Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/7d689d02309ab4996dad6f89d912a0/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.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/77/047ba7c8aafd4f00175a73129e1472/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/047ba7c8aafd4f00175a73129e1472/.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 FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bam --METRICS_FILE FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
08:33:21.238 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 08:33:21 GMT 2026] MarkDuplicates --INPUT FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bam --METRICS_FILE FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 08:33:21 GMT 2026] Executing as ?@nf-77047ba7c8aafd4f00175a73129e1472-3a593-js62b 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 08:33:21 MarkDuplicates Start of doWork freeMemory: 105492552; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 08:33:21 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 08:33:21 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 08:33:25 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:1,387,115
INFO 2026-06-08 08:33:25 MarkDuplicates Tracking 4003 as yet unmatched pairs. 337 records in RAM.
INFO 2026-06-08 08:33:28 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: chr1:6,085,219
INFO 2026-06-08 08:33:28 MarkDuplicates Tracking 8010 as yet unmatched pairs. 1254 records in RAM.
INFO 2026-06-08 08:33:30 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 2s. Last read position: chr1:9,717,013
INFO 2026-06-08 08:33:30 MarkDuplicates Tracking 11158 as yet unmatched pairs. 1473 records in RAM.
INFO 2026-06-08 08:33:32 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 2s. Last read position: chr1:12,112,011
INFO 2026-06-08 08:33:32 MarkDuplicates Tracking 13660 as yet unmatched pairs. 811 records in RAM.
INFO 2026-06-08 08:33:35 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 2s. Last read position: chr1:17,022,691
INFO 2026-06-08 08:33:35 MarkDuplicates Tracking 16265 as yet unmatched pairs. 695 records in RAM.
INFO 2026-06-08 08:33:37 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: chr1:21,706,773
INFO 2026-06-08 08:33:37 MarkDuplicates Tracking 18617 as yet unmatched pairs. 453 records in RAM.
INFO 2026-06-08 08:33:39 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr1:24,927,592
INFO 2026-06-08 08:33:39 MarkDuplicates Tracking 23150 as yet unmatched pairs. 2406 records in RAM.
INFO 2026-06-08 08:33:41 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 2s. Last read position: chr1:27,409,900
INFO 2026-06-08 08:33:41 MarkDuplicates Tracking 24486 as yet unmatched pairs. 763 records in RAM.
INFO 2026-06-08 08:33:43 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: chr1:30,739,910
INFO 2026-06-08 08:33:43 MarkDuplicates Tracking 40988 as yet unmatched pairs. 14413 records in RAM.
INFO 2026-06-08 08:33:46 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 2s. Last read position: chr1:32,825,364
INFO 2026-06-08 08:33:46 MarkDuplicates Tracking 30369 as yet unmatched pairs. 1041 records in RAM.
INFO 2026-06-08 08:33:47 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 1s. Last read position: chr1:36,301,644
INFO 2026-06-08 08:33:47 MarkDuplicates Tracking 32448 as yet unmatched pairs. 273 records in RAM.
INFO 2026-06-08 08:33:49 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 1s. Last read position: chr1:39,576,024
INFO 2026-06-08 08:33:49 MarkDuplicates Tracking 35173 as yet unmatched pairs. 239 records in RAM.
INFO 2026-06-08 08:33:52 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 2s. Last read position: chr1:43,428,262
INFO 2026-06-08 08:33:52 MarkDuplicates Tracking 38131 as yet unmatched pairs. 318 records in RAM.
INFO 2026-06-08 08:33:54 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 1s. Last read position: chr1:45,693,705
INFO 2026-06-08 08:33:54 MarkDuplicates Tracking 40602 as yet unmatched pairs. 176 records in RAM.
INFO 2026-06-08 08:33:56 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 2s. Last read position: chr1:52,488,909
INFO 2026-06-08 08:33:56 MarkDuplicates Tracking 43720 as yet unmatched pairs. 359 records in RAM.
INFO 2026-06-08 08:33:58 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 2s. Last read position: chr1:70,178,940
INFO 2026-06-08 08:33:58 MarkDuplicates Tracking 46052 as yet unmatched pairs. 199 records in RAM.
INFO 2026-06-08 08:34:00 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 1s. Last read position: chr1:86,715,832
INFO 2026-06-08 08:34:00 MarkDuplicates Tracking 49292 as yet unmatched pairs. 934 records in RAM.
INFO 2026-06-08 08:34:02 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 1s. Last read position: chr1:108,692,737
INFO 2026-06-08 08:34:02 MarkDuplicates Tracking 51007 as yet unmatched pairs. 251 records in RAM.
INFO 2026-06-08 08:34:04 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chr1:111,456,705
INFO 2026-06-08 08:34:04 MarkDuplicates Tracking 54114 as yet unmatched pairs. 832 records in RAM.
INFO 2026-06-08 08:34:06 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 1s. Last read position: chr1:116,393,566
INFO 2026-06-08 08:34:06 MarkDuplicates Tracking 57132 as yet unmatched pairs. 1299 records in RAM.
INFO 2026-06-08 08:34:08 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 1s. Last read position: chr1:146,139,948
INFO 2026-06-08 08:34:08 MarkDuplicates Tracking 58042 as yet unmatched pairs. 178 records in RAM.
INFO 2026-06-08 08:34:10 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 2s. Last read position: chr1:149,841,034
INFO 2026-06-08 08:34:10 MarkDuplicates Tracking 66454 as yet unmatched pairs. 6442 records in RAM.
INFO 2026-06-08 08:34:11 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 1s. Last read position: chr1:150,158,851
INFO 2026-06-08 08:34:11 MarkDuplicates Tracking 63877 as yet unmatched pairs. 2497 records in RAM.
INFO 2026-06-08 08:34:13 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 1s. Last read position: chr1:151,342,881
INFO 2026-06-08 08:34:13 MarkDuplicates Tracking 65424 as yet unmatched pairs. 1293 records in RAM.
INFO 2026-06-08 08:34:15 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 2s. Last read position: chr1:154,157,659
INFO 2026-06-08 08:34:15 MarkDuplicates Tracking 77221 as yet unmatched pairs. 10341 records in RAM.
INFO 2026-06-08 08:34:17 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 1s. Last read position: chr1:154,601,496
INFO 2026-06-08 08:34:17 MarkDuplicates Tracking 72414 as yet unmatched pairs. 3030 records in RAM.
INFO 2026-06-08 08:34:19 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 1s. Last read position: chr1:155,659,916
INFO 2026-06-08 08:34:19 MarkDuplicates Tracking 72886 as yet unmatched pairs. 832 records in RAM.
INFO 2026-06-08 08:34:21 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 1s. Last read position: chr1:156,277,096
INFO 2026-06-08 08:34:21 MarkDuplicates Tracking 75416 as yet unmatched pairs. 461 records in RAM.
INFO 2026-06-08 08:34:23 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 2s. Last read position: chr1:160,290,564
INFO 2026-06-08 08:34:23 MarkDuplicates Tracking 78341 as yet unmatched pairs. 815 records in RAM.
INFO 2026-06-08 08:34:25 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 2s. Last read position: chr1:161,054,637
INFO 2026-06-08 08:34:25 MarkDuplicates Tracking 81087 as yet unmatched pairs. 931 records in RAM.
INFO 2026-06-08 08:34:27 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 1s. Last read position: chr1:169,127,396
INFO 2026-06-08 08:34:27 MarkDuplicates Tracking 84668 as yet unmatched pairs. 1897 records in RAM.
INFO 2026-06-08 08:34:29 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 1s. Last read position: chr1:179,050,320
INFO 2026-06-08 08:34:29 MarkDuplicates Tracking 85414 as yet unmatched pairs. 192 records in RAM.
INFO 2026-06-08 08:34:30 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 1s. Last read position: chr1:186,317,510
INFO 2026-06-08 08:34:30 MarkDuplicates Tracking 89226 as yet unmatched pairs. 1105 records in RAM.
INFO 2026-06-08 08:34:32 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 1s. Last read position: chr1:201,468,616
INFO 2026-06-08 08:34:32 MarkDuplicates Tracking 90724 as yet unmatched pairs. 126 records in RAM.
INFO 2026-06-08 08:34:34 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 1s. Last read position: chr1:206,454,957
INFO 2026-06-08 08:34:34 MarkDuplicates Tracking 93175 as yet unmatched pairs. 40 records in RAM.
INFO 2026-06-08 08:34:36 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 1s. Last read position: chr1:219,997,022
INFO 2026-06-08 08:34:36 MarkDuplicates Tracking 96228 as yet unmatched pairs. 463 records in RAM.
INFO 2026-06-08 08:34:38 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 2s. Last read position: chr1:227,030,438
INFO 2026-06-08 08:34:38 MarkDuplicates Tracking 98660 as yet unmatched pairs. 327 records in RAM.
INFO 2026-06-08 08:34:39 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 1s. Last read position: chr1:235,455,614
INFO 2026-06-08 08:34:39 MarkDuplicates Tracking 101754 as yet unmatched pairs. 165 records in RAM.
INFO 2026-06-08 08:34:41 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 1s. Last read position: chr1:247,134,361
INFO 2026-06-08 08:34:41 MarkDuplicates Tracking 104029 as yet unmatched pairs. 4 records in RAM.
INFO 2026-06-08 08:34:44 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 3s. Last read position: chr2:10,788,935
INFO 2026-06-08 08:34:44 MarkDuplicates Tracking 107676 as yet unmatched pairs. 106347 records in RAM.
INFO 2026-06-08 08:34:47 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 2s. Last read position: chr2:25,427,467
INFO 2026-06-08 08:34:47 MarkDuplicates Tracking 110394 as yet unmatched pairs. 109027 records in RAM.
INFO 2026-06-08 08:34:49 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 1s. Last read position: chr2:27,661,151
INFO 2026-06-08 08:34:49 MarkDuplicates Tracking 112585 as yet unmatched pairs. 111202 records in RAM.
INFO 2026-06-08 08:34:51 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,258
INFO 2026-06-08 08:34:51 MarkDuplicates Tracking 158214 as yet unmatched pairs. 110004 records in RAM.
INFO 2026-06-08 08:34:54 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,264
INFO 2026-06-08 08:34:54 MarkDuplicates Tracking 731044 as yet unmatched pairs. 75446 records in RAM.
INFO 2026-06-08 08:34:55 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,406
INFO 2026-06-08 08:34:55 MarkDuplicates Tracking 974199 as yet unmatched pairs. 60431 records in RAM.
INFO 2026-06-08 08:34:57 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 1s. Last read position: chr2:33,595,535
INFO 2026-06-08 08:34:57 MarkDuplicates Tracking 1039377 as yet unmatched pairs. 56540 records in RAM.
INFO 2026-06-08 08:34:58 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 1s. Last read position: chr2:43,901,437
INFO 2026-06-08 08:34:58 MarkDuplicates Tracking 1037046 as yet unmatched pairs. 54150 records in RAM.
INFO 2026-06-08 08:35:00 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 1s. Last read position: chr2:54,646,215
INFO 2026-06-08 08:35:00 MarkDuplicates Tracking 1035078 as yet unmatched pairs. 52145 records in RAM.
INFO 2026-06-08 08:35:02 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 1s. Last read position: chr2:61,301,385
INFO 2026-06-08 08:35:02 MarkDuplicates Tracking 1031834 as yet unmatched pairs. 48854 records in RAM.
INFO 2026-06-08 08:35:04 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 1s. Last read position: chr2:69,475,926
INFO 2026-06-08 08:35:04 MarkDuplicates Tracking 1029218 as yet unmatched pairs. 46187 records in RAM.
INFO 2026-06-08 08:35:06 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 2s. Last read position: chr2:74,198,633
INFO 2026-06-08 08:35:06 MarkDuplicates Tracking 1026958 as yet unmatched pairs. 43889 records in RAM.
INFO 2026-06-08 08:35:08 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 1s. Last read position: chr2:85,616,194
INFO 2026-06-08 08:35:08 MarkDuplicates Tracking 1023574 as yet unmatched pairs. 40483 records in RAM.
INFO 2026-06-08 08:35:10 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 1s. Last read position: chr2:96,275,268
INFO 2026-06-08 08:35:10 MarkDuplicates Tracking 1021820 as yet unmatched pairs. 38695 records in RAM.
INFO 2026-06-08 08:35:12 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 2s. Last read position: chr2:101,004,221
INFO 2026-06-08 08:35:12 MarkDuplicates Tracking 1025567 as yet unmatched pairs. 42395 records in RAM.
INFO 2026-06-08 08:35:13 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 1s. Last read position: chr2:112,389,012
INFO 2026-06-08 08:35:13 MarkDuplicates Tracking 1015810 as yet unmatched pairs. 32610 records in RAM.
INFO 2026-06-08 08:35:15 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 1s. Last read position: chr2:127,719,619
INFO 2026-06-08 08:35:15 MarkDuplicates Tracking 1013893 as yet unmatched pairs. 30657 records in RAM.
INFO 2026-06-08 08:35:17 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 2s. Last read position: chr2:151,270,757
INFO 2026-06-08 08:35:17 MarkDuplicates Tracking 1011262 as yet unmatched pairs. 27969 records in RAM.
INFO 2026-06-08 08:35:19 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 1s. Last read position: chr2:169,821,091
INFO 2026-06-08 08:35:19 MarkDuplicates Tracking 1008809 as yet unmatched pairs. 25474 records in RAM.
INFO 2026-06-08 08:35:21 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 2s. Last read position: chr2:177,505,543
INFO 2026-06-08 08:35:21 MarkDuplicates Tracking 1006352 as yet unmatched pairs. 22971 records in RAM.
INFO 2026-06-08 08:35:23 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 1s. Last read position: chr2:189,782,421
INFO 2026-06-08 08:35:23 MarkDuplicates Tracking 1004336 as yet unmatched pairs. 20904 records in RAM.
INFO 2026-06-08 08:35:25 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 2s. Last read position: chr2:197,078,748
INFO 2026-06-08 08:35:25 MarkDuplicates Tracking 1001359 as yet unmatched pairs. 17889 records in RAM.
INFO 2026-06-08 08:35:27 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 2s. Last read position: chr2:202,467,531
INFO 2026-06-08 08:35:27 MarkDuplicates Tracking 998724 as yet unmatched pairs. 15206 records in RAM.
INFO 2026-06-08 08:35:30 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 2s. Last read position: chr2:216,192,665
INFO 2026-06-08 08:35:30 MarkDuplicates Tracking 999057 as yet unmatched pairs. 15503 records in RAM.
INFO 2026-06-08 08:35:31 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 1s. Last read position: chr2:219,252,050
INFO 2026-06-08 08:35:31 MarkDuplicates Tracking 995256 as yet unmatched pairs. 11669 records in RAM.
INFO 2026-06-08 08:35:34 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 2s. Last read position: chr2:230,310,784
INFO 2026-06-08 08:35:34 MarkDuplicates Tracking 991979 as yet unmatched pairs. 8358 records in RAM.
INFO 2026-06-08 08:35:35 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 1s. Last read position: chr2:231,712,457
INFO 2026-06-08 08:35:35 MarkDuplicates Tracking 991208 as yet unmatched pairs. 7573 records in RAM.
INFO 2026-06-08 08:35:37 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 1s. Last read position: chr2:240,574,521
INFO 2026-06-08 08:35:37 MarkDuplicates Tracking 985948 as yet unmatched pairs. 2272 records in RAM.
INFO 2026-06-08 08:35:40 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 2s. Last read position: chr3:5,201,791
INFO 2026-06-08 08:35:40 MarkDuplicates Tracking 984409 as yet unmatched pairs. 54549 records in RAM.
INFO 2026-06-08 08:35:41 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 1s. Last read position: chr3:12,605,912
INFO 2026-06-08 08:35:41 MarkDuplicates Tracking 981187 as yet unmatched pairs. 51306 records in RAM.
INFO 2026-06-08 08:35:43 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 1s. Last read position: chr3:16,409,406
INFO 2026-06-08 08:35:43 MarkDuplicates Tracking 977152 as yet unmatched pairs. 47229 records in RAM.
INFO 2026-06-08 08:35:45 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr3:37,129,094
INFO 2026-06-08 08:35:45 MarkDuplicates Tracking 974782 as yet unmatched pairs. 44758 records in RAM.
INFO 2026-06-08 08:35:47 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 1s. Last read position: chr3:42,223,432
INFO 2026-06-08 08:35:47 MarkDuplicates Tracking 972235 as yet unmatched pairs. 42163 records in RAM.
INFO 2026-06-08 08:35:49 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 1s. Last read position: chr3:47,122,402
INFO 2026-06-08 08:35:49 MarkDuplicates Tracking 969564 as yet unmatched pairs. 39467 records in RAM.
INFO 2026-06-08 08:35:50 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 1s. Last read position: chr3:48,751,699
INFO 2026-06-08 08:35:50 MarkDuplicates Tracking 966305 as yet unmatched pairs. 36177 records in RAM.
INFO 2026-06-08 08:35:52 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 1s. Last read position: chr3:49,425,024
INFO 2026-06-08 08:35:52 MarkDuplicates Tracking 963532 as yet unmatched pairs. 33375 records in RAM.
INFO 2026-06-08 08:35:54 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 1s. Last read position: chr3:51,634,021
INFO 2026-06-08 08:35:54 MarkDuplicates Tracking 960296 as yet unmatched pairs. 30117 records in RAM.
INFO 2026-06-08 08:35:56 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 2s. Last read position: chr3:52,934,816
INFO 2026-06-08 08:35:56 MarkDuplicates Tracking 957468 as yet unmatched pairs. 27278 records in RAM.
INFO 2026-06-08 08:35:58 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 1s. Last read position: chr3:73,059,088
INFO 2026-06-08 08:35:58 MarkDuplicates Tracking 955101 as yet unmatched pairs. 24866 records in RAM.
INFO 2026-06-08 08:35:59 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 1s. Last read position: chr3:112,464,315
INFO 2026-06-08 08:35:59 MarkDuplicates Tracking 952468 as yet unmatched pairs. 22202 records in RAM.
INFO 2026-06-08 08:36:01 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 1s. Last read position: chr3:122,404,331
INFO 2026-06-08 08:36:01 MarkDuplicates Tracking 951115 as yet unmatched pairs. 20816 records in RAM.
INFO 2026-06-08 08:36:03 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 1s. Last read position: chr3:127,617,971
INFO 2026-06-08 08:36:03 MarkDuplicates Tracking 948241 as yet unmatched pairs. 17915 records in RAM.
INFO 2026-06-08 08:36:05 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 1s. Last read position: chr3:132,675,309
INFO 2026-06-08 08:36:05 MarkDuplicates Tracking 944866 as yet unmatched pairs. 14507 records in RAM.
INFO 2026-06-08 08:36:07 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 2s. Last read position: chr3:143,176,434
INFO 2026-06-08 08:36:07 MarkDuplicates Tracking 942277 as yet unmatched pairs. 11864 records in RAM.
INFO 2026-06-08 08:36:09 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 2s. Last read position: chr3:167,704,845
INFO 2026-06-08 08:36:09 MarkDuplicates Tracking 940185 as yet unmatched pairs. 9707 records in RAM.
INFO 2026-06-08 08:36:11 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 1s. Last read position: chr3:183,037,349
INFO 2026-06-08 08:36:11 MarkDuplicates Tracking 937630 as yet unmatched pairs. 7126 records in RAM.
INFO 2026-06-08 08:36:14 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 2s. Last read position: chr3:186,105,329
INFO 2026-06-08 08:36:14 MarkDuplicates Tracking 935283 as yet unmatched pairs. 4746 records in RAM.
INFO 2026-06-08 08:36:16 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 2s. Last read position: chr3:196,733,786
INFO 2026-06-08 08:36:16 MarkDuplicates Tracking 931807 as yet unmatched pairs. 1228 records in RAM.
INFO 2026-06-08 08:36:18 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 2s. Last read position: chr4:1,721,556
INFO 2026-06-08 08:36:18 MarkDuplicates Tracking 929048 as yet unmatched pairs. 27802 records in RAM.
INFO 2026-06-08 08:36:19 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 1s. Last read position: chr4:2,963,273
INFO 2026-06-08 08:36:19 MarkDuplicates Tracking 925795 as yet unmatched pairs. 24514 records in RAM.
INFO 2026-06-08 08:36:21 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 1s. Last read position: chr4:13,599,203
INFO 2026-06-08 08:36:21 MarkDuplicates Tracking 923092 as yet unmatched pairs. 21783 records in RAM.
INFO 2026-06-08 08:36:23 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 1s. Last read position: chr4:39,456,484
INFO 2026-06-08 08:36:23 MarkDuplicates Tracking 922806 as yet unmatched pairs. 21381 records in RAM.
INFO 2026-06-08 08:36:25 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 1s. Last read position: chr4:55,443,729
INFO 2026-06-08 08:36:25 MarkDuplicates Tracking 918038 as yet unmatched pairs. 16549 records in RAM.
INFO 2026-06-08 08:36:27 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 1s. Last read position: chr4:75,661,978
INFO 2026-06-08 08:36:27 MarkDuplicates Tracking 917095 as yet unmatched pairs. 15588 records in RAM.
INFO 2026-06-08 08:36:29 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 1s. Last read position: chr4:87,105,638
INFO 2026-06-08 08:36:29 MarkDuplicates Tracking 914147 as yet unmatched pairs. 12607 records in RAM.
INFO 2026-06-08 08:36:30 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 1s. Last read position: chr4:105,241,390
INFO 2026-06-08 08:36:30 MarkDuplicates Tracking 910701 as yet unmatched pairs. 9135 records in RAM.
INFO 2026-06-08 08:36:32 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 1s. Last read position: chr4:128,846,434
INFO 2026-06-08 08:36:32 MarkDuplicates Tracking 908551 as yet unmatched pairs. 6941 records in RAM.
INFO 2026-06-08 08:36:34 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 1s. Last read position: chr4:151,101,022
INFO 2026-06-08 08:36:34 MarkDuplicates Tracking 914123 as yet unmatched pairs. 12466 records in RAM.
INFO 2026-06-08 08:36:36 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 1s. Last read position: chr4:173,332,937
INFO 2026-06-08 08:36:36 MarkDuplicates Tracking 904304 as yet unmatched pairs. 2614 records in RAM.
INFO 2026-06-08 08:36:38 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 2s. Last read position: chr5:1,466,881
INFO 2026-06-08 08:36:38 MarkDuplicates Tracking 902055 as yet unmatched pairs. 53749 records in RAM.
INFO 2026-06-08 08:36:40 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 2s. Last read position: chr5:14,366,929
INFO 2026-06-08 08:36:40 MarkDuplicates Tracking 899139 as yet unmatched pairs. 50801 records in RAM.
INFO 2026-06-08 08:36:42 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 1s. Last read position: chr5:33,549,256
INFO 2026-06-08 08:36:42 MarkDuplicates Tracking 894669 as yet unmatched pairs. 46300 records in RAM.
INFO 2026-06-08 08:36:43 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 1s. Last read position: chr5:57,231,184
INFO 2026-06-08 08:36:43 MarkDuplicates Tracking 892785 as yet unmatched pairs. 44385 records in RAM.
INFO 2026-06-08 08:36:45 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: chr5:71,602,588
INFO 2026-06-08 08:36:45 MarkDuplicates Tracking 890485 as yet unmatched pairs. 42072 records in RAM.
INFO 2026-06-08 08:36:47 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 1s. Last read position: chr5:82,276,412
INFO 2026-06-08 08:36:47 MarkDuplicates Tracking 895788 as yet unmatched pairs. 47354 records in RAM.
INFO 2026-06-08 08:36:48 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 1s. Last read position: chr5:98,896,235
INFO 2026-06-08 08:36:48 MarkDuplicates Tracking 885801 as yet unmatched pairs. 37338 records in RAM.
INFO 2026-06-08 08:36:50 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 1s. Last read position: chr5:126,818,982
INFO 2026-06-08 08:36:50 MarkDuplicates Tracking 884106 as yet unmatched pairs. 35616 records in RAM.
INFO 2026-06-08 08:36:52 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 1s. Last read position: chr5:134,788,575
INFO 2026-06-08 08:36:52 MarkDuplicates Tracking 880805 as yet unmatched pairs. 32297 records in RAM.
INFO 2026-06-08 08:36:54 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 1s. Last read position: chr5:139,614,724
INFO 2026-06-08 08:36:54 MarkDuplicates Tracking 878288 as yet unmatched pairs. 29737 records in RAM.
INFO 2026-06-08 08:36:56 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 1s. Last read position: chr5:144,160,371
INFO 2026-06-08 08:36:56 MarkDuplicates Tracking 875148 as yet unmatched pairs. 26566 records in RAM.
INFO 2026-06-08 08:36:57 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 1s. Last read position: chr5:150,402,218
INFO 2026-06-08 08:36:57 MarkDuplicates Tracking 961258 as yet unmatched pairs. 112644 records in RAM.
INFO 2026-06-08 08:36:59 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 1s. Last read position: chr5:150,405,123
INFO 2026-06-08 08:36:59 MarkDuplicates Tracking 972884 as yet unmatched pairs. 124237 records in RAM.
INFO 2026-06-08 08:37:01 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 2s. Last read position: chr5:150,444,262
INFO 2026-06-08 08:37:01 MarkDuplicates Tracking 870345 as yet unmatched pairs. 21667 records in RAM.
INFO 2026-06-08 08:37:04 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 2s. Last read position: chr5:151,223,911
INFO 2026-06-08 08:37:04 MarkDuplicates Tracking 863929 as yet unmatched pairs. 15220 records in RAM.
INFO 2026-06-08 08:37:07 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 3s. Last read position: chr5:163,442,046
INFO 2026-06-08 08:37:07 MarkDuplicates Tracking 863058 as yet unmatched pairs. 14302 records in RAM.
INFO 2026-06-08 08:37:10 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 2s. Last read position: chr5:171,391,786
INFO 2026-06-08 08:37:10 MarkDuplicates Tracking 881614 as yet unmatched pairs. 32833 records in RAM.
INFO 2026-06-08 08:37:11 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 1s. Last read position: chr5:176,384,056
INFO 2026-06-08 08:37:11 MarkDuplicates Tracking 857643 as yet unmatched pairs. 8837 records in RAM.
INFO 2026-06-08 08:37:13 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 1s. Last read position: chr5:177,536,713
INFO 2026-06-08 08:37:13 MarkDuplicates Tracking 854238 as yet unmatched pairs. 5426 records in RAM.
INFO 2026-06-08 08:37:15 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 1s. Last read position: chr5:179,824,297
INFO 2026-06-08 08:37:15 MarkDuplicates Tracking 855556 as yet unmatched pairs. 6701 records in RAM.
INFO 2026-06-08 08:37:18 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 2s. Last read position: chr6:394,967
INFO 2026-06-08 08:37:18 MarkDuplicates Tracking 856146 as yet unmatched pairs. 73792 records in RAM.
INFO 2026-06-08 08:37:19 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 1s. Last read position: chr6:7,246,762
INFO 2026-06-08 08:37:19 MarkDuplicates Tracking 845975 as yet unmatched pairs. 63568 records in RAM.
INFO 2026-06-08 08:37:21 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 1s. Last read position: chr6:17,632,649
INFO 2026-06-08 08:37:21 MarkDuplicates Tracking 843653 as yet unmatched pairs. 61215 records in RAM.
INFO 2026-06-08 08:37:23 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 1s. Last read position: chr6:26,123,655
INFO 2026-06-08 08:37:23 MarkDuplicates Tracking 843485 as yet unmatched pairs. 61013 records in RAM.
INFO 2026-06-08 08:37:25 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 1s. Last read position: chr6:26,271,263
INFO 2026-06-08 08:37:25 MarkDuplicates Tracking 837397 as yet unmatched pairs. 54886 records in RAM.
INFO 2026-06-08 08:37:26 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 1s. Last read position: chr6:27,814,369
INFO 2026-06-08 08:37:26 MarkDuplicates Tracking 844882 as yet unmatched pairs. 62363 records in RAM.
INFO 2026-06-08 08:37:28 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 1s. Last read position: chr6:28,245,898
INFO 2026-06-08 08:37:28 MarkDuplicates Tracking 832812 as yet unmatched pairs. 50270 records in RAM.
INFO 2026-06-08 08:37:30 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 1s. Last read position: chr6:30,491,566
INFO 2026-06-08 08:37:30 MarkDuplicates Tracking 833090 as yet unmatched pairs. 50532 records in RAM.
INFO 2026-06-08 08:37:31 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 1s. Last read position: chr6:31,271,104
INFO 2026-06-08 08:37:31 MarkDuplicates Tracking 838191 as yet unmatched pairs. 55619 records in RAM.
INFO 2026-06-08 08:37:33 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 1s. Last read position: chr6:31,631,446
INFO 2026-06-08 08:37:33 MarkDuplicates Tracking 825596 as yet unmatched pairs. 43002 records in RAM.
INFO 2026-06-08 08:37:35 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 1s. Last read position: chr6:31,962,781
INFO 2026-06-08 08:37:35 MarkDuplicates Tracking 822560 as yet unmatched pairs. 39946 records in RAM.
INFO 2026-06-08 08:37:37 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 1s. Last read position: chr6:32,845,299
INFO 2026-06-08 08:37:37 MarkDuplicates Tracking 820581 as yet unmatched pairs. 37956 records in RAM.
INFO 2026-06-08 08:37:38 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 1s. Last read position: chr6:33,089,229
INFO 2026-06-08 08:37:38 MarkDuplicates Tracking 816611 as yet unmatched pairs. 33963 records in RAM.
INFO 2026-06-08 08:37:40 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 1s. Last read position: chr6:33,683,206
INFO 2026-06-08 08:37:40 MarkDuplicates Tracking 814422 as yet unmatched pairs. 31753 records in RAM.
INFO 2026-06-08 08:37:42 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 2s. Last read position: chr6:36,970,044
INFO 2026-06-08 08:37:42 MarkDuplicates Tracking 812753 as yet unmatched pairs. 30027 records in RAM.
INFO 2026-06-08 08:37:44 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 1s. Last read position: chr6:43,058,208
INFO 2026-06-08 08:37:44 MarkDuplicates Tracking 808054 as yet unmatched pairs. 25281 records in RAM.
INFO 2026-06-08 08:37:46 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 1s. Last read position: chr6:44,253,639
INFO 2026-06-08 08:37:46 MarkDuplicates Tracking 805399 as yet unmatched pairs. 22602 records in RAM.
INFO 2026-06-08 08:37:48 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 1s. Last read position: chr6:56,640,220
INFO 2026-06-08 08:37:48 MarkDuplicates Tracking 803318 as yet unmatched pairs. 20499 records in RAM.
INFO 2026-06-08 08:37:49 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 1s. Last read position: chr6:81,749,837
INFO 2026-06-08 08:37:49 MarkDuplicates Tracking 800297 as yet unmatched pairs. 17417 records in RAM.
INFO 2026-06-08 08:37:51 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr6:89,819,524
INFO 2026-06-08 08:37:51 MarkDuplicates Tracking 798087 as yet unmatched pairs. 15183 records in RAM.
INFO 2026-06-08 08:37:53 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 1s. Last read position: chr6:110,746,111
INFO 2026-06-08 08:37:53 MarkDuplicates Tracking 794880 as yet unmatched pairs. 11940 records in RAM.
INFO 2026-06-08 08:37:55 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 1s. Last read position: chr6:128,005,217
INFO 2026-06-08 08:37:55 MarkDuplicates Tracking 792188 as yet unmatched pairs. 9233 records in RAM.
INFO 2026-06-08 08:37:56 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 1s. Last read position: chr6:144,428,835
INFO 2026-06-08 08:37:56 MarkDuplicates Tracking 790460 as yet unmatched pairs. 7451 records in RAM.
INFO 2026-06-08 08:37:58 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 1s. Last read position: chr6:157,207,227
INFO 2026-06-08 08:37:58 MarkDuplicates Tracking 788347 as yet unmatched pairs. 5314 records in RAM.
INFO 2026-06-08 08:38:00 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 1s. Last read position: chr6:163,478,821
INFO 2026-06-08 08:38:00 MarkDuplicates Tracking 785057 as yet unmatched pairs. 1999 records in RAM.
INFO 2026-06-08 08:38:02 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 2s. Last read position: chr7:2,235,435
INFO 2026-06-08 08:38:02 MarkDuplicates Tracking 782127 as yet unmatched pairs. 56092 records in RAM.
INFO 2026-06-08 08:38:04 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 2s. Last read position: chr7:5,527,532
INFO 2026-06-08 08:38:04 MarkDuplicates Tracking 779322 as yet unmatched pairs. 53263 records in RAM.
INFO 2026-06-08 08:38:06 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 1s. Last read position: chr7:5,528,412
INFO 2026-06-08 08:38:06 MarkDuplicates Tracking 805707 as yet unmatched pairs. 79601 records in RAM.
INFO 2026-06-08 08:38:07 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 1s. Last read position: chr7:5,529,546
INFO 2026-06-08 08:38:07 MarkDuplicates Tracking 809986 as yet unmatched pairs. 83860 records in RAM.
INFO 2026-06-08 08:38:09 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 1s. Last read position: chr7:20,154,249
INFO 2026-06-08 08:38:09 MarkDuplicates Tracking 770265 as yet unmatched pairs. 44109 records in RAM.
INFO 2026-06-08 08:38:11 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 1s. Last read position: chr7:30,622,436
INFO 2026-06-08 08:38:11 MarkDuplicates Tracking 767906 as yet unmatched pairs. 41724 records in RAM.
INFO 2026-06-08 08:38:12 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 1s. Last read position: chr7:44,392,384
INFO 2026-06-08 08:38:12 MarkDuplicates Tracking 764345 as yet unmatched pairs. 38135 records in RAM.
INFO 2026-06-08 08:38:14 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 1s. Last read position: chr7:55,472,926
INFO 2026-06-08 08:38:14 MarkDuplicates Tracking 763616 as yet unmatched pairs. 37372 records in RAM.
INFO 2026-06-08 08:38:16 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 2s. Last read position: chr7:73,200,529
INFO 2026-06-08 08:38:16 MarkDuplicates Tracking 759044 as yet unmatched pairs. 32764 records in RAM.
INFO 2026-06-08 08:38:18 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 1s. Last read position: chr7:74,777,266
INFO 2026-06-08 08:38:18 MarkDuplicates Tracking 759380 as yet unmatched pairs. 33069 records in RAM.
INFO 2026-06-08 08:38:20 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 2s. Last read position: chr7:76,329,724
INFO 2026-06-08 08:38:20 MarkDuplicates Tracking 755497 as yet unmatched pairs. 29164 records in RAM.
INFO 2026-06-08 08:38:22 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 1s. Last read position: chr7:92,774,805
INFO 2026-06-08 08:38:22 MarkDuplicates Tracking 754294 as yet unmatched pairs. 27913 records in RAM.
INFO 2026-06-08 08:38:24 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 1s. Last read position: chr7:99,435,006
INFO 2026-06-08 08:38:24 MarkDuplicates Tracking 750059 as yet unmatched pairs. 23660 records in RAM.
INFO 2026-06-08 08:38:26 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 1s. Last read position: chr7:100,585,916
INFO 2026-06-08 08:38:26 MarkDuplicates Tracking 747734 as yet unmatched pairs. 21318 records in RAM.
INFO 2026-06-08 08:38:27 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 1s. Last read position: chr7:102,560,839
INFO 2026-06-08 08:38:27 MarkDuplicates Tracking 745846 as yet unmatched pairs. 19412 records in RAM.
INFO 2026-06-08 08:38:29 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 1s. Last read position: chr7:116,972,648
INFO 2026-06-08 08:38:29 MarkDuplicates Tracking 742511 as yet unmatched pairs. 16030 records in RAM.
INFO 2026-06-08 08:38:31 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 1s. Last read position: chr7:128,337,157
INFO 2026-06-08 08:38:31 MarkDuplicates Tracking 739421 as yet unmatched pairs. 12919 records in RAM.
INFO 2026-06-08 08:38:32 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr7:137,882,460
INFO 2026-06-08 08:38:32 MarkDuplicates Tracking 739438 as yet unmatched pairs. 12891 records in RAM.
INFO 2026-06-08 08:38:34 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 1s. Last read position: chr7:141,615,519
INFO 2026-06-08 08:38:34 MarkDuplicates Tracking 734926 as yet unmatched pairs. 8336 records in RAM.
INFO 2026-06-08 08:38:36 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 1s. Last read position: chr7:150,372,550
INFO 2026-06-08 08:38:36 MarkDuplicates Tracking 733103 as yet unmatched pairs. 6476 records in RAM.
INFO 2026-06-08 08:38:38 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 1s. Last read position: chr7:155,707,021
INFO 2026-06-08 08:38:38 MarkDuplicates Tracking 728896 as yet unmatched pairs. 2254 records in RAM.
INFO 2026-06-08 08:38:40 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 2s. Last read position: chr8:17,953,138
INFO 2026-06-08 08:38:40 MarkDuplicates Tracking 725470 as yet unmatched pairs. 35390 records in RAM.
INFO 2026-06-08 08:38:41 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 1s. Last read position: chr8:26,634,784
INFO 2026-06-08 08:38:41 MarkDuplicates Tracking 721948 as yet unmatched pairs. 31834 records in RAM.
INFO 2026-06-08 08:38:43 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:05:20s. Time for last 1,000,000: 1s. Last read position: chr8:37,872,112
INFO 2026-06-08 08:38:43 MarkDuplicates Tracking 719226 as yet unmatched pairs. 29093 records in RAM.
INFO 2026-06-08 08:38:45 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 1s. Last read position: chr8:41,529,322
INFO 2026-06-08 08:38:45 MarkDuplicates Tracking 717048 as yet unmatched pairs. 26908 records in RAM.
INFO 2026-06-08 08:38:47 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 1s. Last read position: chr8:55,799,110
INFO 2026-06-08 08:38:47 MarkDuplicates Tracking 714287 as yet unmatched pairs. 24125 records in RAM.
INFO 2026-06-08 08:38:49 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 1s. Last read position: chr8:70,156,967
INFO 2026-06-08 08:38:49 MarkDuplicates Tracking 713358 as yet unmatched pairs. 23181 records in RAM.
INFO 2026-06-08 08:38:52 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 3s. Last read position: chr8:94,851,591
INFO 2026-06-08 08:38:52 MarkDuplicates Tracking 709361 as yet unmatched pairs. 19147 records in RAM.
INFO 2026-06-08 08:38:54 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 2s. Last read position: chr8:100,706,968
INFO 2026-06-08 08:38:54 MarkDuplicates Tracking 711991 as yet unmatched pairs. 21755 records in RAM.
INFO 2026-06-08 08:38:56 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 1s. Last read position: chr8:103,420,308
INFO 2026-06-08 08:38:56 MarkDuplicates Tracking 704317 as yet unmatched pairs. 14065 records in RAM.
INFO 2026-06-08 08:38:58 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 2s. Last read position: chr8:127,738,898
INFO 2026-06-08 08:38:58 MarkDuplicates Tracking 704449 as yet unmatched pairs. 14178 records in RAM.
INFO 2026-06-08 08:39:00 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 1s. Last read position: chr8:143,608,110
INFO 2026-06-08 08:39:00 MarkDuplicates Tracking 697899 as yet unmatched pairs. 7600 records in RAM.
INFO 2026-06-08 08:39:03 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 2s. Last read position: chr8:144,106,221
INFO 2026-06-08 08:39:03 MarkDuplicates Tracking 694445 as yet unmatched pairs. 4133 records in RAM.
INFO 2026-06-08 08:39:05 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 2s. Last read position: chr8:144,931,493
INFO 2026-06-08 08:39:05 MarkDuplicates Tracking 690425 as yet unmatched pairs. 99 records in RAM.
INFO 2026-06-08 08:39:07 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 2s. Last read position: chr9:6,981,033
INFO 2026-06-08 08:39:07 MarkDuplicates Tracking 688144 as yet unmatched pairs. 41810 records in RAM.
INFO 2026-06-08 08:39:09 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 2s. Last read position: chr9:33,135,411
INFO 2026-06-08 08:39:09 MarkDuplicates Tracking 688280 as yet unmatched pairs. 41853 records in RAM.
INFO 2026-06-08 08:39:11 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 1s. Last read position: chr9:35,704,128
INFO 2026-06-08 08:39:11 MarkDuplicates Tracking 683983 as yet unmatched pairs. 37537 records in RAM.
INFO 2026-06-08 08:39:13 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 1s. Last read position: chr9:36,839,132
INFO 2026-06-08 08:39:13 MarkDuplicates Tracking 681409 as yet unmatched pairs. 34946 records in RAM.
INFO 2026-06-08 08:39:15 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 1s. Last read position: chr9:75,133,303
INFO 2026-06-08 08:39:15 MarkDuplicates Tracking 677332 as yet unmatched pairs. 30847 records in RAM.
INFO 2026-06-08 08:39:16 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 1s. Last read position: chr9:92,222,530
INFO 2026-06-08 08:39:16 MarkDuplicates Tracking 675793 as yet unmatched pairs. 29296 records in RAM.
INFO 2026-06-08 08:39:18 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 1s. Last read position: chr9:100,052,530
INFO 2026-06-08 08:39:18 MarkDuplicates Tracking 673166 as yet unmatched pairs. 26641 records in RAM.
INFO 2026-06-08 08:39:20 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 1s. Last read position: chr9:114,346,705
INFO 2026-06-08 08:39:20 MarkDuplicates Tracking 670307 as yet unmatched pairs. 23763 records in RAM.
INFO 2026-06-08 08:39:22 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 1s. Last read position: chr9:122,879,755
INFO 2026-06-08 08:39:22 MarkDuplicates Tracking 666696 as yet unmatched pairs. 20132 records in RAM.
INFO 2026-06-08 08:39:24 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 1s. Last read position: chr9:127,715,087
INFO 2026-06-08 08:39:24 MarkDuplicates Tracking 664178 as yet unmatched pairs. 17576 records in RAM.
INFO 2026-06-08 08:39:26 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 1s. Last read position: chr9:128,706,901
INFO 2026-06-08 08:39:26 MarkDuplicates Tracking 661137 as yet unmatched pairs. 14524 records in RAM.
INFO 2026-06-08 08:39:27 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 1s. Last read position: chr9:130,884,947
INFO 2026-06-08 08:39:27 MarkDuplicates Tracking 659518 as yet unmatched pairs. 12881 records in RAM.
INFO 2026-06-08 08:39:29 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 1s. Last read position: chr9:133,108,389
INFO 2026-06-08 08:39:29 MarkDuplicates Tracking 656062 as yet unmatched pairs. 9407 records in RAM.
INFO 2026-06-08 08:39:31 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:06:09s. Time for last 1,000,000: 2s. Last read position: chr9:136,474,135
INFO 2026-06-08 08:39:31 MarkDuplicates Tracking 653607 as yet unmatched pairs. 6937 records in RAM.
INFO 2026-06-08 08:39:34 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 2s. Last read position: chr9:137,181,732
INFO 2026-06-08 08:39:34 MarkDuplicates Tracking 649667 as yet unmatched pairs. 2978 records in RAM.
INFO 2026-06-08 08:39:38 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 3s. Last read position: chr10:5,456,147
INFO 2026-06-08 08:39:38 MarkDuplicates Tracking 645719 as yet unmatched pairs. 33637 records in RAM.
INFO 2026-06-08 08:39:40 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 2s. Last read position: chr10:15,078,735
INFO 2026-06-08 08:39:40 MarkDuplicates Tracking 643064 as yet unmatched pairs. 30944 records in RAM.
INFO 2026-06-08 08:39:42 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 2s. Last read position: chr10:32,033,869
INFO 2026-06-08 08:39:42 MarkDuplicates Tracking 640920 as yet unmatched pairs. 28761 records in RAM.
INFO 2026-06-08 08:39:43 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 1s. Last read position: chr10:46,131,058
INFO 2026-06-08 08:39:43 MarkDuplicates Tracking 638632 as yet unmatched pairs. 26457 records in RAM.
INFO 2026-06-08 08:39:45 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 1s. Last read position: chr10:59,794,516
INFO 2026-06-08 08:39:45 MarkDuplicates Tracking 636786 as yet unmatched pairs. 24594 records in RAM.
INFO 2026-06-08 08:39:47 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 2s. Last read position: chr10:71,834,456
INFO 2026-06-08 08:39:47 MarkDuplicates Tracking 633440 as yet unmatched pairs. 21220 records in RAM.
INFO 2026-06-08 08:39:49 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 2s. Last read position: chr10:78,033,888
INFO 2026-06-08 08:39:49 MarkDuplicates Tracking 631937 as yet unmatched pairs. 19700 records in RAM.
INFO 2026-06-08 08:39:51 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 2s. Last read position: chr10:87,933,025
INFO 2026-06-08 08:39:51 MarkDuplicates Tracking 629309 as yet unmatched pairs. 17059 records in RAM.
INFO 2026-06-08 08:39:53 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:06:30s. Time for last 1,000,000: 1s. Last read position: chr10:95,823,280
INFO 2026-06-08 08:39:53 MarkDuplicates Tracking 627194 as yet unmatched pairs. 14913 records in RAM.
INFO 2026-06-08 08:39:55 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 1s. Last read position: chr10:97,460,109
INFO 2026-06-08 08:39:55 MarkDuplicates Tracking 623819 as yet unmatched pairs. 11516 records in RAM.
INFO 2026-06-08 08:39:57 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 1s. Last read position: chr10:102,158,046
INFO 2026-06-08 08:39:57 MarkDuplicates Tracking 620985 as yet unmatched pairs. 8664 records in RAM.
INFO 2026-06-08 08:39:59 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 1s. Last read position: chr10:110,876,012
INFO 2026-06-08 08:39:59 MarkDuplicates Tracking 618840 as yet unmatched pairs. 6501 records in RAM.
INFO 2026-06-08 08:40:02 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 2s. Last read position: chr10:123,162,720
INFO 2026-06-08 08:40:02 MarkDuplicates Tracking 615715 as yet unmatched pairs. 3372 records in RAM.
INFO 2026-06-08 08:40:04 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 2s. Last read position: chr10:133,402,225
INFO 2026-06-08 08:40:04 MarkDuplicates Tracking 613626 as yet unmatched pairs. 1249 records in RAM.
INFO 2026-06-08 08:40:07 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:06:44s. Time for last 1,000,000: 2s. Last read position: chr11:771,069
INFO 2026-06-08 08:40:07 MarkDuplicates Tracking 610160 as yet unmatched pairs. 64342 records in RAM.
INFO 2026-06-08 08:40:09 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:06:46s. Time for last 1,000,000: 2s. Last read position: chr11:4,070,158
INFO 2026-06-08 08:40:09 MarkDuplicates Tracking 606435 as yet unmatched pairs. 60599 records in RAM.
INFO 2026-06-08 08:40:12 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 2s. Last read position: chr11:8,914,887
INFO 2026-06-08 08:40:12 MarkDuplicates Tracking 603711 as yet unmatched pairs. 57862 records in RAM.
INFO 2026-06-08 08:40:15 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 2s. Last read position: chr11:18,295,129
INFO 2026-06-08 08:40:15 MarkDuplicates Tracking 601372 as yet unmatched pairs. 55507 records in RAM.
INFO 2026-06-08 08:40:17 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 1s. Last read position: chr11:35,206,057
INFO 2026-06-08 08:40:17 MarkDuplicates Tracking 598716 as yet unmatched pairs. 52833 records in RAM.
INFO 2026-06-08 08:40:18 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 1s. Last read position: chr11:47,311,820
INFO 2026-06-08 08:40:18 MarkDuplicates Tracking 595722 as yet unmatched pairs. 49818 records in RAM.
INFO 2026-06-08 08:40:20 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:06:57s. Time for last 1,000,000: 1s. Last read position: chr11:59,126,050
INFO 2026-06-08 08:40:20 MarkDuplicates Tracking 593081 as yet unmatched pairs. 47165 records in RAM.
INFO 2026-06-08 08:40:22 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 1s. Last read position: chr11:60,922,106
INFO 2026-06-08 08:40:22 MarkDuplicates Tracking 591263 as yet unmatched pairs. 45328 records in RAM.
INFO 2026-06-08 08:40:24 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 1s. Last read position: chr11:62,570,968
INFO 2026-06-08 08:40:24 MarkDuplicates Tracking 590470 as yet unmatched pairs. 44509 records in RAM.
INFO 2026-06-08 08:40:26 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:07:03s. Time for last 1,000,000: 2s. Last read position: chr11:63,904,067
INFO 2026-06-08 08:40:26 MarkDuplicates Tracking 585624 as yet unmatched pairs. 39657 records in RAM.
INFO 2026-06-08 08:40:28 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 1s. Last read position: chr11:64,355,615
INFO 2026-06-08 08:40:28 MarkDuplicates Tracking 583201 as yet unmatched pairs. 37217 records in RAM.
INFO 2026-06-08 08:40:30 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:07:07s. Time for last 1,000,000: 1s. Last read position: chr11:65,131,508
INFO 2026-06-08 08:40:30 MarkDuplicates Tracking 579549 as yet unmatched pairs. 33552 records in RAM.
INFO 2026-06-08 08:40:31 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:07:09s. Time for last 1,000,000: 1s. Last read position: chr11:65,661,967
INFO 2026-06-08 08:40:31 MarkDuplicates Tracking 576212 as yet unmatched pairs. 30165 records in RAM.
INFO 2026-06-08 08:40:34 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:07:11s. Time for last 1,000,000: 2s. Last read position: chr11:66,593,249
INFO 2026-06-08 08:40:34 MarkDuplicates Tracking 572035 as yet unmatched pairs. 25972 records in RAM.
INFO 2026-06-08 08:40:36 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 1s. Last read position: chr11:67,440,727
INFO 2026-06-08 08:40:36 MarkDuplicates Tracking 568693 as yet unmatched pairs. 22613 records in RAM.
INFO 2026-06-08 08:40:38 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:07:15s. Time for last 1,000,000: 1s. Last read position: chr11:69,054,630
INFO 2026-06-08 08:40:38 MarkDuplicates Tracking 564964 as yet unmatched pairs. 18866 records in RAM.
INFO 2026-06-08 08:40:40 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:07:17s. Time for last 1,000,000: 1s. Last read position: chr11:72,984,148
INFO 2026-06-08 08:40:40 MarkDuplicates Tracking 562757 as yet unmatched pairs. 16650 records in RAM.
INFO 2026-06-08 08:40:41 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:07:18s. Time for last 1,000,000: 1s. Last read position: chr11:77,991,234
INFO 2026-06-08 08:40:41 MarkDuplicates Tracking 558987 as yet unmatched pairs. 12857 records in RAM.
INFO 2026-06-08 08:40:43 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:07:20s. Time for last 1,000,000: 1s. Last read position: chr11:102,350,072
INFO 2026-06-08 08:40:43 MarkDuplicates Tracking 557184 as yet unmatched pairs. 11020 records in RAM.
INFO 2026-06-08 08:40:45 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:07:22s. Time for last 1,000,000: 2s. Last read position: chr11:117,167,552
INFO 2026-06-08 08:40:45 MarkDuplicates Tracking 554125 as yet unmatched pairs. 7941 records in RAM.
INFO 2026-06-08 08:40:47 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:07:24s. Time for last 1,000,000: 1s. Last read position: chr11:119,068,998
INFO 2026-06-08 08:40:47 MarkDuplicates Tracking 551255 as yet unmatched pairs. 5065 records in RAM.
INFO 2026-06-08 08:40:49 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:07:26s. Time for last 1,000,000: 1s. Last read position: chr11:123,061,139
INFO 2026-06-08 08:40:49 MarkDuplicates Tracking 553844 as yet unmatched pairs. 7646 records in RAM.
INFO 2026-06-08 08:40:51 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:07:28s. Time for last 1,000,000: 2s. Last read position: chr12:753,525
INFO 2026-06-08 08:40:51 MarkDuplicates Tracking 548061 as yet unmatched pairs. 65094 records in RAM.
INFO 2026-06-08 08:40:53 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:07:30s. Time for last 1,000,000: 1s. Last read position: chr12:4,659,059
INFO 2026-06-08 08:40:53 MarkDuplicates Tracking 543899 as yet unmatched pairs. 60919 records in RAM.
INFO 2026-06-08 08:40:54 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:07:32s. Time for last 1,000,000: 1s. Last read position: chr12:6,863,295
INFO 2026-06-08 08:40:54 MarkDuplicates Tracking 541092 as yet unmatched pairs. 58086 records in RAM.
INFO 2026-06-08 08:40:56 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:07:33s. Time for last 1,000,000: 1s. Last read position: chr12:8,946,253
INFO 2026-06-08 08:40:56 MarkDuplicates Tracking 538485 as yet unmatched pairs. 55474 records in RAM.
INFO 2026-06-08 08:40:58 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:07:35s. Time for last 1,000,000: 1s. Last read position: chr12:14,947,872
INFO 2026-06-08 08:40:58 MarkDuplicates Tracking 540360 as yet unmatched pairs. 57320 records in RAM.
INFO 2026-06-08 08:41:00 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:07:37s. Time for last 1,000,000: 1s. Last read position: chr12:26,657,716
INFO 2026-06-08 08:41:00 MarkDuplicates Tracking 534651 as yet unmatched pairs. 51577 records in RAM.
INFO 2026-06-08 08:41:02 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:07:39s. Time for last 1,000,000: 1s. Last read position: chr12:42,446,590
INFO 2026-06-08 08:41:02 MarkDuplicates Tracking 530721 as yet unmatched pairs. 47623 records in RAM.
INFO 2026-06-08 08:41:03 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:07:41s. Time for last 1,000,000: 1s. Last read position: chr12:49,041,927
INFO 2026-06-08 08:41:03 MarkDuplicates Tracking 528589 as yet unmatched pairs. 45474 records in RAM.
INFO 2026-06-08 08:41:06 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:07:43s. Time for last 1,000,000: 2s. Last read position: chr12:49,997,179
INFO 2026-06-08 08:41:06 MarkDuplicates Tracking 525738 as yet unmatched pairs. 42620 records in RAM.
INFO 2026-06-08 08:41:09 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:07:46s. Time for last 1,000,000: 3s. Last read position: chr12:53,306,237
INFO 2026-06-08 08:41:09 MarkDuplicates Tracking 522986 as yet unmatched pairs. 39850 records in RAM.
INFO 2026-06-08 08:41:12 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:07:49s. Time for last 1,000,000: 2s. Last read position: chr12:54,325,157
INFO 2026-06-08 08:41:12 MarkDuplicates Tracking 520900 as yet unmatched pairs. 37754 records in RAM.
INFO 2026-06-08 08:41:15 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:07:52s. Time for last 1,000,000: 2s. Last read position: chr12:56,245,153
INFO 2026-06-08 08:41:15 MarkDuplicates Tracking 518625 as yet unmatched pairs. 35462 records in RAM.
INFO 2026-06-08 08:41:17 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:07:54s. Time for last 1,000,000: 2s. Last read position: chr12:56,714,427
INFO 2026-06-08 08:41:17 MarkDuplicates Tracking 527329 as yet unmatched pairs. 44153 records in RAM.
INFO 2026-06-08 08:41:19 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:07:56s. Time for last 1,000,000: 1s. Last read position: chr12:57,500,378
INFO 2026-06-08 08:41:19 MarkDuplicates Tracking 514091 as yet unmatched pairs. 30908 records in RAM.
INFO 2026-06-08 08:42:35 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:09:12s. Time for last 1,000,000: 76s. Last read position: chr12:67,657,649
INFO 2026-06-08 08:42:35 MarkDuplicates Tracking 510189 as yet unmatched pairs. 26989 records in RAM.
INFO 2026-06-08 08:42:39 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 3s. Last read position: chr12:79,832,462
INFO 2026-06-08 08:42:39 MarkDuplicates Tracking 507766 as yet unmatched pairs. 24537 records in RAM.
INFO 2026-06-08 08:42:42 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:09:19s. Time for last 1,000,000: 3s. Last read position: chr12:98,601,406
INFO 2026-06-08 08:42:42 MarkDuplicates Tracking 507073 as yet unmatched pairs. 23818 records in RAM.
INFO 2026-06-08 08:42:45 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 2s. Last read position: chr12:105,366,618
INFO 2026-06-08 08:42:45 MarkDuplicates Tracking 505880 as yet unmatched pairs. 22604 records in RAM.
INFO 2026-06-08 08:42:47 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:09:24s. Time for last 1,000,000: 2s. Last read position: chr12:111,447,125
INFO 2026-06-08 08:42:47 MarkDuplicates Tracking 501218 as yet unmatched pairs. 17933 records in RAM.
INFO 2026-06-08 08:42:49 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:09:26s. Time for last 1,000,000: 1s. Last read position: chr12:112,950,708
INFO 2026-06-08 08:42:49 MarkDuplicates Tracking 498193 as yet unmatched pairs. 14894 records in RAM.
INFO 2026-06-08 08:42:51 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:09:28s. Time for last 1,000,000: 2s. Last read position: chr12:120,131,261
INFO 2026-06-08 08:42:51 MarkDuplicates Tracking 495766 as yet unmatched pairs. 12420 records in RAM.
INFO 2026-06-08 08:42:53 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:09:30s. Time for last 1,000,000: 2s. Last read position: chr12:121,423,501
INFO 2026-06-08 08:42:53 MarkDuplicates Tracking 492865 as yet unmatched pairs. 9509 records in RAM.
INFO 2026-06-08 08:42:55 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:09:33s. Time for last 1,000,000: 2s. Last read position: chr12:124,325,557
INFO 2026-06-08 08:42:55 MarkDuplicates Tracking 489919 as yet unmatched pairs. 6515 records in RAM.
INFO 2026-06-08 08:42:57 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 1s. Last read position: chr12:131,941,435
INFO 2026-06-08 08:42:57 MarkDuplicates Tracking 487023 as yet unmatched pairs. 3603 records in RAM.
INFO 2026-06-08 08:42:59 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 2s. Last read position: chr13:19,741,582
INFO 2026-06-08 08:42:59 MarkDuplicates Tracking 483869 as yet unmatched pairs. 15328 records in RAM.
INFO 2026-06-08 08:43:02 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:09:39s. Time for last 1,000,000: 2s. Last read position: chr13:28,139,050
INFO 2026-06-08 08:43:02 MarkDuplicates Tracking 481437 as yet unmatched pairs. 12882 records in RAM.
INFO 2026-06-08 08:43:04 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:09:41s. Time for last 1,000,000: 2s. Last read position: chr13:42,298,719
INFO 2026-06-08 08:43:04 MarkDuplicates Tracking 478737 as yet unmatched pairs. 10167 records in RAM.
INFO 2026-06-08 08:43:07 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 2s. Last read position: chr13:46,777,522
INFO 2026-06-08 08:43:07 MarkDuplicates Tracking 476078 as yet unmatched pairs. 7486 records in RAM.
INFO 2026-06-08 08:43:09 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:09:46s. Time for last 1,000,000: 2s. Last read position: chr13:77,139,102
INFO 2026-06-08 08:43:09 MarkDuplicates Tracking 474081 as yet unmatched pairs. 5486 records in RAM.
INFO 2026-06-08 08:43:11 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:09:48s. Time for last 1,000,000: 1s. Last read position: chr13:102,674,342
INFO 2026-06-08 08:43:11 MarkDuplicates Tracking 471190 as yet unmatched pairs. 2558 records in RAM.
INFO 2026-06-08 08:43:13 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:09:50s. Time for last 1,000,000: 2s. Last read position: chr14:20,781,813
INFO 2026-06-08 08:43:13 MarkDuplicates Tracking 467909 as yet unmatched pairs. 42475 records in RAM.
INFO 2026-06-08 08:43:16 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:09:53s. Time for last 1,000,000: 3s. Last read position: chr14:23,061,171
INFO 2026-06-08 08:43:16 MarkDuplicates Tracking 465586 as yet unmatched pairs. 40139 records in RAM.
INFO 2026-06-08 08:43:19 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:09:56s. Time for last 1,000,000: 2s. Last read position: chr14:24,164,888
INFO 2026-06-08 08:43:19 MarkDuplicates Tracking 465061 as yet unmatched pairs. 39601 records in RAM.
INFO 2026-06-08 08:43:21 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:09:58s. Time for last 1,000,000: 2s. Last read position: chr14:34,773,651
INFO 2026-06-08 08:43:21 MarkDuplicates Tracking 460187 as yet unmatched pairs. 34719 records in RAM.
INFO 2026-06-08 08:43:23 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:10:00s. Time for last 1,000,000: 1s. Last read position: chr14:49,846,181
INFO 2026-06-08 08:43:23 MarkDuplicates Tracking 457905 as yet unmatched pairs. 32376 records in RAM.
INFO 2026-06-08 08:43:25 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:10:02s. Time for last 1,000,000: 2s. Last read position: chr14:57,390,879
INFO 2026-06-08 08:43:25 MarkDuplicates Tracking 454854 as yet unmatched pairs. 29256 records in RAM.
INFO 2026-06-08 08:43:27 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:10:04s. Time for last 1,000,000: 1s. Last read position: chr14:64,175,079
INFO 2026-06-08 08:43:27 MarkDuplicates Tracking 453532 as yet unmatched pairs. 27932 records in RAM.
INFO 2026-06-08 08:43:29 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 1s. Last read position: chr14:69,768,824
INFO 2026-06-08 08:43:29 MarkDuplicates Tracking 452404 as yet unmatched pairs. 26793 records in RAM.
INFO 2026-06-08 08:43:31 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:10:08s. Time for last 1,000,000: 2s. Last read position: chr14:74,763,646
INFO 2026-06-08 08:43:31 MarkDuplicates Tracking 447732 as yet unmatched pairs. 22100 records in RAM.
INFO 2026-06-08 08:43:35 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 3s. Last read position: chr14:91,273,050
INFO 2026-06-08 08:43:35 MarkDuplicates Tracking 444568 as yet unmatched pairs. 18913 records in RAM.
INFO 2026-06-08 08:43:37 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:10:14s. Time for last 1,000,000: 2s. Last read position: chr14:95,710,567
INFO 2026-06-08 08:43:37 MarkDuplicates Tracking 449816 as yet unmatched pairs. 24145 records in RAM.
INFO 2026-06-08 08:43:39 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:10:16s. Time for last 1,000,000: 2s. Last read position: chr14:102,083,788
INFO 2026-06-08 08:43:39 MarkDuplicates Tracking 439790 as yet unmatched pairs. 14106 records in RAM.
INFO 2026-06-08 08:43:41 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:10:18s. Time for last 1,000,000: 1s. Last read position: chr14:105,624,960
INFO 2026-06-08 08:43:41 MarkDuplicates Tracking 435643 as yet unmatched pairs. 9946 records in RAM.
INFO 2026-06-08 08:43:43 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:10:20s. Time for last 1,000,000: 2s. Last read position: chr14:105,769,405
INFO 2026-06-08 08:43:43 MarkDuplicates Tracking 448599 as yet unmatched pairs. 22879 records in RAM.
INFO 2026-06-08 08:43:45 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:10:22s. Time for last 1,000,000: 1s. Last read position: chr14:105,770,140
INFO 2026-06-08 08:43:45 MarkDuplicates Tracking 450275 as yet unmatched pairs. 24552 records in RAM.
INFO 2026-06-08 08:43:47 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:10:25s. Time for last 1,000,000: 2s. Last read position: chr14:105,771,225
INFO 2026-06-08 08:43:47 MarkDuplicates Tracking 476373 as yet unmatched pairs. 50644 records in RAM.
INFO 2026-06-08 08:43:50 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:10:27s. Time for last 1,000,000: 2s. Last read position: chr14:105,926,296
INFO 2026-06-08 08:43:50 MarkDuplicates Tracking 434869 as yet unmatched pairs. 9134 records in RAM.
INFO 2026-06-08 08:43:53 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:10:30s. Time for last 1,000,000: 3s. Last read position: chr15:22,786,711
INFO 2026-06-08 08:43:53 MarkDuplicates Tracking 425793 as yet unmatched pairs. 34451 records in RAM.
INFO 2026-06-08 08:43:56 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:10:33s. Time for last 1,000,000: 2s. Last read position: chr15:34,528,204
INFO 2026-06-08 08:43:56 MarkDuplicates Tracking 424491 as yet unmatched pairs. 33141 records in RAM.
INFO 2026-06-08 08:43:58 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:10:35s. Time for last 1,000,000: 1s. Last read position: chr15:41,699,125
INFO 2026-06-08 08:43:58 MarkDuplicates Tracking 421099 as yet unmatched pairs. 29735 records in RAM.
INFO 2026-06-08 08:44:00 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:10:37s. Time for last 1,000,000: 1s. Last read position: chr15:43,770,538
INFO 2026-06-08 08:44:00 MarkDuplicates Tracking 419025 as yet unmatched pairs. 27649 records in RAM.
INFO 2026-06-08 08:44:02 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:10:39s. Time for last 1,000,000: 1s. Last read position: chr15:50,612,649
INFO 2026-06-08 08:44:02 MarkDuplicates Tracking 415594 as yet unmatched pairs. 24212 records in RAM.
INFO 2026-06-08 08:44:04 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:10:41s. Time for last 1,000,000: 1s. Last read position: chr15:59,217,905
INFO 2026-06-08 08:44:04 MarkDuplicates Tracking 413385 as yet unmatched pairs. 22000 records in RAM.
INFO 2026-06-08 08:44:06 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:10:43s. Time for last 1,000,000: 2s. Last read position: chr15:64,816,615
INFO 2026-06-08 08:44:06 MarkDuplicates Tracking 410871 as yet unmatched pairs. 19485 records in RAM.
INFO 2026-06-08 08:44:08 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 2s. Last read position: chr15:69,452,870
INFO 2026-06-08 08:44:08 MarkDuplicates Tracking 411783 as yet unmatched pairs. 20388 records in RAM.
INFO 2026-06-08 08:44:11 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:10:48s. Time for last 1,000,000: 2s. Last read position: chr15:74,034,483
INFO 2026-06-08 08:44:11 MarkDuplicates Tracking 410504 as yet unmatched pairs. 19088 records in RAM.
INFO 2026-06-08 08:44:14 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:10:51s. Time for last 1,000,000: 3s. Last read position: chr15:75,206,983
INFO 2026-06-08 08:44:14 MarkDuplicates Tracking 402883 as yet unmatched pairs. 11441 records in RAM.
INFO 2026-06-08 08:44:17 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:10:54s. Time for last 1,000,000: 2s. Last read position: chr15:78,798,080
INFO 2026-06-08 08:44:17 MarkDuplicates Tracking 398704 as yet unmatched pairs. 7244 records in RAM.
INFO 2026-06-08 08:44:19 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:10:57s. Time for last 1,000,000: 2s. Last read position: chr15:85,723,228
INFO 2026-06-08 08:44:19 MarkDuplicates Tracking 396660 as yet unmatched pairs. 5189 records in RAM.
INFO 2026-06-08 08:44:22 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:10:59s. Time for last 1,000,000: 2s. Last read position: chr15:92,942,984
INFO 2026-06-08 08:44:22 MarkDuplicates Tracking 393270 as yet unmatched pairs. 1786 records in RAM.
INFO 2026-06-08 08:44:25 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:11:02s. Time for last 1,000,000: 3s. Last read position: chr16:547,468
INFO 2026-06-08 08:44:25 MarkDuplicates Tracking 391144 as yet unmatched pairs. 68145 records in RAM.
INFO 2026-06-08 08:44:27 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:11:05s. Time for last 1,000,000: 2s. Last read position: chr16:1,777,085
INFO 2026-06-08 08:44:27 MarkDuplicates Tracking 387465 as yet unmatched pairs. 64466 records in RAM.
INFO 2026-06-08 08:44:30 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:11:07s. Time for last 1,000,000: 2s. Last read position: chr16:2,445,491
INFO 2026-06-08 08:44:30 MarkDuplicates Tracking 382832 as yet unmatched pairs. 59825 records in RAM.
INFO 2026-06-08 08:44:32 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:11:09s. Time for last 1,000,000: 2s. Last read position: chr16:2,974,060
INFO 2026-06-08 08:44:32 MarkDuplicates Tracking 380632 as yet unmatched pairs. 57618 records in RAM.
INFO 2026-06-08 08:44:35 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:11:12s. Time for last 1,000,000: 2s. Last read position: chr16:4,814,567
INFO 2026-06-08 08:44:35 MarkDuplicates Tracking 377662 as yet unmatched pairs. 54645 records in RAM.
INFO 2026-06-08 08:44:37 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:11:14s. Time for last 1,000,000: 2s. Last read position: chr16:11,966,265
INFO 2026-06-08 08:44:37 MarkDuplicates Tracking 375103 as yet unmatched pairs. 52072 records in RAM.
INFO 2026-06-08 08:44:40 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:11:17s. Time for last 1,000,000: 2s. Last read position: chr16:16,114,872
INFO 2026-06-08 08:44:40 MarkDuplicates Tracking 373344 as yet unmatched pairs. 50305 records in RAM.
INFO 2026-06-08 08:44:42 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:11:19s. Time for last 1,000,000: 1s. Last read position: chr16:18,547,260
INFO 2026-06-08 08:44:42 MarkDuplicates Tracking 371890 as yet unmatched pairs. 48851 records in RAM.
INFO 2026-06-08 08:44:44 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:11:21s. Time for last 1,000,000: 2s. Last read position: chr16:21,427,372
INFO 2026-06-08 08:44:44 MarkDuplicates Tracking 368544 as yet unmatched pairs. 45496 records in RAM.
INFO 2026-06-08 08:44:46 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:11:23s. Time for last 1,000,000: 2s. Last read position: chr16:22,460,810
INFO 2026-06-08 08:44:46 MarkDuplicates Tracking 367736 as yet unmatched pairs. 44672 records in RAM.
INFO 2026-06-08 08:44:47 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:11:25s. Time for last 1,000,000: 1s. Last read position: chr16:24,172,248
INFO 2026-06-08 08:44:47 MarkDuplicates Tracking 367744 as yet unmatched pairs. 44676 records in RAM.
INFO 2026-06-08 08:44:50 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:11:27s. Time for last 1,000,000: 2s. Last read position: chr16:28,826,909
INFO 2026-06-08 08:44:50 MarkDuplicates Tracking 364659 as yet unmatched pairs. 41590 records in RAM.
INFO 2026-06-08 08:44:52 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:11:29s. Time for last 1,000,000: 2s. Last read position: chr16:29,454,060
INFO 2026-06-08 08:44:52 MarkDuplicates Tracking 367159 as yet unmatched pairs. 44082 records in RAM.
INFO 2026-06-08 08:44:53 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:11:31s. Time for last 1,000,000: 1s. Last read position: chr16:29,983,537
INFO 2026-06-08 08:44:53 MarkDuplicates Tracking 359474 as yet unmatched pairs. 36393 records in RAM.
INFO 2026-06-08 08:44:55 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:11:32s. Time for last 1,000,000: 1s. Last read position: chr16:30,203,537
INFO 2026-06-08 08:44:55 MarkDuplicates Tracking 356295 as yet unmatched pairs. 33210 records in RAM.
INFO 2026-06-08 08:44:57 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:11:34s. Time for last 1,000,000: 1s. Last read position: chr16:30,720,761
INFO 2026-06-08 08:44:57 MarkDuplicates Tracking 354514 as yet unmatched pairs. 31429 records in RAM.
INFO 2026-06-08 08:45:00 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:11:37s. Time for last 1,000,000: 3s. Last read position: chr16:31,190,965
INFO 2026-06-08 08:45:00 MarkDuplicates Tracking 351173 as yet unmatched pairs. 28088 records in RAM.
INFO 2026-06-08 08:45:02 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:11:39s. Time for last 1,000,000: 1s. Last read position: chr16:53,304,593
INFO 2026-06-08 08:45:02 MarkDuplicates Tracking 348254 as yet unmatched pairs. 25157 records in RAM.
INFO 2026-06-08 08:45:04 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:11:42s. Time for last 1,000,000: 2s. Last read position: chr16:57,365,095
INFO 2026-06-08 08:45:04 MarkDuplicates Tracking 347962 as yet unmatched pairs. 24858 records in RAM.
INFO 2026-06-08 08:45:07 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:11:44s. Time for last 1,000,000: 2s. Last read position: chr16:67,228,519
INFO 2026-06-08 08:45:07 MarkDuplicates Tracking 343335 as yet unmatched pairs. 20208 records in RAM.
INFO 2026-06-08 08:45:09 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:11:46s. Time for last 1,000,000: 2s. Last read position: chr16:68,919,210
INFO 2026-06-08 08:45:09 MarkDuplicates Tracking 339794 as yet unmatched pairs. 16667 records in RAM.
INFO 2026-06-08 08:45:11 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:11:48s. Time for last 1,000,000: 1s. Last read position: chr16:70,563,921
INFO 2026-06-08 08:45:11 MarkDuplicates Tracking 337018 as yet unmatched pairs. 13870 records in RAM.
INFO 2026-06-08 08:45:13 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:11:51s. Time for last 1,000,000: 2s. Last read position: chr16:81,090,625
INFO 2026-06-08 08:45:13 MarkDuplicates Tracking 334721 as yet unmatched pairs. 11567 records in RAM.
INFO 2026-06-08 08:45:16 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:11:53s. Time for last 1,000,000: 2s. Last read position: chr16:85,920,181
INFO 2026-06-08 08:45:16 MarkDuplicates Tracking 335025 as yet unmatched pairs. 11860 records in RAM.
INFO 2026-06-08 08:45:18 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:11:56s. Time for last 1,000,000: 2s. Last read position: chr16:88,741,565
INFO 2026-06-08 08:45:18 MarkDuplicates Tracking 328837 as yet unmatched pairs. 5671 records in RAM.
INFO 2026-06-08 08:45:21 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:11:58s. Time for last 1,000,000: 2s. Last read position: chr16:89,737,916
INFO 2026-06-08 08:45:21 MarkDuplicates Tracking 324809 as yet unmatched pairs. 1634 records in RAM.
INFO 2026-06-08 08:45:25 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:12:02s. Time for last 1,000,000: 3s. Last read position: chr17:1,650,794
INFO 2026-06-08 08:45:25 MarkDuplicates Tracking 321980 as yet unmatched pairs. 80412 records in RAM.
INFO 2026-06-08 08:45:27 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:12:04s. Time for last 1,000,000: 2s. Last read position: chr17:3,897,743
INFO 2026-06-08 08:45:27 MarkDuplicates Tracking 318406 as yet unmatched pairs. 76833 records in RAM.
INFO 2026-06-08 08:45:30 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:12:07s. Time for last 1,000,000: 3s. Last read position: chr17:4,948,271
INFO 2026-06-08 08:45:30 MarkDuplicates Tracking 323491 as yet unmatched pairs. 81914 records in RAM.
INFO 2026-06-08 08:45:34 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:12:11s. Time for last 1,000,000: 3s. Last read position: chr17:7,252,943
INFO 2026-06-08 08:45:34 MarkDuplicates Tracking 312636 as yet unmatched pairs. 71046 records in RAM.
INFO 2026-06-08 08:45:36 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:12:14s. Time for last 1,000,000: 2s. Last read position: chr17:7,591,830
INFO 2026-06-08 08:45:36 MarkDuplicates Tracking 309682 as yet unmatched pairs. 68092 records in RAM.
INFO 2026-06-08 08:45:39 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:12:16s. Time for last 1,000,000: 2s. Last read position: chr17:8,803,378
INFO 2026-06-08 08:45:39 MarkDuplicates Tracking 307505 as yet unmatched pairs. 65915 records in RAM.
INFO 2026-06-08 08:45:42 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:12:19s. Time for last 1,000,000: 2s. Last read position: chr17:16,952,500
INFO 2026-06-08 08:45:42 MarkDuplicates Tracking 304670 as yet unmatched pairs. 63072 records in RAM.
INFO 2026-06-08 08:45:43 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:12:21s. Time for last 1,000,000: 1s. Last read position: chr17:20,232,334
INFO 2026-06-08 08:45:43 MarkDuplicates Tracking 301528 as yet unmatched pairs. 59924 records in RAM.
INFO 2026-06-08 08:45:45 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:12:23s. Time for last 1,000,000: 2s. Last read position: chr17:28,637,007
INFO 2026-06-08 08:45:45 MarkDuplicates Tracking 299841 as yet unmatched pairs. 58231 records in RAM.
INFO 2026-06-08 08:45:47 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:12:25s. Time for last 1,000,000: 1s. Last read position: chr17:30,510,890
INFO 2026-06-08 08:45:47 MarkDuplicates Tracking 295851 as yet unmatched pairs. 54239 records in RAM.
INFO 2026-06-08 08:45:49 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:12:26s. Time for last 1,000,000: 1s. Last read position: chr17:35,479,647
INFO 2026-06-08 08:45:49 MarkDuplicates Tracking 294255 as yet unmatched pairs. 52637 records in RAM.
INFO 2026-06-08 08:45:51 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:12:28s. Time for last 1,000,000: 1s. Last read position: chr17:37,226,381
INFO 2026-06-08 08:45:51 MarkDuplicates Tracking 291069 as yet unmatched pairs. 49443 records in RAM.
INFO 2026-06-08 08:45:53 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:12:30s. Time for last 1,000,000: 1s. Last read position: chr17:38,852,648
INFO 2026-06-08 08:45:53 MarkDuplicates Tracking 299359 as yet unmatched pairs. 57727 records in RAM.
INFO 2026-06-08 08:45:55 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:12:32s. Time for last 1,000,000: 1s. Last read position: chr17:40,273,796
INFO 2026-06-08 08:45:55 MarkDuplicates Tracking 285654 as yet unmatched pairs. 44015 records in RAM.
INFO 2026-06-08 08:45:58 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:12:36s. Time for last 1,000,000: 3s. Last read position: chr17:42,490,556
INFO 2026-06-08 08:45:58 MarkDuplicates Tracking 283363 as yet unmatched pairs. 41709 records in RAM.
INFO 2026-06-08 08:46:01 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:12:38s. Time for last 1,000,000: 2s. Last read position: chr17:44,040,210
INFO 2026-06-08 08:46:01 MarkDuplicates Tracking 280501 as yet unmatched pairs. 38844 records in RAM.
INFO 2026-06-08 08:46:04 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:12:41s. Time for last 1,000,000: 2s. Last read position: chr17:45,430,132
INFO 2026-06-08 08:46:04 MarkDuplicates Tracking 277324 as yet unmatched pairs. 35655 records in RAM.
INFO 2026-06-08 08:46:06 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:12:44s. Time for last 1,000,000: 2s. Last read position: chr17:47,976,796
INFO 2026-06-08 08:46:06 MarkDuplicates Tracking 276680 as yet unmatched pairs. 35002 records in RAM.
INFO 2026-06-08 08:46:09 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:12:46s. Time for last 1,000,000: 2s. Last read position: chr17:51,171,608
INFO 2026-06-08 08:46:09 MarkDuplicates Tracking 271779 as yet unmatched pairs. 30094 records in RAM.
INFO 2026-06-08 08:46:12 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:12:49s. Time for last 1,000,000: 2s. Last read position: chr17:59,674,699
INFO 2026-06-08 08:46:12 MarkDuplicates Tracking 271594 as yet unmatched pairs. 29902 records in RAM.
INFO 2026-06-08 08:46:15 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:12:52s. Time for last 1,000,000: 2s. Last read position: chr17:63,818,031
INFO 2026-06-08 08:46:15 MarkDuplicates Tracking 267490 as yet unmatched pairs. 25786 records in RAM.
INFO 2026-06-08 08:46:17 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:12:55s. Time for last 1,000,000: 2s. Last read position: chr17:68,450,817
INFO 2026-06-08 08:46:17 MarkDuplicates Tracking 264234 as yet unmatched pairs. 22528 records in RAM.
INFO 2026-06-08 08:46:20 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:12:57s. Time for last 1,000,000: 2s. Last read position: chr17:75,489,275
INFO 2026-06-08 08:46:20 MarkDuplicates Tracking 262249 as yet unmatched pairs. 20525 records in RAM.
INFO 2026-06-08 08:46:23 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:13:00s. Time for last 1,000,000: 2s. Last read position: chr17:76,736,174
INFO 2026-06-08 08:46:23 MarkDuplicates Tracking 261752 as yet unmatched pairs. 20028 records in RAM.
INFO 2026-06-08 08:46:25 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:13:03s. Time for last 1,000,000: 2s. Last read position: chr17:78,171,872
INFO 2026-06-08 08:46:25 MarkDuplicates Tracking 261323 as yet unmatched pairs. 19596 records in RAM.
INFO 2026-06-08 08:46:28 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:13:05s. Time for last 1,000,000: 2s. Last read position: chr17:80,346,123
INFO 2026-06-08 08:46:28 MarkDuplicates Tracking 254752 as yet unmatched pairs. 13016 records in RAM.
INFO 2026-06-08 08:46:31 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:13:08s. Time for last 1,000,000: 2s. Last read position: chr17:81,512,223
INFO 2026-06-08 08:46:31 MarkDuplicates Tracking 253894 as yet unmatched pairs. 12155 records in RAM.
INFO 2026-06-08 08:46:34 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:13:11s. Time for last 1,000,000: 2s. Last read position: chr17:82,054,004
INFO 2026-06-08 08:46:34 MarkDuplicates Tracking 247390 as yet unmatched pairs. 5637 records in RAM.
INFO 2026-06-08 08:46:36 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:13:13s. Time for last 1,000,000: 2s. Last read position: chr17:82,929,412
INFO 2026-06-08 08:46:36 MarkDuplicates Tracking 242190 as yet unmatched pairs. 412 records in RAM.
INFO 2026-06-08 08:46:38 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:13:16s. Time for last 1,000,000: 2s. Last read position: chr18:12,817,341
INFO 2026-06-08 08:46:38 MarkDuplicates Tracking 239431 as yet unmatched pairs. 10833 records in RAM.
INFO 2026-06-08 08:46:40 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:13:17s. Time for last 1,000,000: 1s. Last read position: chr18:35,702,939
INFO 2026-06-08 08:46:40 MarkDuplicates Tracking 236930 as yet unmatched pairs. 8314 records in RAM.
INFO 2026-06-08 08:46:42 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:13:19s. Time for last 1,000,000: 1s. Last read position: chr18:51,176,370
INFO 2026-06-08 08:46:42 MarkDuplicates Tracking 234475 as yet unmatched pairs. 5851 records in RAM.
INFO 2026-06-08 08:46:44 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:13:21s. Time for last 1,000,000: 2s. Last read position: chr18:63,318,467
INFO 2026-06-08 08:46:44 MarkDuplicates Tracking 236756 as yet unmatched pairs. 8124 records in RAM.
INFO 2026-06-08 08:46:47 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:13:24s. Time for last 1,000,000: 3s. Last read position: chr19:629,846
INFO 2026-06-08 08:46:47 MarkDuplicates Tracking 228106 as yet unmatched pairs. 105570 records in RAM.
INFO 2026-06-08 08:46:50 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:13:27s. Time for last 1,000,000: 2s. Last read position: chr19:1,105,656
INFO 2026-06-08 08:46:50 MarkDuplicates Tracking 225246 as yet unmatched pairs. 102702 records in RAM.
INFO 2026-06-08 08:46:53 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:13:30s. Time for last 1,000,000: 3s. Last read position: chr19:1,625,676
INFO 2026-06-08 08:46:53 MarkDuplicates Tracking 224328 as yet unmatched pairs. 101782 records in RAM.
INFO 2026-06-08 08:46:56 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:13:33s. Time for last 1,000,000: 2s. Last read position: chr19:2,216,583
INFO 2026-06-08 08:46:56 MarkDuplicates Tracking 218291 as yet unmatched pairs. 95740 records in RAM.
INFO 2026-06-08 08:46:58 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:13:35s. Time for last 1,000,000: 2s. Last read position: chr19:3,532,039
INFO 2026-06-08 08:46:58 MarkDuplicates Tracking 213729 as yet unmatched pairs. 91177 records in RAM.
INFO 2026-06-08 08:47:01 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:13:38s. Time for last 1,000,000: 2s. Last read position: chr19:4,839,242
INFO 2026-06-08 08:47:01 MarkDuplicates Tracking 211232 as yet unmatched pairs. 88678 records in RAM.
INFO 2026-06-08 08:47:03 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:13:40s. Time for last 1,000,000: 1s. Last read position: chr19:6,416,636
INFO 2026-06-08 08:47:03 MarkDuplicates Tracking 208361 as yet unmatched pairs. 85793 records in RAM.
INFO 2026-06-08 08:47:05 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:13:42s. Time for last 1,000,000: 2s. Last read position: chr19:7,689,231
INFO 2026-06-08 08:47:05 MarkDuplicates Tracking 212815 as yet unmatched pairs. 90244 records in RAM.
INFO 2026-06-08 08:47:07 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:13:44s. Time for last 1,000,000: 2s. Last read position: chr19:10,106,608
INFO 2026-06-08 08:47:07 MarkDuplicates Tracking 201976 as yet unmatched pairs. 79403 records in RAM.
INFO 2026-06-08 08:47:09 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:13:46s. Time for last 1,000,000: 2s. Last read position: chr19:10,379,617
INFO 2026-06-08 08:47:09 MarkDuplicates Tracking 197169 as yet unmatched pairs. 74596 records in RAM.
INFO 2026-06-08 08:47:13 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:13:50s. Time for last 1,000,000: 3s. Last read position: chr19:11,436,115
INFO 2026-06-08 08:47:13 MarkDuplicates Tracking 194936 as yet unmatched pairs. 72363 records in RAM.
INFO 2026-06-08 08:47:16 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:13:53s. Time for last 1,000,000: 3s. Last read position: chr19:12,928,644
INFO 2026-06-08 08:47:16 MarkDuplicates Tracking 191984 as yet unmatched pairs. 69406 records in RAM.
INFO 2026-06-08 08:47:18 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:13:55s. Time for last 1,000,000: 1s. Last read position: chr19:14,410,137
INFO 2026-06-08 08:47:18 MarkDuplicates Tracking 189207 as yet unmatched pairs. 66628 records in RAM.
INFO 2026-06-08 08:47:20 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:13:57s. Time for last 1,000,000: 1s. Last read position: chr19:15,427,441
INFO 2026-06-08 08:47:20 MarkDuplicates Tracking 185407 as yet unmatched pairs. 62822 records in RAM.
INFO 2026-06-08 08:47:22 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:13:59s. Time for last 1,000,000: 1s. Last read position: chr19:17,268,789
INFO 2026-06-08 08:47:22 MarkDuplicates Tracking 182567 as yet unmatched pairs. 59982 records in RAM.
INFO 2026-06-08 08:47:24 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:14:01s. Time for last 1,000,000: 2s. Last read position: chr19:18,177,274
INFO 2026-06-08 08:47:24 MarkDuplicates Tracking 183479 as yet unmatched pairs. 60893 records in RAM.
INFO 2026-06-08 08:47:27 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:14:04s. Time for last 1,000,000: 2s. Last read position: chr19:19,147,729
INFO 2026-06-08 08:47:27 MarkDuplicates Tracking 176657 as yet unmatched pairs. 54064 records in RAM.
INFO 2026-06-08 08:47:30 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:14:08s. Time for last 1,000,000: 3s. Last read position: chr19:32,692,062
INFO 2026-06-08 08:47:30 MarkDuplicates Tracking 172327 as yet unmatched pairs. 49727 records in RAM.
INFO 2026-06-08 08:47:33 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:14:10s. Time for last 1,000,000: 2s. Last read position: chr19:35,716,617
INFO 2026-06-08 08:47:33 MarkDuplicates Tracking 169161 as yet unmatched pairs. 46559 records in RAM.
INFO 2026-06-08 08:47:35 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:14:12s. Time for last 1,000,000: 2s. Last read position: chr19:38,595,485
INFO 2026-06-08 08:47:35 MarkDuplicates Tracking 168800 as yet unmatched pairs. 46195 records in RAM.
INFO 2026-06-08 08:47:37 MarkDuplicates Read 368,000,000 records. Elapsed time: 00:14:14s. Time for last 1,000,000: 2s. Last read position: chr19:39,415,215
INFO 2026-06-08 08:47:37 MarkDuplicates Tracking 163588 as yet unmatched pairs. 40980 records in RAM.
INFO 2026-06-08 08:47:39 MarkDuplicates Read 369,000,000 records. Elapsed time: 00:14:16s. Time for last 1,000,000: 1s. Last read position: chr19:40,578,509
INFO 2026-06-08 08:47:39 MarkDuplicates Tracking 161382 as yet unmatched pairs. 38773 records in RAM.
INFO 2026-06-08 08:47:41 MarkDuplicates Read 370,000,000 records. Elapsed time: 00:14:18s. Time for last 1,000,000: 1s. Last read position: chr19:41,879,276
INFO 2026-06-08 08:47:41 MarkDuplicates Tracking 164173 as yet unmatched pairs. 41563 records in RAM.
INFO 2026-06-08 08:47:44 MarkDuplicates Read 371,000,000 records. Elapsed time: 00:14:21s. Time for last 1,000,000: 2s. Last read position: chr19:42,254,987
INFO 2026-06-08 08:47:44 MarkDuplicates Tracking 154348 as yet unmatched pairs. 31733 records in RAM.
INFO 2026-06-08 08:47:46 MarkDuplicates Read 372,000,000 records. Elapsed time: 00:14:23s. Time for last 1,000,000: 2s. Last read position: chr19:44,176,041
INFO 2026-06-08 08:47:46 MarkDuplicates Tracking 151108 as yet unmatched pairs. 28491 records in RAM.
INFO 2026-06-08 08:47:48 MarkDuplicates Read 373,000,000 records. Elapsed time: 00:14:25s. Time for last 1,000,000: 1s. Last read position: chr19:45,792,513
INFO 2026-06-08 08:47:48 MarkDuplicates Tracking 147661 as yet unmatched pairs. 25044 records in RAM.
INFO 2026-06-08 08:47:50 MarkDuplicates Read 374,000,000 records. Elapsed time: 00:14:27s. Time for last 1,000,000: 1s. Last read position: chr19:47,373,612
INFO 2026-06-08 08:47:50 MarkDuplicates Tracking 144420 as yet unmatched pairs. 21800 records in RAM.
INFO 2026-06-08 08:47:52 MarkDuplicates Read 375,000,000 records. Elapsed time: 00:14:30s. Time for last 1,000,000: 2s. Last read position: chr19:48,956,317
INFO 2026-06-08 08:47:52 MarkDuplicates Tracking 145104 as yet unmatched pairs. 22484 records in RAM.
INFO 2026-06-08 08:47:56 MarkDuplicates Read 376,000,000 records. Elapsed time: 00:14:33s. Time for last 1,000,000: 3s. Last read position: chr19:49,594,832
INFO 2026-06-08 08:47:56 MarkDuplicates Tracking 138974 as yet unmatched pairs. 16346 records in RAM.
INFO 2026-06-08 08:47:59 MarkDuplicates Read 377,000,000 records. Elapsed time: 00:14:36s. Time for last 1,000,000: 2s. Last read position: chr19:49,890,261
INFO 2026-06-08 08:47:59 MarkDuplicates Tracking 139001 as yet unmatched pairs. 16372 records in RAM.
INFO 2026-06-08 08:48:01 MarkDuplicates Read 378,000,000 records. Elapsed time: 00:14:38s. Time for last 1,000,000: 1s. Last read position: chr19:52,652,893
INFO 2026-06-08 08:48:01 MarkDuplicates Tracking 131457 as yet unmatched pairs. 8828 records in RAM.
INFO 2026-06-08 08:48:02 MarkDuplicates Read 379,000,000 records. Elapsed time: 00:14:40s. Time for last 1,000,000: 1s. Last read position: chr19:55,236,932
INFO 2026-06-08 08:48:02 MarkDuplicates Tracking 130692 as yet unmatched pairs. 8060 records in RAM.
INFO 2026-06-08 08:48:04 MarkDuplicates Read 380,000,000 records. Elapsed time: 00:14:41s. Time for last 1,000,000: 1s. Last read position: chr19:57,487,930
INFO 2026-06-08 08:48:04 MarkDuplicates Tracking 125171 as yet unmatched pairs. 2538 records in RAM.
INFO 2026-06-08 08:48:07 MarkDuplicates Read 381,000,000 records. Elapsed time: 00:14:44s. Time for last 1,000,000: 2s. Last read position: chr20:648,908
INFO 2026-06-08 08:48:07 MarkDuplicates Tracking 122097 as yet unmatched pairs. 27605 records in RAM.
INFO 2026-06-08 08:48:08 MarkDuplicates Read 382,000,000 records. Elapsed time: 00:14:46s. Time for last 1,000,000: 1s. Last read position: chr20:5,942,681
INFO 2026-06-08 08:48:08 MarkDuplicates Tracking 118903 as yet unmatched pairs. 24409 records in RAM.
INFO 2026-06-08 08:48:11 MarkDuplicates Read 383,000,000 records. Elapsed time: 00:14:48s. Time for last 1,000,000: 2s. Last read position: chr20:31,550,063
INFO 2026-06-08 08:48:11 MarkDuplicates Tracking 117171 as yet unmatched pairs. 22675 records in RAM.
INFO 2026-06-08 08:48:14 MarkDuplicates Read 384,000,000 records. Elapsed time: 00:14:51s. Time for last 1,000,000: 2s. Last read position: chr20:35,502,518
INFO 2026-06-08 08:48:14 MarkDuplicates Tracking 113512 as yet unmatched pairs. 19016 records in RAM.
INFO 2026-06-08 08:48:16 MarkDuplicates Read 385,000,000 records. Elapsed time: 00:14:53s. Time for last 1,000,000: 2s. Last read position: chr20:38,835,910
INFO 2026-06-08 08:48:16 MarkDuplicates Tracking 111763 as yet unmatched pairs. 17254 records in RAM.
INFO 2026-06-08 08:48:19 MarkDuplicates Read 386,000,000 records. Elapsed time: 00:14:56s. Time for last 1,000,000: 2s. Last read position: chr20:45,814,403
INFO 2026-06-08 08:48:19 MarkDuplicates Tracking 109076 as yet unmatched pairs. 14554 records in RAM.
INFO 2026-06-08 08:48:21 MarkDuplicates Read 387,000,000 records. Elapsed time: 00:14:58s. Time for last 1,000,000: 2s. Last read position: chr20:49,025,347
INFO 2026-06-08 08:48:21 MarkDuplicates Tracking 105320 as yet unmatched pairs. 10798 records in RAM.
INFO 2026-06-08 08:48:24 MarkDuplicates Read 388,000,000 records. Elapsed time: 00:15:01s. Time for last 1,000,000: 2s. Last read position: chr20:58,673,629
INFO 2026-06-08 08:48:24 MarkDuplicates Tracking 102987 as yet unmatched pairs. 8448 records in RAM.
INFO 2026-06-08 08:48:26 MarkDuplicates Read 389,000,000 records. Elapsed time: 00:15:03s. Time for last 1,000,000: 2s. Last read position: chr20:62,879,490
INFO 2026-06-08 08:48:26 MarkDuplicates Tracking 99464 as yet unmatched pairs. 4925 records in RAM.
INFO 2026-06-08 08:48:28 MarkDuplicates Read 390,000,000 records. Elapsed time: 00:15:05s. Time for last 1,000,000: 1s. Last read position: chr20:63,966,411
INFO 2026-06-08 08:48:28 MarkDuplicates Tracking 95924 as yet unmatched pairs. 1382 records in RAM.
INFO 2026-06-08 08:48:30 MarkDuplicates Read 391,000,000 records. Elapsed time: 00:15:07s. Time for last 1,000,000: 1s. Last read position: chr21:8,216,957
INFO 2026-06-08 08:48:30 MarkDuplicates Tracking 92566 as yet unmatched pairs. 14236 records in RAM.
INFO 2026-06-08 08:48:31 MarkDuplicates Read 392,000,000 records. Elapsed time: 00:15:08s. Time for last 1,000,000: 1s. Last read position: chr21:8,399,082
INFO 2026-06-08 08:48:31 MarkDuplicates Tracking 92040 as yet unmatched pairs. 13708 records in RAM.
INFO 2026-06-08 08:48:33 MarkDuplicates Read 393,000,000 records. Elapsed time: 00:15:10s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,543
INFO 2026-06-08 08:48:33 MarkDuplicates Tracking 107959 as yet unmatched pairs. 29627 records in RAM.
INFO 2026-06-08 08:48:36 MarkDuplicates Read 394,000,000 records. Elapsed time: 00:15:13s. Time for last 1,000,000: 3s. Last read position: chr21:33,532,372
INFO 2026-06-08 08:48:36 MarkDuplicates Tracking 87917 as yet unmatched pairs. 9584 records in RAM.
INFO 2026-06-08 08:48:39 MarkDuplicates Read 395,000,000 records. Elapsed time: 00:15:16s. Time for last 1,000,000: 2s. Last read position: chr21:41,430,569
INFO 2026-06-08 08:48:39 MarkDuplicates Tracking 87752 as yet unmatched pairs. 9419 records in RAM.
INFO 2026-06-08 08:48:41 MarkDuplicates Read 396,000,000 records. Elapsed time: 00:15:18s. Time for last 1,000,000: 2s. Last read position: chr21:44,133,820
INFO 2026-06-08 08:48:41 MarkDuplicates Tracking 81702 as yet unmatched pairs. 3369 records in RAM.
INFO 2026-06-08 08:48:43 MarkDuplicates Read 397,000,000 records. Elapsed time: 00:15:20s. Time for last 1,000,000: 2s. Last read position: chr21:46,401,623
INFO 2026-06-08 08:48:43 MarkDuplicates Tracking 79025 as yet unmatched pairs. 692 records in RAM.
INFO 2026-06-08 08:48:46 MarkDuplicates Read 398,000,000 records. Elapsed time: 00:15:23s. Time for last 1,000,000: 3s. Last read position: chr22:20,712,516
INFO 2026-06-08 08:48:46 MarkDuplicates Tracking 76191 as yet unmatched pairs. 33675 records in RAM.
INFO 2026-06-08 08:48:49 MarkDuplicates Read 399,000,000 records. Elapsed time: 00:15:26s. Time for last 1,000,000: 2s. Last read position: chr22:24,091,635
INFO 2026-06-08 08:48:49 MarkDuplicates Tracking 73447 as yet unmatched pairs. 30931 records in RAM.
INFO 2026-06-08 08:48:51 MarkDuplicates Read 400,000,000 records. Elapsed time: 00:15:28s. Time for last 1,000,000: 2s. Last read position: chr22:29,287,030
INFO 2026-06-08 08:48:51 MarkDuplicates Tracking 75849 as yet unmatched pairs. 33333 records in RAM.
INFO 2026-06-08 08:48:54 MarkDuplicates Read 401,000,000 records. Elapsed time: 00:15:31s. Time for last 1,000,000: 3s. Last read position: chr22:30,663,456
INFO 2026-06-08 08:48:54 MarkDuplicates Tracking 66909 as yet unmatched pairs. 24393 records in RAM.
INFO 2026-06-08 08:48:57 MarkDuplicates Read 402,000,000 records. Elapsed time: 00:15:34s. Time for last 1,000,000: 2s. Last read position: chr22:36,288,733
INFO 2026-06-08 08:48:57 MarkDuplicates Tracking 65095 as yet unmatched pairs. 22576 records in RAM.
INFO 2026-06-08 08:48:59 MarkDuplicates Read 403,000,000 records. Elapsed time: 00:15:36s. Time for last 1,000,000: 2s. Last read position: chr22:37,231,319
INFO 2026-06-08 08:48:59 MarkDuplicates Tracking 67983 as yet unmatched pairs. 25464 records in RAM.
INFO 2026-06-08 08:49:01 MarkDuplicates Read 404,000,000 records. Elapsed time: 00:15:38s. Time for last 1,000,000: 1s. Last read position: chr22:38,729,606
INFO 2026-06-08 08:49:01 MarkDuplicates Tracking 59606 as yet unmatched pairs. 17087 records in RAM.
INFO 2026-06-08 08:49:03 MarkDuplicates Read 405,000,000 records. Elapsed time: 00:15:40s. Time for last 1,000,000: 2s. Last read position: chr22:40,779,043
INFO 2026-06-08 08:49:03 MarkDuplicates Tracking 55469 as yet unmatched pairs. 12938 records in RAM.
INFO 2026-06-08 08:49:05 MarkDuplicates Read 406,000,000 records. Elapsed time: 00:15:42s. Time for last 1,000,000: 2s. Last read position: chr22:41,900,339
INFO 2026-06-08 08:49:05 MarkDuplicates Tracking 54571 as yet unmatched pairs. 12040 records in RAM.
INFO 2026-06-08 08:49:07 MarkDuplicates Read 407,000,000 records. Elapsed time: 00:15:44s. Time for last 1,000,000: 1s. Last read position: chr22:45,178,378
INFO 2026-06-08 08:49:07 MarkDuplicates Tracking 50023 as yet unmatched pairs. 7486 records in RAM.
INFO 2026-06-08 08:49:10 MarkDuplicates Read 408,000,000 records. Elapsed time: 00:15:47s. Time for last 1,000,000: 2s. Last read position: chr22:50,313,659
INFO 2026-06-08 08:49:10 MarkDuplicates Tracking 46532 as yet unmatched pairs. 3992 records in RAM.
INFO 2026-06-08 08:49:13 MarkDuplicates Read 409,000,000 records. Elapsed time: 00:15:50s. Time for last 1,000,000: 3s. Last read position: chrX:1,389,407
INFO 2026-06-08 08:49:13 MarkDuplicates Tracking 45368 as yet unmatched pairs. 34260 records in RAM.
INFO 2026-06-08 08:49:16 MarkDuplicates Read 410,000,000 records. Elapsed time: 00:15:53s. Time for last 1,000,000: 2s. Last read position: chrX:16,853,682
INFO 2026-06-08 08:49:16 MarkDuplicates Tracking 39780 as yet unmatched pairs. 28672 records in RAM.
INFO 2026-06-08 08:49:18 MarkDuplicates Read 411,000,000 records. Elapsed time: 00:15:55s. Time for last 1,000,000: 2s. Last read position: chrX:40,597,535
INFO 2026-06-08 08:49:18 MarkDuplicates Tracking 37010 as yet unmatched pairs. 25902 records in RAM.
INFO 2026-06-08 08:49:20 MarkDuplicates Read 412,000,000 records. Elapsed time: 00:15:57s. Time for last 1,000,000: 2s. Last read position: chrX:48,461,739
INFO 2026-06-08 08:49:20 MarkDuplicates Tracking 34905 as yet unmatched pairs. 23794 records in RAM.
INFO 2026-06-08 08:49:22 MarkDuplicates Read 413,000,000 records. Elapsed time: 00:16:00s. Time for last 1,000,000: 2s. Last read position: chrX:53,201,909
INFO 2026-06-08 08:49:22 MarkDuplicates Tracking 31318 as yet unmatched pairs. 20207 records in RAM.
INFO 2026-06-08 08:49:25 MarkDuplicates Read 414,000,000 records. Elapsed time: 00:16:02s. Time for last 1,000,000: 2s. Last read position: chrX:56,564,170
INFO 2026-06-08 08:49:25 MarkDuplicates Tracking 28488 as yet unmatched pairs. 17377 records in RAM.
INFO 2026-06-08 08:49:28 MarkDuplicates Read 415,000,000 records. Elapsed time: 00:16:05s. Time for last 1,000,000: 2s. Last read position: chrX:71,533,321
INFO 2026-06-08 08:49:28 MarkDuplicates Tracking 27884 as yet unmatched pairs. 16773 records in RAM.
INFO 2026-06-08 08:49:32 MarkDuplicates Read 416,000,000 records. Elapsed time: 00:16:09s. Time for last 1,000,000: 4s. Last read position: chrX:78,113,955
INFO 2026-06-08 08:49:32 MarkDuplicates Tracking 26188 as yet unmatched pairs. 15077 records in RAM.
INFO 2026-06-08 08:49:34 MarkDuplicates Read 417,000,000 records. Elapsed time: 00:16:12s. Time for last 1,000,000: 2s. Last read position: chrX:119,468,472
INFO 2026-06-08 08:49:34 MarkDuplicates Tracking 22883 as yet unmatched pairs. 11770 records in RAM.
INFO 2026-06-08 08:49:37 MarkDuplicates Read 418,000,000 records. Elapsed time: 00:16:14s. Time for last 1,000,000: 2s. Last read position: chrX:135,303,531
INFO 2026-06-08 08:49:37 MarkDuplicates Tracking 18268 as yet unmatched pairs. 7155 records in RAM.
INFO 2026-06-08 08:49:40 MarkDuplicates Read 419,000,000 records. Elapsed time: 00:16:17s. Time for last 1,000,000: 2s. Last read position: chrX:153,954,223
INFO 2026-06-08 08:49:40 MarkDuplicates Tracking 16461 as yet unmatched pairs. 5347 records in RAM.
INFO 2026-06-08 08:49:42 MarkDuplicates Read 420,000,000 records. Elapsed time: 00:16:20s. Time for last 1,000,000: 2s. Last read position: chrX:154,449,230
INFO 2026-06-08 08:49:42 MarkDuplicates Tracking 12884 as yet unmatched pairs. 1770 records in RAM.
INFO 2026-06-08 08:49:45 MarkDuplicates Read 421,000,000 records. Elapsed time: 00:16:22s. Time for last 1,000,000: 2s. Last read position: GL000220.1:114,133
INFO 2026-06-08 08:49:45 MarkDuplicates Tracking 9709 as yet unmatched pairs. 1234 records in RAM.
INFO 2026-06-08 08:49:47 MarkDuplicates Read 422,000,000 records. Elapsed time: 00:16:24s. Time for last 1,000,000: 1s. Last read position: GL000220.1:158,135
INFO 2026-06-08 08:49:47 MarkDuplicates Tracking 8551 as yet unmatched pairs. 76 records in RAM.
INFO 2026-06-08 08:49:48 MarkDuplicates Read 423,000,000 records. Elapsed time: 00:16:26s. Time for last 1,000,000: 1s. Last read position: KI270733.1:132,329
INFO 2026-06-08 08:49:48 MarkDuplicates Tracking 3856 as yet unmatched pairs. 3847 records in RAM.
INFO 2026-06-08 08:49:51 MarkDuplicates Read 424,000,000 records. Elapsed time: 00:16:28s. Time for last 1,000,000: 2s. Last read position: KI270733.1:178,327
INFO 2026-06-08 08:49:51 MarkDuplicates Tracking 39 as yet unmatched pairs. 30 records in RAM.
INFO 2026-06-08 08:49:52 MarkDuplicates Read 424343186 records. 0 pairs never matched.
INFO 2026-06-08 08:50:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 37834189792; totalMemory: 54022635520; maxMemory: 63585648640
INFO 2026-06-08 08:50:49 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:51:11 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:51:55 OpticalDuplicateFinder Large duplicate set. size = 1678
INFO 2026-06-08 08:51:55 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-21,675
INFO 2026-06-08 08:51:57 OpticalDuplicateFinder Large duplicate set. size = 1228
INFO 2026-06-08 08:51:57 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,713
INFO 2026-06-08 08:52:12 OpticalDuplicateFinder Large duplicate set. size = 1227
INFO 2026-06-08 08:52:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:5,401
INFO 2026-06-08 08:52:12 MarkDuplicates Traversing fragment information and detecting duplicates.
WARNING 2026-06-08 08:52:13 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
INFO 2026-06-08 08:53:05 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:53:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 37301373936; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-08 08:53:15 MarkDuplicates Marking 191967260 records as duplicates.
INFO 2026-06-08 08:53:15 MarkDuplicates Found 26432222 optical duplicate clusters.
INFO 2026-06-08 08:53:15 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 08:53:38 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:23s. Time for last 10,000,000: 23s. Last read position: chr1:32,825,364
INFO 2026-06-08 08:54:05 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:50s. Time for last 10,000,000: 27s. Last read position: chr1:116,393,566
INFO 2026-06-08 08:54:32 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:17s. Time for last 10,000,000: 27s. Last read position: chr1:161,054,637
INFO 2026-06-08 08:54:58 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:42s. Time for last 10,000,000: 25s. Last read position: chr2:10,788,935
INFO 2026-06-08 08:55:22 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:02:06s. Time for last 10,000,000: 24s. Last read position: chr2:69,475,926
INFO 2026-06-08 08:55:47 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:31s. Time for last 10,000,000: 24s. Last read position: chr2:189,782,421
INFO 2026-06-08 08:56:14 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:58s. Time for last 10,000,000: 26s. Last read position: chr3:16,409,406
INFO 2026-06-08 08:56:40 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:03:24s. Time for last 10,000,000: 26s. Last read position: chr3:122,404,331
INFO 2026-06-08 08:57:06 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:03:51s. Time for last 10,000,000: 26s. Last read position: chr4:13,599,203
INFO 2026-06-08 08:57:32 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:04:16s. Time for last 10,000,000: 25s. Last read position: chr5:14,366,929
INFO 2026-06-08 08:57:58 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:04:43s. Time for last 10,000,000: 26s. Last read position: chr5:150,402,218
INFO 2026-06-08 08:58:22 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:05:06s. Time for last 10,000,000: 23s. Last read position: chr6:7,246,762
INFO 2026-06-08 08:58:48 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:05:32s. Time for last 10,000,000: 26s. Last read position: chr6:32,845,299
INFO 2026-06-08 08:59:16 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:06:00s. Time for last 10,000,000: 28s. Last read position: chr6:128,005,217
INFO 2026-06-08 08:59:40 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:06:25s. Time for last 10,000,000: 24s. Last read position: chr7:44,392,384
INFO 2026-06-08 09:00:06 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:06:50s. Time for last 10,000,000: 25s. Last read position: chr7:128,337,157
INFO 2026-06-08 09:00:32 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:07:16s. Time for last 10,000,000: 25s. Last read position: chr8:70,156,967
INFO 2026-06-08 09:00:58 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:07:42s. Time for last 10,000,000: 26s. Last read position: chr9:35,704,128
INFO 2026-06-08 09:01:24 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:08:08s. Time for last 10,000,000: 26s. Last read position: chr9:133,108,389
INFO 2026-06-08 09:01:49 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:08:33s. Time for last 10,000,000: 24s. Last read position: chr10:87,933,025
INFO 2026-06-08 09:02:15 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:09:00s. Time for last 10,000,000: 26s. Last read position: chr11:18,295,129
INFO 2026-06-08 09:02:45 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:09:30s. Time for last 10,000,000: 30s. Last read position: chr11:66,593,249
INFO 2026-06-08 09:03:11 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:09:56s. Time for last 10,000,000: 25s. Last read position: chr12:4,659,059
INFO 2026-06-08 09:03:37 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:10:21s. Time for last 10,000,000: 25s. Last read position: chr12:56,245,153
INFO 2026-06-08 09:04:02 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:10:47s. Time for last 10,000,000: 25s. Last read position: chr12:121,423,501
INFO 2026-06-08 09:04:29 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:11:13s. Time for last 10,000,000: 26s. Last read position: chr14:23,061,171
INFO 2026-06-08 09:05:00 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:11:44s. Time for last 10,000,000: 31s. Last read position: chr14:102,083,788
INFO 2026-06-08 09:05:27 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:12:12s. Time for last 10,000,000: 27s. Last read position: chr15:50,612,649
INFO 2026-06-08 09:05:54 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:12:38s. Time for last 10,000,000: 26s. Last read position: chr16:1,777,085
INFO 2026-06-08 09:06:21 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:13:05s. Time for last 10,000,000: 27s. Last read position: chr16:28,826,909
INFO 2026-06-08 09:06:48 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:13:32s. Time for last 10,000,000: 26s. Last read position: chr16:70,563,921
INFO 2026-06-08 09:07:15 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:13:59s. Time for last 10,000,000: 27s. Last read position: chr17:8,803,378
INFO 2026-06-08 09:07:42 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:14:26s. Time for last 10,000,000: 26s. Last read position: chr17:44,040,210
INFO 2026-06-08 09:08:08 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:14:53s. Time for last 10,000,000: 26s. Last read position: chr17:80,346,123
INFO 2026-06-08 09:08:33 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:15:17s. Time for last 10,000,000: 24s. Last read position: chr19:1,625,676
INFO 2026-06-08 09:08:59 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:15:43s. Time for last 10,000,000: 26s. Last read position: chr19:14,410,137
INFO 2026-06-08 09:09:25 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:16:09s. Time for last 10,000,000: 25s. Last read position: chr19:41,879,276
INFO 2026-06-08 09:09:51 MarkDuplicates Written 380,000,000 records. Elapsed time: 00:16:36s. Time for last 10,000,000: 26s. Last read position: chr19:57,487,930
INFO 2026-06-08 09:10:17 MarkDuplicates Written 390,000,000 records. Elapsed time: 00:17:02s. Time for last 10,000,000: 26s. Last read position: chr20:63,966,411
INFO 2026-06-08 09:10:43 MarkDuplicates Written 400,000,000 records. Elapsed time: 00:17:27s. Time for last 10,000,000: 25s. Last read position: chr22:29,287,030
INFO 2026-06-08 09:11:06 MarkDuplicates Written 410,000,000 records. Elapsed time: 00:17:50s. Time for last 10,000,000: 23s. Last read position: chrX:16,853,682
INFO 2026-06-08 09:11:31 MarkDuplicates Written 420,000,000 records. Elapsed time: 00:18:16s. Time for last 10,000,000: 25s. Last read position: chrX:154,449,230
INFO 2026-06-08 09:11:50 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 09:11:50 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 09:11:50 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 09:11:51 MarkDuplicates Before output close freeMemory: 202061136; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 09:11:51 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 09:11:51 MarkDuplicates After output close freeMemory: 104839760; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 09:11:51 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 38.50 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory