
INFO 2026-06-08 08:01:48 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 2s. Last read position: chr4:90,838,917
INFO 2026-06-08 08:01:48 MarkDuplicates Tracking 501214 as yet unmatched pairs. 3238 records in RAM.
INFO 2026-06-08 08:01:51 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 2s. Last read position: chr4:168,894,578
INFO 2026-06-08 08:01:51 MarkDuplicates Tracking 498656 as yet unmatched pairs. 661 records in RAM.
INFO 2026-06-08 08:01:55 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 3s. Last read position: chr5:14,482,673
INFO 2026-06-08 08:01:55 MarkDuplicates Tracking 495426 as yet unmatched pairs. 24343 records in RAM.
INFO 2026-06-08 08:01:58 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 2s. Last read position: chr5:67,165,868
INFO 2026-06-08 08:01:58 MarkDuplicates Tracking 492754 as yet unmatched pairs. 21671 records in RAM.
INFO 2026-06-08 08:02:00 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 2s. Last read position: chr5:83,541,110
INFO 2026-06-08 08:02:00 MarkDuplicates Tracking 490540 as yet unmatched pairs. 19456 records in RAM.
INFO 2026-06-08 08:02:03 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 2s. Last read position: chr5:133,097,175
INFO 2026-06-08 08:02:03 MarkDuplicates Tracking 487519 as yet unmatched pairs. 16433 records in RAM.
INFO 2026-06-08 08:02:06 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 2s. Last read position: chr5:140,690,861
INFO 2026-06-08 08:02:06 MarkDuplicates Tracking 485124 as yet unmatched pairs. 14018 records in RAM.
INFO 2026-06-08 08:02:09 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 2s. Last read position: chr5:146,132,956
INFO 2026-06-08 08:02:09 MarkDuplicates Tracking 482741 as yet unmatched pairs. 11635 records in RAM.
INFO 2026-06-08 08:02:11 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 1s. Last read position: chr5:150,405,123
INFO 2026-06-08 08:02:11 MarkDuplicates Tracking 486686 as yet unmatched pairs. 15579 records in RAM.
INFO 2026-06-08 08:02:13 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 1s. Last read position: chr5:160,010,742
INFO 2026-06-08 08:02:13 MarkDuplicates Tracking 477249 as yet unmatched pairs. 6142 records in RAM.
INFO 2026-06-08 08:02:16 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 3s. Last read position: chr5:177,483,661
INFO 2026-06-08 08:02:16 MarkDuplicates Tracking 475762 as yet unmatched pairs. 4650 records in RAM.
INFO 2026-06-08 08:02:19 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 2s. Last read position: chr5:179,840,899
INFO 2026-06-08 08:02:19 MarkDuplicates Tracking 472073 as yet unmatched pairs. 960 records in RAM.
INFO 2026-06-08 08:02:22 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 3s. Last read position: chr6:18,148,994
INFO 2026-06-08 08:02:22 MarkDuplicates Tracking 469103 as yet unmatched pairs. 29110 records in RAM.
INFO 2026-06-08 08:02:25 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 2s. Last read position: chr6:30,916,888
INFO 2026-06-08 08:02:25 MarkDuplicates Tracking 466512 as yet unmatched pairs. 26518 records in RAM.
INFO 2026-06-08 08:02:27 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: chr6:31,829,537
INFO 2026-06-08 08:02:27 MarkDuplicates Tracking 464958 as yet unmatched pairs. 24964 records in RAM.
INFO 2026-06-08 08:02:29 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 2s. Last read position: chr6:32,096,787
INFO 2026-06-08 08:02:29 MarkDuplicates Tracking 462422 as yet unmatched pairs. 22428 records in RAM.
INFO 2026-06-08 08:02:31 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 2s. Last read position: chr6:33,415,989
INFO 2026-06-08 08:02:31 MarkDuplicates Tracking 458988 as yet unmatched pairs. 18994 records in RAM.
INFO 2026-06-08 08:02:34 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 2s. Last read position: chr6:42,978,477
INFO 2026-06-08 08:02:34 MarkDuplicates Tracking 455052 as yet unmatched pairs. 15057 records in RAM.
INFO 2026-06-08 08:02:37 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 3s. Last read position: chr6:56,459,124
INFO 2026-06-08 08:02:37 MarkDuplicates Tracking 452447 as yet unmatched pairs. 12451 records in RAM.
INFO 2026-06-08 08:02:40 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 2s. Last read position: chr6:99,409,270
INFO 2026-06-08 08:02:40 MarkDuplicates Tracking 449245 as yet unmatched pairs. 9245 records in RAM.
INFO 2026-06-08 08:02:43 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 2s. Last read position: chr6:137,198,119
INFO 2026-06-08 08:02:43 MarkDuplicates Tracking 446535 as yet unmatched pairs. 6535 records in RAM.
INFO 2026-06-08 08:02:45 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 2s. Last read position: chr6:152,094,431
INFO 2026-06-08 08:02:45 MarkDuplicates Tracking 443968 as yet unmatched pairs. 3967 records in RAM.
INFO 2026-06-08 08:02:48 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 3s. Last read position: chr6:169,225,277
INFO 2026-06-08 08:02:48 MarkDuplicates Tracking 441674 as yet unmatched pairs. 1672 records in RAM.
INFO 2026-06-08 08:02:52 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 3s. Last read position: chr7:5,376,182
INFO 2026-06-08 08:02:52 MarkDuplicates Tracking 438120 as yet unmatched pairs. 26555 records in RAM.
INFO 2026-06-08 08:02:55 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 2s. Last read position: chr7:44,040,327
INFO 2026-06-08 08:02:55 MarkDuplicates Tracking 435206 as yet unmatched pairs. 23639 records in RAM.
INFO 2026-06-08 08:02:58 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 2s. Last read position: chr7:73,537,288
INFO 2026-06-08 08:02:58 MarkDuplicates Tracking 432729 as yet unmatched pairs. 21157 records in RAM.
INFO 2026-06-08 08:03:00 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 2s. Last read position: chr7:77,196,749
INFO 2026-06-08 08:03:00 MarkDuplicates Tracking 430432 as yet unmatched pairs. 18858 records in RAM.
INFO 2026-06-08 08:03:04 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 3s. Last read position: chr7:97,966,813
INFO 2026-06-08 08:03:04 MarkDuplicates Tracking 427612 as yet unmatched pairs. 16037 records in RAM.
INFO 2026-06-08 08:03:06 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 2s. Last read position: chr7:100,866,416
INFO 2026-06-08 08:03:06 MarkDuplicates Tracking 425033 as yet unmatched pairs. 13457 records in RAM.
INFO 2026-06-08 08:03:09 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 2s. Last read position: chr7:102,561,048
INFO 2026-06-08 08:03:09 MarkDuplicates Tracking 423652 as yet unmatched pairs. 12076 records in RAM.
INFO 2026-06-08 08:03:11 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 1s. Last read position: chr7:128,835,495
INFO 2026-06-08 08:03:11 MarkDuplicates Tracking 421312 as yet unmatched pairs. 9734 records in RAM.
INFO 2026-06-08 08:03:13 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 2s. Last read position: chr7:137,253,558
INFO 2026-06-08 08:03:13 MarkDuplicates Tracking 418052 as yet unmatched pairs. 6474 records in RAM.
INFO 2026-06-08 08:03:16 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 2s. Last read position: chr7:149,224,407
INFO 2026-06-08 08:03:16 MarkDuplicates Tracking 415141 as yet unmatched pairs. 3562 records in RAM.
INFO 2026-06-08 08:03:18 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 2s. Last read position: chr7:158,829,368
INFO 2026-06-08 08:03:18 MarkDuplicates Tracking 411690 as yet unmatched pairs. 109 records in RAM.
INFO 2026-06-08 08:03:20 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 2s. Last read position: chr8:22,618,385
INFO 2026-06-08 08:03:20 MarkDuplicates Tracking 409064 as yet unmatched pairs. 22018 records in RAM.
INFO 2026-06-08 08:03:22 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 1s. Last read position: chr8:37,765,594
INFO 2026-06-08 08:03:22 MarkDuplicates Tracking 405778 as yet unmatched pairs. 18731 records in RAM.
INFO 2026-06-08 08:03:24 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 2s. Last read position: chr8:38,843,291
INFO 2026-06-08 08:03:24 MarkDuplicates Tracking 403380 as yet unmatched pairs. 16333 records in RAM.
INFO 2026-06-08 08:03:27 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 2s. Last read position: chr8:74,321,084
INFO 2026-06-08 08:03:27 MarkDuplicates Tracking 400119 as yet unmatched pairs. 13071 records in RAM.
INFO 2026-06-08 08:03:31 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 3s. Last read position: chr8:120,367,221
INFO 2026-06-08 08:03:31 MarkDuplicates Tracking 398686 as yet unmatched pairs. 11636 records in RAM.
INFO 2026-06-08 08:03:34 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 2s. Last read position: chr8:143,580,191
INFO 2026-06-08 08:03:34 MarkDuplicates Tracking 394978 as yet unmatched pairs. 7923 records in RAM.
INFO 2026-06-08 08:03:36 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 2s. Last read position: chr8:143,923,516
INFO 2026-06-08 08:03:36 MarkDuplicates Tracking 392191 as yet unmatched pairs. 5136 records in RAM.
INFO 2026-06-08 08:03:39 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 2s. Last read position: chr8:144,398,784
INFO 2026-06-08 08:03:39 MarkDuplicates Tracking 388195 as yet unmatched pairs. 1140 records in RAM.
INFO 2026-06-08 08:03:42 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 3s. Last read position: chr9:33,914,834
INFO 2026-06-08 08:03:42 MarkDuplicates Tracking 385080 as yet unmatched pairs. 24180 records in RAM.
INFO 2026-06-08 08:03:45 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 3s. Last read position: chr9:77,922,205
INFO 2026-06-08 08:03:45 MarkDuplicates Tracking 382516 as yet unmatched pairs. 21613 records in RAM.
INFO 2026-06-08 08:03:49 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 3s. Last read position: chr9:98,807,916
INFO 2026-06-08 08:03:49 MarkDuplicates Tracking 379374 as yet unmatched pairs. 18469 records in RAM.
INFO 2026-06-08 08:03:52 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 2s. Last read position: chr9:115,026,582
INFO 2026-06-08 08:03:52 MarkDuplicates Tracking 377363 as yet unmatched pairs. 16458 records in RAM.
INFO 2026-06-08 08:03:54 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 2s. Last read position: chr9:123,411,730
INFO 2026-06-08 08:03:54 MarkDuplicates Tracking 373694 as yet unmatched pairs. 12788 records in RAM.
INFO 2026-06-08 08:03:58 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 3s. Last read position: chr9:128,508,938
INFO 2026-06-08 08:03:58 MarkDuplicates Tracking 370796 as yet unmatched pairs. 9884 records in RAM.
INFO 2026-06-08 08:04:00 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 2s. Last read position: chr9:131,470,955
INFO 2026-06-08 08:04:00 MarkDuplicates Tracking 368198 as yet unmatched pairs. 7285 records in RAM.
INFO 2026-06-08 08:04:03 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 2s. Last read position: chr9:136,334,488
INFO 2026-06-08 08:04:03 MarkDuplicates Tracking 364978 as yet unmatched pairs. 4064 records in RAM.
INFO 2026-06-08 08:04:06 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 2s. Last read position: chr9:137,467,429
INFO 2026-06-08 08:04:06 MarkDuplicates Tracking 361414 as yet unmatched pairs. 492 records in RAM.
INFO 2026-06-08 08:04:09 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 3s. Last read position: chr10:17,233,829
INFO 2026-06-08 08:04:09 MarkDuplicates Tracking 359398 as yet unmatched pairs. 18849 records in RAM.
INFO 2026-06-08 08:04:12 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 3s. Last read position: chr10:34,411,721
INFO 2026-06-08 08:04:12 MarkDuplicates Tracking 355808 as yet unmatched pairs. 15258 records in RAM.
INFO 2026-06-08 08:04:16 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 3s. Last read position: chr10:68,737,869
INFO 2026-06-08 08:04:16 MarkDuplicates Tracking 353427 as yet unmatched pairs. 12870 records in RAM.
INFO 2026-06-08 08:04:19 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 3s. Last read position: chr10:75,401,227
INFO 2026-06-08 08:04:19 MarkDuplicates Tracking 350615 as yet unmatched pairs. 10057 records in RAM.
INFO 2026-06-08 08:04:22 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 2s. Last read position: chr10:89,588,741
INFO 2026-06-08 08:04:22 MarkDuplicates Tracking 347995 as yet unmatched pairs. 7436 records in RAM.
INFO 2026-06-08 08:04:24 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:05:20s. Time for last 1,000,000: 2s. Last read position: chr10:102,141,597
INFO 2026-06-08 08:04:24 MarkDuplicates Tracking 345083 as yet unmatched pairs. 4523 records in RAM.
INFO 2026-06-08 08:04:27 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 2s. Last read position: chr10:122,461,810
INFO 2026-06-08 08:04:27 MarkDuplicates Tracking 342542 as yet unmatched pairs. 1981 records in RAM.
INFO 2026-06-08 08:04:31 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 3s. Last read position: chr11:1,277,188
INFO 2026-06-08 08:04:31 MarkDuplicates Tracking 338776 as yet unmatched pairs. 42658 records in RAM.
INFO 2026-06-08 08:04:34 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 3s. Last read position: chr11:2,138,232
INFO 2026-06-08 08:04:34 MarkDuplicates Tracking 336267 as yet unmatched pairs. 40149 records in RAM.
INFO 2026-06-08 08:04:37 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 3s. Last read position: chr11:6,630,507
INFO 2026-06-08 08:04:37 MarkDuplicates Tracking 332670 as yet unmatched pairs. 36552 records in RAM.
INFO 2026-06-08 08:04:40 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 2s. Last read position: chr11:17,719,958
INFO 2026-06-08 08:04:40 MarkDuplicates Tracking 329843 as yet unmatched pairs. 33724 records in RAM.
INFO 2026-06-08 08:04:43 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 2s. Last read position: chr11:20,083,119
INFO 2026-06-08 08:04:43 MarkDuplicates Tracking 327300 as yet unmatched pairs. 31181 records in RAM.
INFO 2026-06-08 08:04:46 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 3s. Last read position: chr11:47,358,843
INFO 2026-06-08 08:04:46 MarkDuplicates Tracking 324436 as yet unmatched pairs. 28316 records in RAM.
INFO 2026-06-08 08:04:49 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 2s. Last read position: chr11:62,517,006
INFO 2026-06-08 08:04:49 MarkDuplicates Tracking 321422 as yet unmatched pairs. 25285 records in RAM.
INFO 2026-06-08 08:04:52 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 2s. Last read position: chr11:62,677,809
INFO 2026-06-08 08:04:52 MarkDuplicates Tracking 318823 as yet unmatched pairs. 22686 records in RAM.
INFO 2026-06-08 08:04:55 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 2s. Last read position: chr11:65,130,314
INFO 2026-06-08 08:04:55 MarkDuplicates Tracking 315303 as yet unmatched pairs. 19166 records in RAM.
INFO 2026-06-08 08:04:58 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 2s. Last read position: chr11:65,890,975
INFO 2026-06-08 08:04:58 MarkDuplicates Tracking 312685 as yet unmatched pairs. 16523 records in RAM.
INFO 2026-06-08 08:05:00 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 2s. Last read position: chr11:68,036,471
INFO 2026-06-08 08:05:00 MarkDuplicates Tracking 308799 as yet unmatched pairs. 12637 records in RAM.
INFO 2026-06-08 08:05:03 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 2s. Last read position: chr11:72,228,391
INFO 2026-06-08 08:05:03 MarkDuplicates Tracking 306113 as yet unmatched pairs. 9949 records in RAM.
INFO 2026-06-08 08:05:07 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 3s. Last read position: chr11:83,168,926
INFO 2026-06-08 08:05:07 MarkDuplicates Tracking 302992 as yet unmatched pairs. 6827 records in RAM.
INFO 2026-06-08 08:05:09 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 2s. Last read position: chr11:117,282,001
INFO 2026-06-08 08:05:09 MarkDuplicates Tracking 300237 as yet unmatched pairs. 4070 records in RAM.
INFO 2026-06-08 08:05:12 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 2s. Last read position: chr11:123,060,655
INFO 2026-06-08 08:05:12 MarkDuplicates Tracking 297937 as yet unmatched pairs. 1769 records in RAM.
INFO 2026-06-08 08:05:15 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 3s. Last read position: chr12:6,073,731
INFO 2026-06-08 08:05:15 MarkDuplicates Tracking 295257 as yet unmatched pairs. 34458 records in RAM.
INFO 2026-06-08 08:05:18 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 2s. Last read position: chr12:7,156,918
INFO 2026-06-08 08:05:18 MarkDuplicates Tracking 292498 as yet unmatched pairs. 31698 records in RAM.
INFO 2026-06-08 08:05:21 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 2s. Last read position: chr12:26,122,209
INFO 2026-06-08 08:05:21 MarkDuplicates Tracking 289862 as yet unmatched pairs. 29059 records in RAM.
INFO 2026-06-08 08:05:24 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 2s. Last read position: chr12:49,103,568
INFO 2026-06-08 08:05:24 MarkDuplicates Tracking 287207 as yet unmatched pairs. 26402 records in RAM.
INFO 2026-06-08 08:05:27 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 3s. Last read position: chr12:53,097,815
INFO 2026-06-08 08:05:27 MarkDuplicates Tracking 285641 as yet unmatched pairs. 24836 records in RAM.
INFO 2026-06-08 08:05:31 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 3s. Last read position: chr12:55,701,024
INFO 2026-06-08 08:05:31 MarkDuplicates Tracking 283768 as yet unmatched pairs. 22961 records in RAM.
INFO 2026-06-08 08:05:34 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 2s. Last read position: chr12:57,105,182
INFO 2026-06-08 08:05:34 MarkDuplicates Tracking 279838 as yet unmatched pairs. 19031 records in RAM.
INFO 2026-06-08 08:05:37 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 2s. Last read position: chr12:57,201,829
INFO 2026-06-08 08:05:37 MarkDuplicates Tracking 276950 as yet unmatched pairs. 16143 records in RAM.
INFO 2026-06-08 08:05:40 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:06:35s. Time for last 1,000,000: 2s. Last read position: chr12:76,030,617
INFO 2026-06-08 08:05:40 MarkDuplicates Tracking 274059 as yet unmatched pairs. 13251 records in RAM.
INFO 2026-06-08 08:05:42 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 1s. Last read position: chr12:107,754,094
INFO 2026-06-08 08:05:42 MarkDuplicates Tracking 270700 as yet unmatched pairs. 9892 records in RAM.
INFO 2026-06-08 08:05:44 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 1s. Last read position: chr12:119,734,214
INFO 2026-06-08 08:05:44 MarkDuplicates Tracking 267741 as yet unmatched pairs. 6932 records in RAM.
INFO 2026-06-08 08:05:47 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 3s. Last read position: chr12:124,336,849
INFO 2026-06-08 08:05:47 MarkDuplicates Tracking 265846 as yet unmatched pairs. 5037 records in RAM.
INFO 2026-06-08 08:05:49 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 2s. Last read position: chr12:132,508,239
INFO 2026-06-08 08:05:49 MarkDuplicates Tracking 262160 as yet unmatched pairs. 1351 records in RAM.
INFO 2026-06-08 08:05:52 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 2s. Last read position: chr13:75,853,106
INFO 2026-06-08 08:05:52 MarkDuplicates Tracking 259282 as yet unmatched pairs. 3755 records in RAM.
INFO 2026-06-08 08:05:55 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:06:51s. Time for last 1,000,000: 3s. Last read position: chr13:110,506,448
INFO 2026-06-08 08:05:55 MarkDuplicates Tracking 257164 as yet unmatched pairs. 1633 records in RAM.
INFO 2026-06-08 08:05:58 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 2s. Last read position: chr14:23,321,640
INFO 2026-06-08 08:05:58 MarkDuplicates Tracking 254732 as yet unmatched pairs. 17305 records in RAM.
INFO 2026-06-08 08:06:00 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 2s. Last read position: chr14:50,758,396
INFO 2026-06-08 08:06:00 MarkDuplicates Tracking 250897 as yet unmatched pairs. 13470 records in RAM.
INFO 2026-06-08 08:06:02 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 1s. Last read position: chr14:68,902,550
INFO 2026-06-08 08:06:02 MarkDuplicates Tracking 249364 as yet unmatched pairs. 11936 records in RAM.
INFO 2026-06-08 08:06:05 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:07:00s. Time for last 1,000,000: 2s. Last read position: chr14:74,798,553
INFO 2026-06-08 08:06:05 MarkDuplicates Tracking 245998 as yet unmatched pairs. 8570 records in RAM.
INFO 2026-06-08 08:06:07 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 2s. Last read position: chr14:100,128,652
INFO 2026-06-08 08:06:07 MarkDuplicates Tracking 243060 as yet unmatched pairs. 5615 records in RAM.
INFO 2026-06-08 08:06:09 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:07:04s. Time for last 1,000,000: 2s. Last read position: chr14:104,941,830
INFO 2026-06-08 08:06:09 MarkDuplicates Tracking 240453 as yet unmatched pairs. 3008 records in RAM.
INFO 2026-06-08 08:06:11 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:07:07s. Time for last 1,000,000: 2s. Last read position: chr15:22,875,247
INFO 2026-06-08 08:06:11 MarkDuplicates Tracking 237346 as yet unmatched pairs. 19372 records in RAM.
INFO 2026-06-08 08:06:14 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:07:09s. Time for last 1,000,000: 2s. Last read position: chr15:40,407,694
INFO 2026-06-08 08:06:14 MarkDuplicates Tracking 235132 as yet unmatched pairs. 17155 records in RAM.
INFO 2026-06-08 08:06:16 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:07:11s. Time for last 1,000,000: 2s. Last read position: chr15:45,111,100
INFO 2026-06-08 08:06:16 MarkDuplicates Tracking 232689 as yet unmatched pairs. 14712 records in RAM.
INFO 2026-06-08 08:06:18 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:07:14s. Time for last 1,000,000: 2s. Last read position: chr15:64,130,305
INFO 2026-06-08 08:06:18 MarkDuplicates Tracking 229818 as yet unmatched pairs. 11837 records in RAM.
INFO 2026-06-08 08:06:21 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:07:16s. Time for last 1,000,000: 2s. Last read position: chr15:73,927,631
INFO 2026-06-08 08:06:21 MarkDuplicates Tracking 227894 as yet unmatched pairs. 9898 records in RAM.
INFO 2026-06-08 08:06:23 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:07:19s. Time for last 1,000,000: 2s. Last read position: chr15:75,676,139
INFO 2026-06-08 08:06:23 MarkDuplicates Tracking 224519 as yet unmatched pairs. 6522 records in RAM.
INFO 2026-06-08 08:06:26 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:07:22s. Time for last 1,000,000: 2s. Last read position: chr15:85,743,808
INFO 2026-06-08 08:06:26 MarkDuplicates Tracking 221326 as yet unmatched pairs. 3328 records in RAM.
INFO 2026-06-08 08:06:29 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:07:25s. Time for last 1,000,000: 3s. Last read position: chr16:79,386
INFO 2026-06-08 08:06:29 MarkDuplicates Tracking 218036 as yet unmatched pairs. 36137 records in RAM.
INFO 2026-06-08 08:06:32 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:07:28s. Time for last 1,000,000: 2s. Last read position: chr16:1,778,486
INFO 2026-06-08 08:06:32 MarkDuplicates Tracking 214524 as yet unmatched pairs. 32619 records in RAM.
INFO 2026-06-08 08:06:35 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:07:30s. Time for last 1,000,000: 2s. Last read position: chr16:2,756,521
INFO 2026-06-08 08:06:35 MarkDuplicates Tracking 211654 as yet unmatched pairs. 29748 records in RAM.
INFO 2026-06-08 08:06:38 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:07:33s. Time for last 1,000,000: 2s. Last read position: chr16:4,381,175
INFO 2026-06-08 08:06:38 MarkDuplicates Tracking 208272 as yet unmatched pairs. 26365 records in RAM.
INFO 2026-06-08 08:06:40 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:07:35s. Time for last 1,000,000: 2s. Last read position: chr16:14,945,882
INFO 2026-06-08 08:06:40 MarkDuplicates Tracking 205995 as yet unmatched pairs. 24088 records in RAM.
INFO 2026-06-08 08:06:42 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:07:37s. Time for last 1,000,000: 1s. Last read position: chr16:16,359,514
INFO 2026-06-08 08:06:42 MarkDuplicates Tracking 204805 as yet unmatched pairs. 22893 records in RAM.
INFO 2026-06-08 08:06:44 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:07:39s. Time for last 1,000,000: 2s. Last read position: chr16:19,524,058
INFO 2026-06-08 08:06:44 MarkDuplicates Tracking 203187 as yet unmatched pairs. 21274 records in RAM.
INFO 2026-06-08 08:06:47 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:07:43s. Time for last 1,000,000: 3s. Last read position: chr16:22,535,072
INFO 2026-06-08 08:06:47 MarkDuplicates Tracking 202515 as yet unmatched pairs. 20602 records in RAM.
INFO 2026-06-08 08:06:51 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:07:46s. Time for last 1,000,000: 3s. Last read position: chr16:29,385,520
INFO 2026-06-08 08:06:51 MarkDuplicates Tracking 200511 as yet unmatched pairs. 18597 records in RAM.
INFO 2026-06-08 08:06:53 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:07:48s. Time for last 1,000,000: 2s. Last read position: chr16:30,239,919
INFO 2026-06-08 08:06:53 MarkDuplicates Tracking 197982 as yet unmatched pairs. 16066 records in RAM.
INFO 2026-06-08 08:06:55 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:07:50s. Time for last 1,000,000: 1s. Last read position: chr16:31,189,757
INFO 2026-06-08 08:06:55 MarkDuplicates Tracking 195363 as yet unmatched pairs. 13447 records in RAM.
INFO 2026-06-08 08:06:57 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:07:52s. Time for last 1,000,000: 1s. Last read position: chr16:57,458,339
INFO 2026-06-08 08:06:57 MarkDuplicates Tracking 192071 as yet unmatched pairs. 10155 records in RAM.
INFO 2026-06-08 08:06:58 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:07:54s. Time for last 1,000,000: 1s. Last read position: chr16:69,316,312
INFO 2026-06-08 08:06:58 MarkDuplicates Tracking 188802 as yet unmatched pairs. 6883 records in RAM.
INFO 2026-06-08 08:07:00 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:07:56s. Time for last 1,000,000: 1s. Last read position: chr16:81,710,635
INFO 2026-06-08 08:07:00 MarkDuplicates Tracking 185861 as yet unmatched pairs. 3942 records in RAM.
INFO 2026-06-08 08:07:02 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:07:58s. Time for last 1,000,000: 2s. Last read position: chr16:89,556,955
INFO 2026-06-08 08:07:02 MarkDuplicates Tracking 182802 as yet unmatched pairs. 883 records in RAM.
INFO 2026-06-08 08:07:05 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:08:00s. Time for last 1,000,000: 2s. Last read position: chr17:2,387,629
INFO 2026-06-08 08:07:05 MarkDuplicates Tracking 180012 as yet unmatched pairs. 51779 records in RAM.
INFO 2026-06-08 08:07:07 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:08:03s. Time for last 1,000,000: 2s. Last read position: chr17:7,316,043
INFO 2026-06-08 08:07:07 MarkDuplicates Tracking 177146 as yet unmatched pairs. 48913 records in RAM.
INFO 2026-06-08 08:07:09 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 1s. Last read position: chr17:8,264,506
INFO 2026-06-08 08:07:09 MarkDuplicates Tracking 174446 as yet unmatched pairs. 46212 records in RAM.
INFO 2026-06-08 08:07:12 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:08:07s. Time for last 1,000,000: 2s. Last read position: chr17:18,263,993
INFO 2026-06-08 08:07:12 MarkDuplicates Tracking 171657 as yet unmatched pairs. 43422 records in RAM.
INFO 2026-06-08 08:07:14 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:08:09s. Time for last 1,000,000: 2s. Last read position: chr17:29,566,757
INFO 2026-06-08 08:07:14 MarkDuplicates Tracking 168887 as yet unmatched pairs. 40652 records in RAM.
INFO 2026-06-08 08:07:16 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:08:11s. Time for last 1,000,000: 1s. Last read position: chr17:38,467,101
INFO 2026-06-08 08:07:16 MarkDuplicates Tracking 166741 as yet unmatched pairs. 38506 records in RAM.
INFO 2026-06-08 08:07:18 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:08:14s. Time for last 1,000,000: 2s. Last read position: chr17:41,822,321
INFO 2026-06-08 08:07:18 MarkDuplicates Tracking 163506 as yet unmatched pairs. 35271 records in RAM.
INFO 2026-06-08 08:07:21 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:08:17s. Time for last 1,000,000: 3s. Last read position: chr17:44,557,969
INFO 2026-06-08 08:07:21 MarkDuplicates Tracking 160097 as yet unmatched pairs. 31861 records in RAM.
INFO 2026-06-08 08:07:23 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 1s. Last read position: chr17:50,175,293
INFO 2026-06-08 08:07:23 MarkDuplicates Tracking 157732 as yet unmatched pairs. 29495 records in RAM.
INFO 2026-06-08 08:07:25 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 2s. Last read position: chr17:50,188,554
INFO 2026-06-08 08:07:25 MarkDuplicates Tracking 166230 as yet unmatched pairs. 37993 records in RAM.
INFO 2026-06-08 08:07:28 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 2s. Last read position: chr17:50,190,049
INFO 2026-06-08 08:07:28 MarkDuplicates Tracking 169911 as yet unmatched pairs. 41674 records in RAM.
INFO 2026-06-08 08:07:31 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:08:27s. Time for last 1,000,000: 3s. Last read position: chr17:50,192,993
INFO 2026-06-08 08:07:31 MarkDuplicates Tracking 161041 as yet unmatched pairs. 32803 records in RAM.
INFO 2026-06-08 08:07:35 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:08:30s. Time for last 1,000,000: 3s. Last read position: chr17:50,195,469
INFO 2026-06-08 08:07:35 MarkDuplicates Tracking 158825 as yet unmatched pairs. 30586 records in RAM.
INFO 2026-06-08 08:07:39 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 3s. Last read position: chr17:50,197,034
INFO 2026-06-08 08:07:39 MarkDuplicates Tracking 164880 as yet unmatched pairs. 36627 records in RAM.
INFO 2026-06-08 08:07:42 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 3s. Last read position: chr17:50,744,730
INFO 2026-06-08 08:07:42 MarkDuplicates Tracking 139088 as yet unmatched pairs. 10835 records in RAM.
INFO 2026-06-08 08:07:45 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 2s. Last read position: chr17:64,800,698
INFO 2026-06-08 08:07:45 MarkDuplicates Tracking 136567 as yet unmatched pairs. 8314 records in RAM.
INFO 2026-06-08 08:07:48 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:08:43s. Time for last 1,000,000: 2s. Last read position: chr17:75,779,059
INFO 2026-06-08 08:07:48 MarkDuplicates Tracking 133574 as yet unmatched pairs. 5320 records in RAM.
INFO 2026-06-08 08:07:51 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:08:46s. Time for last 1,000,000: 2s. Last read position: chr17:80,754,100
INFO 2026-06-08 08:07:51 MarkDuplicates Tracking 130454 as yet unmatched pairs. 2200 records in RAM.
INFO 2026-06-08 08:07:53 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 2s. Last read position: chr18:9,614,141
INFO 2026-06-08 08:07:53 MarkDuplicates Tracking 127356 as yet unmatched pairs. 4772 records in RAM.
INFO 2026-06-08 08:07:55 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:08:50s. Time for last 1,000,000: 1s. Last read position: chr18:51,078,339
INFO 2026-06-08 08:07:55 MarkDuplicates Tracking 124604 as yet unmatched pairs. 2020 records in RAM.
INFO 2026-06-08 08:07:58 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:08:53s. Time for last 1,000,000: 2s. Last read position: chr19:1,080,367
INFO 2026-06-08 08:07:58 MarkDuplicates Tracking 121058 as yet unmatched pairs. 52555 records in RAM.
INFO 2026-06-08 08:08:00 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:08:55s. Time for last 1,000,000: 2s. Last read position: chr19:2,269,686
INFO 2026-06-08 08:08:00 MarkDuplicates Tracking 118019 as yet unmatched pairs. 49516 records in RAM.
INFO 2026-06-08 08:08:02 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:08:58s. Time for last 1,000,000: 2s. Last read position: chr19:5,144,889
INFO 2026-06-08 08:08:02 MarkDuplicates Tracking 114477 as yet unmatched pairs. 45971 records in RAM.
INFO 2026-06-08 08:08:04 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:09:00s. Time for last 1,000,000: 1s. Last read position: chr19:9,157,324
INFO 2026-06-08 08:08:04 MarkDuplicates Tracking 111036 as yet unmatched pairs. 42530 records in RAM.
INFO 2026-06-08 08:08:06 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:09:02s. Time for last 1,000,000: 1s. Last read position: chr19:11,447,740
INFO 2026-06-08 08:08:06 MarkDuplicates Tracking 108625 as yet unmatched pairs. 40119 records in RAM.
INFO 2026-06-08 08:08:08 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:09:04s. Time for last 1,000,000: 2s. Last read position: chr19:14,388,774
INFO 2026-06-08 08:08:08 MarkDuplicates Tracking 105132 as yet unmatched pairs. 36626 records in RAM.
INFO 2026-06-08 08:08:10 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:09:06s. Time for last 1,000,000: 2s. Last read position: chr19:16,078,079
INFO 2026-06-08 08:08:10 MarkDuplicates Tracking 101693 as yet unmatched pairs. 33186 records in RAM.
INFO 2026-06-08 08:08:13 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 2s. Last read position: chr19:18,538,246
INFO 2026-06-08 08:08:13 MarkDuplicates Tracking 98315 as yet unmatched pairs. 29808 records in RAM.
INFO 2026-06-08 08:08:15 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:09:11s. Time for last 1,000,000: 2s. Last read position: chr19:35,718,183
INFO 2026-06-08 08:08:15 MarkDuplicates Tracking 94747 as yet unmatched pairs. 26240 records in RAM.
INFO 2026-06-08 08:08:17 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:09:13s. Time for last 1,000,000: 2s. Last read position: chr19:39,406,997
INFO 2026-06-08 08:08:17 MarkDuplicates Tracking 93117 as yet unmatched pairs. 24610 records in RAM.
INFO 2026-06-08 08:08:20 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:09:15s. Time for last 1,000,000: 2s. Last read position: chr19:41,231,007
INFO 2026-06-08 08:08:20 MarkDuplicates Tracking 88435 as yet unmatched pairs. 19921 records in RAM.
INFO 2026-06-08 08:08:23 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:09:18s. Time for last 1,000,000: 2s. Last read position: chr19:42,274,161
INFO 2026-06-08 08:08:23 MarkDuplicates Tracking 87458 as yet unmatched pairs. 18944 records in RAM.
INFO 2026-06-08 08:08:26 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:09:21s. Time for last 1,000,000: 2s. Last read position: chr19:45,395,594
INFO 2026-06-08 08:08:26 MarkDuplicates Tracking 82728 as yet unmatched pairs. 14213 records in RAM.
INFO 2026-06-08 08:08:28 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:09:23s. Time for last 1,000,000: 2s. Last read position: chr19:47,716,585
INFO 2026-06-08 08:08:28 MarkDuplicates Tracking 79996 as yet unmatched pairs. 11481 records in RAM.
INFO 2026-06-08 08:08:30 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 1s. Last read position: chr19:49,594,781
INFO 2026-06-08 08:08:30 MarkDuplicates Tracking 76796 as yet unmatched pairs. 8281 records in RAM.
INFO 2026-06-08 08:08:32 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:09:27s. Time for last 1,000,000: 1s. Last read position: chr19:53,483,803
INFO 2026-06-08 08:08:32 MarkDuplicates Tracking 73711 as yet unmatched pairs. 5195 records in RAM.
INFO 2026-06-08 08:08:34 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:09:29s. Time for last 1,000,000: 2s. Last read position: chr19:55,517,835
INFO 2026-06-08 08:08:34 MarkDuplicates Tracking 71613 as yet unmatched pairs. 3097 records in RAM.
INFO 2026-06-08 08:08:37 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:09:32s. Time for last 1,000,000: 2s. Last read position: chr20:2,836,293
INFO 2026-06-08 08:08:37 MarkDuplicates Tracking 67905 as yet unmatched pairs. 15148 records in RAM.
INFO 2026-06-08 08:08:40 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 2s. Last read position: chr20:23,353,982
INFO 2026-06-08 08:08:40 MarkDuplicates Tracking 64889 as yet unmatched pairs. 12131 records in RAM.
INFO 2026-06-08 08:08:42 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:09:38s. Time for last 1,000,000: 2s. Last read position: chr20:36,815,488
INFO 2026-06-08 08:08:42 MarkDuplicates Tracking 62254 as yet unmatched pairs. 9494 records in RAM.
INFO 2026-06-08 08:08:45 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:09:40s. Time for last 1,000,000: 2s. Last read position: chr20:45,891,343
INFO 2026-06-08 08:08:45 MarkDuplicates Tracking 58725 as yet unmatched pairs. 5963 records in RAM.
INFO 2026-06-08 08:08:47 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:09:43s. Time for last 1,000,000: 2s. Last read position: chr20:62,065,418
INFO 2026-06-08 08:08:47 MarkDuplicates Tracking 55207 as yet unmatched pairs. 2445 records in RAM.
INFO 2026-06-08 08:08:50 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:09:46s. Time for last 1,000,000: 3s. Last read position: chr21:7,769,263
INFO 2026-06-08 08:08:50 MarkDuplicates Tracking 52530 as yet unmatched pairs. 13935 records in RAM.
INFO 2026-06-08 08:08:53 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:09:48s. Time for last 1,000,000: 2s. Last read position: chr21:8,399,872
INFO 2026-06-08 08:08:53 MarkDuplicates Tracking 51617 as yet unmatched pairs. 13017 records in RAM.
INFO 2026-06-08 08:08:54 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:09:50s. Time for last 1,000,000: 1s. Last read position: chr21:26,966,194
INFO 2026-06-08 08:08:54 MarkDuplicates Tracking 48741 as yet unmatched pairs. 10140 records in RAM.
INFO 2026-06-08 08:08:57 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:09:52s. Time for last 1,000,000: 2s. Last read position: chr21:44,143,303
INFO 2026-06-08 08:08:57 MarkDuplicates Tracking 45957 as yet unmatched pairs. 7356 records in RAM.
INFO 2026-06-08 08:08:59 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:09:54s. Time for last 1,000,000: 2s. Last read position: chr21:45,997,717
INFO 2026-06-08 08:08:59 MarkDuplicates Tracking 43372 as yet unmatched pairs. 4770 records in RAM.
INFO 2026-06-08 08:09:01 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:09:56s. Time for last 1,000,000: 1s. Last read position: chr21:46,132,415
INFO 2026-06-08 08:09:01 MarkDuplicates Tracking 40563 as yet unmatched pairs. 1961 records in RAM.
INFO 2026-06-08 08:09:03 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:09:58s. Time for last 1,000,000: 2s. Last read position: chr22:25,351,849
INFO 2026-06-08 08:09:03 MarkDuplicates Tracking 36600 as yet unmatched pairs. 17987 records in RAM.
INFO 2026-06-08 08:09:05 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:10:01s. Time for last 1,000,000: 2s. Last read position: chr22:36,300,225
INFO 2026-06-08 08:09:05 MarkDuplicates Tracking 34009 as yet unmatched pairs. 15395 records in RAM.
INFO 2026-06-08 08:09:07 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:10:02s. Time for last 1,000,000: 1s. Last read position: chr22:38,294,160
INFO 2026-06-08 08:09:07 MarkDuplicates Tracking 31346 as yet unmatched pairs. 12732 records in RAM.
INFO 2026-06-08 08:09:10 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 3s. Last read position: chr22:40,826,621
INFO 2026-06-08 08:09:10 MarkDuplicates Tracking 28153 as yet unmatched pairs. 9538 records in RAM.
INFO 2026-06-08 08:09:14 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 3s. Last read position: chr22:42,980,933
INFO 2026-06-08 08:09:14 MarkDuplicates Tracking 25177 as yet unmatched pairs. 6562 records in RAM.
INFO 2026-06-08 08:09:16 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:10:11s. Time for last 1,000,000: 2s. Last read position: chr22:50,276,662
INFO 2026-06-08 08:09:16 MarkDuplicates Tracking 22146 as yet unmatched pairs. 3531 records in RAM.
INFO 2026-06-08 08:09:18 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:10:13s. Time for last 1,000,000: 1s. Last read position: chr22:50,721,718
INFO 2026-06-08 08:09:18 MarkDuplicates Tracking 19291 as yet unmatched pairs. 676 records in RAM.
INFO 2026-06-08 08:09:20 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:10:15s. Time for last 1,000,000: 1s. Last read position: chrX:41,144,619
INFO 2026-06-08 08:09:20 MarkDuplicates Tracking 15886 as yet unmatched pairs. 11721 records in RAM.
INFO 2026-06-08 08:09:22 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:10:17s. Time for last 1,000,000: 1s. Last read position: chrX:53,195,263
INFO 2026-06-08 08:09:22 MarkDuplicates Tracking 13254 as yet unmatched pairs. 9089 records in RAM.
INFO 2026-06-08 08:09:23 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:10:19s. Time for last 1,000,000: 1s. Last read position: chrX:74,105,533
INFO 2026-06-08 08:09:23 MarkDuplicates Tracking 10838 as yet unmatched pairs. 6673 records in RAM.
INFO 2026-06-08 08:09:25 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:10:21s. Time for last 1,000,000: 1s. Last read position: chrX:131,286,011
INFO 2026-06-08 08:09:25 MarkDuplicates Tracking 8090 as yet unmatched pairs. 3924 records in RAM.
INFO 2026-06-08 08:09:27 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:10:23s. Time for last 1,000,000: 2s. Last read position: chrX:154,365,359
INFO 2026-06-08 08:09:27 MarkDuplicates Tracking 6037 as yet unmatched pairs. 1871 records in RAM.
INFO 2026-06-08 08:09:29 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:10:25s. Time for last 1,000,000: 1s. Last read position: GL000220.1:152,850
INFO 2026-06-08 08:09:29 MarkDuplicates Tracking 3353 as yet unmatched pairs. 86 records in RAM.
INFO 2026-06-08 08:09:31 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 1s. Last read position: KI270733.1:133,655
INFO 2026-06-08 08:09:31 MarkDuplicates Tracking 577 as yet unmatched pairs. 574 records in RAM.
INFO 2026-06-08 08:09:32 MarkDuplicates Read 233609943 records. 0 pairs never matched.
INFO 2026-06-08 08:09:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 35073069600; totalMemory: 61807263744; maxMemory: 63585648640
INFO 2026-06-08 08:09:49 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:09:56 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:10:37 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 08:10:55 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:11:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300842000; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-08 08:11:04 MarkDuplicates Marking 178561700 records as duplicates.
INFO 2026-06-08 08:11:04 MarkDuplicates Found 3803156 optical duplicate clusters.
INFO 2026-06-08 08:11:04 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 08:11:27 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:22s. Time for last 10,000,000: 22s. Last read position: chr1:149,064,458
INFO 2026-06-08 08:11:50 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:45s. Time for last 10,000,000: 23s. Last read position: chr1:201,212,815
INFO 2026-06-08 08:12:12 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:07s. Time for last 10,000,000: 22s. Last read position: chr2:55,049,755
INFO 2026-06-08 08:12:31 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:26s. Time for last 10,000,000: 19s. Last read position: chr2:219,176,224
INFO 2026-06-08 08:12:54 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:49s. Time for last 10,000,000: 22s. Last read position: chr3:129,569,857
INFO 2026-06-08 08:13:16 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:11s. Time for last 10,000,000: 22s. Last read position: chr5:83,541,110
INFO 2026-06-08 08:13:38 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:33s. Time for last 10,000,000: 21s. Last read position: chr6:31,829,537
INFO 2026-06-08 08:13:59 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:54s. Time for last 10,000,000: 21s. Last read position: chr7:44,040,327
INFO 2026-06-08 08:14:20 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:03:16s. Time for last 10,000,000: 21s. Last read position: chr8:22,618,385
INFO 2026-06-08 08:14:41 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:03:36s. Time for last 10,000,000: 20s. Last read position: chr9:98,807,916
INFO 2026-06-08 08:15:03 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:03:58s. Time for last 10,000,000: 21s. Last read position: chr10:75,401,227
INFO 2026-06-08 08:15:25 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:04:21s. Time for last 10,000,000: 22s. Last read position: chr11:62,517,006
INFO 2026-06-08 08:15:49 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:04:44s. Time for last 10,000,000: 23s. Last read position: chr12:7,156,918
INFO 2026-06-08 08:16:09 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:05:04s. Time for last 10,000,000: 19s. Last read position: chr12:124,336,849
INFO 2026-06-08 08:16:28 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:05:24s. Time for last 10,000,000: 19s. Last read position: chr15:22,875,247
INFO 2026-06-08 08:16:48 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:05:43s. Time for last 10,000,000: 19s. Last read position: chr16:4,381,175
INFO 2026-06-08 08:17:06 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:06:01s. Time for last 10,000,000: 18s. Last read position: chr16:81,710,635
INFO 2026-06-08 08:17:25 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:06:21s. Time for last 10,000,000: 19s. Last read position: chr17:50,175,293
INFO 2026-06-08 08:17:44 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:06:40s. Time for last 10,000,000: 18s. Last read position: chr18:9,614,141
INFO 2026-06-08 08:18:03 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:06:59s. Time for last 10,000,000: 18s. Last read position: chr19:35,718,183
INFO 2026-06-08 08:18:21 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:07:16s. Time for last 10,000,000: 17s. Last read position: chr20:23,353,982
INFO 2026-06-08 08:18:39 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:07:34s. Time for last 10,000,000: 18s. Last read position: chr22:25,351,849
INFO 2026-06-08 08:18:57 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:07:52s. Time for last 10,000,000: 18s. Last read position: chrX:131,286,011
INFO 2026-06-08 08:19:08 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:19:08 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:19:08 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:19:08 MarkDuplicates Before output close freeMemory: 17283833448; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-08 08:19:08 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:19:09 MarkDuplicates After output close freeMemory: 204003440; totalMemory: 234881024; maxMemory: 63585648640
[Mon Jun 08 08:19:09 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 20.11 minutes.
Runtime.totalMemory()=234881024
ls: *cram: No such file or directory
ls: *.crai: No such file or directory