Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/5c6d4c19fc27fd75afd80962bd7ea9/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/5c6d4c19fc27fd75afd80962bd7ea9/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/d4e748c570fc5361d6ed1cefa6a876/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)
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 aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.md.bam --METRICS_FILE aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
08:00:43.198 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 08:00:43 GMT 2026] MarkDuplicates --INPUT aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.md.bam --METRICS_FILE aih-tih-sc-2f84cc-R1_B23WHYVLT4_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 08:00:43 GMT 2026] Executing as ?@nf-705c6d4c19fc27fd75afd80962bd7ea9-4f928-bj4xc 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 08:00:43 MarkDuplicates Start of doWork freeMemory: 105828960; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 08:00:43 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 08:00:43 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 08:00:48 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:8,356,099
INFO 2026-06-08 08:00:48 MarkDuplicates Tracking 3230 as yet unmatched pairs. 46 records in RAM.
INFO 2026-06-08 08:00:51 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: chr1:13,780,609
INFO 2026-06-08 08:00:51 MarkDuplicates Tracking 6303 as yet unmatched pairs. 230 records in RAM.
INFO 2026-06-08 08:00:54 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 2s. Last read position: chr1:19,906,548
INFO 2026-06-08 08:00:54 MarkDuplicates Tracking 8889 as yet unmatched pairs. 3 records in RAM.
INFO 2026-06-08 08:00:56 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 2s. Last read position: chr1:24,535,126
INFO 2026-06-08 08:00:56 MarkDuplicates Tracking 11876 as yet unmatched pairs. 14 records in RAM.
INFO 2026-06-08 08:00:59 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: chr1:28,329,148
INFO 2026-06-08 08:00:59 MarkDuplicates Tracking 14606 as yet unmatched pairs. 5 records in RAM.
INFO 2026-06-08 08:01:01 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr1:35,841,301
INFO 2026-06-08 08:01:01 MarkDuplicates Tracking 17603 as yet unmatched pairs. 34 records in RAM.
INFO 2026-06-08 08:01:04 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 2s. Last read position: chr1:40,258,256
INFO 2026-06-08 08:01:04 MarkDuplicates Tracking 20383 as yet unmatched pairs. 21 records in RAM.
INFO 2026-06-08 08:01:06 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 2s. Last read position: chr1:46,716,324
INFO 2026-06-08 08:01:06 MarkDuplicates Tracking 23331 as yet unmatched pairs. 182 records in RAM.
INFO 2026-06-08 08:01:09 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 2s. Last read position: chr1:70,250,721
INFO 2026-06-08 08:01:09 MarkDuplicates Tracking 25998 as yet unmatched pairs. 176 records in RAM.
INFO 2026-06-08 08:01:11 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 2s. Last read position: chr1:100,911,097
INFO 2026-06-08 08:01:11 MarkDuplicates Tracking 28460 as yet unmatched pairs. 98 records in RAM.
INFO 2026-06-08 08:01:14 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 2s. Last read position: chr1:114,402,762
INFO 2026-06-08 08:01:14 MarkDuplicates Tracking 31020 as yet unmatched pairs. 70 records in RAM.
INFO 2026-06-08 08:01:16 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 2s. Last read position: chr1:120,519,316
INFO 2026-06-08 08:01:16 MarkDuplicates Tracking 33286 as yet unmatched pairs. 6 records in RAM.
INFO 2026-06-08 08:01:18 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 1s. Last read position: chr1:146,164,751
INFO 2026-06-08 08:01:18 MarkDuplicates Tracking 35191 as yet unmatched pairs. 661 records in RAM.
INFO 2026-06-08 08:01:20 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 1s. Last read position: chr1:149,463,661
INFO 2026-06-08 08:01:20 MarkDuplicates Tracking 35653 as yet unmatched pairs. 79 records in RAM.
INFO 2026-06-08 08:01:22 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 2s. Last read position: chr1:151,315,642
INFO 2026-06-08 08:01:22 MarkDuplicates Tracking 37964 as yet unmatched pairs. 135 records in RAM.
INFO 2026-06-08 08:01:24 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 2s. Last read position: chr1:154,246,288
INFO 2026-06-08 08:01:24 MarkDuplicates Tracking 40420 as yet unmatched pairs. 71 records in RAM.
INFO 2026-06-08 08:01:27 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chr1:155,766,336
INFO 2026-06-08 08:01:27 MarkDuplicates Tracking 43067 as yet unmatched pairs. 123 records in RAM.
INFO 2026-06-08 08:01:29 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 1s. Last read position: chr1:159,015,919
INFO 2026-06-08 08:01:29 MarkDuplicates Tracking 46116 as yet unmatched pairs. 239 records in RAM.
INFO 2026-06-08 08:01:31 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 1s. Last read position: chr1:161,210,638
INFO 2026-06-08 08:01:31 MarkDuplicates Tracking 48727 as yet unmatched pairs. 9 records in RAM.
INFO 2026-06-08 08:01:33 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 1s. Last read position: chr1:171,557,550
INFO 2026-06-08 08:01:33 MarkDuplicates Tracking 51930 as yet unmatched pairs. 756 records in RAM.
INFO 2026-06-08 08:01:35 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 2s. Last read position: chr1:183,023,991
INFO 2026-06-08 08:01:35 MarkDuplicates Tracking 53880 as yet unmatched pairs. 22 records in RAM.
INFO 2026-06-08 08:01:37 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 2s. Last read position: chr1:198,639,265
INFO 2026-06-08 08:01:37 MarkDuplicates Tracking 58106 as yet unmatched pairs. 1805 records in RAM.
INFO 2026-06-08 08:01:39 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 1s. Last read position: chr1:204,429,970
INFO 2026-06-08 08:01:39 MarkDuplicates Tracking 59237 as yet unmatched pairs. 83 records in RAM.
INFO 2026-06-08 08:01:41 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 1s. Last read position: chr1:209,762,538
INFO 2026-06-08 08:01:41 MarkDuplicates Tracking 61743 as yet unmatched pairs. 51 records in RAM.
INFO 2026-06-08 08:01:42 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 1s. Last read position: chr1:228,272,080
INFO 2026-06-08 08:01:42 MarkDuplicates Tracking 64373 as yet unmatched pairs. 37 records in RAM.
INFO 2026-06-08 08:01:44 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 2s. Last read position: chr1:244,856,748
INFO 2026-06-08 08:01:44 MarkDuplicates Tracking 67372 as yet unmatched pairs. 99 records in RAM.
INFO 2026-06-08 08:01:47 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 3s. Last read position: chr2:23,869,727
INFO 2026-06-08 08:01:47 MarkDuplicates Tracking 70021 as yet unmatched pairs. 69752 records in RAM.
INFO 2026-06-08 08:01:50 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 2s. Last read position: chr2:30,231,652
INFO 2026-06-08 08:01:50 MarkDuplicates Tracking 73334 as yet unmatched pairs. 73055 records in RAM.
INFO 2026-06-08 08:01:52 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,264
INFO 2026-06-08 08:01:52 MarkDuplicates Tracking 214666 as yet unmatched pairs. 66530 records in RAM.
INFO 2026-06-08 08:01:55 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,406
INFO 2026-06-08 08:01:55 MarkDuplicates Tracking 603477 as yet unmatched pairs. 46309 records in RAM.
INFO 2026-06-08 08:01:58 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 2s. Last read position: chr2:40,164,974
INFO 2026-06-08 08:01:58 MarkDuplicates Tracking 641507 as yet unmatched pairs. 43176 records in RAM.
INFO 2026-06-08 08:02:01 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 3s. Last read position: chr2:43,571,821
INFO 2026-06-08 08:02:01 MarkDuplicates Tracking 639325 as yet unmatched pairs. 40986 records in RAM.
INFO 2026-06-08 08:02:04 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 2s. Last read position: chr2:55,418,881
INFO 2026-06-08 08:02:04 MarkDuplicates Tracking 635875 as yet unmatched pairs. 37529 records in RAM.
INFO 2026-06-08 08:02:06 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 2s. Last read position: chr2:70,087,727
INFO 2026-06-08 08:02:06 MarkDuplicates Tracking 633350 as yet unmatched pairs. 34992 records in RAM.
INFO 2026-06-08 08:02:08 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 2s. Last read position: chr2:85,623,659
INFO 2026-06-08 08:02:08 MarkDuplicates Tracking 630407 as yet unmatched pairs. 32044 records in RAM.
INFO 2026-06-08 08:02:10 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 2s. Last read position: chr2:97,245,447
INFO 2026-06-08 08:02:10 MarkDuplicates Tracking 628295 as yet unmatched pairs. 29925 records in RAM.
INFO 2026-06-08 08:02:13 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 2s. Last read position: chr2:108,755,195
INFO 2026-06-08 08:02:13 MarkDuplicates Tracking 626239 as yet unmatched pairs. 27860 records in RAM.
INFO 2026-06-08 08:02:15 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 2s. Last read position: chr2:113,197,750
INFO 2026-06-08 08:02:15 MarkDuplicates Tracking 624256 as yet unmatched pairs. 25876 records in RAM.
INFO 2026-06-08 08:02:18 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 2s. Last read position: chr2:136,115,405
INFO 2026-06-08 08:02:18 MarkDuplicates Tracking 622103 as yet unmatched pairs. 23720 records in RAM.
INFO 2026-06-08 08:02:20 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 2s. Last read position: chr2:168,140,738
INFO 2026-06-08 08:02:20 MarkDuplicates Tracking 618851 as yet unmatched pairs. 20446 records in RAM.
INFO 2026-06-08 08:02:22 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 2s. Last read position: chr2:178,553,738
INFO 2026-06-08 08:02:22 MarkDuplicates Tracking 616200 as yet unmatched pairs. 17785 records in RAM.
INFO 2026-06-08 08:02:26 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 4s. Last read position: chr2:178,652,304
INFO 2026-06-08 08:02:26 MarkDuplicates Tracking 614285 as yet unmatched pairs. 15868 records in RAM.
INFO 2026-06-08 08:02:29 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 3s. Last read position: chr2:178,759,022
INFO 2026-06-08 08:02:29 MarkDuplicates Tracking 612061 as yet unmatched pairs. 13632 records in RAM.
INFO 2026-06-08 08:02:32 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 2s. Last read position: chr2:197,392,445
INFO 2026-06-08 08:02:32 MarkDuplicates Tracking 609589 as yet unmatched pairs. 11143 records in RAM.
INFO 2026-06-08 08:02:35 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 3s. Last read position: chr2:208,339,423
INFO 2026-06-08 08:02:35 MarkDuplicates Tracking 606605 as yet unmatched pairs. 8159 records in RAM.
INFO 2026-06-08 08:02:37 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 2s. Last read position: chr2:224,816,663
INFO 2026-06-08 08:02:37 MarkDuplicates Tracking 603880 as yet unmatched pairs. 5423 records in RAM.
INFO 2026-06-08 08:02:40 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 2s. Last read position: chr2:233,170,506
INFO 2026-06-08 08:02:40 MarkDuplicates Tracking 601191 as yet unmatched pairs. 2725 records in RAM.
INFO 2026-06-08 08:02:43 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 2s. Last read position: chr3:5,211,117
INFO 2026-06-08 08:02:43 MarkDuplicates Tracking 597986 as yet unmatched pairs. 34380 records in RAM.
INFO 2026-06-08 08:02:45 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 2s. Last read position: chr3:14,198,054
INFO 2026-06-08 08:02:45 MarkDuplicates Tracking 594768 as yet unmatched pairs. 31154 records in RAM.
INFO 2026-06-08 08:02:49 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 3s. Last read position: chr3:36,833,621
INFO 2026-06-08 08:02:49 MarkDuplicates Tracking 592097 as yet unmatched pairs. 28466 records in RAM.
INFO 2026-06-08 08:02:51 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 2s. Last read position: chr3:45,955,275
INFO 2026-06-08 08:02:51 MarkDuplicates Tracking 589315 as yet unmatched pairs. 25675 records in RAM.
INFO 2026-06-08 08:02:54 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 2s. Last read position: chr3:49,006,700
INFO 2026-06-08 08:02:54 MarkDuplicates Tracking 586480 as yet unmatched pairs. 22838 records in RAM.
INFO 2026-06-08 08:02:57 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 3s. Last read position: chr3:51,993,898
INFO 2026-06-08 08:02:57 MarkDuplicates Tracking 583656 as yet unmatched pairs. 20011 records in RAM.
INFO 2026-06-08 08:03:00 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 2s. Last read position: chr3:63,996,153
INFO 2026-06-08 08:03:00 MarkDuplicates Tracking 580837 as yet unmatched pairs. 17183 records in RAM.
INFO 2026-06-08 08:03:02 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 2s. Last read position: chr3:108,688,886
INFO 2026-06-08 08:03:02 MarkDuplicates Tracking 578063 as yet unmatched pairs. 14382 records in RAM.
INFO 2026-06-08 08:03:05 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 2s. Last read position: chr3:122,700,627
INFO 2026-06-08 08:03:05 MarkDuplicates Tracking 575874 as yet unmatched pairs. 12181 records in RAM.
INFO 2026-06-08 08:03:07 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 2s. Last read position: chr3:133,612,482
INFO 2026-06-08 08:03:07 MarkDuplicates Tracking 572688 as yet unmatched pairs. 8981 records in RAM.
INFO 2026-06-08 08:03:11 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 3s. Last read position: chr3:158,822,026
INFO 2026-06-08 08:03:11 MarkDuplicates Tracking 569795 as yet unmatched pairs. 6082 records in RAM.
INFO 2026-06-08 08:03:13 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 2s. Last read position: chr3:184,317,474
INFO 2026-06-08 08:03:13 MarkDuplicates Tracking 567147 as yet unmatched pairs. 3415 records in RAM.
INFO 2026-06-08 08:03:16 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 2s. Last read position: chr3:196,827,255
INFO 2026-06-08 08:03:16 MarkDuplicates Tracking 564479 as yet unmatched pairs. 739 records in RAM.
INFO 2026-06-08 08:03:19 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 2s. Last read position: chr4:2,908,513
INFO 2026-06-08 08:03:19 MarkDuplicates Tracking 561388 as yet unmatched pairs. 16413 records in RAM.
INFO 2026-06-08 08:03:22 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 3s. Last read position: chr4:25,847,506
INFO 2026-06-08 08:03:22 MarkDuplicates Tracking 559030 as yet unmatched pairs. 14051 records in RAM.
INFO 2026-06-08 08:03:25 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 2s. Last read position: chr4:55,444,714
INFO 2026-06-08 08:03:25 MarkDuplicates Tracking 555870 as yet unmatched pairs. 10886 records in RAM.
INFO 2026-06-08 08:03:27 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 2s. Last read position: chr4:82,355,306
INFO 2026-06-08 08:03:27 MarkDuplicates Tracking 553523 as yet unmatched pairs. 8535 records in RAM.
INFO 2026-06-08 08:03:29 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 2s. Last read position: chr4:102,607,149
INFO 2026-06-08 08:03:29 MarkDuplicates Tracking 550737 as yet unmatched pairs. 5745 records in RAM.
INFO 2026-06-08 08:03:32 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 2s. Last read position: chr4:140,622,181
INFO 2026-06-08 08:03:32 MarkDuplicates Tracking 548395 as yet unmatched pairs. 3398 records in RAM.
INFO 2026-06-08 08:03:35 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 3s. Last read position: chr4:173,318,507
INFO 2026-06-08 08:03:35 MarkDuplicates Tracking 545693 as yet unmatched pairs. 682 records in RAM.
INFO 2026-06-08 08:03:37 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 2s. Last read position: chr5:14,498,229
INFO 2026-06-08 08:03:37 MarkDuplicates Tracking 542984 as yet unmatched pairs. 35229 records in RAM.
INFO 2026-06-08 08:03:40 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 2s. Last read position: chr5:40,981,463
INFO 2026-06-08 08:03:40 MarkDuplicates Tracking 540160 as yet unmatched pairs. 32396 records in RAM.
INFO 2026-06-08 08:03:42 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 2s. Last read position: chr5:69,626,701
INFO 2026-06-08 08:03:42 MarkDuplicates Tracking 537520 as yet unmatched pairs. 29753 records in RAM.
INFO 2026-06-08 08:03:45 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 2s. Last read position: chr5:83,540,110
INFO 2026-06-08 08:03:45 MarkDuplicates Tracking 535622 as yet unmatched pairs. 27847 records in RAM.
INFO 2026-06-08 08:03:48 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 3s. Last read position: chr5:119,166,701
INFO 2026-06-08 08:03:48 MarkDuplicates Tracking 533130 as yet unmatched pairs. 25329 records in RAM.
INFO 2026-06-08 08:03:50 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 2s. Last read position: chr5:138,392,032
INFO 2026-06-08 08:03:50 MarkDuplicates Tracking 530302 as yet unmatched pairs. 22500 records in RAM.
INFO 2026-06-08 08:03:53 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 2s. Last read position: chr5:144,165,573
INFO 2026-06-08 08:03:53 MarkDuplicates Tracking 527639 as yet unmatched pairs. 19785 records in RAM.
INFO 2026-06-08 08:03:55 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 2s. Last read position: chr5:150,402,205
INFO 2026-06-08 08:03:55 MarkDuplicates Tracking 545962 as yet unmatched pairs. 38107 records in RAM.
INFO 2026-06-08 08:03:58 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 3s. Last read position: chr5:150,405,117
INFO 2026-06-08 08:03:58 MarkDuplicates Tracking 532449 as yet unmatched pairs. 24588 records in RAM.
INFO 2026-06-08 08:04:01 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 2s. Last read position: chr5:150,407,246
INFO 2026-06-08 08:04:01 MarkDuplicates Tracking 524138 as yet unmatched pairs. 16264 records in RAM.
INFO 2026-06-08 08:04:03 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 2s. Last read position: chr5:157,489,123
INFO 2026-06-08 08:04:03 MarkDuplicates Tracking 515795 as yet unmatched pairs. 7921 records in RAM.
INFO 2026-06-08 08:04:05 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 2s. Last read position: chr5:172,935,247
INFO 2026-06-08 08:04:05 MarkDuplicates Tracking 513237 as yet unmatched pairs. 5359 records in RAM.
INFO 2026-06-08 08:04:08 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 2s. Last read position: chr5:179,733,122
INFO 2026-06-08 08:04:08 MarkDuplicates Tracking 510536 as yet unmatched pairs. 2657 records in RAM.
INFO 2026-06-08 08:04:11 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 3s. Last read position: chr6:7,181,223
INFO 2026-06-08 08:04:11 MarkDuplicates Tracking 507082 as yet unmatched pairs. 36981 records in RAM.
INFO 2026-06-08 08:04:13 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 2s. Last read position: chr6:26,027,095
INFO 2026-06-08 08:04:13 MarkDuplicates Tracking 504268 as yet unmatched pairs. 34156 records in RAM.
INFO 2026-06-08 08:04:16 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 2s. Last read position: chr6:29,889,363
INFO 2026-06-08 08:04:16 MarkDuplicates Tracking 501754 as yet unmatched pairs. 31640 records in RAM.
INFO 2026-06-08 08:04:19 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 2s. Last read position: chr6:31,355,375
INFO 2026-06-08 08:04:19 MarkDuplicates Tracking 499319 as yet unmatched pairs. 29196 records in RAM.
INFO 2026-06-08 08:04:21 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 2s. Last read position: chr6:32,043,256
INFO 2026-06-08 08:04:21 MarkDuplicates Tracking 495707 as yet unmatched pairs. 25582 records in RAM.
INFO 2026-06-08 08:04:23 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 2s. Last read position: chr6:32,978,379
INFO 2026-06-08 08:04:23 MarkDuplicates Tracking 493119 as yet unmatched pairs. 22990 records in RAM.
INFO 2026-06-08 08:04:26 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 2s. Last read position: chr6:34,870,931
INFO 2026-06-08 08:04:26 MarkDuplicates Tracking 490108 as yet unmatched pairs. 19977 records in RAM.
INFO 2026-06-08 08:04:28 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 2s. Last read position: chr6:43,171,834
INFO 2026-06-08 08:04:28 MarkDuplicates Tracking 487079 as yet unmatched pairs. 16944 records in RAM.
INFO 2026-06-08 08:04:31 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 2s. Last read position: chr6:73,055,576
INFO 2026-06-08 08:04:31 MarkDuplicates Tracking 484267 as yet unmatched pairs. 14131 records in RAM.
INFO 2026-06-08 08:04:33 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 2s. Last read position: chr6:89,951,379
INFO 2026-06-08 08:04:33 MarkDuplicates Tracking 481642 as yet unmatched pairs. 11501 records in RAM.
INFO 2026-06-08 08:04:36 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 2s. Last read position: chr6:116,399,400
INFO 2026-06-08 08:04:36 MarkDuplicates Tracking 479042 as yet unmatched pairs. 8884 records in RAM.
INFO 2026-06-08 08:04:38 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 2s. Last read position: chr6:143,941,929
INFO 2026-06-08 08:04:38 MarkDuplicates Tracking 476530 as yet unmatched pairs. 6364 records in RAM.
INFO 2026-06-08 08:04:40 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 2s. Last read position: chr6:156,901,469
INFO 2026-06-08 08:04:40 MarkDuplicates Tracking 473647 as yet unmatched pairs. 3473 records in RAM.
INFO 2026-06-08 08:04:42 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 1s. Last read position: chr6:169,723,818
INFO 2026-06-08 08:04:42 MarkDuplicates Tracking 470481 as yet unmatched pairs. 293 records in RAM.
INFO 2026-06-08 08:04:44 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 2s. Last read position: chr7:5,528,106
INFO 2026-06-08 08:04:44 MarkDuplicates Tracking 469584 as yet unmatched pairs. 31569 records in RAM.
INFO 2026-06-08 08:04:46 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 1s. Last read position: chr7:19,117,190
INFO 2026-06-08 08:04:46 MarkDuplicates Tracking 464251 as yet unmatched pairs. 26219 records in RAM.
INFO 2026-06-08 08:04:47 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 1s. Last read position: chr7:44,003,745
INFO 2026-06-08 08:04:47 MarkDuplicates Tracking 461576 as yet unmatched pairs. 23542 records in RAM.
INFO 2026-06-08 08:04:50 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 2s. Last read position: chr7:65,198,438
INFO 2026-06-08 08:04:50 MarkDuplicates Tracking 458685 as yet unmatched pairs. 20644 records in RAM.
INFO 2026-06-08 08:04:52 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 2s. Last read position: chr7:74,849,610
INFO 2026-06-08 08:04:52 MarkDuplicates Tracking 457061 as yet unmatched pairs. 19017 records in RAM.
INFO 2026-06-08 08:04:54 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 2s. Last read position: chr7:87,184,550
INFO 2026-06-08 08:04:54 MarkDuplicates Tracking 455400 as yet unmatched pairs. 17352 records in RAM.
INFO 2026-06-08 08:04:57 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 2s. Last read position: chr7:98,953,247
INFO 2026-06-08 08:04:57 MarkDuplicates Tracking 452814 as yet unmatched pairs. 14762 records in RAM.
INFO 2026-06-08 08:04:59 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 2s. Last read position: chr7:100,886,848
INFO 2026-06-08 08:04:59 MarkDuplicates Tracking 449684 as yet unmatched pairs. 11626 records in RAM.
INFO 2026-06-08 08:05:00 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 1s. Last read position: chr7:102,777,248
INFO 2026-06-08 08:05:00 MarkDuplicates Tracking 448070 as yet unmatched pairs. 10000 records in RAM.
INFO 2026-06-08 08:05:02 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 1s. Last read position: chr7:128,085,710
INFO 2026-06-08 08:05:02 MarkDuplicates Tracking 445650 as yet unmatched pairs. 7578 records in RAM.
INFO 2026-06-08 08:05:03 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 1s. Last read position: chr7:140,808,026
INFO 2026-06-08 08:05:03 MarkDuplicates Tracking 442980 as yet unmatched pairs. 4897 records in RAM.
INFO 2026-06-08 08:05:05 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 1s. Last read position: chr7:150,804,879
INFO 2026-06-08 08:05:05 MarkDuplicates Tracking 440313 as yet unmatched pairs. 2222 records in RAM.
INFO 2026-06-08 08:05:07 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 2s. Last read position: chr8:9,748,180
INFO 2026-06-08 08:05:07 MarkDuplicates Tracking 437280 as yet unmatched pairs. 21422 records in RAM.
INFO 2026-06-08 08:05:09 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 1s. Last read position: chr8:24,335,602
INFO 2026-06-08 08:05:09 MarkDuplicates Tracking 434422 as yet unmatched pairs. 18558 records in RAM.
INFO 2026-06-08 08:05:11 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr8:38,787,601
INFO 2026-06-08 08:05:11 MarkDuplicates Tracking 431807 as yet unmatched pairs. 15942 records in RAM.
INFO 2026-06-08 08:05:12 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr8:59,018,406
INFO 2026-06-08 08:05:12 MarkDuplicates Tracking 428710 as yet unmatched pairs. 12839 records in RAM.
INFO 2026-06-08 08:05:14 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 1s. Last read position: chr8:94,731,461
INFO 2026-06-08 08:05:14 MarkDuplicates Tracking 426275 as yet unmatched pairs. 10396 records in RAM.
INFO 2026-06-08 08:05:16 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 1s. Last read position: chr8:108,228,325
INFO 2026-06-08 08:05:16 MarkDuplicates Tracking 423800 as yet unmatched pairs. 7917 records in RAM.
INFO 2026-06-08 08:05:17 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 1s. Last read position: chr8:140,879,510
INFO 2026-06-08 08:05:17 MarkDuplicates Tracking 420978 as yet unmatched pairs. 5086 records in RAM.
INFO 2026-06-08 08:05:20 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 2s. Last read position: chr8:144,179,492
INFO 2026-06-08 08:05:20 MarkDuplicates Tracking 417306 as yet unmatched pairs. 1409 records in RAM.
INFO 2026-06-08 08:05:22 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 2s. Last read position: chr9:6,460,713
INFO 2026-06-08 08:05:22 MarkDuplicates Tracking 414437 as yet unmatched pairs. 27308 records in RAM.
INFO 2026-06-08 08:05:24 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 1s. Last read position: chr9:35,032,544
INFO 2026-06-08 08:05:24 MarkDuplicates Tracking 411512 as yet unmatched pairs. 24381 records in RAM.
INFO 2026-06-08 08:05:26 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 1s. Last read position: chr9:37,020,696
INFO 2026-06-08 08:05:26 MarkDuplicates Tracking 408767 as yet unmatched pairs. 21625 records in RAM.
INFO 2026-06-08 08:05:28 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 1s. Last read position: chr9:89,379,432
INFO 2026-06-08 08:05:28 MarkDuplicates Tracking 406394 as yet unmatched pairs. 19252 records in RAM.
INFO 2026-06-08 08:05:29 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 1s. Last read position: chr9:107,283,684
INFO 2026-06-08 08:05:29 MarkDuplicates Tracking 403431 as yet unmatched pairs. 16284 records in RAM.
INFO 2026-06-08 08:05:31 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 2s. Last read position: chr9:115,086,437
INFO 2026-06-08 08:05:31 MarkDuplicates Tracking 400613 as yet unmatched pairs. 13465 records in RAM.
INFO 2026-06-08 08:05:34 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 2s. Last read position: chr9:125,239,021
INFO 2026-06-08 08:05:34 MarkDuplicates Tracking 397976 as yet unmatched pairs. 10817 records in RAM.
INFO 2026-06-08 08:05:36 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 2s. Last read position: chr9:129,858,537
INFO 2026-06-08 08:05:36 MarkDuplicates Tracking 394943 as yet unmatched pairs. 7781 records in RAM.
INFO 2026-06-08 08:05:38 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 2s. Last read position: chr9:133,031,048
INFO 2026-06-08 08:05:38 MarkDuplicates Tracking 392241 as yet unmatched pairs. 5070 records in RAM.
INFO 2026-06-08 08:05:40 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 2s. Last read position: chr9:136,979,011
INFO 2026-06-08 08:05:40 MarkDuplicates Tracking 389212 as yet unmatched pairs. 2040 records in RAM.
INFO 2026-06-08 08:05:43 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 2s. Last read position: chr10:7,367,652
INFO 2026-06-08 08:05:43 MarkDuplicates Tracking 386033 as yet unmatched pairs. 21476 records in RAM.
INFO 2026-06-08 08:05:45 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 2s. Last read position: chr10:28,608,329
INFO 2026-06-08 08:05:45 MarkDuplicates Tracking 383470 as yet unmatched pairs. 18908 records in RAM.
INFO 2026-06-08 08:05:47 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 2s. Last read position: chr10:45,910,607
INFO 2026-06-08 08:05:47 MarkDuplicates Tracking 380840 as yet unmatched pairs. 16277 records in RAM.
INFO 2026-06-08 08:05:50 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 2s. Last read position: chr10:59,792,966
INFO 2026-06-08 08:05:50 MarkDuplicates Tracking 378693 as yet unmatched pairs. 14128 records in RAM.
INFO 2026-06-08 08:05:53 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 2s. Last read position: chr10:73,766,099
INFO 2026-06-08 08:05:53 MarkDuplicates Tracking 375783 as yet unmatched pairs. 11212 records in RAM.
INFO 2026-06-08 08:05:55 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 2s. Last read position: chr10:89,417,328
INFO 2026-06-08 08:05:55 MarkDuplicates Tracking 373346 as yet unmatched pairs. 8767 records in RAM.
INFO 2026-06-08 08:05:57 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 2s. Last read position: chr10:98,435,691
INFO 2026-06-08 08:05:57 MarkDuplicates Tracking 370736 as yet unmatched pairs. 6153 records in RAM.
INFO 2026-06-08 08:05:59 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 2s. Last read position: chr10:111,016,878
INFO 2026-06-08 08:05:59 MarkDuplicates Tracking 367707 as yet unmatched pairs. 3111 records in RAM.
INFO 2026-06-08 08:06:02 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 2s. Last read position: chr10:133,267,972
INFO 2026-06-08 08:06:02 MarkDuplicates Tracking 365099 as yet unmatched pairs. 499 records in RAM.
INFO 2026-06-08 08:06:04 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 2s. Last read position: chr11:2,396,680
INFO 2026-06-08 08:06:04 MarkDuplicates Tracking 361953 as yet unmatched pairs. 40533 records in RAM.
INFO 2026-06-08 08:06:06 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 2s. Last read position: chr11:10,799,616
INFO 2026-06-08 08:06:06 MarkDuplicates Tracking 358942 as yet unmatched pairs. 37521 records in RAM.
INFO 2026-06-08 08:06:09 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 2s. Last read position: chr11:43,404,093
INFO 2026-06-08 08:06:09 MarkDuplicates Tracking 356077 as yet unmatched pairs. 34654 records in RAM.
INFO 2026-06-08 08:06:11 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 2s. Last read position: chr11:58,527,641
INFO 2026-06-08 08:06:11 MarkDuplicates Tracking 353088 as yet unmatched pairs. 31660 records in RAM.
INFO 2026-06-08 08:06:14 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 2s. Last read position: chr11:60,469,609
INFO 2026-06-08 08:06:14 MarkDuplicates Tracking 352994 as yet unmatched pairs. 31566 records in RAM.
INFO 2026-06-08 08:06:16 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 2s. Last read position: chr11:62,531,023
INFO 2026-06-08 08:06:16 MarkDuplicates Tracking 348396 as yet unmatched pairs. 26963 records in RAM.
INFO 2026-06-08 08:06:18 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 2s. Last read position: chr11:64,730,101
INFO 2026-06-08 08:06:18 MarkDuplicates Tracking 345311 as yet unmatched pairs. 23872 records in RAM.
INFO 2026-06-08 08:06:21 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 2s. Last read position: chr11:65,628,590
INFO 2026-06-08 08:06:21 MarkDuplicates Tracking 341758 as yet unmatched pairs. 20318 records in RAM.
INFO 2026-06-08 08:06:23 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 2s. Last read position: chr11:67,301,598
INFO 2026-06-08 08:06:23 MarkDuplicates Tracking 338379 as yet unmatched pairs. 16938 records in RAM.
INFO 2026-06-08 08:06:25 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 2s. Last read position: chr11:72,009,080
INFO 2026-06-08 08:06:25 MarkDuplicates Tracking 334959 as yet unmatched pairs. 13515 records in RAM.
INFO 2026-06-08 08:06:27 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 2s. Last read position: chr11:77,162,148
INFO 2026-06-08 08:06:27 MarkDuplicates Tracking 331784 as yet unmatched pairs. 10339 records in RAM.
INFO 2026-06-08 08:06:29 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 2s. Last read position: chr11:102,324,611
INFO 2026-06-08 08:06:29 MarkDuplicates Tracking 329658 as yet unmatched pairs. 8203 records in RAM.
INFO 2026-06-08 08:06:32 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 2s. Last read position: chr11:117,986,412
INFO 2026-06-08 08:06:32 MarkDuplicates Tracking 326650 as yet unmatched pairs. 5191 records in RAM.
INFO 2026-06-08 08:06:34 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 2s. Last read position: chr11:120,469,330
INFO 2026-06-08 08:06:34 MarkDuplicates Tracking 323751 as yet unmatched pairs. 2289 records in RAM.
INFO 2026-06-08 08:06:36 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 2s. Last read position: chr12:754,107
INFO 2026-06-08 08:06:36 MarkDuplicates Tracking 321186 as yet unmatched pairs. 37650 records in RAM.
INFO 2026-06-08 08:06:39 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 2s. Last read position: chr12:6,936,938
INFO 2026-06-08 08:06:39 MarkDuplicates Tracking 318276 as yet unmatched pairs. 34740 records in RAM.
INFO 2026-06-08 08:06:41 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 2s. Last read position: chr12:11,869,521
INFO 2026-06-08 08:06:41 MarkDuplicates Tracking 316220 as yet unmatched pairs. 32674 records in RAM.
INFO 2026-06-08 08:06:43 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 2s. Last read position: chr12:30,734,970
INFO 2026-06-08 08:06:43 MarkDuplicates Tracking 313069 as yet unmatched pairs. 29518 records in RAM.
INFO 2026-06-08 08:06:46 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 2s. Last read position: chr12:48,679,738
INFO 2026-06-08 08:06:46 MarkDuplicates Tracking 310542 as yet unmatched pairs. 26987 records in RAM.
INFO 2026-06-08 08:06:47 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 1s. Last read position: chr12:50,780,191
INFO 2026-06-08 08:06:47 MarkDuplicates Tracking 307916 as yet unmatched pairs. 24361 records in RAM.
INFO 2026-06-08 08:06:49 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 1s. Last read position: chr12:54,369,951
INFO 2026-06-08 08:06:49 MarkDuplicates Tracking 305262 as yet unmatched pairs. 21704 records in RAM.
INFO 2026-06-08 08:06:50 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 1s. Last read position: chr12:56,712,826
INFO 2026-06-08 08:06:50 MarkDuplicates Tracking 303341 as yet unmatched pairs. 19782 records in RAM.
INFO 2026-06-08 08:06:52 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 1s. Last read position: chr12:57,514,998
INFO 2026-06-08 08:06:52 MarkDuplicates Tracking 299922 as yet unmatched pairs. 16361 records in RAM.
INFO 2026-06-08 08:06:54 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:06:09s. Time for last 1,000,000: 2s. Last read position: chr12:75,481,047
INFO 2026-06-08 08:06:54 MarkDuplicates Tracking 297255 as yet unmatched pairs. 13694 records in RAM.
INFO 2026-06-08 08:06:56 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 2s. Last read position: chr12:103,941,524
INFO 2026-06-08 08:06:56 MarkDuplicates Tracking 294571 as yet unmatched pairs. 11009 records in RAM.
INFO 2026-06-08 08:06:58 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 2s. Last read position: chr12:112,141,053
INFO 2026-06-08 08:06:58 MarkDuplicates Tracking 291848 as yet unmatched pairs. 8276 records in RAM.
INFO 2026-06-08 08:07:00 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 1s. Last read position: chr12:120,737,929
INFO 2026-06-08 08:07:00 MarkDuplicates Tracking 289007 as yet unmatched pairs. 5427 records in RAM.
INFO 2026-06-08 08:07:02 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 1s. Last read position: chr12:124,426,671
INFO 2026-06-08 08:07:02 MarkDuplicates Tracking 286219 as yet unmatched pairs. 2635 records in RAM.
INFO 2026-06-08 08:07:03 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 1s. Last read position: chr13:20,002,861
INFO 2026-06-08 08:07:03 MarkDuplicates Tracking 283791 as yet unmatched pairs. 10989 records in RAM.
INFO 2026-06-08 08:07:05 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 1s. Last read position: chr13:39,013,222
INFO 2026-06-08 08:07:05 MarkDuplicates Tracking 280950 as yet unmatched pairs. 8134 records in RAM.
INFO 2026-06-08 08:07:07 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 1s. Last read position: chr13:49,460,145
INFO 2026-06-08 08:07:07 MarkDuplicates Tracking 277988 as yet unmatched pairs. 5172 records in RAM.
INFO 2026-06-08 08:07:09 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 1s. Last read position: chr13:98,860,433
INFO 2026-06-08 08:07:09 MarkDuplicates Tracking 275368 as yet unmatched pairs. 2545 records in RAM.
INFO 2026-06-08 08:07:11 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 1s. Last read position: chr14:20,407,926
INFO 2026-06-08 08:07:11 MarkDuplicates Tracking 272616 as yet unmatched pairs. 25711 records in RAM.
INFO 2026-06-08 08:07:12 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 1s. Last read position: chr14:24,165,168
INFO 2026-06-08 08:07:12 MarkDuplicates Tracking 269655 as yet unmatched pairs. 22743 records in RAM.
INFO 2026-06-08 08:07:14 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 1s. Last read position: chr14:49,621,683
INFO 2026-06-08 08:07:14 MarkDuplicates Tracking 266904 as yet unmatched pairs. 19990 records in RAM.
INFO 2026-06-08 08:07:16 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:06:31s. Time for last 1,000,000: 1s. Last read position: chr14:64,025,308
INFO 2026-06-08 08:07:16 MarkDuplicates Tracking 264268 as yet unmatched pairs. 17354 records in RAM.
INFO 2026-06-08 08:07:17 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 1s. Last read position: chr14:71,587,899
INFO 2026-06-08 08:07:17 MarkDuplicates Tracking 261521 as yet unmatched pairs. 14598 records in RAM.
INFO 2026-06-08 08:07:19 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 1s. Last read position: chr14:90,263,400
INFO 2026-06-08 08:07:19 MarkDuplicates Tracking 258713 as yet unmatched pairs. 11786 records in RAM.
INFO 2026-06-08 08:07:20 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:06:35s. Time for last 1,000,000: 1s. Last read position: chr14:100,141,735
INFO 2026-06-08 08:07:20 MarkDuplicates Tracking 256013 as yet unmatched pairs. 9075 records in RAM.
INFO 2026-06-08 08:07:22 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 1s. Last read position: chr14:105,583,850
INFO 2026-06-08 08:07:22 MarkDuplicates Tracking 254688 as yet unmatched pairs. 7741 records in RAM.
INFO 2026-06-08 08:07:24 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 1s. Last read position: chr14:105,707,364
INFO 2026-06-08 08:07:24 MarkDuplicates Tracking 253448 as yet unmatched pairs. 6496 records in RAM.
INFO 2026-06-08 08:07:25 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 1s. Last read position: chr14:105,769,707
INFO 2026-06-08 08:07:25 MarkDuplicates Tracking 249344 as yet unmatched pairs. 2390 records in RAM.
INFO 2026-06-08 08:07:27 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 1s. Last read position: chr15:22,607,905
INFO 2026-06-08 08:07:27 MarkDuplicates Tracking 246804 as yet unmatched pairs. 22209 records in RAM.
INFO 2026-06-08 08:07:29 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:06:44s. Time for last 1,000,000: 1s. Last read position: chr15:34,920,332
INFO 2026-06-08 08:07:29 MarkDuplicates Tracking 244647 as yet unmatched pairs. 20049 records in RAM.
INFO 2026-06-08 08:07:31 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:06:47s. Time for last 1,000,000: 2s. Last read position: chr15:42,529,738
INFO 2026-06-08 08:07:31 MarkDuplicates Tracking 241874 as yet unmatched pairs. 17275 records in RAM.
INFO 2026-06-08 08:07:33 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 1s. Last read position: chr15:51,450,263
INFO 2026-06-08 08:07:33 MarkDuplicates Tracking 239138 as yet unmatched pairs. 14539 records in RAM.
INFO 2026-06-08 08:07:35 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 1s. Last read position: chr15:63,069,784
INFO 2026-06-08 08:07:35 MarkDuplicates Tracking 236503 as yet unmatched pairs. 11898 records in RAM.
INFO 2026-06-08 08:07:37 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 2s. Last read position: chr15:70,096,712
INFO 2026-06-08 08:07:37 MarkDuplicates Tracking 233621 as yet unmatched pairs. 9013 records in RAM.
INFO 2026-06-08 08:07:39 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 1s. Last read position: chr15:76,261,165
INFO 2026-06-08 08:07:39 MarkDuplicates Tracking 230664 as yet unmatched pairs. 6054 records in RAM.
INFO 2026-06-08 08:07:40 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 1s. Last read position: chr15:85,579,980
INFO 2026-06-08 08:07:40 MarkDuplicates Tracking 228186 as yet unmatched pairs. 3566 records in RAM.
INFO 2026-06-08 08:07:42 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:06:57s. Time for last 1,000,000: 1s. Last read position: chr15:99,712,647
INFO 2026-06-08 08:07:42 MarkDuplicates Tracking 225245 as yet unmatched pairs. 622 records in RAM.
INFO 2026-06-08 08:07:44 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 1s. Last read position: chr16:2,061,992
INFO 2026-06-08 08:07:44 MarkDuplicates Tracking 221909 as yet unmatched pairs. 40971 records in RAM.
INFO 2026-06-08 08:07:45 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:07:00s. Time for last 1,000,000: 1s. Last read position: chr16:2,766,669
INFO 2026-06-08 08:07:45 MarkDuplicates Tracking 219979 as yet unmatched pairs. 39041 records in RAM.
INFO 2026-06-08 08:07:47 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 2s. Last read position: chr16:8,781,307
INFO 2026-06-08 08:07:47 MarkDuplicates Tracking 215903 as yet unmatched pairs. 34965 records in RAM.
INFO 2026-06-08 08:07:50 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 2s. Last read position: chr16:14,240,252
INFO 2026-06-08 08:07:50 MarkDuplicates Tracking 213168 as yet unmatched pairs. 32229 records in RAM.
INFO 2026-06-08 08:07:51 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 1s. Last read position: chr16:16,337,053
INFO 2026-06-08 08:07:51 MarkDuplicates Tracking 211684 as yet unmatched pairs. 30745 records in RAM.
INFO 2026-06-08 08:07:53 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 1s. Last read position: chr16:19,629,780
INFO 2026-06-08 08:07:53 MarkDuplicates Tracking 210097 as yet unmatched pairs. 29158 records in RAM.
INFO 2026-06-08 08:07:55 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 1s. Last read position: chr16:21,406,519
INFO 2026-06-08 08:07:55 MarkDuplicates Tracking 210269 as yet unmatched pairs. 29330 records in RAM.
INFO 2026-06-08 08:07:57 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:07:12s. Time for last 1,000,000: 2s. Last read position: chr16:21,837,437
INFO 2026-06-08 08:07:57 MarkDuplicates Tracking 209072 as yet unmatched pairs. 28133 records in RAM.
INFO 2026-06-08 08:07:58 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 1s. Last read position: chr16:22,527,842
INFO 2026-06-08 08:07:58 MarkDuplicates Tracking 207618 as yet unmatched pairs. 26679 records in RAM.
INFO 2026-06-08 08:08:00 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:07:15s. Time for last 1,000,000: 1s. Last read position: chr16:22,535,328
INFO 2026-06-08 08:08:00 MarkDuplicates Tracking 207027 as yet unmatched pairs. 26088 records in RAM.
INFO 2026-06-08 08:08:01 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:07:16s. Time for last 1,000,000: 1s. Last read position: chr16:28,724,918
INFO 2026-06-08 08:08:01 MarkDuplicates Tracking 204751 as yet unmatched pairs. 23812 records in RAM.
INFO 2026-06-08 08:08:02 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:07:17s. Time for last 1,000,000: 1s. Last read position: chr16:29,416,205
INFO 2026-06-08 08:08:02 MarkDuplicates Tracking 203885 as yet unmatched pairs. 22946 records in RAM.
INFO 2026-06-08 08:08:04 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:07:19s. Time for last 1,000,000: 1s. Last read position: chr16:29,806,785
INFO 2026-06-08 08:08:04 MarkDuplicates Tracking 202252 as yet unmatched pairs. 21313 records in RAM.
INFO 2026-06-08 08:08:05 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:07:20s. Time for last 1,000,000: 1s. Last read position: chr16:30,225,746
INFO 2026-06-08 08:08:05 MarkDuplicates Tracking 200254 as yet unmatched pairs. 19315 records in RAM.
INFO 2026-06-08 08:08:06 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:07:21s. Time for last 1,000,000: 1s. Last read position: chr16:30,961,363
INFO 2026-06-08 08:08:06 MarkDuplicates Tracking 198182 as yet unmatched pairs. 17241 records in RAM.
INFO 2026-06-08 08:08:08 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:07:23s. Time for last 1,000,000: 1s. Last read position: chr16:50,315,128
INFO 2026-06-08 08:08:08 MarkDuplicates Tracking 195373 as yet unmatched pairs. 14432 records in RAM.
INFO 2026-06-08 08:08:09 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:07:25s. Time for last 1,000,000: 1s. Last read position: chr16:58,526,025
INFO 2026-06-08 08:08:09 MarkDuplicates Tracking 192535 as yet unmatched pairs. 11593 records in RAM.
INFO 2026-06-08 08:08:12 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 2s. Last read position: chr16:68,860,239
INFO 2026-06-08 08:08:12 MarkDuplicates Tracking 189519 as yet unmatched pairs. 8576 records in RAM.
INFO 2026-06-08 08:08:14 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:07:29s. Time for last 1,000,000: 2s. Last read position: chr16:79,594,464
INFO 2026-06-08 08:08:14 MarkDuplicates Tracking 186727 as yet unmatched pairs. 5781 records in RAM.
INFO 2026-06-08 08:08:16 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:07:31s. Time for last 1,000,000: 2s. Last read position: chr16:88,699,037
INFO 2026-06-08 08:08:16 MarkDuplicates Tracking 183549 as yet unmatched pairs. 2603 records in RAM.
INFO 2026-06-08 08:08:19 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:07:34s. Time for last 1,000,000: 2s. Last read position: chr17:1,471,920
INFO 2026-06-08 08:08:19 MarkDuplicates Tracking 180183 as yet unmatched pairs. 44850 records in RAM.
INFO 2026-06-08 08:08:20 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:07:35s. Time for last 1,000,000: 1s. Last read position: chr17:4,142,832
INFO 2026-06-08 08:08:20 MarkDuplicates Tracking 177170 as yet unmatched pairs. 41837 records in RAM.
INFO 2026-06-08 08:08:22 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:07:37s. Time for last 1,000,000: 1s. Last read position: chr17:7,346,897
INFO 2026-06-08 08:08:22 MarkDuplicates Tracking 174200 as yet unmatched pairs. 38867 records in RAM.
INFO 2026-06-08 08:08:23 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:07:38s. Time for last 1,000,000: 1s. Last read position: chr17:8,369,997
INFO 2026-06-08 08:08:23 MarkDuplicates Tracking 171554 as yet unmatched pairs. 36221 records in RAM.
INFO 2026-06-08 08:08:25 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:07:40s. Time for last 1,000,000: 1s. Last read position: chr17:18,671,417
INFO 2026-06-08 08:08:25 MarkDuplicates Tracking 168899 as yet unmatched pairs. 33566 records in RAM.
INFO 2026-06-08 08:08:26 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:07:42s. Time for last 1,000,000: 1s. Last read position: chr17:29,534,224
INFO 2026-06-08 08:08:26 MarkDuplicates Tracking 165973 as yet unmatched pairs. 30633 records in RAM.
INFO 2026-06-08 08:08:28 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:07:43s. Time for last 1,000,000: 1s. Last read position: chr17:35,817,719
INFO 2026-06-08 08:08:28 MarkDuplicates Tracking 164532 as yet unmatched pairs. 29192 records in RAM.
INFO 2026-06-08 08:08:29 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:07:45s. Time for last 1,000,000: 1s. Last read position: chr17:39,184,050
INFO 2026-06-08 08:08:29 MarkDuplicates Tracking 161186 as yet unmatched pairs. 25845 records in RAM.
INFO 2026-06-08 08:08:31 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:07:46s. Time for last 1,000,000: 1s. Last read position: chr17:42,325,016
INFO 2026-06-08 08:08:31 MarkDuplicates Tracking 158561 as yet unmatched pairs. 23220 records in RAM.
INFO 2026-06-08 08:08:33 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:07:48s. Time for last 1,000,000: 1s. Last read position: chr17:45,503,334
INFO 2026-06-08 08:08:33 MarkDuplicates Tracking 155483 as yet unmatched pairs. 20138 records in RAM.
INFO 2026-06-08 08:08:35 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:07:50s. Time for last 1,000,000: 1s. Last read position: chr17:47,924,973
INFO 2026-06-08 08:08:35 MarkDuplicates Tracking 153762 as yet unmatched pairs. 18416 records in RAM.
INFO 2026-06-08 08:08:36 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:07:51s. Time for last 1,000,000: 1s. Last read position: chr17:58,352,085
INFO 2026-06-08 08:08:36 MarkDuplicates Tracking 150620 as yet unmatched pairs. 15273 records in RAM.
INFO 2026-06-08 08:08:39 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:07:54s. Time for last 1,000,000: 2s. Last read position: chr17:64,053,303
INFO 2026-06-08 08:08:39 MarkDuplicates Tracking 147931 as yet unmatched pairs. 12582 records in RAM.
INFO 2026-06-08 08:08:40 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:07:56s. Time for last 1,000,000: 1s. Last read position: chr17:69,043,536
INFO 2026-06-08 08:08:40 MarkDuplicates Tracking 145439 as yet unmatched pairs. 10089 records in RAM.
INFO 2026-06-08 08:08:42 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:07:57s. Time for last 1,000,000: 1s. Last read position: chr17:76,742,004
INFO 2026-06-08 08:08:42 MarkDuplicates Tracking 142285 as yet unmatched pairs. 6934 records in RAM.
INFO 2026-06-08 08:08:43 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:07:59s. Time for last 1,000,000: 1s. Last read position: chr17:80,345,200
INFO 2026-06-08 08:08:43 MarkDuplicates Tracking 139319 as yet unmatched pairs. 3966 records in RAM.
INFO 2026-06-08 08:08:45 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:08:00s. Time for last 1,000,000: 1s. Last read position: chr17:82,441,092
INFO 2026-06-08 08:08:45 MarkDuplicates Tracking 136207 as yet unmatched pairs. 854 records in RAM.
INFO 2026-06-08 08:08:47 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:08:02s. Time for last 1,000,000: 1s. Last read position: chr18:21,574,066
INFO 2026-06-08 08:08:47 MarkDuplicates Tracking 133502 as yet unmatched pairs. 6264 records in RAM.
INFO 2026-06-08 08:08:48 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:08:03s. Time for last 1,000,000: 1s. Last read position: chr18:50,940,291
INFO 2026-06-08 08:08:48 MarkDuplicates Tracking 130882 as yet unmatched pairs. 3642 records in RAM.
INFO 2026-06-08 08:08:50 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 1s. Last read position: chr18:76,980,385
INFO 2026-06-08 08:08:50 MarkDuplicates Tracking 127983 as yet unmatched pairs. 743 records in RAM.
INFO 2026-06-08 08:08:52 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:08:07s. Time for last 1,000,000: 1s. Last read position: chr19:1,116,829
INFO 2026-06-08 08:08:52 MarkDuplicates Tracking 124544 as yet unmatched pairs. 55878 records in RAM.
INFO 2026-06-08 08:08:53 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:08:08s. Time for last 1,000,000: 1s. Last read position: chr19:2,757,762
INFO 2026-06-08 08:08:53 MarkDuplicates Tracking 120934 as yet unmatched pairs. 52267 records in RAM.
INFO 2026-06-08 08:08:55 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:08:10s. Time for last 1,000,000: 1s. Last read position: chr19:6,467,929
INFO 2026-06-08 08:08:55 MarkDuplicates Tracking 117968 as yet unmatched pairs. 49301 records in RAM.
INFO 2026-06-08 08:08:56 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:08:11s. Time for last 1,000,000: 1s. Last read position: chr19:8,471,331
INFO 2026-06-08 08:08:56 MarkDuplicates Tracking 114702 as yet unmatched pairs. 46035 records in RAM.
INFO 2026-06-08 08:08:58 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:08:13s. Time for last 1,000,000: 1s. Last read position: chr19:11,445,430
INFO 2026-06-08 08:08:58 MarkDuplicates Tracking 111550 as yet unmatched pairs. 42883 records in RAM.
INFO 2026-06-08 08:08:59 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:08:14s. Time for last 1,000,000: 1s. Last read position: chr19:14,529,678
INFO 2026-06-08 08:08:59 MarkDuplicates Tracking 108599 as yet unmatched pairs. 39932 records in RAM.
INFO 2026-06-08 08:09:01 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 1s. Last read position: chr19:16,413,786
INFO 2026-06-08 08:09:01 MarkDuplicates Tracking 105640 as yet unmatched pairs. 36972 records in RAM.
INFO 2026-06-08 08:09:03 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:08:18s. Time for last 1,000,000: 1s. Last read position: chr19:18,009,820
INFO 2026-06-08 08:09:03 MarkDuplicates Tracking 102507 as yet unmatched pairs. 33837 records in RAM.
INFO 2026-06-08 08:09:04 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 1s. Last read position: chr19:20,793,782
INFO 2026-06-08 08:09:04 MarkDuplicates Tracking 99159 as yet unmatched pairs. 30488 records in RAM.
INFO 2026-06-08 08:09:06 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 1s. Last read position: chr19:35,732,632
INFO 2026-06-08 08:09:06 MarkDuplicates Tracking 95930 as yet unmatched pairs. 27258 records in RAM.
INFO 2026-06-08 08:09:08 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 2s. Last read position: chr19:39,407,754
INFO 2026-06-08 08:09:08 MarkDuplicates Tracking 93711 as yet unmatched pairs. 25039 records in RAM.
INFO 2026-06-08 08:09:10 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 2s. Last read position: chr19:41,860,799
INFO 2026-06-08 08:09:10 MarkDuplicates Tracking 90271 as yet unmatched pairs. 21598 records in RAM.
INFO 2026-06-08 08:09:12 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:08:27s. Time for last 1,000,000: 2s. Last read position: chr19:42,122,344
INFO 2026-06-08 08:09:12 MarkDuplicates Tracking 87507 as yet unmatched pairs. 18834 records in RAM.
INFO 2026-06-08 08:09:14 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 1s. Last read position: chr19:44,907,822
INFO 2026-06-08 08:09:14 MarkDuplicates Tracking 84562 as yet unmatched pairs. 15886 records in RAM.
INFO 2026-06-08 08:09:15 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:08:30s. Time for last 1,000,000: 1s. Last read position: chr19:47,780,874
INFO 2026-06-08 08:09:15 MarkDuplicates Tracking 81157 as yet unmatched pairs. 12481 records in RAM.
INFO 2026-06-08 08:09:17 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 1s. Last read position: chr19:49,594,986
INFO 2026-06-08 08:09:17 MarkDuplicates Tracking 78006 as yet unmatched pairs. 9330 records in RAM.
INFO 2026-06-08 08:09:19 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 1s. Last read position: chr19:51,573,341
INFO 2026-06-08 08:09:19 MarkDuplicates Tracking 74989 as yet unmatched pairs. 6313 records in RAM.
INFO 2026-06-08 08:09:20 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 1s. Last read position: chr19:54,664,833
INFO 2026-06-08 08:09:20 MarkDuplicates Tracking 72422 as yet unmatched pairs. 3746 records in RAM.
INFO 2026-06-08 08:09:22 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 1s. Last read position: chr19:58,294,783
INFO 2026-06-08 08:09:22 MarkDuplicates Tracking 69339 as yet unmatched pairs. 660 records in RAM.
INFO 2026-06-08 08:09:24 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:08:39s. Time for last 1,000,000: 2s. Last read position: chr20:17,948,895
INFO 2026-06-08 08:09:24 MarkDuplicates Tracking 66466 as yet unmatched pairs. 14200 records in RAM.
INFO 2026-06-08 08:09:27 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:08:42s. Time for last 1,000,000: 2s. Last read position: chr20:35,630,743
INFO 2026-06-08 08:09:27 MarkDuplicates Tracking 63493 as yet unmatched pairs. 11225 records in RAM.
INFO 2026-06-08 08:09:29 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:08:44s. Time for last 1,000,000: 1s. Last read position: chr20:45,363,620
INFO 2026-06-08 08:09:29 MarkDuplicates Tracking 60575 as yet unmatched pairs. 8306 records in RAM.
INFO 2026-06-08 08:09:30 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:08:45s. Time for last 1,000,000: 1s. Last read position: chr20:50,892,987
INFO 2026-06-08 08:09:30 MarkDuplicates Tracking 57892 as yet unmatched pairs. 5623 records in RAM.
INFO 2026-06-08 08:09:32 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:08:47s. Time for last 1,000,000: 1s. Last read position: chr20:62,812,554
INFO 2026-06-08 08:09:32 MarkDuplicates Tracking 54294 as yet unmatched pairs. 2023 records in RAM.
INFO 2026-06-08 08:09:33 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 1s. Last read position: chr21:8,254,531
INFO 2026-06-08 08:09:33 MarkDuplicates Tracking 51292 as yet unmatched pairs. 7851 records in RAM.
INFO 2026-06-08 08:09:34 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:08:50s. Time for last 1,000,000: 1s. Last read position: chr21:29,326,287
INFO 2026-06-08 08:09:34 MarkDuplicates Tracking 49676 as yet unmatched pairs. 6231 records in RAM.
INFO 2026-06-08 08:09:36 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 1s. Last read position: chr21:39,200,220
INFO 2026-06-08 08:09:36 MarkDuplicates Tracking 46761 as yet unmatched pairs. 3315 records in RAM.
INFO 2026-06-08 08:09:38 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:08:53s. Time for last 1,000,000: 1s. Last read position: chr21:46,416,148
INFO 2026-06-08 08:09:38 MarkDuplicates Tracking 43980 as yet unmatched pairs. 534 records in RAM.
INFO 2026-06-08 08:09:40 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:08:55s. Time for last 1,000,000: 2s. Last read position: chr22:21,959,693
INFO 2026-06-08 08:09:40 MarkDuplicates Tracking 40905 as yet unmatched pairs. 18135 records in RAM.
INFO 2026-06-08 08:09:42 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:08:57s. Time for last 1,000,000: 1s. Last read position: chr22:29,282,427
INFO 2026-06-08 08:09:42 MarkDuplicates Tracking 38340 as yet unmatched pairs. 15570 records in RAM.
INFO 2026-06-08 08:10:47 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:10:03s. Time for last 1,000,000: 65s. Last read position: chr22:35,403,423
INFO 2026-06-08 08:10:47 MarkDuplicates Tracking 35289 as yet unmatched pairs. 12519 records in RAM.
INFO 2026-06-08 08:10:49 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:10:04s. Time for last 1,000,000: 1s. Last read position: chr22:37,855,564
INFO 2026-06-08 08:10:49 MarkDuplicates Tracking 32355 as yet unmatched pairs. 9585 records in RAM.
INFO 2026-06-08 08:10:50 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 1s. Last read position: chr22:41,127,553
INFO 2026-06-08 08:10:50 MarkDuplicates Tracking 29361 as yet unmatched pairs. 6591 records in RAM.
INFO 2026-06-08 08:10:52 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:10:07s. Time for last 1,000,000: 1s. Last read position: chr22:45,672,033
INFO 2026-06-08 08:10:52 MarkDuplicates Tracking 26263 as yet unmatched pairs. 3492 records in RAM.
INFO 2026-06-08 08:10:54 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 1s. Last read position: chrX:291,536
INFO 2026-06-08 08:10:54 MarkDuplicates Tracking 22774 as yet unmatched pairs. 18449 records in RAM.
INFO 2026-06-08 08:10:55 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:10:10s. Time for last 1,000,000: 1s. Last read position: chrX:40,062,884
INFO 2026-06-08 08:10:55 MarkDuplicates Tracking 20171 as yet unmatched pairs. 15843 records in RAM.
INFO 2026-06-08 08:10:57 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 1s. Last read position: chrX:49,031,396
INFO 2026-06-08 08:10:57 MarkDuplicates Tracking 17337 as yet unmatched pairs. 13009 records in RAM.
INFO 2026-06-08 08:10:59 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:10:14s. Time for last 1,000,000: 1s. Last read position: chrX:70,963,198
INFO 2026-06-08 08:10:59 MarkDuplicates Tracking 14561 as yet unmatched pairs. 10232 records in RAM.
INFO 2026-06-08 08:11:00 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:10:15s. Time for last 1,000,000: 1s. Last read position: chrX:77,902,664
INFO 2026-06-08 08:11:00 MarkDuplicates Tracking 12180 as yet unmatched pairs. 7851 records in RAM.
INFO 2026-06-08 08:11:02 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:10:17s. Time for last 1,000,000: 1s. Last read position: chrX:123,885,880
INFO 2026-06-08 08:11:02 MarkDuplicates Tracking 9647 as yet unmatched pairs. 5317 records in RAM.
INFO 2026-06-08 08:11:03 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:10:18s. Time for last 1,000,000: 1s. Last read position: chrX:153,957,038
INFO 2026-06-08 08:11:03 MarkDuplicates Tracking 6722 as yet unmatched pairs. 2389 records in RAM.
INFO 2026-06-08 08:11:05 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:10:20s. Time for last 1,000,000: 1s. Last read position: chrY:14,418,876
INFO 2026-06-08 08:11:05 MarkDuplicates Tracking 3728 as yet unmatched pairs. 389 records in RAM.
INFO 2026-06-08 08:11:06 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:10:21s. Time for last 1,000,000: 1s. Last read position: KI270733.1:131,020
INFO 2026-06-08 08:11:06 MarkDuplicates Tracking 1239 as yet unmatched pairs. 1226 records in RAM.
INFO 2026-06-08 08:11:07 MarkDuplicates Read 267542956 records. 0 pairs never matched.
INFO 2026-06-08 08:11:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 24855266680; totalMemory: 35467034624; maxMemory: 63585648640
INFO 2026-06-08 08:11:17 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:11:27 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:11:43 OpticalDuplicateFinder Large duplicate set. size = 1062
INFO 2026-06-08 08:11:43 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:23,660
INFO 2026-06-08 08:11:43 OpticalDuplicateFinder Large duplicate set. size = 1043
INFO 2026-06-08 08:11:43 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:14,680
INFO 2026-06-08 08:11:43 OpticalDuplicateFinder Large duplicate set. size = 1650
INFO 2026-06-08 08:11:43 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,126
INFO 2026-06-08 08:11:43 OpticalDuplicateFinder Large duplicate set. size = 1120
INFO 2026-06-08 08:11:43 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:4,179
INFO 2026-06-08 08:11:43 OpticalDuplicateFinder Large duplicate set. size = 1619
INFO 2026-06-08 08:11:43 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,202
INFO 2026-06-08 08:11:43 OpticalDuplicateFinder Large duplicate set. size = 1998
INFO 2026-06-08 08:11:43 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,640
INFO 2026-06-08 08:11:43 OpticalDuplicateFinder Large duplicate set. size = 3523
INFO 2026-06-08 08:11:44 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:23,078
INFO 2026-06-08 08:11:44 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-18,552
INFO 2026-06-08 08:11:44 OpticalDuplicateFinder compared 3,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,604
INFO 2026-06-08 08:11:44 OpticalDuplicateFinder Large duplicate set. size = 1068
INFO 2026-06-08 08:11:44 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:23,612
INFO 2026-06-08 08:11:44 OpticalDuplicateFinder Large duplicate set. size = 1452
INFO 2026-06-08 08:11:44 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,885
INFO 2026-06-08 08:11:44 OpticalDuplicateFinder Large duplicate set. size = 1410
INFO 2026-06-08 08:11:44 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,243
INFO 2026-06-08 08:11:55 MarkDuplicates Traversing fragment information and detecting duplicates.
WARNING 2026-06-08 08:11:55 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
INFO 2026-06-08 08:12:32 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:12:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 35421661688; totalMemory: 51371835392; maxMemory: 63585648640
INFO 2026-06-08 08:12:38 MarkDuplicates Marking 134179711 records as duplicates.
INFO 2026-06-08 08:12:38 MarkDuplicates Found 7134692 optical duplicate clusters.
INFO 2026-06-08 08:12:38 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 08:13:03 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:25s. Time for last 10,000,000: 25s. Last read position: chr1:100,911,097
INFO 2026-06-08 08:13:26 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:47s. Time for last 10,000,000: 22s. Last read position: chr1:171,557,550
INFO 2026-06-08 08:13:44 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:06s. Time for last 10,000,000: 18s. Last read position: chr2:32,916,406
INFO 2026-06-08 08:14:04 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:26s. Time for last 10,000,000: 20s. Last read position: chr2:168,140,738
INFO 2026-06-08 08:14:25 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:47s. Time for last 10,000,000: 21s. Last read position: chr3:36,833,621
INFO 2026-06-08 08:14:45 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:07s. Time for last 10,000,000: 19s. Last read position: chr3:196,827,255
INFO 2026-06-08 08:15:08 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:30s. Time for last 10,000,000: 23s. Last read position: chr5:69,626,701
INFO 2026-06-08 08:15:29 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:51s. Time for last 10,000,000: 20s. Last read position: chr5:179,733,122
INFO 2026-06-08 08:15:49 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:03:11s. Time for last 10,000,000: 20s. Last read position: chr6:89,951,379
INFO 2026-06-08 08:16:09 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:03:31s. Time for last 10,000,000: 19s. Last read position: chr7:87,184,550
INFO 2026-06-08 08:16:29 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:03:50s. Time for last 10,000,000: 19s. Last read position: chr8:59,018,406
INFO 2026-06-08 08:16:51 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:04:13s. Time for last 10,000,000: 22s. Last read position: chr9:115,086,437
INFO 2026-06-08 08:17:12 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:04:33s. Time for last 10,000,000: 20s. Last read position: chr10:89,417,328
INFO 2026-06-08 08:17:29 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:04:51s. Time for last 10,000,000: 17s. Last read position: chr11:64,730,101
INFO 2026-06-08 08:17:47 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:05:09s. Time for last 10,000,000: 18s. Last read position: chr12:11,869,521
INFO 2026-06-08 08:18:05 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:05:26s. Time for last 10,000,000: 17s. Last read position: chr12:120,737,929
INFO 2026-06-08 08:18:21 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:05:42s. Time for last 10,000,000: 16s. Last read position: chr14:71,587,899
INFO 2026-06-08 08:18:37 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:05:58s. Time for last 10,000,000: 15s. Last read position: chr15:63,069,784
INFO 2026-06-08 08:18:52 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:06:14s. Time for last 10,000,000: 15s. Last read position: chr16:19,629,780
INFO 2026-06-08 08:19:09 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:06:30s. Time for last 10,000,000: 16s. Last read position: chr16:50,315,128
INFO 2026-06-08 08:19:25 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:06:47s. Time for last 10,000,000: 16s. Last read position: chr17:29,534,224
INFO 2026-06-08 08:19:43 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:07:04s. Time for last 10,000,000: 17s. Last read position: chr17:80,345,200
INFO 2026-06-08 08:19:59 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:07:21s. Time for last 10,000,000: 16s. Last read position: chr19:14,529,678
INFO 2026-06-08 08:20:15 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:07:37s. Time for last 10,000,000: 15s. Last read position: chr19:49,594,986
INFO 2026-06-08 08:20:31 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:07:53s. Time for last 10,000,000: 15s. Last read position: chr21:29,326,287
INFO 2026-06-08 08:20:47 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:08:09s. Time for last 10,000,000: 16s. Last read position: chrX:40,062,884
INFO 2026-06-08 08:21:04 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:21:04 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:21:04 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:21:05 MarkDuplicates Before output close freeMemory: 202412656; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:21:05 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:21:05 MarkDuplicates After output close freeMemory: 104180256; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 08:21:05 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 20.37 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory