Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.md.bam --METRICS_FILE BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
08:02:23.704 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Jun 08 08:02:23 GMT 2026] MarkDuplicates --INPUT BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.md.bam --METRICS_FILE BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 08:02:23 GMT 2026] Executing as ?@nf-0a326c7fb81cf226da2ef8e1fbca9ff5-c82fe-k7pkr on Linux 6.12.88 amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0
INFO 2026-06-08 08:02:23 MarkDuplicates Start of doWork freeMemory: 105826464; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 08:02:23 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 08:02:23 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 08:02:30 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 4s. Last read position: chr1:1,050,448
INFO 2026-06-08 08:02:30 MarkDuplicates Tracking 2805 as yet unmatched pairs. 164 records in RAM.
INFO 2026-06-08 08:02:34 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 4s. Last read position: chr1:1,804,488
INFO 2026-06-08 08:02:34 MarkDuplicates Tracking 5688 as yet unmatched pairs. 159 records in RAM.
INFO 2026-06-08 08:02:38 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 4s. Last read position: chr1:8,364,070
INFO 2026-06-08 08:02:38 MarkDuplicates Tracking 8150 as yet unmatched pairs. 22 records in RAM.
INFO 2026-06-08 08:02:42 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 3s. Last read position: chr1:13,780,775
INFO 2026-06-08 08:02:42 MarkDuplicates Tracking 10932 as yet unmatched pairs. 345 records in RAM.
INFO 2026-06-08 08:02:44 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 2s. Last read position: chr1:18,908,445
INFO 2026-06-08 08:02:44 MarkDuplicates Tracking 12902 as yet unmatched pairs. 86 records in RAM.
INFO 2026-06-08 08:02:47 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 3s. Last read position: chr1:21,852,801
INFO 2026-06-08 08:02:47 MarkDuplicates Tracking 15342 as yet unmatched pairs. 40 records in RAM.
INFO 2026-06-08 08:02:49 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 2s. Last read position: chr1:25,229,104
INFO 2026-06-08 08:02:49 MarkDuplicates Tracking 17283 as yet unmatched pairs. 19 records in RAM.
INFO 2026-06-08 08:02:53 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 3s. Last read position: chr1:27,303,702
INFO 2026-06-08 08:02:53 MarkDuplicates Tracking 19494 as yet unmatched pairs. 15 records in RAM.
INFO 2026-06-08 08:02:56 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 3s. Last read position: chr1:31,632,628
INFO 2026-06-08 08:02:56 MarkDuplicates Tracking 22066 as yet unmatched pairs. 15 records in RAM.
INFO 2026-06-08 08:02:59 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 2s. Last read position: chr1:35,188,035
INFO 2026-06-08 08:02:59 MarkDuplicates Tracking 24513 as yet unmatched pairs. 18 records in RAM.
INFO 2026-06-08 08:03:02 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 3s. Last read position: chr1:39,563,656
INFO 2026-06-08 08:03:02 MarkDuplicates Tracking 27160 as yet unmatched pairs. 302 records in RAM.
INFO 2026-06-08 08:03:05 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 2s. Last read position: chr1:43,588,813
INFO 2026-06-08 08:03:05 MarkDuplicates Tracking 29818 as yet unmatched pairs. 195 records in RAM.
INFO 2026-06-08 08:03:07 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 1s. Last read position: chr1:46,798,911
INFO 2026-06-08 08:03:07 MarkDuplicates Tracking 32114 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 08:03:08 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 1s. Last read position: chr1:63,411,903
INFO 2026-06-08 08:03:08 MarkDuplicates Tracking 34652 as yet unmatched pairs. 8 records in RAM.
INFO 2026-06-08 08:03:11 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: chr1:94,174,177
INFO 2026-06-08 08:03:11 MarkDuplicates Tracking 36919 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 08:03:13 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 2s. Last read position: chr1:109,689,278
INFO 2026-06-08 08:03:13 MarkDuplicates Tracking 40448 as yet unmatched pairs. 1473 records in RAM.
INFO 2026-06-08 08:03:16 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 2s. Last read position: chr1:116,536,135
INFO 2026-06-08 08:03:16 MarkDuplicates Tracking 41407 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 08:03:18 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 1s. Last read position: chr1:145,856,739
INFO 2026-06-08 08:03:18 MarkDuplicates Tracking 43226 as yet unmatched pairs. 78 records in RAM.
INFO 2026-06-08 08:03:19 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 1s. Last read position: chr1:149,811,980
INFO 2026-06-08 08:03:19 MarkDuplicates Tracking 44793 as yet unmatched pairs. 557 records in RAM.
INFO 2026-06-08 08:03:22 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 2s. Last read position: chr1:149,925,926
INFO 2026-06-08 08:03:22 MarkDuplicates Tracking 45818 as yet unmatched pairs. 123 records in RAM.
INFO 2026-06-08 08:03:23 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 1s. Last read position: chr1:151,400,449
INFO 2026-06-08 08:03:23 MarkDuplicates Tracking 47973 as yet unmatched pairs. 88 records in RAM.
INFO 2026-06-08 08:03:26 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 2s. Last read position: chr1:153,960,560
INFO 2026-06-08 08:03:26 MarkDuplicates Tracking 49930 as yet unmatched pairs. 165 records in RAM.
INFO 2026-06-08 08:03:28 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 2s. Last read position: chr1:155,057,351
INFO 2026-06-08 08:03:28 MarkDuplicates Tracking 52173 as yet unmatched pairs. 247 records in RAM.
INFO 2026-06-08 08:03:31 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 3s. Last read position: chr1:156,114,926
INFO 2026-06-08 08:03:31 MarkDuplicates Tracking 54888 as yet unmatched pairs. 770 records in RAM.
INFO 2026-06-08 08:03:34 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 2s. Last read position: chr1:156,670,243
INFO 2026-06-08 08:03:34 MarkDuplicates Tracking 57087 as yet unmatched pairs. 110 records in RAM.
INFO 2026-06-08 08:03:36 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 1s. Last read position: chr1:161,052,741
INFO 2026-06-08 08:03:36 MarkDuplicates Tracking 59566 as yet unmatched pairs. 80 records in RAM.
INFO 2026-06-08 08:03:38 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 1s. Last read position: chr1:169,696,535
INFO 2026-06-08 08:03:38 MarkDuplicates Tracking 61733 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 08:03:40 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 2s. Last read position: chr1:180,809,181
INFO 2026-06-08 08:03:40 MarkDuplicates Tracking 63886 as yet unmatched pairs. 33 records in RAM.
INFO 2026-06-08 08:03:43 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 2s. Last read position: chr1:196,701,294
INFO 2026-06-08 08:03:43 MarkDuplicates Tracking 66108 as yet unmatched pairs. 85 records in RAM.
INFO 2026-06-08 08:03:45 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 2s. Last read position: chr1:203,828,399
INFO 2026-06-08 08:03:45 MarkDuplicates Tracking 68550 as yet unmatched pairs. 153 records in RAM.
INFO 2026-06-08 08:03:48 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 2s. Last read position: chr1:209,618,617
INFO 2026-06-08 08:03:48 MarkDuplicates Tracking 70443 as yet unmatched pairs. 13 records in RAM.
INFO 2026-06-08 08:03:51 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 2s. Last read position: chr1:225,422,100
INFO 2026-06-08 08:03:51 MarkDuplicates Tracking 72667 as yet unmatched pairs. 34 records in RAM.
INFO 2026-06-08 08:03:53 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 2s. Last read position: chr1:228,457,465
INFO 2026-06-08 08:03:53 MarkDuplicates Tracking 75195 as yet unmatched pairs. 188 records in RAM.
INFO 2026-06-08 08:03:56 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 2s. Last read position: chr1:243,142,317
INFO 2026-06-08 08:03:56 MarkDuplicates Tracking 77737 as yet unmatched pairs. 21 records in RAM.
INFO 2026-06-08 08:04:00 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 4s. Last read position: chr2:9,555,512
INFO 2026-06-08 08:04:00 MarkDuplicates Tracking 80173 as yet unmatched pairs. 80096 records in RAM.
INFO 2026-06-08 08:04:04 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 3s. Last read position: chr2:20,204,235
INFO 2026-06-08 08:04:04 MarkDuplicates Tracking 84649 as yet unmatched pairs. 84567 records in RAM.
INFO 2026-06-08 08:04:07 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 2s. Last read position: chr2:27,378,492
INFO 2026-06-08 08:04:07 MarkDuplicates Tracking 84903 as yet unmatched pairs. 84816 records in RAM.
INFO 2026-06-08 08:04:10 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,264
INFO 2026-06-08 08:04:10 MarkDuplicates Tracking 116782 as yet unmatched pairs. 84061 records in RAM.
INFO 2026-06-08 08:04:13 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 3s. Last read position: chr2:32,916,403
INFO 2026-06-08 08:04:13 MarkDuplicates Tracking 693749 as yet unmatched pairs. 35991 records in RAM.
INFO 2026-06-08 08:04:15 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 1s. Last read position: chr2:33,134,853
INFO 2026-06-08 08:04:15 MarkDuplicates Tracking 738688 as yet unmatched pairs. 32477 records in RAM.
INFO 2026-06-08 08:04:17 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 1s. Last read position: chr2:43,976,170
INFO 2026-06-08 08:04:17 MarkDuplicates Tracking 736142 as yet unmatched pairs. 29930 records in RAM.
INFO 2026-06-08 08:04:19 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 2s. Last read position: chr2:60,461,906
INFO 2026-06-08 08:04:19 MarkDuplicates Tracking 733580 as yet unmatched pairs. 27366 records in RAM.
INFO 2026-06-08 08:04:21 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 1s. Last read position: chr2:72,961,186
INFO 2026-06-08 08:04:21 MarkDuplicates Tracking 731399 as yet unmatched pairs. 25179 records in RAM.
INFO 2026-06-08 08:04:23 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 2s. Last read position: chr2:85,596,844
INFO 2026-06-08 08:04:23 MarkDuplicates Tracking 728963 as yet unmatched pairs. 22742 records in RAM.
INFO 2026-06-08 08:04:26 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 2s. Last read position: chr2:99,405,991
INFO 2026-06-08 08:04:26 MarkDuplicates Tracking 726388 as yet unmatched pairs. 20162 records in RAM.
INFO 2026-06-08 08:04:29 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 3s. Last read position: chr2:110,115,698
INFO 2026-06-08 08:04:29 MarkDuplicates Tracking 724509 as yet unmatched pairs. 18280 records in RAM.
INFO 2026-06-08 08:04:32 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 3s. Last read position: chr2:130,190,476
INFO 2026-06-08 08:04:32 MarkDuplicates Tracking 722716 as yet unmatched pairs. 16483 records in RAM.
INFO 2026-06-08 08:04:35 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 2s. Last read position: chr2:161,367,862
INFO 2026-06-08 08:04:35 MarkDuplicates Tracking 720563 as yet unmatched pairs. 14318 records in RAM.
INFO 2026-06-08 08:04:38 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 2s. Last read position: chr2:182,838,604
INFO 2026-06-08 08:04:38 MarkDuplicates Tracking 718680 as yet unmatched pairs. 12432 records in RAM.
INFO 2026-06-08 08:04:41 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 2s. Last read position: chr2:195,680,285
INFO 2026-06-08 08:04:41 MarkDuplicates Tracking 716129 as yet unmatched pairs. 9878 records in RAM.
INFO 2026-06-08 08:04:44 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 3s. Last read position: chr2:215,365,530
INFO 2026-06-08 08:04:44 MarkDuplicates Tracking 714326 as yet unmatched pairs. 8073 records in RAM.
INFO 2026-06-08 08:04:47 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 2s. Last read position: chr2:218,400,060
INFO 2026-06-08 08:04:47 MarkDuplicates Tracking 711489 as yet unmatched pairs. 5234 records in RAM.
INFO 2026-06-08 08:04:50 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 2s. Last read position: chr2:231,712,899
INFO 2026-06-08 08:04:50 MarkDuplicates Tracking 709062 as yet unmatched pairs. 2781 records in RAM.
INFO 2026-06-08 08:04:53 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 3s. Last read position: chr2:241,249,885
INFO 2026-06-08 08:04:53 MarkDuplicates Tracking 706688 as yet unmatched pairs. 403 records in RAM.
INFO 2026-06-08 08:04:57 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 3s. Last read position: chr3:12,587,569
INFO 2026-06-08 08:04:57 MarkDuplicates Tracking 704466 as yet unmatched pairs. 35522 records in RAM.
INFO 2026-06-08 08:04:59 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 2s. Last read position: chr3:32,128,154
INFO 2026-06-08 08:04:59 MarkDuplicates Tracking 702186 as yet unmatched pairs. 33239 records in RAM.
INFO 2026-06-08 08:05:01 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 1s. Last read position: chr3:39,408,662
INFO 2026-06-08 08:05:01 MarkDuplicates Tracking 700890 as yet unmatched pairs. 31942 records in RAM.
INFO 2026-06-08 08:05:03 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 1s. Last read position: chr3:45,110,640
INFO 2026-06-08 08:05:03 MarkDuplicates Tracking 697412 as yet unmatched pairs. 28464 records in RAM.
INFO 2026-06-08 08:05:05 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 1s. Last read position: chr3:48,440,302
INFO 2026-06-08 08:05:05 MarkDuplicates Tracking 694999 as yet unmatched pairs. 26050 records in RAM.
INFO 2026-06-08 08:05:07 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 1s. Last read position: chr3:49,362,508
INFO 2026-06-08 08:05:07 MarkDuplicates Tracking 692239 as yet unmatched pairs. 23287 records in RAM.
INFO 2026-06-08 08:05:09 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 2s. Last read position: chr3:52,491,422
INFO 2026-06-08 08:05:09 MarkDuplicates Tracking 689609 as yet unmatched pairs. 20655 records in RAM.
INFO 2026-06-08 08:05:11 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 2s. Last read position: chr3:77,546,379
INFO 2026-06-08 08:05:11 MarkDuplicates Tracking 687364 as yet unmatched pairs. 18401 records in RAM.
INFO 2026-06-08 08:05:13 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 1s. Last read position: chr3:114,350,532
INFO 2026-06-08 08:05:13 MarkDuplicates Tracking 685257 as yet unmatched pairs. 16291 records in RAM.
INFO 2026-06-08 08:05:15 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 1s. Last read position: chr3:127,017,825
INFO 2026-06-08 08:05:15 MarkDuplicates Tracking 682924 as yet unmatched pairs. 13956 records in RAM.
INFO 2026-06-08 08:05:17 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 1s. Last read position: chr3:136,002,440
INFO 2026-06-08 08:05:17 MarkDuplicates Tracking 680529 as yet unmatched pairs. 11559 records in RAM.
INFO 2026-06-08 08:05:19 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 2s. Last read position: chr3:157,159,915
INFO 2026-06-08 08:05:19 MarkDuplicates Tracking 677867 as yet unmatched pairs. 8895 records in RAM.
INFO 2026-06-08 08:05:21 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 2s. Last read position: chr3:183,736,723
INFO 2026-06-08 08:05:21 MarkDuplicates Tracking 675660 as yet unmatched pairs. 6687 records in RAM.
INFO 2026-06-08 08:05:23 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 1s. Last read position: chr3:186,081,162
INFO 2026-06-08 08:05:23 MarkDuplicates Tracking 673269 as yet unmatched pairs. 4296 records in RAM.
INFO 2026-06-08 08:05:25 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 2s. Last read position: chr3:195,721,001
INFO 2026-06-08 08:05:25 MarkDuplicates Tracking 671721 as yet unmatched pairs. 2744 records in RAM.
INFO 2026-06-08 08:05:27 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 1s. Last read position: chr3:195,895,253
INFO 2026-06-08 08:05:27 MarkDuplicates Tracking 670210 as yet unmatched pairs. 1232 records in RAM.
INFO 2026-06-08 08:05:29 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 2s. Last read position: chr4:1,731,230
INFO 2026-06-08 08:05:29 MarkDuplicates Tracking 667740 as yet unmatched pairs. 28838 records in RAM.
INFO 2026-06-08 08:05:31 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 2s. Last read position: chr4:1,799,251
INFO 2026-06-08 08:05:31 MarkDuplicates Tracking 667944 as yet unmatched pairs. 29042 records in RAM.
INFO 2026-06-08 08:05:34 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 2s. Last read position: chr4:1,801,659
INFO 2026-06-08 08:05:34 MarkDuplicates Tracking 663921 as yet unmatched pairs. 25019 records in RAM.
INFO 2026-06-08 08:05:35 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 1s. Last read position: chr4:1,804,958
INFO 2026-06-08 08:05:35 MarkDuplicates Tracking 663410 as yet unmatched pairs. 24508 records in RAM.
INFO 2026-06-08 08:05:37 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 1s. Last read position: chr4:1,806,557
INFO 2026-06-08 08:05:37 MarkDuplicates Tracking 658066 as yet unmatched pairs. 19164 records in RAM.
INFO 2026-06-08 08:05:39 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 1s. Last read position: chr4:2,829,518
INFO 2026-06-08 08:05:39 MarkDuplicates Tracking 653236 as yet unmatched pairs. 14334 records in RAM.
INFO 2026-06-08 08:05:41 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 1s. Last read position: chr4:9,234,361
INFO 2026-06-08 08:05:41 MarkDuplicates Tracking 651180 as yet unmatched pairs. 12276 records in RAM.
INFO 2026-06-08 08:05:42 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 1s. Last read position: chr4:39,342,420
INFO 2026-06-08 08:05:42 MarkDuplicates Tracking 649271 as yet unmatched pairs. 10362 records in RAM.
INFO 2026-06-08 08:05:44 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 1s. Last read position: chr4:71,567,034
INFO 2026-06-08 08:05:44 MarkDuplicates Tracking 646848 as yet unmatched pairs. 7937 records in RAM.
INFO 2026-06-08 08:05:46 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 1s. Last read position: chr4:86,772,943
INFO 2026-06-08 08:05:46 MarkDuplicates Tracking 644627 as yet unmatched pairs. 5711 records in RAM.
INFO 2026-06-08 08:05:48 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: chr4:121,681,730
INFO 2026-06-08 08:05:48 MarkDuplicates Tracking 642562 as yet unmatched pairs. 3643 records in RAM.
INFO 2026-06-08 08:05:51 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 3s. Last read position: chr4:155,710,913
INFO 2026-06-08 08:05:51 MarkDuplicates Tracking 640505 as yet unmatched pairs. 1578 records in RAM.
INFO 2026-06-08 08:05:54 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 2s. Last read position: chr5:1,083,770
INFO 2026-06-08 08:05:54 MarkDuplicates Tracking 638420 as yet unmatched pairs. 28417 records in RAM.
INFO 2026-06-08 08:05:55 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 1s. Last read position: chr5:16,701,298
INFO 2026-06-08 08:05:55 MarkDuplicates Tracking 635741 as yet unmatched pairs. 25738 records in RAM.
INFO 2026-06-08 08:05:58 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 2s. Last read position: chr5:56,504,785
INFO 2026-06-08 08:05:58 MarkDuplicates Tracking 633588 as yet unmatched pairs. 23585 records in RAM.
INFO 2026-06-08 08:06:00 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 2s. Last read position: chr5:73,504,356
INFO 2026-06-08 08:06:00 MarkDuplicates Tracking 632071 as yet unmatched pairs. 22065 records in RAM.
INFO 2026-06-08 08:06:02 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 1s. Last read position: chr5:96,985,080
INFO 2026-06-08 08:06:02 MarkDuplicates Tracking 629757 as yet unmatched pairs. 19750 records in RAM.
INFO 2026-06-08 08:06:04 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 2s. Last read position: chr5:133,104,358
INFO 2026-06-08 08:06:04 MarkDuplicates Tracking 627663 as yet unmatched pairs. 17652 records in RAM.
INFO 2026-06-08 08:06:07 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 2s. Last read position: chr5:139,316,094
INFO 2026-06-08 08:06:07 MarkDuplicates Tracking 625402 as yet unmatched pairs. 15390 records in RAM.
INFO 2026-06-08 08:06:09 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 2s. Last read position: chr5:141,864,158
INFO 2026-06-08 08:06:09 MarkDuplicates Tracking 623381 as yet unmatched pairs. 13260 records in RAM.
INFO 2026-06-08 08:06:12 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 2s. Last read position: chr5:150,402,174
INFO 2026-06-08 08:06:12 MarkDuplicates Tracking 621903 as yet unmatched pairs. 11782 records in RAM.
INFO 2026-06-08 08:06:15 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 3s. Last read position: chr5:154,813,916
INFO 2026-06-08 08:06:15 MarkDuplicates Tracking 618811 as yet unmatched pairs. 8690 records in RAM.
INFO 2026-06-08 08:06:18 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 2s. Last read position: chr5:172,769,669
INFO 2026-06-08 08:06:18 MarkDuplicates Tracking 616568 as yet unmatched pairs. 6443 records in RAM.
INFO 2026-06-08 08:06:20 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 2s. Last read position: chr5:179,158,753
INFO 2026-06-08 08:06:20 MarkDuplicates Tracking 613767 as yet unmatched pairs. 3639 records in RAM.
INFO 2026-06-08 08:06:23 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 2s. Last read position: chr5:179,835,177
INFO 2026-06-08 08:06:23 MarkDuplicates Tracking 612541 as yet unmatched pairs. 2413 records in RAM.
INFO 2026-06-08 08:06:26 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 3s. Last read position: chr6:7,230,735
INFO 2026-06-08 08:06:26 MarkDuplicates Tracking 608772 as yet unmatched pairs. 35719 records in RAM.
INFO 2026-06-08 08:06:29 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 2s. Last read position: chr6:26,020,777
INFO 2026-06-08 08:06:29 MarkDuplicates Tracking 606085 as yet unmatched pairs. 33028 records in RAM.
INFO 2026-06-08 08:06:31 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 1s. Last read position: chr6:27,810,247
INFO 2026-06-08 08:06:31 MarkDuplicates Tracking 604266 as yet unmatched pairs. 31207 records in RAM.
INFO 2026-06-08 08:06:33 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 1s. Last read position: chr6:30,668,165
INFO 2026-06-08 08:06:33 MarkDuplicates Tracking 601511 as yet unmatched pairs. 28452 records in RAM.
INFO 2026-06-08 08:06:34 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 1s. Last read position: chr6:31,633,499
INFO 2026-06-08 08:06:34 MarkDuplicates Tracking 599269 as yet unmatched pairs. 26210 records in RAM.
INFO 2026-06-08 08:06:36 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 1s. Last read position: chr6:31,828,419
INFO 2026-06-08 08:06:36 MarkDuplicates Tracking 597711 as yet unmatched pairs. 24652 records in RAM.
INFO 2026-06-08 08:06:38 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 1s. Last read position: chr6:32,977,930
INFO 2026-06-08 08:06:38 MarkDuplicates Tracking 595237 as yet unmatched pairs. 22178 records in RAM.
INFO 2026-06-08 08:06:40 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 1s. Last read position: chr6:35,468,835
INFO 2026-06-08 08:06:40 MarkDuplicates Tracking 593151 as yet unmatched pairs. 20086 records in RAM.
INFO 2026-06-08 08:06:42 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 2s. Last read position: chr6:43,225,722
INFO 2026-06-08 08:06:42 MarkDuplicates Tracking 590282 as yet unmatched pairs. 17214 records in RAM.
INFO 2026-06-08 08:06:44 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 2s. Last read position: chr6:53,508,650
INFO 2026-06-08 08:06:44 MarkDuplicates Tracking 587985 as yet unmatched pairs. 14916 records in RAM.
INFO 2026-06-08 08:06:46 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 2s. Last read position: chr6:87,259,554
INFO 2026-06-08 08:06:46 MarkDuplicates Tracking 585681 as yet unmatched pairs. 12610 records in RAM.
INFO 2026-06-08 08:06:49 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 2s. Last read position: chr6:112,172,680
INFO 2026-06-08 08:06:49 MarkDuplicates Tracking 583310 as yet unmatched pairs. 10235 records in RAM.
INFO 2026-06-08 08:06:51 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 1s. Last read position: chr6:137,011,355
INFO 2026-06-08 08:06:51 MarkDuplicates Tracking 580965 as yet unmatched pairs. 7886 records in RAM.
INFO 2026-06-08 08:06:53 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 2s. Last read position: chr6:151,349,716
INFO 2026-06-08 08:06:53 MarkDuplicates Tracking 578450 as yet unmatched pairs. 5370 records in RAM.
INFO 2026-06-08 08:06:55 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 2s. Last read position: chr6:159,755,155
INFO 2026-06-08 08:06:55 MarkDuplicates Tracking 576288 as yet unmatched pairs. 3204 records in RAM.
INFO 2026-06-08 08:06:57 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 1s. Last read position: chr6:169,232,676
INFO 2026-06-08 08:06:57 MarkDuplicates Tracking 573971 as yet unmatched pairs. 885 records in RAM.
INFO 2026-06-08 08:07:00 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 2s. Last read position: chr7:2,652,826
INFO 2026-06-08 08:07:00 MarkDuplicates Tracking 571077 as yet unmatched pairs. 38604 records in RAM.
INFO 2026-06-08 08:07:03 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 2s. Last read position: chr7:5,528,069
INFO 2026-06-08 08:07:03 MarkDuplicates Tracking 569235 as yet unmatched pairs. 36761 records in RAM.
INFO 2026-06-08 08:07:06 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 2s. Last read position: chr7:11,022,948
INFO 2026-06-08 08:07:06 MarkDuplicates Tracking 565215 as yet unmatched pairs. 32740 records in RAM.
INFO 2026-06-08 08:07:08 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 2s. Last read position: chr7:38,774,217
INFO 2026-06-08 08:07:08 MarkDuplicates Tracking 563234 as yet unmatched pairs. 30755 records in RAM.
INFO 2026-06-08 08:07:10 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 1s. Last read position: chr7:47,280,334
INFO 2026-06-08 08:07:10 MarkDuplicates Tracking 560735 as yet unmatched pairs. 28255 records in RAM.
INFO 2026-06-08 08:07:12 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 1s. Last read position: chr7:72,942,309
INFO 2026-06-08 08:07:12 MarkDuplicates Tracking 558759 as yet unmatched pairs. 26274 records in RAM.
INFO 2026-06-08 08:07:13 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 1s. Last read position: chr7:74,783,026
INFO 2026-06-08 08:07:13 MarkDuplicates Tracking 557235 as yet unmatched pairs. 24750 records in RAM.
INFO 2026-06-08 08:07:15 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 2s. Last read position: chr7:76,302,984
INFO 2026-06-08 08:07:15 MarkDuplicates Tracking 557113 as yet unmatched pairs. 24628 records in RAM.
INFO 2026-06-08 08:07:17 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 2s. Last read position: chr7:80,758,286
INFO 2026-06-08 08:07:17 MarkDuplicates Tracking 553314 as yet unmatched pairs. 20828 records in RAM.
INFO 2026-06-08 08:07:21 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 3s. Last read position: chr7:94,427,651
INFO 2026-06-08 08:07:21 MarkDuplicates Tracking 551005 as yet unmatched pairs. 18519 records in RAM.
INFO 2026-06-08 08:07:24 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 3s. Last read position: chr7:100,199,314
INFO 2026-06-08 08:07:24 MarkDuplicates Tracking 548385 as yet unmatched pairs. 15899 records in RAM.
INFO 2026-06-08 08:07:26 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 2s. Last read position: chr7:101,232,362
INFO 2026-06-08 08:07:26 MarkDuplicates Tracking 546039 as yet unmatched pairs. 13550 records in RAM.
INFO 2026-06-08 08:07:27 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 1s. Last read position: chr7:102,653,454
INFO 2026-06-08 08:07:27 MarkDuplicates Tracking 544955 as yet unmatched pairs. 12466 records in RAM.
INFO 2026-06-08 08:07:29 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 1s. Last read position: chr7:123,692,565
INFO 2026-06-08 08:07:29 MarkDuplicates Tracking 543218 as yet unmatched pairs. 10724 records in RAM.
INFO 2026-06-08 08:07:32 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 2s. Last read position: chr7:134,928,855
INFO 2026-06-08 08:07:32 MarkDuplicates Tracking 540931 as yet unmatched pairs. 8434 records in RAM.
INFO 2026-06-08 08:07:34 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 1s. Last read position: chr7:140,479,157
INFO 2026-06-08 08:07:34 MarkDuplicates Tracking 538700 as yet unmatched pairs. 6203 records in RAM.
INFO 2026-06-08 08:07:35 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr7:144,362,909
INFO 2026-06-08 08:07:35 MarkDuplicates Tracking 536699 as yet unmatched pairs. 4201 records in RAM.
INFO 2026-06-08 08:07:38 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 2s. Last read position: chr7:151,234,165
INFO 2026-06-08 08:07:38 MarkDuplicates Tracking 534028 as yet unmatched pairs. 1527 records in RAM.
INFO 2026-06-08 08:07:41 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 3s. Last read position: chr8:13,115,586
INFO 2026-06-08 08:07:41 MarkDuplicates Tracking 531555 as yet unmatched pairs. 29217 records in RAM.
INFO 2026-06-08 08:07:44 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 2s. Last read position: chr8:34,874,549
INFO 2026-06-08 08:07:44 MarkDuplicates Tracking 529405 as yet unmatched pairs. 27067 records in RAM.
INFO 2026-06-08 08:07:47 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 2s. Last read position: chr8:42,180,488
INFO 2026-06-08 08:07:47 MarkDuplicates Tracking 527087 as yet unmatched pairs. 24747 records in RAM.
INFO 2026-06-08 08:07:50 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 2s. Last read position: chr8:60,856,129
INFO 2026-06-08 08:07:50 MarkDuplicates Tracking 524708 as yet unmatched pairs. 22363 records in RAM.
INFO 2026-06-08 08:07:52 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 2s. Last read position: chr8:73,081,147
INFO 2026-06-08 08:07:52 MarkDuplicates Tracking 522076 as yet unmatched pairs. 19730 records in RAM.
INFO 2026-06-08 08:07:54 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 1s. Last read position: chr8:100,704,989
INFO 2026-06-08 08:07:54 MarkDuplicates Tracking 520309 as yet unmatched pairs. 17960 records in RAM.
INFO 2026-06-08 08:07:56 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 1s. Last read position: chr8:119,873,849
INFO 2026-06-08 08:07:56 MarkDuplicates Tracking 517633 as yet unmatched pairs. 15283 records in RAM.
INFO 2026-06-08 08:07:58 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 1s. Last read position: chr8:140,549,184
INFO 2026-06-08 08:07:58 MarkDuplicates Tracking 515130 as yet unmatched pairs. 12775 records in RAM.
INFO 2026-06-08 08:08:00 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 1s. Last read position: chr8:143,792,976
INFO 2026-06-08 08:08:00 MarkDuplicates Tracking 512161 as yet unmatched pairs. 9803 records in RAM.
INFO 2026-06-08 08:08:01 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 1s. Last read position: chr8:143,861,003
INFO 2026-06-08 08:08:01 MarkDuplicates Tracking 511166 as yet unmatched pairs. 8806 records in RAM.
INFO 2026-06-08 08:08:03 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 1s. Last read position: chr8:143,864,263
INFO 2026-06-08 08:08:03 MarkDuplicates Tracking 510529 as yet unmatched pairs. 8169 records in RAM.
INFO 2026-06-08 08:08:04 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 1s. Last read position: chr8:143,917,583
INFO 2026-06-08 08:08:04 MarkDuplicates Tracking 509301 as yet unmatched pairs. 6940 records in RAM.
INFO 2026-06-08 08:08:06 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 2s. Last read position: chr8:144,095,970
INFO 2026-06-08 08:08:06 MarkDuplicates Tracking 505329 as yet unmatched pairs. 2966 records in RAM.
INFO 2026-06-08 08:08:08 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 1s. Last read position: chr8:144,882,206
INFO 2026-06-08 08:08:08 MarkDuplicates Tracking 502413 as yet unmatched pairs. 47 records in RAM.
INFO 2026-06-08 08:08:10 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 2s. Last read position: chr9:27,567,074
INFO 2026-06-08 08:08:10 MarkDuplicates Tracking 500158 as yet unmatched pairs. 26357 records in RAM.
INFO 2026-06-08 08:08:12 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 2s. Last read position: chr9:35,699,974
INFO 2026-06-08 08:08:12 MarkDuplicates Tracking 497731 as yet unmatched pairs. 23928 records in RAM.
INFO 2026-06-08 08:08:14 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 2s. Last read position: chr9:78,304,782
INFO 2026-06-08 08:08:14 MarkDuplicates Tracking 495705 as yet unmatched pairs. 21875 records in RAM.
INFO 2026-06-08 08:08:17 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 2s. Last read position: chr9:93,452,314
INFO 2026-06-08 08:08:17 MarkDuplicates Tracking 493242 as yet unmatched pairs. 19409 records in RAM.
INFO 2026-06-08 08:08:19 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 1s. Last read position: chr9:109,106,550
INFO 2026-06-08 08:08:19 MarkDuplicates Tracking 491032 as yet unmatched pairs. 17198 records in RAM.
INFO 2026-06-08 08:08:22 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 2s. Last read position: chr9:121,328,956
INFO 2026-06-08 08:08:22 MarkDuplicates Tracking 488415 as yet unmatched pairs. 14580 records in RAM.
INFO 2026-06-08 08:08:24 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 2s. Last read position: chr9:128,167,117
INFO 2026-06-08 08:08:24 MarkDuplicates Tracking 485824 as yet unmatched pairs. 11987 records in RAM.
INFO 2026-06-08 08:08:26 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 2s. Last read position: chr9:130,636,032
INFO 2026-06-08 08:08:26 MarkDuplicates Tracking 483004 as yet unmatched pairs. 9167 records in RAM.
INFO 2026-06-08 08:08:27 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 1s. Last read position: chr9:133,352,507
INFO 2026-06-08 08:08:27 MarkDuplicates Tracking 480953 as yet unmatched pairs. 7116 records in RAM.
INFO 2026-06-08 08:08:29 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 1s. Last read position: chr9:136,475,744
INFO 2026-06-08 08:08:29 MarkDuplicates Tracking 478169 as yet unmatched pairs. 4331 records in RAM.
INFO 2026-06-08 08:08:31 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 1s. Last read position: chr9:137,241,395
INFO 2026-06-08 08:08:31 MarkDuplicates Tracking 475469 as yet unmatched pairs. 1630 records in RAM.
INFO 2026-06-08 08:08:34 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 2s. Last read position: chr10:4,995,829
INFO 2026-06-08 08:08:34 MarkDuplicates Tracking 473046 as yet unmatched pairs. 20682 records in RAM.
INFO 2026-06-08 08:08:36 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 2s. Last read position: chr10:15,558,076
INFO 2026-06-08 08:08:36 MarkDuplicates Tracking 470497 as yet unmatched pairs. 18130 records in RAM.
INFO 2026-06-08 08:08:38 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 1s. Last read position: chr10:32,037,602
INFO 2026-06-08 08:08:38 MarkDuplicates Tracking 468694 as yet unmatched pairs. 16326 records in RAM.
INFO 2026-06-08 08:08:39 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 1s. Last read position: chr10:46,416,006
INFO 2026-06-08 08:08:39 MarkDuplicates Tracking 466471 as yet unmatched pairs. 14103 records in RAM.
INFO 2026-06-08 08:08:41 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 1s. Last read position: chr10:71,299,126
INFO 2026-06-08 08:08:41 MarkDuplicates Tracking 464460 as yet unmatched pairs. 12089 records in RAM.
INFO 2026-06-08 08:08:43 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 1s. Last read position: chr10:80,489,258
INFO 2026-06-08 08:08:43 MarkDuplicates Tracking 462338 as yet unmatched pairs. 9965 records in RAM.
INFO 2026-06-08 08:08:45 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 1s. Last read position: chr10:95,238,028
INFO 2026-06-08 08:08:45 MarkDuplicates Tracking 460179 as yet unmatched pairs. 7805 records in RAM.
INFO 2026-06-08 08:08:47 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 1s. Last read position: chr10:102,484,290
INFO 2026-06-08 08:08:47 MarkDuplicates Tracking 457687 as yet unmatched pairs. 5313 records in RAM.
INFO 2026-06-08 08:08:49 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 2s. Last read position: chr10:119,042,203
INFO 2026-06-08 08:08:49 MarkDuplicates Tracking 455818 as yet unmatched pairs. 3435 records in RAM.
INFO 2026-06-08 08:08:51 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 2s. Last read position: chr10:130,166,939
INFO 2026-06-08 08:08:51 MarkDuplicates Tracking 453398 as yet unmatched pairs. 1009 records in RAM.
INFO 2026-06-08 08:08:53 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 2s. Last read position: chr11:581,971
INFO 2026-06-08 08:08:53 MarkDuplicates Tracking 450895 as yet unmatched pairs. 52989 records in RAM.
INFO 2026-06-08 08:08:55 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 2s. Last read position: chr11:2,133,003
INFO 2026-06-08 08:08:55 MarkDuplicates Tracking 451975 as yet unmatched pairs. 54067 records in RAM.
INFO 2026-06-08 08:08:57 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:06:31s. Time for last 1,000,000: 1s. Last read position: chr11:2,133,643
INFO 2026-06-08 08:08:57 MarkDuplicates Tracking 451361 as yet unmatched pairs. 53453 records in RAM.
INFO 2026-06-08 08:08:59 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:06:33s. Time for last 1,000,000: 1s. Last read position: chr11:7,987,434
INFO 2026-06-08 08:08:59 MarkDuplicates Tracking 442570 as yet unmatched pairs. 44661 records in RAM.
INFO 2026-06-08 08:09:01 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:06:35s. Time for last 1,000,000: 1s. Last read position: chr11:27,889,196
INFO 2026-06-08 08:09:01 MarkDuplicates Tracking 439900 as yet unmatched pairs. 41987 records in RAM.
INFO 2026-06-08 08:09:03 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 1s. Last read position: chr11:46,382,585
INFO 2026-06-08 08:09:03 MarkDuplicates Tracking 437673 as yet unmatched pairs. 39758 records in RAM.
INFO 2026-06-08 08:09:05 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 1s. Last read position: chr11:57,809,443
INFO 2026-06-08 08:09:05 MarkDuplicates Tracking 435302 as yet unmatched pairs. 37387 records in RAM.
INFO 2026-06-08 08:09:07 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 2s. Last read position: chr11:62,521,869
INFO 2026-06-08 08:09:07 MarkDuplicates Tracking 433138 as yet unmatched pairs. 35212 records in RAM.
INFO 2026-06-08 08:09:10 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:06:44s. Time for last 1,000,000: 2s. Last read position: chr11:63,826,986
INFO 2026-06-08 08:09:10 MarkDuplicates Tracking 430575 as yet unmatched pairs. 32649 records in RAM.
INFO 2026-06-08 08:09:12 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:06:46s. Time for last 1,000,000: 2s. Last read position: chr11:65,111,487
INFO 2026-06-08 08:09:12 MarkDuplicates Tracking 427886 as yet unmatched pairs. 29959 records in RAM.
INFO 2026-06-08 08:09:14 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 2s. Last read position: chr11:65,654,869
INFO 2026-06-08 08:09:14 MarkDuplicates Tracking 425584 as yet unmatched pairs. 27655 records in RAM.
INFO 2026-06-08 08:09:16 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 2s. Last read position: chr11:66,315,404
INFO 2026-06-08 08:09:16 MarkDuplicates Tracking 422458 as yet unmatched pairs. 24527 records in RAM.
INFO 2026-06-08 08:09:18 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 1s. Last read position: chr11:67,302,172
INFO 2026-06-08 08:09:18 MarkDuplicates Tracking 419420 as yet unmatched pairs. 21489 records in RAM.
INFO 2026-06-08 08:09:20 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 1s. Last read position: chr11:68,262,040
INFO 2026-06-08 08:09:20 MarkDuplicates Tracking 416656 as yet unmatched pairs. 18724 records in RAM.
INFO 2026-06-08 08:09:22 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 1s. Last read position: chr11:69,643,888
INFO 2026-06-08 08:09:22 MarkDuplicates Tracking 415581 as yet unmatched pairs. 17648 records in RAM.
INFO 2026-06-08 08:09:24 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 1s. Last read position: chr11:72,008,711
INFO 2026-06-08 08:09:24 MarkDuplicates Tracking 413017 as yet unmatched pairs. 15083 records in RAM.
INFO 2026-06-08 08:09:26 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:07:00s. Time for last 1,000,000: 2s. Last read position: chr11:72,714,215
INFO 2026-06-08 08:09:26 MarkDuplicates Tracking 409984 as yet unmatched pairs. 12050 records in RAM.
INFO 2026-06-08 08:09:29 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:07:03s. Time for last 1,000,000: 2s. Last read position: chr11:77,123,725
INFO 2026-06-08 08:09:29 MarkDuplicates Tracking 407318 as yet unmatched pairs. 9383 records in RAM.
INFO 2026-06-08 08:09:31 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 2s. Last read position: chr11:104,000,219
INFO 2026-06-08 08:09:31 MarkDuplicates Tracking 404786 as yet unmatched pairs. 6847 records in RAM.
INFO 2026-06-08 08:09:34 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 2s. Last read position: chr11:118,903,425
INFO 2026-06-08 08:09:34 MarkDuplicates Tracking 402512 as yet unmatched pairs. 4570 records in RAM.
INFO 2026-06-08 08:09:36 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 2s. Last read position: chr11:123,059,698
INFO 2026-06-08 08:09:36 MarkDuplicates Tracking 400596 as yet unmatched pairs. 2653 records in RAM.
INFO 2026-06-08 08:09:39 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 3s. Last read position: chr12:14,870
INFO 2026-06-08 08:09:39 MarkDuplicates Tracking 397970 as yet unmatched pairs. 42582 records in RAM.
INFO 2026-06-08 08:09:42 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:07:16s. Time for last 1,000,000: 2s. Last read position: chr12:6,341,803
INFO 2026-06-08 08:09:42 MarkDuplicates Tracking 396017 as yet unmatched pairs. 40629 records in RAM.
INFO 2026-06-08 08:09:44 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:07:18s. Time for last 1,000,000: 2s. Last read position: chr12:7,080,941
INFO 2026-06-08 08:09:44 MarkDuplicates Tracking 393594 as yet unmatched pairs. 38205 records in RAM.
INFO 2026-06-08 08:09:46 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:07:20s. Time for last 1,000,000: 2s. Last read position: chr12:16,354,318
INFO 2026-06-08 08:09:46 MarkDuplicates Tracking 391454 as yet unmatched pairs. 36065 records in RAM.
INFO 2026-06-08 08:09:48 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:07:22s. Time for last 1,000,000: 1s. Last read position: chr12:46,370,466
INFO 2026-06-08 08:09:48 MarkDuplicates Tracking 389080 as yet unmatched pairs. 33688 records in RAM.
INFO 2026-06-08 08:09:49 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:07:23s. Time for last 1,000,000: 1s. Last read position: chr12:49,128,052
INFO 2026-06-08 08:09:49 MarkDuplicates Tracking 386961 as yet unmatched pairs. 31568 records in RAM.
INFO 2026-06-08 08:09:51 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:07:25s. Time for last 1,000,000: 1s. Last read position: chr12:50,981,748
INFO 2026-06-08 08:09:51 MarkDuplicates Tracking 384540 as yet unmatched pairs. 29144 records in RAM.
INFO 2026-06-08 08:09:53 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 1s. Last read position: chr12:52,904,917
INFO 2026-06-08 08:09:53 MarkDuplicates Tracking 381958 as yet unmatched pairs. 26562 records in RAM.
INFO 2026-06-08 08:09:55 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:07:28s. Time for last 1,000,000: 1s. Last read position: chr12:54,283,903
INFO 2026-06-08 08:09:55 MarkDuplicates Tracking 380164 as yet unmatched pairs. 24767 records in RAM.
INFO 2026-06-08 08:09:56 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:07:30s. Time for last 1,000,000: 1s. Last read position: chr12:56,314,937
INFO 2026-06-08 08:09:56 MarkDuplicates Tracking 377568 as yet unmatched pairs. 22169 records in RAM.
INFO 2026-06-08 08:09:58 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:07:32s. Time for last 1,000,000: 1s. Last read position: chr12:57,105,317
INFO 2026-06-08 08:09:58 MarkDuplicates Tracking 375461 as yet unmatched pairs. 20062 records in RAM.
INFO 2026-06-08 08:10:00 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:07:34s. Time for last 1,000,000: 1s. Last read position: chr12:63,802,379
INFO 2026-06-08 08:10:00 MarkDuplicates Tracking 373037 as yet unmatched pairs. 17637 records in RAM.
INFO 2026-06-08 08:10:03 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:07:37s. Time for last 1,000,000: 2s. Last read position: chr12:89,350,682
INFO 2026-06-08 08:10:03 MarkDuplicates Tracking 370990 as yet unmatched pairs. 15589 records in RAM.
INFO 2026-06-08 08:10:05 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:07:39s. Time for last 1,000,000: 2s. Last read position: chr12:106,239,624
INFO 2026-06-08 08:10:05 MarkDuplicates Tracking 368850 as yet unmatched pairs. 13448 records in RAM.
INFO 2026-06-08 08:10:07 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:07:41s. Time for last 1,000,000: 1s. Last read position: chr12:112,283,272
INFO 2026-06-08 08:10:07 MarkDuplicates Tracking 366407 as yet unmatched pairs. 11005 records in RAM.
INFO 2026-06-08 08:10:09 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:07:43s. Time for last 1,000,000: 1s. Last read position: chr12:114,680,907
INFO 2026-06-08 08:10:09 MarkDuplicates Tracking 363893 as yet unmatched pairs. 8491 records in RAM.
INFO 2026-06-08 08:10:10 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:07:44s. Time for last 1,000,000: 1s. Last read position: chr12:120,845,061
INFO 2026-06-08 08:10:10 MarkDuplicates Tracking 361295 as yet unmatched pairs. 5893 records in RAM.
INFO 2026-06-08 08:10:12 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:07:46s. Time for last 1,000,000: 1s. Last read position: chr12:124,334,564
INFO 2026-06-08 08:10:12 MarkDuplicates Tracking 358980 as yet unmatched pairs. 3575 records in RAM.
INFO 2026-06-08 08:10:14 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:07:48s. Time for last 1,000,000: 2s. Last read position: chr12:132,677,380
INFO 2026-06-08 08:10:14 MarkDuplicates Tracking 356155 as yet unmatched pairs. 748 records in RAM.
INFO 2026-06-08 08:10:16 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:07:50s. Time for last 1,000,000: 1s. Last read position: chr13:26,682,824
INFO 2026-06-08 08:10:16 MarkDuplicates Tracking 353967 as yet unmatched pairs. 10051 records in RAM.
INFO 2026-06-08 08:10:18 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:07:52s. Time for last 1,000,000: 2s. Last read position: chr13:40,559,635
INFO 2026-06-08 08:10:18 MarkDuplicates Tracking 352089 as yet unmatched pairs. 8172 records in RAM.
INFO 2026-06-08 08:10:20 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:07:54s. Time for last 1,000,000: 1s. Last read position: chr13:95,166,190
INFO 2026-06-08 08:10:20 MarkDuplicates Tracking 349880 as yet unmatched pairs. 5959 records in RAM.
INFO 2026-06-08 08:10:22 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:07:56s. Time for last 1,000,000: 2s. Last read position: chr13:110,205,511
INFO 2026-06-08 08:10:22 MarkDuplicates Tracking 347293 as yet unmatched pairs. 3371 records in RAM.
INFO 2026-06-08 08:10:24 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:07:58s. Time for last 1,000,000: 1s. Last read position: chr13:113,322,298
INFO 2026-06-08 08:10:24 MarkDuplicates Tracking 344496 as yet unmatched pairs. 571 records in RAM.
INFO 2026-06-08 08:10:26 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:08:00s. Time for last 1,000,000: 2s. Last read position: chr14:23,033,604
INFO 2026-06-08 08:10:26 MarkDuplicates Tracking 342121 as yet unmatched pairs. 20371 records in RAM.
INFO 2026-06-08 08:10:28 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:08:02s. Time for last 1,000,000: 1s. Last read position: chr14:24,159,923
INFO 2026-06-08 08:10:28 MarkDuplicates Tracking 339371 as yet unmatched pairs. 17621 records in RAM.
INFO 2026-06-08 08:10:30 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:08:04s. Time for last 1,000,000: 2s. Last read position: chr14:38,254,581
INFO 2026-06-08 08:10:30 MarkDuplicates Tracking 337072 as yet unmatched pairs. 15321 records in RAM.
INFO 2026-06-08 08:10:32 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:08:06s. Time for last 1,000,000: 1s. Last read position: chr14:60,879,714
INFO 2026-06-08 08:10:32 MarkDuplicates Tracking 335136 as yet unmatched pairs. 13382 records in RAM.
INFO 2026-06-08 08:10:34 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:08:08s. Time for last 1,000,000: 1s. Last read position: chr14:69,886,015
INFO 2026-06-08 08:10:34 MarkDuplicates Tracking 332775 as yet unmatched pairs. 11020 records in RAM.
INFO 2026-06-08 08:10:36 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:08:10s. Time for last 1,000,000: 1s. Last read position: chr14:75,281,033
INFO 2026-06-08 08:10:36 MarkDuplicates Tracking 330734 as yet unmatched pairs. 8977 records in RAM.
INFO 2026-06-08 08:10:37 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:08:11s. Time for last 1,000,000: 1s. Last read position: chr14:93,242,918
INFO 2026-06-08 08:10:37 MarkDuplicates Tracking 327915 as yet unmatched pairs. 6150 records in RAM.
INFO 2026-06-08 08:10:39 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:08:13s. Time for last 1,000,000: 1s. Last read position: chr14:102,209,302
INFO 2026-06-08 08:10:39 MarkDuplicates Tracking 325444 as yet unmatched pairs. 3668 records in RAM.
INFO 2026-06-08 08:10:41 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:08:15s. Time for last 1,000,000: 1s. Last read position: chr14:105,392,832
INFO 2026-06-08 08:10:41 MarkDuplicates Tracking 322757 as yet unmatched pairs. 979 records in RAM.
INFO 2026-06-08 08:10:43 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:08:17s. Time for last 1,000,000: 1s. Last read position: chr15:29,708,801
INFO 2026-06-08 08:10:43 MarkDuplicates Tracking 320680 as yet unmatched pairs. 19624 records in RAM.
INFO 2026-06-08 08:10:45 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 1s. Last read position: chr15:41,243,722
INFO 2026-06-08 08:10:45 MarkDuplicates Tracking 318794 as yet unmatched pairs. 17737 records in RAM.
INFO 2026-06-08 08:10:47 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 1s. Last read position: chr15:43,793,764
INFO 2026-06-08 08:10:47 MarkDuplicates Tracking 317647 as yet unmatched pairs. 16588 records in RAM.
INFO 2026-06-08 08:10:48 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:08:22s. Time for last 1,000,000: 1s. Last read position: chr15:57,706,751
INFO 2026-06-08 08:10:48 MarkDuplicates Tracking 314190 as yet unmatched pairs. 13129 records in RAM.
INFO 2026-06-08 08:10:50 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:08:24s. Time for last 1,000,000: 2s. Last read position: chr15:65,869,528
INFO 2026-06-08 08:10:50 MarkDuplicates Tracking 311657 as yet unmatched pairs. 10595 records in RAM.
INFO 2026-06-08 08:10:53 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:08:27s. Time for last 1,000,000: 2s. Last read position: chr15:73,998,081
INFO 2026-06-08 08:10:53 MarkDuplicates Tracking 309459 as yet unmatched pairs. 8396 records in RAM.
INFO 2026-06-08 08:10:55 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 2s. Last read position: chr15:76,931,855
INFO 2026-06-08 08:10:55 MarkDuplicates Tracking 306558 as yet unmatched pairs. 5493 records in RAM.
INFO 2026-06-08 08:10:56 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:08:30s. Time for last 1,000,000: 1s. Last read position: chr15:88,527,629
INFO 2026-06-08 08:10:56 MarkDuplicates Tracking 304157 as yet unmatched pairs. 3092 records in RAM.
INFO 2026-06-08 08:10:58 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 1s. Last read position: chr15:96,334,116
INFO 2026-06-08 08:10:58 MarkDuplicates Tracking 301889 as yet unmatched pairs. 823 records in RAM.
INFO 2026-06-08 08:11:00 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 2s. Last read position: chr16:660,658
INFO 2026-06-08 08:11:00 MarkDuplicates Tracking 299289 as yet unmatched pairs. 44021 records in RAM.
INFO 2026-06-08 08:11:02 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:08:36s. Time for last 1,000,000: 1s. Last read position: chr16:1,788,176
INFO 2026-06-08 08:11:02 MarkDuplicates Tracking 296391 as yet unmatched pairs. 41123 records in RAM.
INFO 2026-06-08 08:11:04 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:08:38s. Time for last 1,000,000: 1s. Last read position: chr16:2,622,693
INFO 2026-06-08 08:11:04 MarkDuplicates Tracking 292874 as yet unmatched pairs. 37606 records in RAM.
INFO 2026-06-08 08:11:06 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 1s. Last read position: chr16:3,849,378
INFO 2026-06-08 08:11:06 MarkDuplicates Tracking 290150 as yet unmatched pairs. 34882 records in RAM.
INFO 2026-06-08 08:11:08 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:08:42s. Time for last 1,000,000: 1s. Last read position: chr16:14,218,906
INFO 2026-06-08 08:11:08 MarkDuplicates Tracking 287502 as yet unmatched pairs. 32234 records in RAM.
INFO 2026-06-08 08:11:09 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:08:43s. Time for last 1,000,000: 1s. Last read position: chr16:15,949,764
INFO 2026-06-08 08:11:09 MarkDuplicates Tracking 286111 as yet unmatched pairs. 30842 records in RAM.
INFO 2026-06-08 08:11:11 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:08:45s. Time for last 1,000,000: 1s. Last read position: chr16:18,351,334
INFO 2026-06-08 08:11:11 MarkDuplicates Tracking 285395 as yet unmatched pairs. 30126 records in RAM.
INFO 2026-06-08 08:11:12 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:08:46s. Time for last 1,000,000: 1s. Last read position: chr16:21,402,739
INFO 2026-06-08 08:11:12 MarkDuplicates Tracking 283725 as yet unmatched pairs. 28456 records in RAM.
INFO 2026-06-08 08:11:14 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 1s. Last read position: chr16:22,326,193
INFO 2026-06-08 08:11:14 MarkDuplicates Tracking 282840 as yet unmatched pairs. 27571 records in RAM.
INFO 2026-06-08 08:11:16 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:08:50s. Time for last 1,000,000: 1s. Last read position: chr16:27,461,431
INFO 2026-06-08 08:11:16 MarkDuplicates Tracking 281672 as yet unmatched pairs. 26403 records in RAM.
INFO 2026-06-08 08:11:18 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:08:52s. Time for last 1,000,000: 2s. Last read position: chr16:29,383,857
INFO 2026-06-08 08:11:18 MarkDuplicates Tracking 279648 as yet unmatched pairs. 24379 records in RAM.
INFO 2026-06-08 08:11:20 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 2s. Last read position: chr16:29,986,880
INFO 2026-06-08 08:11:20 MarkDuplicates Tracking 277966 as yet unmatched pairs. 22697 records in RAM.
INFO 2026-06-08 08:11:22 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:08:56s. Time for last 1,000,000: 1s. Last read position: chr16:30,555,192
INFO 2026-06-08 08:11:22 MarkDuplicates Tracking 276031 as yet unmatched pairs. 20762 records in RAM.
INFO 2026-06-08 08:11:24 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:08:58s. Time for last 1,000,000: 1s. Last read position: chr16:31,112,156
INFO 2026-06-08 08:11:24 MarkDuplicates Tracking 273572 as yet unmatched pairs. 18296 records in RAM.
INFO 2026-06-08 08:11:26 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:09:00s. Time for last 1,000,000: 1s. Last read position: chr16:55,482,988
INFO 2026-06-08 08:11:26 MarkDuplicates Tracking 271175 as yet unmatched pairs. 15895 records in RAM.
INFO 2026-06-08 08:11:27 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:09:01s. Time for last 1,000,000: 1s. Last read position: chr16:67,163,296
INFO 2026-06-08 08:11:27 MarkDuplicates Tracking 268789 as yet unmatched pairs. 13504 records in RAM.
INFO 2026-06-08 08:11:29 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:09:03s. Time for last 1,000,000: 1s. Last read position: chr16:69,109,922
INFO 2026-06-08 08:11:29 MarkDuplicates Tracking 266450 as yet unmatched pairs. 11165 records in RAM.
INFO 2026-06-08 08:11:31 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 1s. Last read position: chr16:71,849,955
INFO 2026-06-08 08:11:31 MarkDuplicates Tracking 263776 as yet unmatched pairs. 8490 records in RAM.
INFO 2026-06-08 08:11:32 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:09:06s. Time for last 1,000,000: 1s. Last read position: chr16:81,082,821
INFO 2026-06-08 08:11:32 MarkDuplicates Tracking 261486 as yet unmatched pairs. 6195 records in RAM.
INFO 2026-06-08 08:11:34 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 1s. Last read position: chr16:88,650,956
INFO 2026-06-08 08:11:34 MarkDuplicates Tracking 258738 as yet unmatched pairs. 3442 records in RAM.
INFO 2026-06-08 08:11:36 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:09:10s. Time for last 1,000,000: 1s. Last read position: chr16:89,770,166
INFO 2026-06-08 08:11:36 MarkDuplicates Tracking 256207 as yet unmatched pairs. 911 records in RAM.
INFO 2026-06-08 08:11:39 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:09:13s. Time for last 1,000,000: 3s. Last read position: chr17:2,387,871
INFO 2026-06-08 08:11:39 MarkDuplicates Tracking 253371 as yet unmatched pairs. 66759 records in RAM.
INFO 2026-06-08 08:11:41 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:09:15s. Time for last 1,000,000: 2s. Last read position: chr17:7,229,642
INFO 2026-06-08 08:11:41 MarkDuplicates Tracking 250656 as yet unmatched pairs. 64043 records in RAM.
INFO 2026-06-08 08:11:43 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:09:17s. Time for last 1,000,000: 2s. Last read position: chr17:7,849,073
INFO 2026-06-08 08:11:43 MarkDuplicates Tracking 248379 as yet unmatched pairs. 61766 records in RAM.
INFO 2026-06-08 08:11:46 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:09:19s. Time for last 1,000,000: 2s. Last read position: chr17:17,794,155
INFO 2026-06-08 08:11:46 MarkDuplicates Tracking 246126 as yet unmatched pairs. 59512 records in RAM.
INFO 2026-06-08 08:11:48 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 2s. Last read position: chr17:28,554,894
INFO 2026-06-08 08:11:48 MarkDuplicates Tracking 244008 as yet unmatched pairs. 57394 records in RAM.
INFO 2026-06-08 08:11:50 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:09:24s. Time for last 1,000,000: 2s. Last read position: chr17:28,906,144
INFO 2026-06-08 08:11:50 MarkDuplicates Tracking 241690 as yet unmatched pairs. 55075 records in RAM.
INFO 2026-06-08 08:11:52 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:09:26s. Time for last 1,000,000: 2s. Last read position: chr17:35,650,773
INFO 2026-06-08 08:11:52 MarkDuplicates Tracking 239592 as yet unmatched pairs. 52976 records in RAM.
INFO 2026-06-08 08:11:54 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:09:28s. Time for last 1,000,000: 1s. Last read position: chr17:38,063,906
INFO 2026-06-08 08:11:54 MarkDuplicates Tracking 238186 as yet unmatched pairs. 51570 records in RAM.
INFO 2026-06-08 08:13:11 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:10:45s. Time for last 1,000,000: 76s. Last read position: chr17:38,735,201
INFO 2026-06-08 08:13:11 MarkDuplicates Tracking 235886 as yet unmatched pairs. 49270 records in RAM.
INFO 2026-06-08 08:13:15 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:10:49s. Time for last 1,000,000: 3s. Last read position: chr17:39,709,382
INFO 2026-06-08 08:13:15 MarkDuplicates Tracking 233843 as yet unmatched pairs. 47226 records in RAM.
INFO 2026-06-08 08:13:17 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:10:51s. Time for last 1,000,000: 1s. Last read position: chr17:39,724,726
INFO 2026-06-08 08:13:17 MarkDuplicates Tracking 230976 as yet unmatched pairs. 44359 records in RAM.
INFO 2026-06-08 08:13:19 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:10:53s. Time for last 1,000,000: 1s. Last read position: chr17:40,134,237
INFO 2026-06-08 08:13:19 MarkDuplicates Tracking 228083 as yet unmatched pairs. 41466 records in RAM.
INFO 2026-06-08 08:13:20 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:10:54s. Time for last 1,000,000: 1s. Last read position: chr17:41,527,939
INFO 2026-06-08 08:13:20 MarkDuplicates Tracking 225970 as yet unmatched pairs. 39352 records in RAM.
INFO 2026-06-08 08:13:22 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:10:56s. Time for last 1,000,000: 1s. Last read position: chr17:42,867,662
INFO 2026-06-08 08:13:22 MarkDuplicates Tracking 222637 as yet unmatched pairs. 36019 records in RAM.
INFO 2026-06-08 08:13:24 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 1s. Last read position: chr17:46,576,233
INFO 2026-06-08 08:13:24 MarkDuplicates Tracking 220770 as yet unmatched pairs. 34150 records in RAM.
INFO 2026-06-08 08:13:26 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:11:00s. Time for last 1,000,000: 1s. Last read position: chr17:50,187,524
INFO 2026-06-08 08:13:26 MarkDuplicates Tracking 221980 as yet unmatched pairs. 35360 records in RAM.
INFO 2026-06-08 08:13:28 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:11:02s. Time for last 1,000,000: 1s. Last read position: chr17:50,190,034
INFO 2026-06-08 08:13:28 MarkDuplicates Tracking 219111 as yet unmatched pairs. 32491 records in RAM.
INFO 2026-06-08 08:13:30 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:11:04s. Time for last 1,000,000: 2s. Last read position: chr17:50,194,129
INFO 2026-06-08 08:13:30 MarkDuplicates Tracking 218068 as yet unmatched pairs. 31448 records in RAM.
INFO 2026-06-08 08:13:32 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:11:06s. Time for last 1,000,000: 1s. Last read position: chr17:50,196,487
INFO 2026-06-08 08:13:32 MarkDuplicates Tracking 213428 as yet unmatched pairs. 26808 records in RAM.
INFO 2026-06-08 08:13:34 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:11:08s. Time for last 1,000,000: 2s. Last read position: chr17:50,679,807
INFO 2026-06-08 08:13:34 MarkDuplicates Tracking 208871 as yet unmatched pairs. 22251 records in RAM.
INFO 2026-06-08 08:13:37 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:11:11s. Time for last 1,000,000: 3s. Last read position: chr17:61,403,084
INFO 2026-06-08 08:13:37 MarkDuplicates Tracking 206522 as yet unmatched pairs. 19901 records in RAM.
INFO 2026-06-08 08:13:39 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:11:13s. Time for last 1,000,000: 1s. Last read position: chr17:67,940,439
INFO 2026-06-08 08:13:39 MarkDuplicates Tracking 204072 as yet unmatched pairs. 17450 records in RAM.
INFO 2026-06-08 08:13:41 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:11:15s. Time for last 1,000,000: 1s. Last read position: chr17:75,501,949
INFO 2026-06-08 08:13:41 MarkDuplicates Tracking 201562 as yet unmatched pairs. 14936 records in RAM.
INFO 2026-06-08 08:13:43 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:11:17s. Time for last 1,000,000: 1s. Last read position: chr17:76,265,929
INFO 2026-06-08 08:13:43 MarkDuplicates Tracking 198854 as yet unmatched pairs. 12228 records in RAM.
INFO 2026-06-08 08:13:45 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:11:19s. Time for last 1,000,000: 1s. Last read position: chr17:78,976,044
INFO 2026-06-08 08:13:45 MarkDuplicates Tracking 196224 as yet unmatched pairs. 9598 records in RAM.
INFO 2026-06-08 08:13:46 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:11:20s. Time for last 1,000,000: 1s. Last read position: chr17:81,510,712
INFO 2026-06-08 08:13:46 MarkDuplicates Tracking 193496 as yet unmatched pairs. 6868 records in RAM.
INFO 2026-06-08 08:13:48 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:11:22s. Time for last 1,000,000: 1s. Last read position: chr17:81,996,683
INFO 2026-06-08 08:13:48 MarkDuplicates Tracking 190701 as yet unmatched pairs. 4073 records in RAM.
INFO 2026-06-08 08:13:50 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:11:24s. Time for last 1,000,000: 1s. Last read position: chr17:82,419,815
INFO 2026-06-08 08:13:50 MarkDuplicates Tracking 187539 as yet unmatched pairs. 910 records in RAM.
INFO 2026-06-08 08:13:52 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:11:26s. Time for last 1,000,000: 1s. Last read position: chr18:10,539,797
INFO 2026-06-08 08:13:52 MarkDuplicates Tracking 185151 as yet unmatched pairs. 6180 records in RAM.
INFO 2026-06-08 08:13:54 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:11:28s. Time for last 1,000,000: 1s. Last read position: chr18:46,035,073
INFO 2026-06-08 08:13:54 MarkDuplicates Tracking 182741 as yet unmatched pairs. 3769 records in RAM.
INFO 2026-06-08 08:13:56 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:11:29s. Time for last 1,000,000: 1s. Last read position: chr18:62,716,157
INFO 2026-06-08 08:13:56 MarkDuplicates Tracking 180573 as yet unmatched pairs. 1600 records in RAM.
INFO 2026-06-08 08:13:59 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:11:33s. Time for last 1,000,000: 3s. Last read position: chr19:799,409
INFO 2026-06-08 08:13:59 MarkDuplicates Tracking 177956 as yet unmatched pairs. 76798 records in RAM.
INFO 2026-06-08 08:14:01 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:11:35s. Time for last 1,000,000: 2s. Last read position: chr19:1,430,351
INFO 2026-06-08 08:14:01 MarkDuplicates Tracking 174551 as yet unmatched pairs. 73392 records in RAM.
INFO 2026-06-08 08:14:03 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:11:37s. Time for last 1,000,000: 2s. Last read position: chr19:2,046,397
INFO 2026-06-08 08:14:03 MarkDuplicates Tracking 171434 as yet unmatched pairs. 70274 records in RAM.
INFO 2026-06-08 08:14:06 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:11:40s. Time for last 1,000,000: 2s. Last read position: chr19:3,551,111
INFO 2026-06-08 08:14:06 MarkDuplicates Tracking 168519 as yet unmatched pairs. 67358 records in RAM.
INFO 2026-06-08 08:14:08 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:11:42s. Time for last 1,000,000: 2s. Last read position: chr19:5,151,328
INFO 2026-06-08 08:14:08 MarkDuplicates Tracking 165755 as yet unmatched pairs. 64593 records in RAM.
INFO 2026-06-08 08:14:10 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:11:44s. Time for last 1,000,000: 1s. Last read position: chr19:7,467,521
INFO 2026-06-08 08:14:10 MarkDuplicates Tracking 162942 as yet unmatched pairs. 61778 records in RAM.
INFO 2026-06-08 08:14:12 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:11:46s. Time for last 1,000,000: 2s. Last read position: chr19:9,828,029
INFO 2026-06-08 08:14:12 MarkDuplicates Tracking 160490 as yet unmatched pairs. 59326 records in RAM.
INFO 2026-06-08 08:14:14 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:11:48s. Time for last 1,000,000: 1s. Last read position: chr19:10,923,160
INFO 2026-06-08 08:14:14 MarkDuplicates Tracking 157607 as yet unmatched pairs. 56442 records in RAM.
INFO 2026-06-08 08:14:16 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:11:50s. Time for last 1,000,000: 1s. Last read position: chr19:12,730,957
INFO 2026-06-08 08:14:16 MarkDuplicates Tracking 155350 as yet unmatched pairs. 54185 records in RAM.
INFO 2026-06-08 08:14:18 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:11:52s. Time for last 1,000,000: 1s. Last read position: chr19:13,993,726
INFO 2026-06-08 08:14:18 MarkDuplicates Tracking 152549 as yet unmatched pairs. 51383 records in RAM.
INFO 2026-06-08 08:14:20 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:11:54s. Time for last 1,000,000: 1s. Last read position: chr19:15,167,382
INFO 2026-06-08 08:14:20 MarkDuplicates Tracking 150148 as yet unmatched pairs. 48981 records in RAM.
INFO 2026-06-08 08:14:22 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:11:56s. Time for last 1,000,000: 2s. Last read position: chr19:15,243,365
INFO 2026-06-08 08:14:22 MarkDuplicates Tracking 147561 as yet unmatched pairs. 46394 records in RAM.
INFO 2026-06-08 08:14:24 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:11:58s. Time for last 1,000,000: 2s. Last read position: chr19:16,869,746
INFO 2026-06-08 08:14:24 MarkDuplicates Tracking 144659 as yet unmatched pairs. 43491 records in RAM.
INFO 2026-06-08 08:14:26 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:12:00s. Time for last 1,000,000: 1s. Last read position: chr19:18,280,693
INFO 2026-06-08 08:14:26 MarkDuplicates Tracking 142175 as yet unmatched pairs. 41006 records in RAM.
INFO 2026-06-08 08:14:28 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:12:02s. Time for last 1,000,000: 1s. Last read position: chr19:19,180,696
INFO 2026-06-08 08:14:28 MarkDuplicates Tracking 139018 as yet unmatched pairs. 37847 records in RAM.
INFO 2026-06-08 08:14:30 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:12:04s. Time for last 1,000,000: 1s. Last read position: chr19:33,302,335
INFO 2026-06-08 08:14:30 MarkDuplicates Tracking 136483 as yet unmatched pairs. 35309 records in RAM.
INFO 2026-06-08 08:14:31 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:12:05s. Time for last 1,000,000: 1s. Last read position: chr19:35,547,181
INFO 2026-06-08 08:14:31 MarkDuplicates Tracking 133639 as yet unmatched pairs. 32465 records in RAM.
INFO 2026-06-08 08:14:33 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:12:07s. Time for last 1,000,000: 1s. Last read position: chr19:38,119,332
INFO 2026-06-08 08:14:33 MarkDuplicates Tracking 130719 as yet unmatched pairs. 29545 records in RAM.
INFO 2026-06-08 08:14:35 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:12:09s. Time for last 1,000,000: 2s. Last read position: chr19:38,945,092
INFO 2026-06-08 08:14:35 MarkDuplicates Tracking 128175 as yet unmatched pairs. 27001 records in RAM.
INFO 2026-06-08 08:14:37 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:12:11s. Time for last 1,000,000: 1s. Last read position: chr19:39,423,890
INFO 2026-06-08 08:14:37 MarkDuplicates Tracking 126185 as yet unmatched pairs. 25011 records in RAM.
INFO 2026-06-08 08:14:39 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:12:13s. Time for last 1,000,000: 1s. Last read position: chr19:40,578,465
INFO 2026-06-08 08:14:39 MarkDuplicates Tracking 123542 as yet unmatched pairs. 22367 records in RAM.
INFO 2026-06-08 08:14:41 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:12:15s. Time for last 1,000,000: 2s. Last read position: chr19:42,272,524
INFO 2026-06-08 08:14:41 MarkDuplicates Tracking 121382 as yet unmatched pairs. 20207 records in RAM.
INFO 2026-06-08 08:14:43 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:12:17s. Time for last 1,000,000: 1s. Last read position: chr19:44,819,581
INFO 2026-06-08 08:14:43 MarkDuplicates Tracking 118632 as yet unmatched pairs. 17442 records in RAM.
INFO 2026-06-08 08:14:45 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:12:19s. Time for last 1,000,000: 1s. Last read position: chr19:45,940,536
INFO 2026-06-08 08:14:45 MarkDuplicates Tracking 115602 as yet unmatched pairs. 14411 records in RAM.
INFO 2026-06-08 08:14:47 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:12:21s. Time for last 1,000,000: 1s. Last read position: chr19:48,615,375
INFO 2026-06-08 08:14:47 MarkDuplicates Tracking 113551 as yet unmatched pairs. 12360 records in RAM.
INFO 2026-06-08 08:14:48 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:12:22s. Time for last 1,000,000: 1s. Last read position: chr19:49,497,192
INFO 2026-06-08 08:14:48 MarkDuplicates Tracking 110845 as yet unmatched pairs. 9654 records in RAM.
INFO 2026-06-08 08:14:50 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:12:24s. Time for last 1,000,000: 1s. Last read position: chr19:50,000,800
INFO 2026-06-08 08:14:50 MarkDuplicates Tracking 107749 as yet unmatched pairs. 6558 records in RAM.
INFO 2026-06-08 08:14:52 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:12:26s. Time for last 1,000,000: 1s. Last read position: chr19:54,457,953
INFO 2026-06-08 08:14:52 MarkDuplicates Tracking 105364 as yet unmatched pairs. 4172 records in RAM.
INFO 2026-06-08 08:14:54 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:12:28s. Time for last 1,000,000: 2s. Last read position: chr19:57,284,607
INFO 2026-06-08 08:14:54 MarkDuplicates Tracking 102727 as yet unmatched pairs. 1534 records in RAM.
INFO 2026-06-08 08:14:56 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:12:30s. Time for last 1,000,000: 2s. Last read position: chr20:1,392,833
INFO 2026-06-08 08:14:56 MarkDuplicates Tracking 100569 as yet unmatched pairs. 23699 records in RAM.
INFO 2026-06-08 08:14:58 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:12:32s. Time for last 1,000,000: 2s. Last read position: chr20:10,640,901
INFO 2026-06-08 08:14:58 MarkDuplicates Tracking 97435 as yet unmatched pairs. 20564 records in RAM.
INFO 2026-06-08 08:15:00 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:12:34s. Time for last 1,000,000: 1s. Last read position: chr20:23,690,237
INFO 2026-06-08 08:15:00 MarkDuplicates Tracking 95116 as yet unmatched pairs. 18244 records in RAM.
INFO 2026-06-08 08:15:02 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:12:36s. Time for last 1,000,000: 1s. Last read position: chr20:33,811,530
INFO 2026-06-08 08:15:02 MarkDuplicates Tracking 92560 as yet unmatched pairs. 15688 records in RAM.
INFO 2026-06-08 08:15:04 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:12:38s. Time for last 1,000,000: 1s. Last read position: chr20:36,185,183
INFO 2026-06-08 08:15:04 MarkDuplicates Tracking 90267 as yet unmatched pairs. 13394 records in RAM.
INFO 2026-06-08 08:15:06 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:12:40s. Time for last 1,000,000: 1s. Last read position: chr20:43,702,620
INFO 2026-06-08 08:15:06 MarkDuplicates Tracking 87854 as yet unmatched pairs. 10978 records in RAM.
INFO 2026-06-08 08:15:08 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:12:42s. Time for last 1,000,000: 2s. Last read position: chr20:45,840,675
INFO 2026-06-08 08:15:08 MarkDuplicates Tracking 85423 as yet unmatched pairs. 8547 records in RAM.
INFO 2026-06-08 08:15:10 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:12:44s. Time for last 1,000,000: 1s. Last read position: chr20:50,191,963
INFO 2026-06-08 08:15:10 MarkDuplicates Tracking 83007 as yet unmatched pairs. 6130 records in RAM.
INFO 2026-06-08 08:15:12 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:12:46s. Time for last 1,000,000: 1s. Last read position: chr20:58,903,698
INFO 2026-06-08 08:15:12 MarkDuplicates Tracking 80739 as yet unmatched pairs. 3861 records in RAM.
INFO 2026-06-08 08:15:14 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:12:48s. Time for last 1,000,000: 1s. Last read position: chr20:63,521,667
INFO 2026-06-08 08:15:14 MarkDuplicates Tracking 78099 as yet unmatched pairs. 1220 records in RAM.
INFO 2026-06-08 08:15:15 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:12:49s. Time for last 1,000,000: 1s. Last read position: chr21:8,214,729
INFO 2026-06-08 08:15:15 MarkDuplicates Tracking 76206 as yet unmatched pairs. 14215 records in RAM.
INFO 2026-06-08 08:15:17 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:12:51s. Time for last 1,000,000: 1s. Last read position: chr21:8,258,955
INFO 2026-06-08 08:15:17 MarkDuplicates Tracking 74349 as yet unmatched pairs. 12330 records in RAM.
INFO 2026-06-08 08:15:18 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:12:52s. Time for last 1,000,000: 1s. Last read position: chr21:8,400,307
INFO 2026-06-08 08:15:18 MarkDuplicates Tracking 73448 as yet unmatched pairs. 11423 records in RAM.
INFO 2026-06-08 08:15:19 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:12:53s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,591
INFO 2026-06-08 08:15:19 MarkDuplicates Tracking 71995 as yet unmatched pairs. 9964 records in RAM.
INFO 2026-06-08 08:15:22 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:12:56s. Time for last 1,000,000: 2s. Last read position: chr21:33,553,185
INFO 2026-06-08 08:15:22 MarkDuplicates Tracking 69585 as yet unmatched pairs. 7554 records in RAM.
INFO 2026-06-08 08:15:24 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:12:58s. Time for last 1,000,000: 2s. Last read position: chr21:42,285,965
INFO 2026-06-08 08:15:24 MarkDuplicates Tracking 67182 as yet unmatched pairs. 5151 records in RAM.
INFO 2026-06-08 08:15:26 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:13:00s. Time for last 1,000,000: 1s. Last read position: chr21:45,468,364
INFO 2026-06-08 08:15:26 MarkDuplicates Tracking 65247 as yet unmatched pairs. 3216 records in RAM.
INFO 2026-06-08 08:15:28 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:13:02s. Time for last 1,000,000: 2s. Last read position: chr22:16,697,553
INFO 2026-06-08 08:15:28 MarkDuplicates Tracking 61992 as yet unmatched pairs. 33022 records in RAM.
INFO 2026-06-08 08:15:30 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:13:04s. Time for last 1,000,000: 1s. Last read position: chr22:20,555,098
INFO 2026-06-08 08:15:30 MarkDuplicates Tracking 59655 as yet unmatched pairs. 30685 records in RAM.
INFO 2026-06-08 08:15:32 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:13:06s. Time for last 1,000,000: 1s. Last read position: chr22:23,271,536
INFO 2026-06-08 08:15:32 MarkDuplicates Tracking 57399 as yet unmatched pairs. 28429 records in RAM.
INFO 2026-06-08 08:15:34 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:13:08s. Time for last 1,000,000: 1s. Last read position: chr22:23,982,938
INFO 2026-06-08 08:15:34 MarkDuplicates Tracking 54139 as yet unmatched pairs. 25169 records in RAM.
INFO 2026-06-08 08:15:37 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:13:11s. Time for last 1,000,000: 2s. Last read position: chr22:25,041,143
INFO 2026-06-08 08:15:37 MarkDuplicates Tracking 51909 as yet unmatched pairs. 22939 records in RAM.
INFO 2026-06-08 08:15:39 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:13:13s. Time for last 1,000,000: 2s. Last read position: chr22:29,286,946
INFO 2026-06-08 08:15:39 MarkDuplicates Tracking 49836 as yet unmatched pairs. 20866 records in RAM.
INFO 2026-06-08 08:15:41 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:13:15s. Time for last 1,000,000: 1s. Last read position: chr22:29,792,486
INFO 2026-06-08 08:15:41 MarkDuplicates Tracking 46909 as yet unmatched pairs. 17939 records in RAM.
INFO 2026-06-08 08:15:43 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:13:17s. Time for last 1,000,000: 1s. Last read position: chr22:31,104,328
INFO 2026-06-08 08:15:43 MarkDuplicates Tracking 44762 as yet unmatched pairs. 15792 records in RAM.
INFO 2026-06-08 08:15:45 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:13:19s. Time for last 1,000,000: 2s. Last read position: chr22:31,857,445
INFO 2026-06-08 08:15:45 MarkDuplicates Tracking 42488 as yet unmatched pairs. 13518 records in RAM.
INFO 2026-06-08 08:15:47 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:13:21s. Time for last 1,000,000: 2s. Last read position: chr22:36,321,758
INFO 2026-06-08 08:15:47 MarkDuplicates Tracking 40124 as yet unmatched pairs. 11154 records in RAM.
INFO 2026-06-08 08:15:49 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:13:23s. Time for last 1,000,000: 1s. Last read position: chr22:38,822,636
INFO 2026-06-08 08:15:49 MarkDuplicates Tracking 37239 as yet unmatched pairs. 8269 records in RAM.
INFO 2026-06-08 08:15:51 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:13:25s. Time for last 1,000,000: 1s. Last read position: chr22:41,878,102
INFO 2026-06-08 08:15:51 MarkDuplicates Tracking 34618 as yet unmatched pairs. 5648 records in RAM.
INFO 2026-06-08 08:15:53 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:13:27s. Time for last 1,000,000: 2s. Last read position: chr22:46,364,599
INFO 2026-06-08 08:15:53 MarkDuplicates Tracking 31671 as yet unmatched pairs. 2701 records in RAM.
INFO 2026-06-08 08:15:55 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:13:29s. Time for last 1,000,000: 2s. Last read position: chrX:345,544
INFO 2026-06-08 08:15:55 MarkDuplicates Tracking 28734 as yet unmatched pairs. 21711 records in RAM.
INFO 2026-06-08 08:15:56 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:13:30s. Time for last 1,000,000: 1s. Last read position: chrX:20,175,199
INFO 2026-06-08 08:15:56 MarkDuplicates Tracking 26663 as yet unmatched pairs. 19632 records in RAM.
INFO 2026-06-08 08:15:58 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:13:32s. Time for last 1,000,000: 1s. Last read position: chrX:47,173,128
INFO 2026-06-08 08:15:58 MarkDuplicates Tracking 24564 as yet unmatched pairs. 17533 records in RAM.
INFO 2026-06-08 08:16:00 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:13:34s. Time for last 1,000,000: 2s. Last read position: chrX:49,281,348
INFO 2026-06-08 08:16:00 MarkDuplicates Tracking 22119 as yet unmatched pairs. 15088 records in RAM.
INFO 2026-06-08 08:16:02 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:13:36s. Time for last 1,000,000: 1s. Last read position: chrX:54,183,102
INFO 2026-06-08 08:16:02 MarkDuplicates Tracking 20094 as yet unmatched pairs. 13063 records in RAM.
INFO 2026-06-08 08:16:04 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:13:38s. Time for last 1,000,000: 1s. Last read position: chrX:72,482,508
INFO 2026-06-08 08:16:04 MarkDuplicates Tracking 17747 as yet unmatched pairs. 10714 records in RAM.
INFO 2026-06-08 08:16:05 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:13:39s. Time for last 1,000,000: 1s. Last read position: chrX:104,186,168
INFO 2026-06-08 08:16:05 MarkDuplicates Tracking 15751 as yet unmatched pairs. 8718 records in RAM.
INFO 2026-06-08 08:16:07 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:13:41s. Time for last 1,000,000: 1s. Last read position: chrX:130,069,400
INFO 2026-06-08 08:16:07 MarkDuplicates Tracking 13365 as yet unmatched pairs. 6332 records in RAM.
INFO 2026-06-08 08:16:09 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:13:43s. Time for last 1,000,000: 1s. Last read position: chrX:153,773,268
INFO 2026-06-08 08:16:09 MarkDuplicates Tracking 11180 as yet unmatched pairs. 4145 records in RAM.
INFO 2026-06-08 08:16:11 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:13:45s. Time for last 1,000,000: 2s. Last read position: chrX:154,399,490
INFO 2026-06-08 08:16:11 MarkDuplicates Tracking 8896 as yet unmatched pairs. 1861 records in RAM.
INFO 2026-06-08 08:16:14 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:13:48s. Time for last 1,000,000: 2s. Last read position: chrM:11,999
INFO 2026-06-08 08:16:14 MarkDuplicates Tracking 6349 as yet unmatched pairs. 71 records in RAM.
INFO 2026-06-08 08:16:15 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:13:49s. Time for last 1,000,000: 1s. Last read position: GL000220.1:153,358
INFO 2026-06-08 08:16:15 MarkDuplicates Tracking 4683 as yet unmatched pairs. 147 records in RAM.
INFO 2026-06-08 08:16:17 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:13:51s. Time for last 1,000,000: 1s. Last read position: KI270733.1:125,548
INFO 2026-06-08 08:16:17 MarkDuplicates Tracking 4489 as yet unmatched pairs. 4453 records in RAM.
INFO 2026-06-08 08:16:18 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:13:52s. Time for last 1,000,000: 1s. Last read position: KI270733.1:174,585
INFO 2026-06-08 08:16:18 MarkDuplicates Tracking 309 as yet unmatched pairs. 273 records in RAM.
INFO 2026-06-08 08:16:19 MarkDuplicates Read 352891605 records. 0 pairs never matched.
INFO 2026-06-08 08:16:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 31017619944; totalMemory: 44291850240; maxMemory: 63585648640
INFO 2026-06-08 08:16:56 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:17:07 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:17:26 OpticalDuplicateFinder Large duplicate set. size = 1319
INFO 2026-06-08 08:17:26 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:1,623
INFO 2026-06-08 08:17:46 OpticalDuplicateFinder Large duplicate set. size = 1030
INFO 2026-06-08 08:17:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,060
INFO 2026-06-08 08:17:46 OpticalDuplicateFinder Large duplicate set. size = 1235
INFO 2026-06-08 08:17:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,388
INFO 2026-06-08 08:17:46 OpticalDuplicateFinder Large duplicate set. size = 1308
INFO 2026-06-08 08:17:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-14,338
INFO 2026-06-08 08:18:10 MarkDuplicates Traversing fragment information and detecting duplicates.
WARNING 2026-06-08 08:18:10 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
INFO 2026-06-08 08:18:52 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:19:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300704432; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-08 08:19:03 MarkDuplicates Marking 264666758 records as duplicates.
INFO 2026-06-08 08:19:03 MarkDuplicates Found 5071143 optical duplicate clusters.
INFO 2026-06-08 08:19:03 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 08:19:21 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:17s. Time for last 10,000,000: 17s. Last read position: chr1:35,188,035
INFO 2026-06-08 08:19:40 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:36s. Time for last 10,000,000: 18s. Last read position: chr1:149,925,926
INFO 2026-06-08 08:19:58 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:55s. Time for last 10,000,000: 18s. Last read position: chr1:203,828,399
INFO 2026-06-08 08:20:17 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:14s. Time for last 10,000,000: 19s. Last read position: chr2:33,134,853
INFO 2026-06-08 08:20:35 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:32s. Time for last 10,000,000: 17s. Last read position: chr2:195,680,285
INFO 2026-06-08 08:20:53 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:50s. Time for last 10,000,000: 18s. Last read position: chr3:49,362,508
INFO 2026-06-08 08:21:11 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:07s. Time for last 10,000,000: 17s. Last read position: chr3:195,895,253
INFO 2026-06-08 08:21:28 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:24s. Time for last 10,000,000: 17s. Last read position: chr4:86,772,943
INFO 2026-06-08 08:21:44 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:40s. Time for last 10,000,000: 15s. Last read position: chr5:141,864,158
INFO 2026-06-08 08:21:59 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:55s. Time for last 10,000,000: 15s. Last read position: chr6:31,633,499
INFO 2026-06-08 08:22:14 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:03:11s. Time for last 10,000,000: 15s. Last read position: chr6:159,755,155
INFO 2026-06-08 08:22:30 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:26s. Time for last 10,000,000: 15s. Last read position: chr7:80,758,286
INFO 2026-06-08 08:22:45 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:41s. Time for last 10,000,000: 15s. Last read position: chr8:13,115,586
INFO 2026-06-08 08:23:00 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:03:56s. Time for last 10,000,000: 15s. Last read position: chr8:143,864,263
INFO 2026-06-08 08:23:17 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:04:13s. Time for last 10,000,000: 17s. Last read position: chr9:128,167,117
INFO 2026-06-08 08:23:34 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:30s. Time for last 10,000,000: 16s. Last read position: chr10:80,489,258
INFO 2026-06-08 08:23:51 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:04:47s. Time for last 10,000,000: 16s. Last read position: chr11:46,382,585
INFO 2026-06-08 08:24:06 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:05:02s. Time for last 10,000,000: 15s. Last read position: chr11:72,008,711
INFO 2026-06-08 08:24:21 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:05:18s. Time for last 10,000,000: 15s. Last read position: chr12:46,370,466
INFO 2026-06-08 08:24:37 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:05:33s. Time for last 10,000,000: 15s. Last read position: chr12:112,283,272
INFO 2026-06-08 08:24:53 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:05:49s. Time for last 10,000,000: 15s. Last read position: chr14:23,033,604
INFO 2026-06-08 08:25:09 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:06:05s. Time for last 10,000,000: 15s. Last read position: chr15:41,243,722
INFO 2026-06-08 08:25:24 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:06:20s. Time for last 10,000,000: 15s. Last read position: chr16:2,622,693
INFO 2026-06-08 08:25:39 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:06:35s. Time for last 10,000,000: 15s. Last read position: chr16:30,555,192
INFO 2026-06-08 08:25:54 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:06:50s. Time for last 10,000,000: 14s. Last read position: chr17:7,229,642
INFO 2026-06-08 08:26:09 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:07:06s. Time for last 10,000,000: 15s. Last read position: chr17:40,134,237
INFO 2026-06-08 08:26:24 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:07:21s. Time for last 10,000,000: 15s. Last read position: chr17:67,940,439
INFO 2026-06-08 08:26:39 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:07:36s. Time for last 10,000,000: 14s. Last read position: chr19:799,409
INFO 2026-06-08 08:26:54 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:07:50s. Time for last 10,000,000: 14s. Last read position: chr19:15,167,382
INFO 2026-06-08 08:27:09 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:08:05s. Time for last 10,000,000: 14s. Last read position: chr19:40,578,465
INFO 2026-06-08 08:27:24 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:08:20s. Time for last 10,000,000: 14s. Last read position: chr20:10,640,901
INFO 2026-06-08 08:27:38 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:08:35s. Time for last 10,000,000: 14s. Last read position: chr21:8,258,955
INFO 2026-06-08 08:27:54 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:08:50s. Time for last 10,000,000: 15s. Last read position: chr22:25,041,143
INFO 2026-06-08 08:28:09 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:09:05s. Time for last 10,000,000: 15s. Last read position: chrX:20,175,199
INFO 2026-06-08 08:28:24 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:09:20s. Time for last 10,000,000: 15s. Last read position: GL000220.1:153,358
INFO 2026-06-08 08:28:34 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:28:34 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:28:34 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:28:34 MarkDuplicates Before output close freeMemory: 202051296; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:28:34 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:28:34 MarkDuplicates After output close freeMemory: 104169136; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 08:28:34 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 26.18 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory