Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/be8a4d08b3debc53836dda7bdcb162/1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam
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/74/199fb4c062c092ae6b510da73c33e6/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/199fb4c062c092ae6b510da73c33e6/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai
==> 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 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bam --METRICS_FILE 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
08:09:09.735 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 08:09:09 GMT 2026] MarkDuplicates --INPUT 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bam --METRICS_FILE 1173_C31_T1_RNA_SLD_01_A23T55JLT4_2.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 08:09:09 GMT 2026] Executing as ?@nf-74199fb4c062c092ae6b510da73c33e6-4fd82-wmn4g 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 08:09:09 MarkDuplicates Start of doWork freeMemory: 105827952; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 08:09:09 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 08:09:09 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 08:09:14 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:2,556,656
INFO 2026-06-08 08:09:14 MarkDuplicates Tracking 3551 as yet unmatched pairs. 183 records in RAM.
INFO 2026-06-08 08:09:17 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: chr1:10,072,082
INFO 2026-06-08 08:09:17 MarkDuplicates Tracking 6777 as yet unmatched pairs. 33 records in RAM.
INFO 2026-06-08 08:09:19 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: chr1:16,130,185
INFO 2026-06-08 08:09:19 MarkDuplicates Tracking 9831 as yet unmatched pairs. 54 records in RAM.
INFO 2026-06-08 08:09:21 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 2s. Last read position: chr1:20,660,966
INFO 2026-06-08 08:09:21 MarkDuplicates Tracking 13063 as yet unmatched pairs. 180 records in RAM.
INFO 2026-06-08 08:09:23 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 2s. Last read position: chr1:22,639,422
INFO 2026-06-08 08:09:23 MarkDuplicates Tracking 16449 as yet unmatched pairs. 164 records in RAM.
INFO 2026-06-08 08:09:27 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 3s. Last read position: chr1:26,346,579
INFO 2026-06-08 08:09:27 MarkDuplicates Tracking 19329 as yet unmatched pairs. 48 records in RAM.
INFO 2026-06-08 08:09:29 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 2s. Last read position: chr1:30,966,024
INFO 2026-06-08 08:09:29 MarkDuplicates Tracking 22477 as yet unmatched pairs. 113 records in RAM.
INFO 2026-06-08 08:09:32 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 3s. Last read position: chr1:35,007,033
INFO 2026-06-08 08:09:32 MarkDuplicates Tracking 25578 as yet unmatched pairs. 30 records in RAM.
INFO 2026-06-08 08:09:34 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 1s. Last read position: chr1:39,571,335
INFO 2026-06-08 08:09:34 MarkDuplicates Tracking 28688 as yet unmatched pairs. 135 records in RAM.
INFO 2026-06-08 08:09:36 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 2s. Last read position: chr1:44,776,127
INFO 2026-06-08 08:09:36 MarkDuplicates Tracking 32342 as yet unmatched pairs. 566 records in RAM.
INFO 2026-06-08 08:09:39 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 3s. Last read position: chr1:52,359,872
INFO 2026-06-08 08:09:39 MarkDuplicates Tracking 34814 as yet unmatched pairs. 61 records in RAM.
INFO 2026-06-08 08:09:42 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 2s. Last read position: chr1:68,159,171
INFO 2026-06-08 08:09:42 MarkDuplicates Tracking 37876 as yet unmatched pairs. 138 records in RAM.
INFO 2026-06-08 08:09:44 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 2s. Last read position: chr1:94,532,418
INFO 2026-06-08 08:09:44 MarkDuplicates Tracking 40624 as yet unmatched pairs. 99 records in RAM.
INFO 2026-06-08 08:09:47 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 3s. Last read position: chr1:111,456,653
INFO 2026-06-08 08:09:47 MarkDuplicates Tracking 43368 as yet unmatched pairs. 53 records in RAM.
INFO 2026-06-08 08:09:50 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 2s. Last read position: chr1:117,622,860
INFO 2026-06-08 08:09:50 MarkDuplicates Tracking 46261 as yet unmatched pairs. 64 records in RAM.
INFO 2026-06-08 08:09:52 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 1s. Last read position: chr1:145,291,580
INFO 2026-06-08 08:09:52 MarkDuplicates Tracking 48694 as yet unmatched pairs. 42 records in RAM.
INFO 2026-06-08 08:09:54 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chr1:149,390,838
INFO 2026-06-08 08:09:54 MarkDuplicates Tracking 50211 as yet unmatched pairs. 77 records in RAM.
INFO 2026-06-08 08:09:56 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 2s. Last read position: chr1:150,817,372
INFO 2026-06-08 08:09:56 MarkDuplicates Tracking 52790 as yet unmatched pairs. 60 records in RAM.
INFO 2026-06-08 08:09:58 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 2s. Last read position: chr1:153,960,616
INFO 2026-06-08 08:09:58 MarkDuplicates Tracking 55866 as yet unmatched pairs. 145 records in RAM.
INFO 2026-06-08 08:10:00 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 1s. Last read position: chr1:155,169,815
INFO 2026-06-08 08:10:00 MarkDuplicates Tracking 59221 as yet unmatched pairs. 686 records in RAM.
INFO 2026-06-08 08:10:03 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 2s. Last read position: chr1:156,134,857
INFO 2026-06-08 08:10:03 MarkDuplicates Tracking 62089 as yet unmatched pairs. 399 records in RAM.
INFO 2026-06-08 08:10:04 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 1s. Last read position: chr1:160,283,623
INFO 2026-06-08 08:10:04 MarkDuplicates Tracking 64966 as yet unmatched pairs. 32 records in RAM.
INFO 2026-06-08 08:10:06 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 2s. Last read position: chr1:169,106,836
INFO 2026-06-08 08:10:06 MarkDuplicates Tracking 70370 as yet unmatched pairs. 2472 records in RAM.
INFO 2026-06-08 08:10:08 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 1s. Last read position: chr1:171,584,505
INFO 2026-06-08 08:10:08 MarkDuplicates Tracking 71044 as yet unmatched pairs. 69 records in RAM.
INFO 2026-06-08 08:10:11 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 3s. Last read position: chr1:184,706,712
INFO 2026-06-08 08:10:11 MarkDuplicates Tracking 74023 as yet unmatched pairs. 68 records in RAM.
INFO 2026-06-08 08:10:14 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 2s. Last read position: chr1:201,898,326
INFO 2026-06-08 08:10:14 MarkDuplicates Tracking 76892 as yet unmatched pairs. 138 records in RAM.
INFO 2026-06-08 08:10:16 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 1s. Last read position: chr1:205,718,265
INFO 2026-06-08 08:10:16 MarkDuplicates Tracking 79966 as yet unmatched pairs. 287 records in RAM.
INFO 2026-06-08 08:10:18 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 2s. Last read position: chr1:206,933,080
INFO 2026-06-08 08:10:18 MarkDuplicates Tracking 86751 as yet unmatched pairs. 4099 records in RAM.
INFO 2026-06-08 08:10:20 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 2s. Last read position: chr1:206,939,348
INFO 2026-06-08 08:10:20 MarkDuplicates Tracking 88531 as yet unmatched pairs. 2578 records in RAM.
INFO 2026-06-08 08:10:22 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 2s. Last read position: chr1:220,210,715
INFO 2026-06-08 08:10:22 MarkDuplicates Tracking 88972 as yet unmatched pairs. 56 records in RAM.
INFO 2026-06-08 08:10:24 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 1s. Last read position: chr1:228,277,757
INFO 2026-06-08 08:10:24 MarkDuplicates Tracking 91784 as yet unmatched pairs. 12 records in RAM.
INFO 2026-06-08 08:10:26 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 1s. Last read position: chr1:244,857,596
INFO 2026-06-08 08:10:26 MarkDuplicates Tracking 95179 as yet unmatched pairs. 314 records in RAM.
INFO 2026-06-08 08:10:29 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 3s. Last read position: chr2:17,701,887
INFO 2026-06-08 08:10:29 MarkDuplicates Tracking 98033 as yet unmatched pairs. 97028 records in RAM.
INFO 2026-06-08 08:10:31 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 2s. Last read position: chr2:27,241,072
INFO 2026-06-08 08:10:31 MarkDuplicates Tracking 101145 as yet unmatched pairs. 100097 records in RAM.
INFO 2026-06-08 08:10:35 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 3s. Last read position: chr2:32,916,256
INFO 2026-06-08 08:10:35 MarkDuplicates Tracking 154399 as yet unmatched pairs. 98495 records in RAM.
INFO 2026-06-08 08:10:37 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,264
INFO 2026-06-08 08:10:37 MarkDuplicates Tracking 513584 as yet unmatched pairs. 75773 records in RAM.
INFO 2026-06-08 08:10:39 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,406
INFO 2026-06-08 08:10:39 MarkDuplicates Tracking 810494 as yet unmatched pairs. 57368 records in RAM.
INFO 2026-06-08 08:10:41 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 1s. Last read position: chr2:37,088,397
INFO 2026-06-08 08:10:41 MarkDuplicates Tracking 868809 as yet unmatched pairs. 52931 records in RAM.
INFO 2026-06-08 08:10:43 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 1s. Last read position: chr2:46,384,582
INFO 2026-06-08 08:10:43 MarkDuplicates Tracking 865811 as yet unmatched pairs. 49900 records in RAM.
INFO 2026-06-08 08:10:45 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 2s. Last read position: chr2:55,544,346
INFO 2026-06-08 08:10:45 MarkDuplicates Tracking 862681 as yet unmatched pairs. 46740 records in RAM.
INFO 2026-06-08 08:10:48 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 2s. Last read position: chr2:70,979,079
INFO 2026-06-08 08:10:48 MarkDuplicates Tracking 859952 as yet unmatched pairs. 43971 records in RAM.
INFO 2026-06-08 08:10:50 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 1s. Last read position: chr2:85,349,477
INFO 2026-06-08 08:10:50 MarkDuplicates Tracking 857065 as yet unmatched pairs. 41040 records in RAM.
INFO 2026-06-08 08:10:51 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 1s. Last read position: chr2:96,832,608
INFO 2026-06-08 08:10:51 MarkDuplicates Tracking 854460 as yet unmatched pairs. 38404 records in RAM.
INFO 2026-06-08 08:10:53 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 1s. Last read position: chr2:108,749,039
INFO 2026-06-08 08:10:53 MarkDuplicates Tracking 852091 as yet unmatched pairs. 36005 records in RAM.
INFO 2026-06-08 08:10:55 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 2s. Last read position: chr2:112,422,549
INFO 2026-06-08 08:10:55 MarkDuplicates Tracking 850269 as yet unmatched pairs. 34173 records in RAM.
INFO 2026-06-08 08:10:57 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 1s. Last read position: chr2:130,346,060
INFO 2026-06-08 08:10:57 MarkDuplicates Tracking 847401 as yet unmatched pairs. 31281 records in RAM.
INFO 2026-06-08 08:11:00 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 2s. Last read position: chr2:160,137,581
INFO 2026-06-08 08:11:00 MarkDuplicates Tracking 844707 as yet unmatched pairs. 28543 records in RAM.
INFO 2026-06-08 08:11:02 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 2s. Last read position: chr2:177,233,268
INFO 2026-06-08 08:11:02 MarkDuplicates Tracking 842124 as yet unmatched pairs. 25911 records in RAM.
INFO 2026-06-08 08:11:05 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 2s. Last read position: chr2:189,001,553
INFO 2026-06-08 08:11:05 MarkDuplicates Tracking 839479 as yet unmatched pairs. 23242 records in RAM.
INFO 2026-06-08 08:11:07 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 2s. Last read position: chr2:197,453,566
INFO 2026-06-08 08:11:07 MarkDuplicates Tracking 835691 as yet unmatched pairs. 19416 records in RAM.
INFO 2026-06-08 08:11:09 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 2s. Last read position: chr2:215,346,869
INFO 2026-06-08 08:11:09 MarkDuplicates Tracking 833018 as yet unmatched pairs. 16705 records in RAM.
INFO 2026-06-08 08:11:11 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 1s. Last read position: chr2:215,404,389
INFO 2026-06-08 08:11:11 MarkDuplicates Tracking 830923 as yet unmatched pairs. 14597 records in RAM.
INFO 2026-06-08 08:11:13 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 1s. Last read position: chr2:217,848,105
INFO 2026-06-08 08:11:13 MarkDuplicates Tracking 827606 as yet unmatched pairs. 11261 records in RAM.
INFO 2026-06-08 08:11:15 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 2s. Last read position: chr2:222,558,360
INFO 2026-06-08 08:11:15 MarkDuplicates Tracking 824349 as yet unmatched pairs. 7964 records in RAM.
INFO 2026-06-08 08:11:17 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 1s. Last read position: chr2:231,798,815
INFO 2026-06-08 08:11:17 MarkDuplicates Tracking 821570 as yet unmatched pairs. 5119 records in RAM.
INFO 2026-06-08 08:11:19 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 1s. Last read position: chr2:239,126,456
INFO 2026-06-08 08:11:19 MarkDuplicates Tracking 818638 as yet unmatched pairs. 2143 records in RAM.
INFO 2026-06-08 08:11:21 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 2s. Last read position: chr3:9,800,226
INFO 2026-06-08 08:11:21 MarkDuplicates Tracking 815688 as yet unmatched pairs. 44886 records in RAM.
INFO 2026-06-08 08:11:24 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 2s. Last read position: chr3:25,596,498
INFO 2026-06-08 08:11:24 MarkDuplicates Tracking 812547 as yet unmatched pairs. 41709 records in RAM.
INFO 2026-06-08 08:11:26 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 1s. Last read position: chr3:40,462,031
INFO 2026-06-08 08:11:26 MarkDuplicates Tracking 809813 as yet unmatched pairs. 38927 records in RAM.
INFO 2026-06-08 08:11:28 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 1s. Last read position: chr3:47,124,046
INFO 2026-06-08 08:11:28 MarkDuplicates Tracking 806735 as yet unmatched pairs. 35823 records in RAM.
INFO 2026-06-08 08:11:30 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 1s. Last read position: chr3:49,057,411
INFO 2026-06-08 08:11:30 MarkDuplicates Tracking 803507 as yet unmatched pairs. 32561 records in RAM.
INFO 2026-06-08 08:11:32 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 1s. Last read position: chr3:50,349,978
INFO 2026-06-08 08:11:32 MarkDuplicates Tracking 800150 as yet unmatched pairs. 29172 records in RAM.
INFO 2026-06-08 08:11:33 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr3:56,624,982
INFO 2026-06-08 08:11:33 MarkDuplicates Tracking 796987 as yet unmatched pairs. 25985 records in RAM.
INFO 2026-06-08 08:11:36 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 2s. Last read position: chr3:71,435,765
INFO 2026-06-08 08:11:36 MarkDuplicates Tracking 794180 as yet unmatched pairs. 23150 records in RAM.
INFO 2026-06-08 08:11:38 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 1s. Last read position: chr3:113,274,553
INFO 2026-06-08 08:11:38 MarkDuplicates Tracking 791505 as yet unmatched pairs. 20436 records in RAM.
INFO 2026-06-08 08:11:40 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 2s. Last read position: chr3:124,927,830
INFO 2026-06-08 08:11:40 MarkDuplicates Tracking 789419 as yet unmatched pairs. 18300 records in RAM.
INFO 2026-06-08 08:11:42 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 2s. Last read position: chr3:133,938,436
INFO 2026-06-08 08:11:42 MarkDuplicates Tracking 785685 as yet unmatched pairs. 14543 records in RAM.
INFO 2026-06-08 08:11:44 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 2s. Last read position: chr3:158,646,206
INFO 2026-06-08 08:11:44 MarkDuplicates Tracking 782893 as yet unmatched pairs. 11713 records in RAM.
INFO 2026-06-08 08:11:46 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 1s. Last read position: chr3:184,182,809
INFO 2026-06-08 08:11:46 MarkDuplicates Tracking 780243 as yet unmatched pairs. 9029 records in RAM.
INFO 2026-06-08 08:11:50 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 3s. Last read position: chr3:190,308,276
INFO 2026-06-08 08:11:50 MarkDuplicates Tracking 777354 as yet unmatched pairs. 6114 records in RAM.
INFO 2026-06-08 08:11:52 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 1s. Last read position: chr3:195,780,279
INFO 2026-06-08 08:11:52 MarkDuplicates Tracking 777929 as yet unmatched pairs. 6669 records in RAM.
INFO 2026-06-08 08:11:53 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 1s. Last read position: chr3:195,783,667
INFO 2026-06-08 08:11:53 MarkDuplicates Tracking 777288 as yet unmatched pairs. 6016 records in RAM.
INFO 2026-06-08 08:11:55 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 2s. Last read position: chr3:195,787,686
INFO 2026-06-08 08:11:55 MarkDuplicates Tracking 773876 as yet unmatched pairs. 2595 records in RAM.
INFO 2026-06-08 08:11:57 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 1s. Last read position: chr4:1,025,241
INFO 2026-06-08 08:11:57 MarkDuplicates Tracking 770429 as yet unmatched pairs. 24389 records in RAM.
INFO 2026-06-08 08:12:00 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 2s. Last read position: chr4:7,768,995
INFO 2026-06-08 08:12:00 MarkDuplicates Tracking 767201 as yet unmatched pairs. 21134 records in RAM.
INFO 2026-06-08 08:12:01 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 1s. Last read position: chr4:39,454,594
INFO 2026-06-08 08:12:01 MarkDuplicates Tracking 764150 as yet unmatched pairs. 18046 records in RAM.
INFO 2026-06-08 08:12:03 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 1s. Last read position: chr4:57,040,915
INFO 2026-06-08 08:12:03 MarkDuplicates Tracking 761366 as yet unmatched pairs. 15237 records in RAM.
INFO 2026-06-08 08:12:05 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 2s. Last read position: chr4:78,776,631
INFO 2026-06-08 08:12:05 MarkDuplicates Tracking 758418 as yet unmatched pairs. 12273 records in RAM.
INFO 2026-06-08 08:12:07 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 1s. Last read position: chr4:102,797,401
INFO 2026-06-08 08:12:07 MarkDuplicates Tracking 755967 as yet unmatched pairs. 9788 records in RAM.
INFO 2026-06-08 08:12:09 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 2s. Last read position: chr4:125,398,891
INFO 2026-06-08 08:12:09 MarkDuplicates Tracking 753182 as yet unmatched pairs. 6969 records in RAM.
INFO 2026-06-08 08:12:11 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 2s. Last read position: chr4:153,270,450
INFO 2026-06-08 08:12:11 MarkDuplicates Tracking 750580 as yet unmatched pairs. 4335 records in RAM.
INFO 2026-06-08 08:12:13 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 2s. Last read position: chr4:186,603,295
INFO 2026-06-08 08:12:13 MarkDuplicates Tracking 747669 as yet unmatched pairs. 1381 records in RAM.
INFO 2026-06-08 08:12:16 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 2s. Last read position: chr5:12,421,860
INFO 2026-06-08 08:12:16 MarkDuplicates Tracking 744478 as yet unmatched pairs. 36507 records in RAM.
INFO 2026-06-08 08:12:18 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 2s. Last read position: chr5:36,995,669
INFO 2026-06-08 08:12:18 MarkDuplicates Tracking 741696 as yet unmatched pairs. 33693 records in RAM.
INFO 2026-06-08 08:12:21 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 2s. Last read position: chr5:68,295,422
INFO 2026-06-08 08:12:21 MarkDuplicates Tracking 739111 as yet unmatched pairs. 31075 records in RAM.
INFO 2026-06-08 08:12:23 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 2s. Last read position: chr5:81,080,132
INFO 2026-06-08 08:12:23 MarkDuplicates Tracking 736618 as yet unmatched pairs. 28552 records in RAM.
INFO 2026-06-08 08:12:25 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 2s. Last read position: chr5:112,259,265
INFO 2026-06-08 08:12:25 MarkDuplicates Tracking 734019 as yet unmatched pairs. 25923 records in RAM.
INFO 2026-06-08 08:12:27 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 2s. Last read position: chr5:133,774,774
INFO 2026-06-08 08:12:27 MarkDuplicates Tracking 731173 as yet unmatched pairs. 23044 records in RAM.
INFO 2026-06-08 08:12:30 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 2s. Last read position: chr5:139,326,201
INFO 2026-06-08 08:12:30 MarkDuplicates Tracking 728246 as yet unmatched pairs. 20103 records in RAM.
INFO 2026-06-08 08:12:32 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 1s. Last read position: chr5:141,924,630
INFO 2026-06-08 08:12:32 MarkDuplicates Tracking 725686 as yet unmatched pairs. 17451 records in RAM.
INFO 2026-06-08 08:12:34 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: chr5:150,402,209
INFO 2026-06-08 08:12:34 MarkDuplicates Tracking 729409 as yet unmatched pairs. 21152 records in RAM.
INFO 2026-06-08 08:12:35 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 1s. Last read position: chr5:150,656,990
INFO 2026-06-08 08:12:35 MarkDuplicates Tracking 719043 as yet unmatched pairs. 10772 records in RAM.
INFO 2026-06-08 08:12:37 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 1s. Last read position: chr5:168,568,696
INFO 2026-06-08 08:12:37 MarkDuplicates Tracking 716178 as yet unmatched pairs. 7886 records in RAM.
INFO 2026-06-08 08:12:39 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 1s. Last read position: chr5:176,571,185
INFO 2026-06-08 08:12:39 MarkDuplicates Tracking 713517 as yet unmatched pairs. 5193 records in RAM.
INFO 2026-06-08 08:12:41 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 2s. Last read position: chr5:179,821,074
INFO 2026-06-08 08:12:41 MarkDuplicates Tracking 711179 as yet unmatched pairs. 2835 records in RAM.
INFO 2026-06-08 08:12:44 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 2s. Last read position: chr6:3,153,856
INFO 2026-06-08 08:12:44 MarkDuplicates Tracking 707456 as yet unmatched pairs. 42494 records in RAM.
INFO 2026-06-08 08:12:45 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 1s. Last read position: chr6:15,487,335
INFO 2026-06-08 08:12:45 MarkDuplicates Tracking 704459 as yet unmatched pairs. 39482 records in RAM.
INFO 2026-06-08 08:12:47 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 1s. Last read position: chr6:27,810,159
INFO 2026-06-08 08:12:47 MarkDuplicates Tracking 701482 as yet unmatched pairs. 36456 records in RAM.
INFO 2026-06-08 08:12:49 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 1s. Last read position: chr6:30,724,280
INFO 2026-06-08 08:12:49 MarkDuplicates Tracking 698566 as yet unmatched pairs. 33513 records in RAM.
INFO 2026-06-08 08:12:51 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 1s. Last read position: chr6:31,659,762
INFO 2026-06-08 08:12:51 MarkDuplicates Tracking 695604 as yet unmatched pairs. 30533 records in RAM.
INFO 2026-06-08 08:12:53 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 2s. Last read position: chr6:32,097,814
INFO 2026-06-08 08:12:53 MarkDuplicates Tracking 693001 as yet unmatched pairs. 27919 records in RAM.
INFO 2026-06-08 08:12:57 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 3s. Last read position: chr6:33,415,809
INFO 2026-06-08 08:12:57 MarkDuplicates Tracking 690031 as yet unmatched pairs. 24940 records in RAM.
INFO 2026-06-08 08:12:59 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 2s. Last read position: chr6:41,684,920
INFO 2026-06-08 08:12:59 MarkDuplicates Tracking 686924 as yet unmatched pairs. 21807 records in RAM.
INFO 2026-06-08 08:13:02 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 2s. Last read position: chr6:47,283,968
INFO 2026-06-08 08:13:02 MarkDuplicates Tracking 683912 as yet unmatched pairs. 18776 records in RAM.
INFO 2026-06-08 08:13:04 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 2s. Last read position: chr6:75,678,671
INFO 2026-06-08 08:13:04 MarkDuplicates Tracking 681349 as yet unmatched pairs. 16161 records in RAM.
INFO 2026-06-08 08:13:07 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 2s. Last read position: chr6:106,971,808
INFO 2026-06-08 08:13:07 MarkDuplicates Tracking 678953 as yet unmatched pairs. 13749 records in RAM.
INFO 2026-06-08 08:13:09 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 1s. Last read position: chr6:129,353,164
INFO 2026-06-08 08:13:09 MarkDuplicates Tracking 675651 as yet unmatched pairs. 10412 records in RAM.
INFO 2026-06-08 08:13:10 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 1s. Last read position: chr6:139,167,016
INFO 2026-06-08 08:13:10 MarkDuplicates Tracking 672784 as yet unmatched pairs. 7528 records in RAM.
INFO 2026-06-08 08:13:12 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 1s. Last read position: chr6:157,206,882
INFO 2026-06-08 08:13:12 MarkDuplicates Tracking 670051 as yet unmatched pairs. 4775 records in RAM.
INFO 2026-06-08 08:13:14 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 1s. Last read position: chr6:160,628,227
INFO 2026-06-08 08:13:14 MarkDuplicates Tracking 666826 as yet unmatched pairs. 1515 records in RAM.
INFO 2026-06-08 08:13:16 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 2s. Last read position: chr7:2,661,700
INFO 2026-06-08 08:13:16 MarkDuplicates Tracking 663489 as yet unmatched pairs. 47110 records in RAM.
INFO 2026-06-08 08:13:18 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 1s. Last read position: chr7:5,529,167
INFO 2026-06-08 08:13:18 MarkDuplicates Tracking 661790 as yet unmatched pairs. 45397 records in RAM.
INFO 2026-06-08 08:13:20 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 1s. Last read position: chr7:22,818,000
INFO 2026-06-08 08:13:20 MarkDuplicates Tracking 657482 as yet unmatched pairs. 41071 records in RAM.
INFO 2026-06-08 08:13:22 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 2s. Last read position: chr7:44,030,812
INFO 2026-06-08 08:13:22 MarkDuplicates Tracking 654416 as yet unmatched pairs. 37977 records in RAM.
INFO 2026-06-08 08:13:24 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 1s. Last read position: chr7:55,472,956
INFO 2026-06-08 08:13:24 MarkDuplicates Tracking 651415 as yet unmatched pairs. 34958 records in RAM.
INFO 2026-06-08 08:13:26 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 1s. Last read position: chr7:73,831,230
INFO 2026-06-08 08:13:26 MarkDuplicates Tracking 649359 as yet unmatched pairs. 32875 records in RAM.
INFO 2026-06-08 08:13:27 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 1s. Last read position: chr7:76,303,806
INFO 2026-06-08 08:13:27 MarkDuplicates Tracking 647572 as yet unmatched pairs. 31075 records in RAM.
INFO 2026-06-08 08:13:29 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 1s. Last read position: chr7:92,701,730
INFO 2026-06-08 08:13:29 MarkDuplicates Tracking 644075 as yet unmatched pairs. 27543 records in RAM.
INFO 2026-06-08 08:13:32 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 2s. Last read position: chr7:98,949,693
INFO 2026-06-08 08:13:32 MarkDuplicates Tracking 640871 as yet unmatched pairs. 24320 records in RAM.
INFO 2026-06-08 08:13:34 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 1s. Last read position: chr7:100,813,676
INFO 2026-06-08 08:13:34 MarkDuplicates Tracking 638006 as yet unmatched pairs. 21445 records in RAM.
INFO 2026-06-08 08:13:36 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 2s. Last read position: chr7:100,995,117
INFO 2026-06-08 08:13:36 MarkDuplicates Tracking 636452 as yet unmatched pairs. 19886 records in RAM.
INFO 2026-06-08 08:13:38 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr7:100,998,310
INFO 2026-06-08 08:13:38 MarkDuplicates Tracking 635366 as yet unmatched pairs. 18798 records in RAM.
INFO 2026-06-08 08:13:39 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 1s. Last read position: chr7:101,001,511
INFO 2026-06-08 08:13:39 MarkDuplicates Tracking 634342 as yet unmatched pairs. 17771 records in RAM.
INFO 2026-06-08 08:13:41 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 1s. Last read position: chr7:101,036,693
INFO 2026-06-08 08:13:41 MarkDuplicates Tracking 633279 as yet unmatched pairs. 16705 records in RAM.
INFO 2026-06-08 08:13:42 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 1s. Last read position: chr7:102,553,292
INFO 2026-06-08 08:13:42 MarkDuplicates Tracking 630951 as yet unmatched pairs. 14362 records in RAM.
INFO 2026-06-08 08:13:44 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 1s. Last read position: chr7:116,731,692
INFO 2026-06-08 08:13:44 MarkDuplicates Tracking 628364 as yet unmatched pairs. 11749 records in RAM.
INFO 2026-06-08 08:13:46 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 1s. Last read position: chr7:129,878,326
INFO 2026-06-08 08:13:46 MarkDuplicates Tracking 625558 as yet unmatched pairs. 8925 records in RAM.
INFO 2026-06-08 08:13:48 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 1s. Last read position: chr7:140,459,110
INFO 2026-06-08 08:13:48 MarkDuplicates Tracking 622886 as yet unmatched pairs. 6237 records in RAM.
INFO 2026-06-08 08:13:49 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 1s. Last read position: chr7:144,365,482
INFO 2026-06-08 08:13:49 MarkDuplicates Tracking 620763 as yet unmatched pairs. 4098 records in RAM.
INFO 2026-06-08 08:13:51 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 1s. Last read position: chr7:155,706,952
INFO 2026-06-08 08:13:51 MarkDuplicates Tracking 617643 as yet unmatched pairs. 949 records in RAM.
INFO 2026-06-08 08:13:53 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 1s. Last read position: chr8:17,940,070
INFO 2026-06-08 08:13:53 MarkDuplicates Tracking 614638 as yet unmatched pairs. 31186 records in RAM.
INFO 2026-06-08 08:13:55 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 1s. Last read position: chr8:27,442,958
INFO 2026-06-08 08:13:55 MarkDuplicates Tracking 611736 as yet unmatched pairs. 28264 records in RAM.
INFO 2026-06-08 08:13:58 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 2s. Last read position: chr8:38,290,526
INFO 2026-06-08 08:13:58 MarkDuplicates Tracking 608327 as yet unmatched pairs. 24814 records in RAM.
INFO 2026-06-08 08:13:59 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 1s. Last read position: chr8:52,642,378
INFO 2026-06-08 08:13:59 MarkDuplicates Tracking 605299 as yet unmatched pairs. 21763 records in RAM.
INFO 2026-06-08 08:14:01 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 1s. Last read position: chr8:74,603,579
INFO 2026-06-08 08:14:01 MarkDuplicates Tracking 602689 as yet unmatched pairs. 19117 records in RAM.
INFO 2026-06-08 08:14:04 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 3s. Last read position: chr8:100,705,617
INFO 2026-06-08 08:14:04 MarkDuplicates Tracking 600241 as yet unmatched pairs. 16645 records in RAM.
INFO 2026-06-08 08:14:07 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 2s. Last read position: chr8:123,798,140
INFO 2026-06-08 08:14:07 MarkDuplicates Tracking 597199 as yet unmatched pairs. 13571 records in RAM.
INFO 2026-06-08 08:14:09 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 2s. Last read position: chr8:143,574,790
INFO 2026-06-08 08:14:09 MarkDuplicates Tracking 594065 as yet unmatched pairs. 10407 records in RAM.
INFO 2026-06-08 08:14:11 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 1s. Last read position: chr8:143,861,253
INFO 2026-06-08 08:14:11 MarkDuplicates Tracking 592256 as yet unmatched pairs. 8592 records in RAM.
INFO 2026-06-08 08:14:12 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 1s. Last read position: chr8:143,865,236
INFO 2026-06-08 08:14:12 MarkDuplicates Tracking 590769 as yet unmatched pairs. 7100 records in RAM.
INFO 2026-06-08 08:14:14 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 1s. Last read position: chr8:143,924,419
INFO 2026-06-08 08:14:14 MarkDuplicates Tracking 588030 as yet unmatched pairs. 4353 records in RAM.
INFO 2026-06-08 08:14:16 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 1s. Last read position: chr8:144,790,415
INFO 2026-06-08 08:14:16 MarkDuplicates Tracking 584247 as yet unmatched pairs. 559 records in RAM.
INFO 2026-06-08 08:14:18 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 2s. Last read position: chr9:19,619,613
INFO 2026-06-08 08:14:18 MarkDuplicates Tracking 581273 as yet unmatched pairs. 31028 records in RAM.
INFO 2026-06-08 08:14:20 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr9:35,704,373
INFO 2026-06-08 08:14:20 MarkDuplicates Tracking 578231 as yet unmatched pairs. 27964 records in RAM.
INFO 2026-06-08 08:14:22 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 1s. Last read position: chr9:75,117,504
INFO 2026-06-08 08:14:22 MarkDuplicates Tracking 575641 as yet unmatched pairs. 25320 records in RAM.
INFO 2026-06-08 08:14:24 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 1s. Last read position: chr9:93,267,848
INFO 2026-06-08 08:14:24 MarkDuplicates Tracking 572672 as yet unmatched pairs. 22326 records in RAM.
INFO 2026-06-08 08:14:26 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 1s. Last read position: chr9:107,485,798
INFO 2026-06-08 08:14:26 MarkDuplicates Tracking 569892 as yet unmatched pairs. 19518 records in RAM.
INFO 2026-06-08 08:14:27 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 1s. Last read position: chr9:121,150,285
INFO 2026-06-08 08:14:27 MarkDuplicates Tracking 566771 as yet unmatched pairs. 16379 records in RAM.
INFO 2026-06-08 08:14:29 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 2s. Last read position: chr9:127,916,480
INFO 2026-06-08 08:14:29 MarkDuplicates Tracking 563583 as yet unmatched pairs. 13169 records in RAM.
INFO 2026-06-08 08:14:31 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:05:20s. Time for last 1,000,000: 2s. Last read position: chr9:129,640,682
INFO 2026-06-08 08:14:31 MarkDuplicates Tracking 560229 as yet unmatched pairs. 9789 records in RAM.
INFO 2026-06-08 08:14:33 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 1s. Last read position: chr9:133,255,569
INFO 2026-06-08 08:14:33 MarkDuplicates Tracking 557587 as yet unmatched pairs. 7117 records in RAM.
INFO 2026-06-08 08:14:35 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 2s. Last read position: chr9:136,523,806
INFO 2026-06-08 08:14:35 MarkDuplicates Tracking 554029 as yet unmatched pairs. 3545 records in RAM.
INFO 2026-06-08 08:14:38 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 2s. Last read position: chr10:885,664
INFO 2026-06-08 08:14:38 MarkDuplicates Tracking 550235 as yet unmatched pairs. 35821 records in RAM.
INFO 2026-06-08 08:14:40 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 2s. Last read position: chr10:21,740,159
INFO 2026-06-08 08:14:40 MarkDuplicates Tracking 547295 as yet unmatched pairs. 32859 records in RAM.
INFO 2026-06-08 08:14:42 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 2s. Last read position: chr10:32,028,508
INFO 2026-06-08 08:14:42 MarkDuplicates Tracking 545631 as yet unmatched pairs. 31169 records in RAM.
INFO 2026-06-08 08:14:44 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 1s. Last read position: chr10:46,015,256
INFO 2026-06-08 08:14:44 MarkDuplicates Tracking 542583 as yet unmatched pairs. 28109 records in RAM.
INFO 2026-06-08 08:14:46 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 1s. Last read position: chr10:68,341,640
INFO 2026-06-08 08:14:46 MarkDuplicates Tracking 539730 as yet unmatched pairs. 25230 records in RAM.
INFO 2026-06-08 08:14:48 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 1s. Last read position: chr10:74,109,038
INFO 2026-06-08 08:14:48 MarkDuplicates Tracking 536831 as yet unmatched pairs. 22311 records in RAM.
INFO 2026-06-08 08:14:50 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 2s. Last read position: chr10:88,935,240
INFO 2026-06-08 08:14:50 MarkDuplicates Tracking 534215 as yet unmatched pairs. 19675 records in RAM.
INFO 2026-06-08 08:14:52 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 1s. Last read position: chr10:97,431,016
INFO 2026-06-08 08:14:52 MarkDuplicates Tracking 531588 as yet unmatched pairs. 17038 records in RAM.
INFO 2026-06-08 08:14:54 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 2s. Last read position: chr10:102,657,198
INFO 2026-06-08 08:14:54 MarkDuplicates Tracking 528132 as yet unmatched pairs. 13574 records in RAM.
INFO 2026-06-08 08:14:56 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 2s. Last read position: chr10:113,141,303
INFO 2026-06-08 08:14:56 MarkDuplicates Tracking 525342 as yet unmatched pairs. 10768 records in RAM.
INFO 2026-06-08 08:14:58 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 1s. Last read position: chr10:122,211,251
INFO 2026-06-08 08:14:58 MarkDuplicates Tracking 522449 as yet unmatched pairs. 7853 records in RAM.
INFO 2026-06-08 08:14:59 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 1s. Last read position: chr10:122,589,225
INFO 2026-06-08 08:14:59 MarkDuplicates Tracking 521041 as yet unmatched pairs. 6430 records in RAM.
INFO 2026-06-08 08:15:01 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 1s. Last read position: chr10:122,606,152
INFO 2026-06-08 08:15:01 MarkDuplicates Tracking 518295 as yet unmatched pairs. 3676 records in RAM.
INFO 2026-06-08 08:15:03 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 1s. Last read position: chr10:124,042,396
INFO 2026-06-08 08:15:03 MarkDuplicates Tracking 516442 as yet unmatched pairs. 1817 records in RAM.
INFO 2026-06-08 08:15:05 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 2s. Last read position: chr11:320,608
INFO 2026-06-08 08:15:05 MarkDuplicates Tracking 514440 as yet unmatched pairs. 58224 records in RAM.
INFO 2026-06-08 08:15:08 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 2s. Last read position: chr11:1,075,731
INFO 2026-06-08 08:15:08 MarkDuplicates Tracking 511352 as yet unmatched pairs. 55117 records in RAM.
INFO 2026-06-08 08:15:10 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 2s. Last read position: chr11:1,244,123
INFO 2026-06-08 08:15:10 MarkDuplicates Tracking 506876 as yet unmatched pairs. 50625 records in RAM.
INFO 2026-06-08 08:15:12 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 1s. Last read position: chr11:6,223,857
INFO 2026-06-08 08:15:12 MarkDuplicates Tracking 504056 as yet unmatched pairs. 47801 records in RAM.
INFO 2026-06-08 08:15:15 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 2s. Last read position: chr11:13,419,554
INFO 2026-06-08 08:15:15 MarkDuplicates Tracking 500795 as yet unmatched pairs. 44529 records in RAM.
INFO 2026-06-08 08:15:17 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 1s. Last read position: chr11:34,464,123
INFO 2026-06-08 08:15:17 MarkDuplicates Tracking 497942 as yet unmatched pairs. 41665 records in RAM.
INFO 2026-06-08 08:15:19 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 1s. Last read position: chr11:46,795,634
INFO 2026-06-08 08:15:19 MarkDuplicates Tracking 494815 as yet unmatched pairs. 38532 records in RAM.
INFO 2026-06-08 08:15:21 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:06:09s. Time for last 1,000,000: 1s. Last read position: chr11:58,612,300
INFO 2026-06-08 08:15:21 MarkDuplicates Tracking 491914 as yet unmatched pairs. 35616 records in RAM.
INFO 2026-06-08 08:15:23 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 1s. Last read position: chr11:62,521,148
INFO 2026-06-08 08:15:23 MarkDuplicates Tracking 489145 as yet unmatched pairs. 32818 records in RAM.
INFO 2026-06-08 08:15:24 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 1s. Last read position: chr11:62,627,321
INFO 2026-06-08 08:15:24 MarkDuplicates Tracking 486407 as yet unmatched pairs. 30077 records in RAM.
INFO 2026-06-08 08:15:26 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 2s. Last read position: chr11:64,804,400
INFO 2026-06-08 08:15:26 MarkDuplicates Tracking 483085 as yet unmatched pairs. 26746 records in RAM.
INFO 2026-06-08 08:15:28 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 1s. Last read position: chr11:65,659,787
INFO 2026-06-08 08:15:28 MarkDuplicates Tracking 479728 as yet unmatched pairs. 23356 records in RAM.
INFO 2026-06-08 08:15:31 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 2s. Last read position: chr11:67,401,069
INFO 2026-06-08 08:15:31 MarkDuplicates Tracking 476287 as yet unmatched pairs. 19910 records in RAM.
INFO 2026-06-08 08:15:33 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 2s. Last read position: chr11:70,435,047
INFO 2026-06-08 08:15:33 MarkDuplicates Tracking 473114 as yet unmatched pairs. 16718 records in RAM.
INFO 2026-06-08 08:15:35 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 1s. Last read position: chr11:75,404,858
INFO 2026-06-08 08:15:35 MarkDuplicates Tracking 469586 as yet unmatched pairs. 13162 records in RAM.
INFO 2026-06-08 08:15:37 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 1s. Last read position: chr11:96,341,611
INFO 2026-06-08 08:15:37 MarkDuplicates Tracking 466868 as yet unmatched pairs. 10421 records in RAM.
INFO 2026-06-08 08:15:39 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 2s. Last read position: chr11:117,202,877
INFO 2026-06-08 08:15:39 MarkDuplicates Tracking 463700 as yet unmatched pairs. 7234 records in RAM.
INFO 2026-06-08 08:15:41 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:06:30s. Time for last 1,000,000: 1s. Last read position: chr11:119,419,488
INFO 2026-06-08 08:15:41 MarkDuplicates Tracking 460739 as yet unmatched pairs. 4257 records in RAM.
INFO 2026-06-08 08:15:43 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:06:31s. Time for last 1,000,000: 1s. Last read position: chr11:129,164,315
INFO 2026-06-08 08:15:43 MarkDuplicates Tracking 457846 as yet unmatched pairs. 1340 records in RAM.
INFO 2026-06-08 08:15:45 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 2s. Last read position: chr12:5,949,046
INFO 2026-06-08 08:15:45 MarkDuplicates Tracking 454924 as yet unmatched pairs. 47470 records in RAM.
INFO 2026-06-08 08:15:47 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 2s. Last read position: chr12:7,062,668
INFO 2026-06-08 08:15:47 MarkDuplicates Tracking 451811 as yet unmatched pairs. 44349 records in RAM.
INFO 2026-06-08 08:15:49 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 1s. Last read position: chr12:12,908,608
INFO 2026-06-08 08:15:49 MarkDuplicates Tracking 449953 as yet unmatched pairs. 42477 records in RAM.
INFO 2026-06-08 08:15:51 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 1s. Last read position: chr12:32,582,110
INFO 2026-06-08 08:15:51 MarkDuplicates Tracking 446200 as yet unmatched pairs. 38713 records in RAM.
INFO 2026-06-08 08:15:53 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 1s. Last read position: chr12:49,051,452
INFO 2026-06-08 08:15:53 MarkDuplicates Tracking 443225 as yet unmatched pairs. 35720 records in RAM.
INFO 2026-06-08 08:15:55 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 1s. Last read position: chr12:51,242,558
INFO 2026-06-08 08:15:55 MarkDuplicates Tracking 440695 as yet unmatched pairs. 33182 records in RAM.
INFO 2026-06-08 08:15:57 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:06:46s. Time for last 1,000,000: 2s. Last read position: chr12:53,443,427
INFO 2026-06-08 08:15:57 MarkDuplicates Tracking 437463 as yet unmatched pairs. 29945 records in RAM.
INFO 2026-06-08 08:16:00 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 2s. Last read position: chr12:56,004,328
INFO 2026-06-08 08:16:00 MarkDuplicates Tracking 434785 as yet unmatched pairs. 27263 records in RAM.
INFO 2026-06-08 08:16:02 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 1s. Last read position: chr12:56,714,602
INFO 2026-06-08 08:16:02 MarkDuplicates Tracking 432725 as yet unmatched pairs. 25189 records in RAM.
INFO 2026-06-08 08:16:03 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 1s. Last read position: chr12:57,190,878
INFO 2026-06-08 08:16:03 MarkDuplicates Tracking 429048 as yet unmatched pairs. 21506 records in RAM.
INFO 2026-06-08 08:16:05 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 1s. Last read position: chr12:66,137,990
INFO 2026-06-08 08:16:05 MarkDuplicates Tracking 426005 as yet unmatched pairs. 18452 records in RAM.
INFO 2026-06-08 08:16:07 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 1s. Last read position: chr12:89,349,511
INFO 2026-06-08 08:16:07 MarkDuplicates Tracking 423206 as yet unmatched pairs. 15636 records in RAM.
INFO 2026-06-08 08:16:09 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:06:57s. Time for last 1,000,000: 1s. Last read position: chr12:104,265,794
INFO 2026-06-08 08:16:09 MarkDuplicates Tracking 420562 as yet unmatched pairs. 12983 records in RAM.
INFO 2026-06-08 08:16:10 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 1s. Last read position: chr12:112,185,090
INFO 2026-06-08 08:16:10 MarkDuplicates Tracking 417454 as yet unmatched pairs. 9858 records in RAM.
INFO 2026-06-08 08:16:12 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 1s. Last read position: chr12:120,212,293
INFO 2026-06-08 08:16:12 MarkDuplicates Tracking 414946 as yet unmatched pairs. 7337 records in RAM.
INFO 2026-06-08 08:16:14 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 1s. Last read position: chr12:123,012,635
INFO 2026-06-08 08:16:14 MarkDuplicates Tracking 411480 as yet unmatched pairs. 3862 records in RAM.
INFO 2026-06-08 08:16:16 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:07:04s. Time for last 1,000,000: 1s. Last read position: chr12:132,583,109
INFO 2026-06-08 08:16:16 MarkDuplicates Tracking 408413 as yet unmatched pairs. 786 records in RAM.
INFO 2026-06-08 08:16:18 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 1s. Last read position: chr13:28,659,175
INFO 2026-06-08 08:16:18 MarkDuplicates Tracking 405613 as yet unmatched pairs. 10853 records in RAM.
INFO 2026-06-08 08:16:20 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 2s. Last read position: chr13:48,233,371
INFO 2026-06-08 08:16:20 MarkDuplicates Tracking 402578 as yet unmatched pairs. 7804 records in RAM.
INFO 2026-06-08 08:16:22 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 2s. Last read position: chr13:77,062,596
INFO 2026-06-08 08:16:22 MarkDuplicates Tracking 399830 as yet unmatched pairs. 5039 records in RAM.
INFO 2026-06-08 08:16:24 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:07:12s. Time for last 1,000,000: 2s. Last read position: chr13:110,457,355
INFO 2026-06-08 08:16:24 MarkDuplicates Tracking 396674 as yet unmatched pairs. 1869 records in RAM.
INFO 2026-06-08 08:16:26 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:07:15s. Time for last 1,000,000: 2s. Last read position: chr14:21,383,860
INFO 2026-06-08 08:16:26 MarkDuplicates Tracking 393409 as yet unmatched pairs. 30464 records in RAM.
INFO 2026-06-08 08:16:28 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:07:17s. Time for last 1,000,000: 1s. Last read position: chr14:24,190,439
INFO 2026-06-08 08:16:28 MarkDuplicates Tracking 390233 as yet unmatched pairs. 27282 records in RAM.
INFO 2026-06-08 08:16:30 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:07:19s. Time for last 1,000,000: 1s. Last read position: chr14:49,618,862
INFO 2026-06-08 08:16:30 MarkDuplicates Tracking 387672 as yet unmatched pairs. 24697 records in RAM.
INFO 2026-06-08 08:16:32 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:07:20s. Time for last 1,000,000: 1s. Last read position: chr14:63,954,770
INFO 2026-06-08 08:16:32 MarkDuplicates Tracking 384661 as yet unmatched pairs. 21659 records in RAM.
INFO 2026-06-08 08:16:34 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:07:22s. Time for last 1,000,000: 1s. Last read position: chr14:70,962,225
INFO 2026-06-08 08:16:34 MarkDuplicates Tracking 381566 as yet unmatched pairs. 18551 records in RAM.
INFO 2026-06-08 08:16:35 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:07:24s. Time for last 1,000,000: 1s. Last read position: chr14:77,298,720
INFO 2026-06-08 08:16:35 MarkDuplicates Tracking 378647 as yet unmatched pairs. 15619 records in RAM.
INFO 2026-06-08 08:16:37 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:07:26s. Time for last 1,000,000: 1s. Last read position: chr14:95,204,353
INFO 2026-06-08 08:16:37 MarkDuplicates Tracking 375868 as yet unmatched pairs. 12830 records in RAM.
INFO 2026-06-08 08:16:39 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:07:28s. Time for last 1,000,000: 1s. Last read position: chr14:103,657,640
INFO 2026-06-08 08:16:39 MarkDuplicates Tracking 372495 as yet unmatched pairs. 9431 records in RAM.
INFO 2026-06-08 08:16:41 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:07:29s. Time for last 1,000,000: 1s. Last read position: chr14:105,487,214
INFO 2026-06-08 08:16:41 MarkDuplicates Tracking 369582 as yet unmatched pairs. 6508 records in RAM.
INFO 2026-06-08 08:16:42 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:07:31s. Time for last 1,000,000: 1s. Last read position: chr14:105,624,685
INFO 2026-06-08 08:16:42 MarkDuplicates Tracking 366558 as yet unmatched pairs. 3470 records in RAM.
INFO 2026-06-08 08:16:44 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:07:33s. Time for last 1,000,000: 1s. Last read position: chr14:105,742,170
INFO 2026-06-08 08:16:44 MarkDuplicates Tracking 364232 as yet unmatched pairs. 1143 records in RAM.
INFO 2026-06-08 08:16:46 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:07:35s. Time for last 1,000,000: 2s. Last read position: chr15:32,600,380
INFO 2026-06-08 08:16:46 MarkDuplicates Tracking 361765 as yet unmatched pairs. 26373 records in RAM.
INFO 2026-06-08 08:16:48 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:07:36s. Time for last 1,000,000: 1s. Last read position: chr15:40,459,051
INFO 2026-06-08 08:16:48 MarkDuplicates Tracking 358862 as yet unmatched pairs. 23453 records in RAM.
INFO 2026-06-08 08:16:50 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:07:39s. Time for last 1,000,000: 2s. Last read position: chr15:43,765,935
INFO 2026-06-08 08:16:50 MarkDuplicates Tracking 356147 as yet unmatched pairs. 20714 records in RAM.
INFO 2026-06-08 08:16:53 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:07:41s. Time for last 1,000,000: 2s. Last read position: chr15:50,648,811
INFO 2026-06-08 08:16:53 MarkDuplicates Tracking 353312 as yet unmatched pairs. 17873 records in RAM.
INFO 2026-06-08 08:16:55 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:07:43s. Time for last 1,000,000: 1s. Last read position: chr15:60,364,500
INFO 2026-06-08 08:16:55 MarkDuplicates Tracking 351022 as yet unmatched pairs. 15570 records in RAM.
INFO 2026-06-08 08:16:56 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:07:45s. Time for last 1,000,000: 1s. Last read position: chr15:66,502,672
INFO 2026-06-08 08:16:56 MarkDuplicates Tracking 347569 as yet unmatched pairs. 12101 records in RAM.
INFO 2026-06-08 08:16:58 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:07:47s. Time for last 1,000,000: 1s. Last read position: chr15:74,035,421
INFO 2026-06-08 08:16:58 MarkDuplicates Tracking 344766 as yet unmatched pairs. 9285 records in RAM.
INFO 2026-06-08 08:17:00 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:07:49s. Time for last 1,000,000: 1s. Last read position: chr15:80,695,845
INFO 2026-06-08 08:17:00 MarkDuplicates Tracking 341074 as yet unmatched pairs. 5574 records in RAM.
INFO 2026-06-08 08:17:02 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:07:50s. Time for last 1,000,000: 1s. Last read position: chr15:89,321,809
INFO 2026-06-08 08:17:02 MarkDuplicates Tracking 338774 as yet unmatched pairs. 3262 records in RAM.
INFO 2026-06-08 08:17:04 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:07:52s. Time for last 1,000,000: 1s. Last read position: chr15:101,971,925
INFO 2026-06-08 08:17:04 MarkDuplicates Tracking 335584 as yet unmatched pairs. 61 records in RAM.
INFO 2026-06-08 08:17:06 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:07:55s. Time for last 1,000,000: 2s. Last read position: chr16:1,775,659
INFO 2026-06-08 08:17:06 MarkDuplicates Tracking 331942 as yet unmatched pairs. 43566 records in RAM.
INFO 2026-06-08 08:17:08 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:07:56s. Time for last 1,000,000: 1s. Last read position: chr16:2,766,068
INFO 2026-06-08 08:17:08 MarkDuplicates Tracking 328521 as yet unmatched pairs. 40136 records in RAM.
INFO 2026-06-08 08:17:11 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:07:59s. Time for last 1,000,000: 2s. Last read position: chr16:4,811,277
INFO 2026-06-08 08:17:11 MarkDuplicates Tracking 325134 as yet unmatched pairs. 36747 records in RAM.
INFO 2026-06-08 08:17:14 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:08:02s. Time for last 1,000,000: 3s. Last read position: chr16:14,951,748
INFO 2026-06-08 08:17:14 MarkDuplicates Tracking 322970 as yet unmatched pairs. 34578 records in RAM.
INFO 2026-06-08 08:17:17 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 3s. Last read position: chr16:16,329,027
INFO 2026-06-08 08:17:17 MarkDuplicates Tracking 320652 as yet unmatched pairs. 32248 records in RAM.
INFO 2026-06-08 08:17:19 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:08:08s. Time for last 1,000,000: 2s. Last read position: chr16:19,474,190
INFO 2026-06-08 08:17:19 MarkDuplicates Tracking 319222 as yet unmatched pairs. 30809 records in RAM.
INFO 2026-06-08 08:17:21 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:08:10s. Time for last 1,000,000: 1s. Last read position: chr16:21,851,764
INFO 2026-06-08 08:17:21 MarkDuplicates Tracking 317973 as yet unmatched pairs. 29556 records in RAM.
INFO 2026-06-08 08:17:23 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:08:11s. Time for last 1,000,000: 1s. Last read position: chr16:24,794,576
INFO 2026-06-08 08:17:23 MarkDuplicates Tracking 316511 as yet unmatched pairs. 28090 records in RAM.
INFO 2026-06-08 08:17:25 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:08:13s. Time for last 1,000,000: 1s. Last read position: chr16:29,381,597
INFO 2026-06-08 08:17:25 MarkDuplicates Tracking 314057 as yet unmatched pairs. 25622 records in RAM.
INFO 2026-06-08 08:17:26 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:08:15s. Time for last 1,000,000: 1s. Last read position: chr16:29,986,616
INFO 2026-06-08 08:17:26 MarkDuplicates Tracking 312159 as yet unmatched pairs. 23723 records in RAM.
INFO 2026-06-08 08:17:29 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:08:17s. Time for last 1,000,000: 2s. Last read position: chr16:30,669,380
INFO 2026-06-08 08:17:29 MarkDuplicates Tracking 309677 as yet unmatched pairs. 21238 records in RAM.
INFO 2026-06-08 08:17:31 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 2s. Last read position: chr16:32,770,392
INFO 2026-06-08 08:17:31 MarkDuplicates Tracking 306599 as yet unmatched pairs. 18153 records in RAM.
INFO 2026-06-08 08:17:33 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:08:22s. Time for last 1,000,000: 2s. Last read position: chr16:57,363,729
INFO 2026-06-08 08:17:33 MarkDuplicates Tracking 303622 as yet unmatched pairs. 15163 records in RAM.
INFO 2026-06-08 08:17:35 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:08:24s. Time for last 1,000,000: 2s. Last read position: chr16:67,879,278
INFO 2026-06-08 08:17:35 MarkDuplicates Tracking 300304 as yet unmatched pairs. 11840 records in RAM.
INFO 2026-06-08 08:17:37 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:08:26s. Time for last 1,000,000: 2s. Last read position: chr16:70,664,116
INFO 2026-06-08 08:17:37 MarkDuplicates Tracking 297308 as yet unmatched pairs. 8835 records in RAM.
INFO 2026-06-08 08:17:39 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:08:28s. Time for last 1,000,000: 2s. Last read position: chr16:81,705,455
INFO 2026-06-08 08:17:39 MarkDuplicates Tracking 294400 as yet unmatched pairs. 5919 records in RAM.
INFO 2026-06-08 08:17:42 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:08:30s. Time for last 1,000,000: 2s. Last read position: chr16:88,722,866
INFO 2026-06-08 08:17:42 MarkDuplicates Tracking 290999 as yet unmatched pairs. 2492 records in RAM.
INFO 2026-06-08 08:17:45 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:08:33s. Time for last 1,000,000: 2s. Last read position: chr17:1,361,191
INFO 2026-06-08 08:17:45 MarkDuplicates Tracking 288378 as yet unmatched pairs. 88647 records in RAM.
INFO 2026-06-08 08:17:47 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 2s. Last read position: chr17:4,072,611
INFO 2026-06-08 08:17:47 MarkDuplicates Tracking 284502 as yet unmatched pairs. 84762 records in RAM.
INFO 2026-06-08 08:17:49 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:08:38s. Time for last 1,000,000: 2s. Last read position: chr17:7,223,177
INFO 2026-06-08 08:17:49 MarkDuplicates Tracking 281392 as yet unmatched pairs. 81641 records in RAM.
INFO 2026-06-08 08:17:51 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 2s. Last read position: chr17:7,846,821
INFO 2026-06-08 08:17:51 MarkDuplicates Tracking 278139 as yet unmatched pairs. 78385 records in RAM.
INFO 2026-06-08 08:17:54 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:08:42s. Time for last 1,000,000: 2s. Last read position: chr17:16,382,055
INFO 2026-06-08 08:17:54 MarkDuplicates Tracking 275821 as yet unmatched pairs. 76061 records in RAM.
INFO 2026-06-08 08:17:56 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:08:44s. Time for last 1,000,000: 1s. Last read position: chr17:22,204,323
INFO 2026-06-08 08:17:56 MarkDuplicates Tracking 272054 as yet unmatched pairs. 72281 records in RAM.
INFO 2026-06-08 08:17:58 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:08:46s. Time for last 1,000,000: 1s. Last read position: chr17:30,184,644
INFO 2026-06-08 08:17:58 MarkDuplicates Tracking 269184 as yet unmatched pairs. 69400 records in RAM.
INFO 2026-06-08 08:18:00 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 1s. Last read position: chr17:36,537,193
INFO 2026-06-08 08:18:00 MarkDuplicates Tracking 266551 as yet unmatched pairs. 66761 records in RAM.
INFO 2026-06-08 08:18:01 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:08:50s. Time for last 1,000,000: 1s. Last read position: chr17:39,700,295
INFO 2026-06-08 08:18:01 MarkDuplicates Tracking 264531 as yet unmatched pairs. 64741 records in RAM.
INFO 2026-06-08 08:18:04 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:08:52s. Time for last 1,000,000: 2s. Last read position: chr17:40,356,165
INFO 2026-06-08 08:18:04 MarkDuplicates Tracking 260659 as yet unmatched pairs. 60866 records in RAM.
INFO 2026-06-08 08:18:05 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 1s. Last read position: chr17:42,567,218
INFO 2026-06-08 08:18:05 MarkDuplicates Tracking 257265 as yet unmatched pairs. 57469 records in RAM.
INFO 2026-06-08 08:18:07 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:08:56s. Time for last 1,000,000: 1s. Last read position: chr17:45,169,252
INFO 2026-06-08 08:18:07 MarkDuplicates Tracking 254201 as yet unmatched pairs. 54399 records in RAM.
INFO 2026-06-08 08:19:14 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:10:03s. Time for last 1,000,000: 67s. Last read position: chr17:48,940,930
INFO 2026-06-08 08:19:14 MarkDuplicates Tracking 251553 as yet unmatched pairs. 51745 records in RAM.
INFO 2026-06-08 08:19:16 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:10:05s. Time for last 1,000,000: 2s. Last read position: chr17:50,186,911
INFO 2026-06-08 08:19:16 MarkDuplicates Tracking 253631 as yet unmatched pairs. 53820 records in RAM.
INFO 2026-06-08 08:19:18 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:10:07s. Time for last 1,000,000: 1s. Last read position: chr17:50,188,752
INFO 2026-06-08 08:19:18 MarkDuplicates Tracking 249679 as yet unmatched pairs. 49858 records in RAM.
INFO 2026-06-08 08:19:20 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 1s. Last read position: chr17:50,190,000
INFO 2026-06-08 08:19:20 MarkDuplicates Tracking 244225 as yet unmatched pairs. 44401 records in RAM.
INFO 2026-06-08 08:19:22 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:10:11s. Time for last 1,000,000: 1s. Last read position: chr17:50,192,662
INFO 2026-06-08 08:19:22 MarkDuplicates Tracking 240611 as yet unmatched pairs. 40787 records in RAM.
INFO 2026-06-08 08:19:24 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 1s. Last read position: chr17:50,194,430
INFO 2026-06-08 08:19:24 MarkDuplicates Tracking 240475 as yet unmatched pairs. 40651 records in RAM.
INFO 2026-06-08 08:19:26 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:10:15s. Time for last 1,000,000: 2s. Last read position: chr17:50,196,180
INFO 2026-06-08 08:19:26 MarkDuplicates Tracking 237230 as yet unmatched pairs. 37400 records in RAM.
INFO 2026-06-08 08:19:28 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:10:17s. Time for last 1,000,000: 2s. Last read position: chr17:50,198,160
INFO 2026-06-08 08:19:28 MarkDuplicates Tracking 228957 as yet unmatched pairs. 29125 records in RAM.
INFO 2026-06-08 08:19:30 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:10:18s. Time for last 1,000,000: 1s. Last read position: chr17:50,201,413
INFO 2026-06-08 08:19:30 MarkDuplicates Tracking 225924 as yet unmatched pairs. 26092 records in RAM.
INFO 2026-06-08 08:19:32 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:10:20s. Time for last 1,000,000: 1s. Last read position: chr17:58,358,025
INFO 2026-06-08 08:19:32 MarkDuplicates Tracking 220999 as yet unmatched pairs. 21156 records in RAM.
INFO 2026-06-08 08:19:34 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:10:22s. Time for last 1,000,000: 2s. Last read position: chr17:63,820,348
INFO 2026-06-08 08:19:34 MarkDuplicates Tracking 217822 as yet unmatched pairs. 17974 records in RAM.
INFO 2026-06-08 08:19:36 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:10:24s. Time for last 1,000,000: 1s. Last read position: chr17:72,121,805
INFO 2026-06-08 08:19:36 MarkDuplicates Tracking 215292 as yet unmatched pairs. 15441 records in RAM.
INFO 2026-06-08 08:19:37 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 1s. Last read position: chr17:75,730,303
INFO 2026-06-08 08:19:37 MarkDuplicates Tracking 212182 as yet unmatched pairs. 12326 records in RAM.
INFO 2026-06-08 08:19:39 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:10:28s. Time for last 1,000,000: 2s. Last read position: chr17:77,213,915
INFO 2026-06-08 08:19:39 MarkDuplicates Tracking 208319 as yet unmatched pairs. 8456 records in RAM.
INFO 2026-06-08 08:19:42 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:10:30s. Time for last 1,000,000: 2s. Last read position: chr17:80,346,725
INFO 2026-06-08 08:19:42 MarkDuplicates Tracking 205044 as yet unmatched pairs. 5176 records in RAM.
INFO 2026-06-08 08:19:44 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:10:32s. Time for last 1,000,000: 1s. Last read position: chr17:82,054,655
INFO 2026-06-08 08:19:44 MarkDuplicates Tracking 201550 as yet unmatched pairs. 1679 records in RAM.
INFO 2026-06-08 08:19:46 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:10:34s. Time for last 1,000,000: 1s. Last read position: chr18:20,955,214
INFO 2026-06-08 08:19:46 MarkDuplicates Tracking 198457 as yet unmatched pairs. 5368 records in RAM.
INFO 2026-06-08 08:19:47 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:10:36s. Time for last 1,000,000: 1s. Last read position: chr18:49,853,527
INFO 2026-06-08 08:19:47 MarkDuplicates Tracking 195738 as yet unmatched pairs. 2642 records in RAM.
INFO 2026-06-08 08:19:50 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:10:39s. Time for last 1,000,000: 2s. Last read position: chr19:582,509
INFO 2026-06-08 08:19:50 MarkDuplicates Tracking 193623 as yet unmatched pairs. 109559 records in RAM.
INFO 2026-06-08 08:19:52 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:10:40s. Time for last 1,000,000: 1s. Last read position: chr19:1,432,615
INFO 2026-06-08 08:19:52 MarkDuplicates Tracking 188749 as yet unmatched pairs. 104683 records in RAM.
INFO 2026-06-08 08:19:54 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:10:42s. Time for last 1,000,000: 1s. Last read position: chr19:3,452,527
INFO 2026-06-08 08:19:54 MarkDuplicates Tracking 184998 as yet unmatched pairs. 100930 records in RAM.
INFO 2026-06-08 08:19:56 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:10:44s. Time for last 1,000,000: 1s. Last read position: chr19:5,691,343
INFO 2026-06-08 08:19:56 MarkDuplicates Tracking 181596 as yet unmatched pairs. 97525 records in RAM.
INFO 2026-06-08 08:19:57 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 1s. Last read position: chr19:6,744,903
INFO 2026-06-08 08:19:57 MarkDuplicates Tracking 178299 as yet unmatched pairs. 94224 records in RAM.
INFO 2026-06-08 08:19:59 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:10:47s. Time for last 1,000,000: 1s. Last read position: chr19:10,090,015
INFO 2026-06-08 08:19:59 MarkDuplicates Tracking 174865 as yet unmatched pairs. 90785 records in RAM.
INFO 2026-06-08 08:20:01 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:10:49s. Time for last 1,000,000: 1s. Last read position: chr19:11,041,365
INFO 2026-06-08 08:20:01 MarkDuplicates Tracking 171546 as yet unmatched pairs. 87460 records in RAM.
INFO 2026-06-08 08:20:03 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:10:51s. Time for last 1,000,000: 1s. Last read position: chr19:12,770,969
INFO 2026-06-08 08:20:03 MarkDuplicates Tracking 168425 as yet unmatched pairs. 84338 records in RAM.
INFO 2026-06-08 08:20:05 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:10:53s. Time for last 1,000,000: 1s. Last read position: chr19:14,478,390
INFO 2026-06-08 08:20:05 MarkDuplicates Tracking 165133 as yet unmatched pairs. 81039 records in RAM.
INFO 2026-06-08 08:20:07 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:10:55s. Time for last 1,000,000: 2s. Last read position: chr19:15,272,964
INFO 2026-06-08 08:20:07 MarkDuplicates Tracking 162627 as yet unmatched pairs. 78531 records in RAM.
INFO 2026-06-08 08:20:09 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:10:57s. Time for last 1,000,000: 2s. Last read position: chr19:17,733,248
INFO 2026-06-08 08:20:09 MarkDuplicates Tracking 158472 as yet unmatched pairs. 74375 records in RAM.
INFO 2026-06-08 08:20:11 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:10:59s. Time for last 1,000,000: 1s. Last read position: chr19:18,777,171
INFO 2026-06-08 08:20:11 MarkDuplicates Tracking 155097 as yet unmatched pairs. 70994 records in RAM.
INFO 2026-06-08 08:20:12 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:11:01s. Time for last 1,000,000: 1s. Last read position: chr19:34,393,260
INFO 2026-06-08 08:20:12 MarkDuplicates Tracking 151709 as yet unmatched pairs. 67605 records in RAM.
INFO 2026-06-08 08:20:14 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:11:03s. Time for last 1,000,000: 1s. Last read position: chr19:35,766,852
INFO 2026-06-08 08:20:14 MarkDuplicates Tracking 148005 as yet unmatched pairs. 63901 records in RAM.
INFO 2026-06-08 08:20:16 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:11:04s. Time for last 1,000,000: 1s. Last read position: chr19:38,801,862
INFO 2026-06-08 08:20:16 MarkDuplicates Tracking 146084 as yet unmatched pairs. 61980 records in RAM.
INFO 2026-06-08 08:20:18 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:11:06s. Time for last 1,000,000: 1s. Last read position: chr19:39,473,421
INFO 2026-06-08 08:20:18 MarkDuplicates Tracking 141701 as yet unmatched pairs. 57597 records in RAM.
INFO 2026-06-08 08:20:20 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:11:08s. Time for last 1,000,000: 1s. Last read position: chr19:39,875,844
INFO 2026-06-08 08:20:20 MarkDuplicates Tracking 138609 as yet unmatched pairs. 54502 records in RAM.
INFO 2026-06-08 08:20:21 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:11:09s. Time for last 1,000,000: 1s. Last read position: chr19:39,878,017
INFO 2026-06-08 08:20:21 MarkDuplicates Tracking 142303 as yet unmatched pairs. 58196 records in RAM.
INFO 2026-06-08 08:20:23 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:11:11s. Time for last 1,000,000: 1s. Last read position: chr19:39,886,069
INFO 2026-06-08 08:20:23 MarkDuplicates Tracking 139097 as yet unmatched pairs. 54990 records in RAM.
INFO 2026-06-08 08:20:24 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:11:13s. Time for last 1,000,000: 1s. Last read position: chr19:39,889,882
INFO 2026-06-08 08:20:24 MarkDuplicates Tracking 142109 as yet unmatched pairs. 57998 records in RAM.
INFO 2026-06-08 08:20:27 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:11:15s. Time for last 1,000,000: 2s. Last read position: chr19:39,892,989
INFO 2026-06-08 08:20:27 MarkDuplicates Tracking 135917 as yet unmatched pairs. 51800 records in RAM.
INFO 2026-06-08 08:20:29 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:11:17s. Time for last 1,000,000: 2s. Last read position: chr19:39,895,933
INFO 2026-06-08 08:20:29 MarkDuplicates Tracking 130801 as yet unmatched pairs. 46684 records in RAM.
INFO 2026-06-08 08:20:30 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:11:19s. Time for last 1,000,000: 1s. Last read position: chr19:39,905,975
INFO 2026-06-08 08:20:30 MarkDuplicates Tracking 129719 as yet unmatched pairs. 45602 records in RAM.
INFO 2026-06-08 08:20:32 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:11:20s. Time for last 1,000,000: 1s. Last read position: chr19:39,927,916
INFO 2026-06-08 08:20:32 MarkDuplicates Tracking 120872 as yet unmatched pairs. 36752 records in RAM.
INFO 2026-06-08 08:20:34 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:11:22s. Time for last 1,000,000: 1s. Last read position: chr19:41,301,615
INFO 2026-06-08 08:20:34 MarkDuplicates Tracking 116365 as yet unmatched pairs. 32242 records in RAM.
INFO 2026-06-08 08:20:35 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:11:24s. Time for last 1,000,000: 1s. Last read position: chr19:41,715,132
INFO 2026-06-08 08:20:35 MarkDuplicates Tracking 116050 as yet unmatched pairs. 31925 records in RAM.
INFO 2026-06-08 08:20:37 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:11:25s. Time for last 1,000,000: 1s. Last read position: chr19:41,720,069
INFO 2026-06-08 08:20:37 MarkDuplicates Tracking 116302 as yet unmatched pairs. 32176 records in RAM.
INFO 2026-06-08 08:20:39 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:11:27s. Time for last 1,000,000: 1s. Last read position: chr19:41,958,315
INFO 2026-06-08 08:20:39 MarkDuplicates Tracking 108020 as yet unmatched pairs. 23890 records in RAM.
INFO 2026-06-08 08:20:41 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:11:29s. Time for last 1,000,000: 1s. Last read position: chr19:43,507,989
INFO 2026-06-08 08:20:41 MarkDuplicates Tracking 105140 as yet unmatched pairs. 20997 records in RAM.
INFO 2026-06-08 08:20:43 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:11:31s. Time for last 1,000,000: 1s. Last read position: chr19:45,778,622
INFO 2026-06-08 08:20:43 MarkDuplicates Tracking 101285 as yet unmatched pairs. 17140 records in RAM.
INFO 2026-06-08 08:20:44 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:11:33s. Time for last 1,000,000: 1s. Last read position: chr19:48,615,891
INFO 2026-06-08 08:20:44 MarkDuplicates Tracking 98299 as yet unmatched pairs. 14151 records in RAM.
INFO 2026-06-08 08:20:46 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:11:35s. Time for last 1,000,000: 1s. Last read position: chr19:49,651,911
INFO 2026-06-08 08:20:46 MarkDuplicates Tracking 94404 as yet unmatched pairs. 10249 records in RAM.
INFO 2026-06-08 08:20:48 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:11:37s. Time for last 1,000,000: 1s. Last read position: chr19:52,221,086
INFO 2026-06-08 08:20:48 MarkDuplicates Tracking 90880 as yet unmatched pairs. 6723 records in RAM.
INFO 2026-06-08 08:20:50 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:11:38s. Time for last 1,000,000: 1s. Last read position: chr19:55,346,945
INFO 2026-06-08 08:20:50 MarkDuplicates Tracking 87538 as yet unmatched pairs. 3379 records in RAM.
INFO 2026-06-08 08:20:52 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:11:41s. Time for last 1,000,000: 2s. Last read position: chr19:58,550,489
INFO 2026-06-08 08:20:52 MarkDuplicates Tracking 84614 as yet unmatched pairs. 454 records in RAM.
INFO 2026-06-08 08:20:55 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:11:44s. Time for last 1,000,000: 2s. Last read position: chr20:10,641,460
INFO 2026-06-08 08:20:55 MarkDuplicates Tracking 81185 as yet unmatched pairs. 18072 records in RAM.
INFO 2026-06-08 08:20:57 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:11:45s. Time for last 1,000,000: 1s. Last read position: chr20:25,296,373
INFO 2026-06-08 08:20:57 MarkDuplicates Tracking 78261 as yet unmatched pairs. 15146 records in RAM.
INFO 2026-06-08 08:20:59 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:11:47s. Time for last 1,000,000: 1s. Last read position: chr20:35,938,930
INFO 2026-06-08 08:20:59 MarkDuplicates Tracking 75053 as yet unmatched pairs. 11932 records in RAM.
INFO 2026-06-08 08:21:00 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:11:49s. Time for last 1,000,000: 1s. Last read position: chr20:45,330,414
INFO 2026-06-08 08:21:00 MarkDuplicates Tracking 72375 as yet unmatched pairs. 9254 records in RAM.
INFO 2026-06-08 08:21:02 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:11:51s. Time for last 1,000,000: 1s. Last read position: chr20:51,523,250
INFO 2026-06-08 08:21:02 MarkDuplicates Tracking 69106 as yet unmatched pairs. 5984 records in RAM.
INFO 2026-06-08 08:21:04 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:11:52s. Time for last 1,000,000: 1s. Last read position: chr20:62,812,794
INFO 2026-06-08 08:21:04 MarkDuplicates Tracking 65442 as yet unmatched pairs. 2319 records in RAM.
INFO 2026-06-08 08:21:06 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:11:54s. Time for last 1,000,000: 1s. Last read position: chr21:8,216,459
INFO 2026-06-08 08:21:06 MarkDuplicates Tracking 62496 as yet unmatched pairs. 12587 records in RAM.
INFO 2026-06-08 08:21:07 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:11:55s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,574
INFO 2026-06-08 08:21:07 MarkDuplicates Tracking 61542 as yet unmatched pairs. 11628 records in RAM.
INFO 2026-06-08 08:21:09 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:11:57s. Time for last 1,000,000: 1s. Last read position: chr21:33,813,982
INFO 2026-06-08 08:21:09 MarkDuplicates Tracking 58707 as yet unmatched pairs. 8790 records in RAM.
INFO 2026-06-08 08:21:10 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:11:58s. Time for last 1,000,000: 1s. Last read position: chr21:41,991,686
INFO 2026-06-08 08:21:10 MarkDuplicates Tracking 55591 as yet unmatched pairs. 5673 records in RAM.
INFO 2026-06-08 08:21:12 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:12:00s. Time for last 1,000,000: 1s. Last read position: chr21:45,981,838
INFO 2026-06-08 08:21:12 MarkDuplicates Tracking 52522 as yet unmatched pairs. 2602 records in RAM.
INFO 2026-06-08 08:21:14 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:12:02s. Time for last 1,000,000: 1s. Last read position: chr22:19,973,307
INFO 2026-06-08 08:21:14 MarkDuplicates Tracking 48697 as yet unmatched pairs. 23304 records in RAM.
INFO 2026-06-08 08:21:15 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:12:04s. Time for last 1,000,000: 1s. Last read position: chr22:23,882,509
INFO 2026-06-08 08:21:15 MarkDuplicates Tracking 45328 as yet unmatched pairs. 19935 records in RAM.
INFO 2026-06-08 08:21:18 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:12:06s. Time for last 1,000,000: 2s. Last read position: chr22:29,331,449
INFO 2026-06-08 08:21:18 MarkDuplicates Tracking 42078 as yet unmatched pairs. 16685 records in RAM.
INFO 2026-06-08 08:21:20 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:12:08s. Time for last 1,000,000: 2s. Last read position: chr22:36,284,432
INFO 2026-06-08 08:21:20 MarkDuplicates Tracking 39232 as yet unmatched pairs. 13836 records in RAM.
INFO 2026-06-08 08:21:21 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:12:10s. Time for last 1,000,000: 1s. Last read position: chr22:37,927,483
INFO 2026-06-08 08:21:21 MarkDuplicates Tracking 35599 as yet unmatched pairs. 10203 records in RAM.
INFO 2026-06-08 08:21:23 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:12:11s. Time for last 1,000,000: 1s. Last read position: chr22:41,339,100
INFO 2026-06-08 08:21:23 MarkDuplicates Tracking 32448 as yet unmatched pairs. 7051 records in RAM.
INFO 2026-06-08 08:21:25 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:12:13s. Time for last 1,000,000: 1s. Last read position: chr22:46,534,085
INFO 2026-06-08 08:21:25 MarkDuplicates Tracking 28994 as yet unmatched pairs. 3596 records in RAM.
INFO 2026-06-08 08:21:27 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:12:15s. Time for last 1,000,000: 1s. Last read position: chrX:1,387,409
INFO 2026-06-08 08:21:27 MarkDuplicates Tracking 25484 as yet unmatched pairs. 21441 records in RAM.
INFO 2026-06-08 08:21:28 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:12:17s. Time for last 1,000,000: 1s. Last read position: chrX:23,785,694
INFO 2026-06-08 08:21:28 MarkDuplicates Tracking 22542 as yet unmatched pairs. 18482 records in RAM.
INFO 2026-06-08 08:21:30 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:12:18s. Time for last 1,000,000: 1s. Last read position: chrX:47,639,004
INFO 2026-06-08 08:21:30 MarkDuplicates Tracking 19388 as yet unmatched pairs. 15326 records in RAM.
INFO 2026-06-08 08:21:31 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:12:20s. Time for last 1,000,000: 1s. Last read position: chrX:53,631,414
INFO 2026-06-08 08:21:31 MarkDuplicates Tracking 16373 as yet unmatched pairs. 12311 records in RAM.
INFO 2026-06-08 08:21:33 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:12:22s. Time for last 1,000,000: 1s. Last read position: chrX:74,186,668
INFO 2026-06-08 08:21:33 MarkDuplicates Tracking 13589 as yet unmatched pairs. 9527 records in RAM.
INFO 2026-06-08 08:21:35 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:12:23s. Time for last 1,000,000: 1s. Last read position: chrX:109,682,752
INFO 2026-06-08 08:21:35 MarkDuplicates Tracking 10895 as yet unmatched pairs. 6833 records in RAM.
INFO 2026-06-08 08:21:36 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:12:25s. Time for last 1,000,000: 1s. Last read position: chrX:153,346,859
INFO 2026-06-08 08:21:36 MarkDuplicates Tracking 8299 as yet unmatched pairs. 4235 records in RAM.
INFO 2026-06-08 08:21:39 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:12:27s. Time for last 1,000,000: 2s. Last read position: chrX:154,428,821
INFO 2026-06-08 08:21:39 MarkDuplicates Tracking 4960 as yet unmatched pairs. 896 records in RAM.
INFO 2026-06-08 08:21:40 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:12:28s. Time for last 1,000,000: 1s. Last read position: GL000220.1:116,898
INFO 2026-06-08 08:21:40 MarkDuplicates Tracking 2116 as yet unmatched pairs. 159 records in RAM.
INFO 2026-06-08 08:21:41 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:12:30s. Time for last 1,000,000: 1s. Last read position: KI270733.1:177,397
INFO 2026-06-08 08:21:41 MarkDuplicates Tracking 45 as yet unmatched pairs. 36 records in RAM.
INFO 2026-06-08 08:21:42 MarkDuplicates Read 337179422 records. 0 pairs never matched.
INFO 2026-06-08 08:22:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 30024037936; totalMemory: 42849009664; maxMemory: 63585648640
INFO 2026-06-08 08:22:07 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:22:12 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:22:22 OpticalDuplicateFinder Large duplicate set. size = 1261
INFO 2026-06-08 08:22:22 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:1,987
INFO 2026-06-08 08:22:22 OpticalDuplicateFinder Large duplicate set. size = 1148
INFO 2026-06-08 08:22:22 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-25,817
INFO 2026-06-08 08:22:25 OpticalDuplicateFinder Large duplicate set. size = 1094
INFO 2026-06-08 08:22:25 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:2,003
INFO 2026-06-08 08:22:25 OpticalDuplicateFinder Large duplicate set. size = 1038
INFO 2026-06-08 08:22:25 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:4,244
INFO 2026-06-08 08:22:26 OpticalDuplicateFinder Large duplicate set. size = 1107
INFO 2026-06-08 08:22:26 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,915
INFO 2026-06-08 08:22:26 OpticalDuplicateFinder Large duplicate set. size = 1312
INFO 2026-06-08 08:22:26 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-13,998
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder Large duplicate set. size = 1005
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:4,066
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder Large duplicate set. size = 1613
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,103
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder Large duplicate set. size = 1063
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,881
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder Large duplicate set. size = 1008
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,756
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder Large duplicate set. size = 1059
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:26,734
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder Large duplicate set. size = 1513
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,026
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder Large duplicate set. size = 1082
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-22,144
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder Large duplicate set. size = 1159
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:5,118
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder Large duplicate set. size = 1713
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:7,440
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder Large duplicate set. size = 1465
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,186
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder Large duplicate set. size = 1132
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:10,797
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder Large duplicate set. size = 1383
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,837
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder Large duplicate set. size = 1224
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,332
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder Large duplicate set. size = 1039
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-25,267
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder Large duplicate set. size = 1336
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,871
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder Large duplicate set. size = 1317
INFO 2026-06-08 08:22:34 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,342
INFO 2026-06-08 08:22:36 OpticalDuplicateFinder Large duplicate set. size = 1074
INFO 2026-06-08 08:22:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:5,822
INFO 2026-06-08 08:22:36 OpticalDuplicateFinder Large duplicate set. size = 1320
INFO 2026-06-08 08:22:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,876
INFO 2026-06-08 08:22:36 OpticalDuplicateFinder Large duplicate set. size = 1088
INFO 2026-06-08 08:22:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:31,451
INFO 2026-06-08 08:22:36 OpticalDuplicateFinder Large duplicate set. size = 1908
INFO 2026-06-08 08:22:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,220
INFO 2026-06-08 08:22:38 MarkDuplicates Traversing fragment information and detecting duplicates.
WARNING 2026-06-08 08:22:39 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
INFO 2026-06-08 08:23:15 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:23:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300674800; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-08 08:23:19 MarkDuplicates Marking 117460204 records as duplicates.
INFO 2026-06-08 08:23:19 MarkDuplicates Found 3431182 optical duplicate clusters.
INFO 2026-06-08 08:23:19 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 08:23:35 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:15s. Time for last 10,000,000: 15s. Last read position: chr1:44,776,127
INFO 2026-06-08 08:23:50 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:31s. Time for last 10,000,000: 15s. Last read position: chr1:155,169,815
INFO 2026-06-08 08:24:06 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:46s. Time for last 10,000,000: 15s. Last read position: chr1:220,210,715
INFO 2026-06-08 08:24:22 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:02s. Time for last 10,000,000: 16s. Last read position: chr2:55,544,346
INFO 2026-06-08 08:24:39 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:19s. Time for last 10,000,000: 16s. Last read position: chr2:197,453,566
INFO 2026-06-08 08:24:55 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:35s. Time for last 10,000,000: 16s. Last read position: chr3:47,124,046
INFO 2026-06-08 08:25:11 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:01:51s. Time for last 10,000,000: 15s. Last read position: chr3:190,308,276
INFO 2026-06-08 08:25:27 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:07s. Time for last 10,000,000: 16s. Last read position: chr4:125,398,891
INFO 2026-06-08 08:25:43 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:23s. Time for last 10,000,000: 16s. Last read position: chr5:141,924,630
INFO 2026-06-08 08:25:58 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:38s. Time for last 10,000,000: 15s. Last read position: chr6:31,659,762
INFO 2026-06-08 08:26:13 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:02:54s. Time for last 10,000,000: 15s. Last read position: chr6:160,628,227
INFO 2026-06-08 08:26:28 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:09s. Time for last 10,000,000: 14s. Last read position: chr7:100,813,676
INFO 2026-06-08 08:26:43 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:23s. Time for last 10,000,000: 14s. Last read position: chr7:155,706,952
INFO 2026-06-08 08:26:58 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:03:39s. Time for last 10,000,000: 15s. Last read position: chr8:143,865,236
INFO 2026-06-08 08:27:13 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:03:54s. Time for last 10,000,000: 15s. Last read position: chr9:129,640,682
INFO 2026-06-08 08:27:29 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:09s. Time for last 10,000,000: 15s. Last read position: chr10:97,431,016
INFO 2026-06-08 08:27:44 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:04:24s. Time for last 10,000,000: 15s. Last read position: chr11:6,223,857
INFO 2026-06-08 08:27:59 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:04:39s. Time for last 10,000,000: 14s. Last read position: chr11:70,435,047
INFO 2026-06-08 08:28:14 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:04:54s. Time for last 10,000,000: 15s. Last read position: chr12:49,051,452
INFO 2026-06-08 08:28:29 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:05:09s. Time for last 10,000,000: 14s. Last read position: chr12:120,212,293
INFO 2026-06-08 08:28:44 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:05:24s. Time for last 10,000,000: 14s. Last read position: chr14:63,954,770
INFO 2026-06-08 08:28:59 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:05:39s. Time for last 10,000,000: 14s. Last read position: chr15:43,765,935
INFO 2026-06-08 08:29:14 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:05:54s. Time for last 10,000,000: 15s. Last read position: chr16:4,811,277
INFO 2026-06-08 08:29:29 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:06:10s. Time for last 10,000,000: 15s. Last read position: chr16:57,363,729
INFO 2026-06-08 08:29:45 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:06:25s. Time for last 10,000,000: 15s. Last read position: chr17:22,204,323
INFO 2026-06-08 08:30:00 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:06:40s. Time for last 10,000,000: 15s. Last read position: chr17:50,190,000
INFO 2026-06-08 08:30:15 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:06:56s. Time for last 10,000,000: 15s. Last read position: chr17:77,213,915
INFO 2026-06-08 08:30:31 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:07:11s. Time for last 10,000,000: 15s. Last read position: chr19:10,090,015
INFO 2026-06-08 08:30:47 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:07:27s. Time for last 10,000,000: 15s. Last read position: chr19:39,473,421
INFO 2026-06-08 08:31:02 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:07:42s. Time for last 10,000,000: 15s. Last read position: chr19:41,715,132
INFO 2026-06-08 08:31:18 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:07:58s. Time for last 10,000,000: 15s. Last read position: chr20:10,641,460
INFO 2026-06-08 08:31:33 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:08:14s. Time for last 10,000,000: 15s. Last read position: chr21:45,981,838
INFO 2026-06-08 08:31:49 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:08:29s. Time for last 10,000,000: 15s. Last read position: chrX:47,639,004
INFO 2026-06-08 08:32:06 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:32:06 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:32:06 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:32:06 MarkDuplicates Before output close freeMemory: 202146008; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:32:06 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:32:06 MarkDuplicates After output close freeMemory: 104147040; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 08:32:06 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 22.95 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory