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/e7/840b5b26a9e3c23007a4e37ae4146c/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/840b5b26a9e3c23007a4e37ae4146c/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/94f87efce0c9ea1070184b2035b932/659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)
Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_6i-T1-TRNA-1_A23MVY2LT4_1.md.bam --METRICS_FILE 659_6i-T1-TRNA-1_A23MVY2LT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
08:16:16.353 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 08:16:16 GMT 2026] MarkDuplicates --INPUT 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_6i-T1-TRNA-1_A23MVY2LT4_1.md.bam --METRICS_FILE 659_6i-T1-TRNA-1_A23MVY2LT4_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 08:16:16 GMT 2026] Executing as ?@nf-e7840b5b26a9e3c23007a4e37ae4146c-88d7c-pgzj5 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 08:16:16 MarkDuplicates Start of doWork freeMemory: 105494400; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 08:16:16 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 08:16:16 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 08:16:20 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:1,739,273
INFO 2026-06-08 08:16:20 MarkDuplicates Tracking 2895 as yet unmatched pairs. 51 records in RAM.
INFO 2026-06-08 08:16:22 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 2s. Last read position: chr1:8,358,551
INFO 2026-06-08 08:16:22 MarkDuplicates Tracking 6243 as yet unmatched pairs. 535 records in RAM.
INFO 2026-06-08 08:16:25 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 2s. Last read position: chr1:11,240,500
INFO 2026-06-08 08:16:25 MarkDuplicates Tracking 8507 as yet unmatched pairs. 237 records in RAM.
INFO 2026-06-08 08:16:27 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 2s. Last read position: chr1:15,937,507
INFO 2026-06-08 08:16:27 MarkDuplicates Tracking 11002 as yet unmatched pairs. 172 records in RAM.
INFO 2026-06-08 08:16:29 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 2s. Last read position: chr1:20,637,974
INFO 2026-06-08 08:16:29 MarkDuplicates Tracking 13426 as yet unmatched pairs. 163 records in RAM.
INFO 2026-06-08 08:16:32 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: chr1:22,639,345
INFO 2026-06-08 08:16:32 MarkDuplicates Tracking 16338 as yet unmatched pairs. 471 records in RAM.
INFO 2026-06-08 08:16:35 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 2s. Last read position: chr1:26,320,214
INFO 2026-06-08 08:16:35 MarkDuplicates Tracking 18402 as yet unmatched pairs. 144 records in RAM.
INFO 2026-06-08 08:16:37 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: chr1:29,097,885
INFO 2026-06-08 08:16:37 MarkDuplicates Tracking 20893 as yet unmatched pairs. 113 records in RAM.
INFO 2026-06-08 08:16:39 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 2s. Last read position: chr1:32,668,819
INFO 2026-06-08 08:16:39 MarkDuplicates Tracking 23573 as yet unmatched pairs. 84 records in RAM.
INFO 2026-06-08 08:16:41 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 2s. Last read position: chr1:36,466,456
INFO 2026-06-08 08:16:41 MarkDuplicates Tracking 26254 as yet unmatched pairs. 72 records in RAM.
INFO 2026-06-08 08:16:43 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 2s. Last read position: chr1:39,748,976
INFO 2026-06-08 08:16:43 MarkDuplicates Tracking 28641 as yet unmatched pairs. 42 records in RAM.
INFO 2026-06-08 08:16:45 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 1s. Last read position: chr1:43,603,491
INFO 2026-06-08 08:16:45 MarkDuplicates Tracking 31309 as yet unmatched pairs. 79 records in RAM.
INFO 2026-06-08 08:16:48 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 2s. Last read position: chr1:46,708,015
INFO 2026-06-08 08:16:48 MarkDuplicates Tracking 33742 as yet unmatched pairs. 141 records in RAM.
INFO 2026-06-08 08:16:50 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 2s. Last read position: chr1:55,134,321
INFO 2026-06-08 08:16:50 MarkDuplicates Tracking 36247 as yet unmatched pairs. 107 records in RAM.
INFO 2026-06-08 08:16:52 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 2s. Last read position: chr1:71,592,934
INFO 2026-06-08 08:16:52 MarkDuplicates Tracking 38475 as yet unmatched pairs. 3 records in RAM.
INFO 2026-06-08 08:16:55 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 2s. Last read position: chr1:92,833,415
INFO 2026-06-08 08:16:55 MarkDuplicates Tracking 41028 as yet unmatched pairs. 220 records in RAM.
INFO 2026-06-08 08:16:57 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 2s. Last read position: chr1:109,252,075
INFO 2026-06-08 08:16:57 MarkDuplicates Tracking 42975 as yet unmatched pairs. 20 records in RAM.
INFO 2026-06-08 08:16:59 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 2s. Last read position: chr1:113,980,591
INFO 2026-06-08 08:16:59 MarkDuplicates Tracking 45390 as yet unmatched pairs. 108 records in RAM.
INFO 2026-06-08 08:17:01 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 1s. Last read position: chr1:119,916,385
INFO 2026-06-08 08:17:01 MarkDuplicates Tracking 48192 as yet unmatched pairs. 523 records in RAM.
INFO 2026-06-08 08:17:03 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: chr1:120,814,840
INFO 2026-06-08 08:17:03 MarkDuplicates Tracking 50084 as yet unmatched pairs. 267 records in RAM.
INFO 2026-06-08 08:17:05 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 1s. Last read position: chr1:146,975,936
INFO 2026-06-08 08:17:05 MarkDuplicates Tracking 51114 as yet unmatched pairs. 90 records in RAM.
INFO 2026-06-08 08:17:06 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 1s. Last read position: chr1:149,513,390
INFO 2026-06-08 08:17:06 MarkDuplicates Tracking 52101 as yet unmatched pairs. 36 records in RAM.
INFO 2026-06-08 08:17:08 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 1s. Last read position: chr1:151,369,106
INFO 2026-06-08 08:17:08 MarkDuplicates Tracking 54416 as yet unmatched pairs. 115 records in RAM.
INFO 2026-06-08 08:17:10 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 1s. Last read position: chr1:154,172,926
INFO 2026-06-08 08:17:10 MarkDuplicates Tracking 57515 as yet unmatched pairs. 910 records in RAM.
INFO 2026-06-08 08:17:12 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 2s. Last read position: chr1:155,264,722
INFO 2026-06-08 08:17:12 MarkDuplicates Tracking 59133 as yet unmatched pairs. 34 records in RAM.
INFO 2026-06-08 08:17:13 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 1s. Last read position: chr1:156,246,221
INFO 2026-06-08 08:17:13 MarkDuplicates Tracking 61764 as yet unmatched pairs. 55 records in RAM.
INFO 2026-06-08 08:17:15 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 1s. Last read position: chr1:160,547,032
INFO 2026-06-08 08:17:15 MarkDuplicates Tracking 64296 as yet unmatched pairs. 75 records in RAM.
INFO 2026-06-08 08:17:17 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 1s. Last read position: chr1:169,378,378
INFO 2026-06-08 08:17:17 MarkDuplicates Tracking 66753 as yet unmatched pairs. 147 records in RAM.
INFO 2026-06-08 08:17:19 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 1s. Last read position: chr1:180,176,020
INFO 2026-06-08 08:17:19 MarkDuplicates Tracking 68982 as yet unmatched pairs. 63 records in RAM.
INFO 2026-06-08 08:17:21 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 2s. Last read position: chr1:186,347,353
INFO 2026-06-08 08:17:21 MarkDuplicates Tracking 71786 as yet unmatched pairs. 628 records in RAM.
INFO 2026-06-08 08:17:24 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 2s. Last read position: chr1:201,783,652
INFO 2026-06-08 08:17:24 MarkDuplicates Tracking 73393 as yet unmatched pairs. 42 records in RAM.
INFO 2026-06-08 08:17:25 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 1s. Last read position: chr1:204,549,375
INFO 2026-06-08 08:17:25 MarkDuplicates Tracking 76154 as yet unmatched pairs. 488 records in RAM.
INFO 2026-06-08 08:17:27 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 1s. Last read position: chr1:209,777,364
INFO 2026-06-08 08:17:27 MarkDuplicates Tracking 78341 as yet unmatched pairs. 107 records in RAM.
INFO 2026-06-08 08:17:29 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 1s. Last read position: chr1:225,514,802
INFO 2026-06-08 08:17:29 MarkDuplicates Tracking 81079 as yet unmatched pairs. 491 records in RAM.
INFO 2026-06-08 08:17:31 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 1s. Last read position: chr1:229,518,319
INFO 2026-06-08 08:17:31 MarkDuplicates Tracking 83394 as yet unmatched pairs. 45 records in RAM.
INFO 2026-06-08 08:17:33 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 2s. Last read position: chr1:243,563,718
INFO 2026-06-08 08:17:33 MarkDuplicates Tracking 86752 as yet unmatched pairs. 751 records in RAM.
INFO 2026-06-08 08:17:37 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 3s. Last read position: chr2:9,354,602
INFO 2026-06-08 08:17:37 MarkDuplicates Tracking 88309 as yet unmatched pairs. 88086 records in RAM.
INFO 2026-06-08 08:17:39 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 2s. Last read position: chr2:24,284,717
INFO 2026-06-08 08:17:39 MarkDuplicates Tracking 90877 as yet unmatched pairs. 90636 records in RAM.
INFO 2026-06-08 08:17:40 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 1s. Last read position: chr2:27,316,043
INFO 2026-06-08 08:17:40 MarkDuplicates Tracking 93294 as yet unmatched pairs. 93039 records in RAM.
INFO 2026-06-08 08:17:42 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 1s. Last read position: chr2:32,468,669
INFO 2026-06-08 08:17:42 MarkDuplicates Tracking 96343 as yet unmatched pairs. 96071 records in RAM.
INFO 2026-06-08 08:17:44 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,264
INFO 2026-06-08 08:17:44 MarkDuplicates Tracking 408059 as yet unmatched pairs. 80255 records in RAM.
INFO 2026-06-08 08:17:46 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,406
INFO 2026-06-08 08:17:46 MarkDuplicates Tracking 818442 as yet unmatched pairs. 60130 records in RAM.
INFO 2026-06-08 08:17:48 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 1s. Last read position: chr2:36,787,261
INFO 2026-06-08 08:17:48 MarkDuplicates Tracking 865639 as yet unmatched pairs. 57174 records in RAM.
INFO 2026-06-08 08:17:49 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 1s. Last read position: chr2:43,224,377
INFO 2026-06-08 08:17:49 MarkDuplicates Tracking 863834 as yet unmatched pairs. 55369 records in RAM.
INFO 2026-06-08 08:17:51 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 1s. Last read position: chr2:50,552,654
INFO 2026-06-08 08:17:51 MarkDuplicates Tracking 860415 as yet unmatched pairs. 51944 records in RAM.
INFO 2026-06-08 08:17:53 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 1s. Last read position: chr2:61,221,554
INFO 2026-06-08 08:17:53 MarkDuplicates Tracking 858134 as yet unmatched pairs. 49657 records in RAM.
INFO 2026-06-08 08:17:55 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 2s. Last read position: chr2:70,181,188
INFO 2026-06-08 08:17:55 MarkDuplicates Tracking 855550 as yet unmatched pairs. 47064 records in RAM.
INFO 2026-06-08 08:17:57 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 2s. Last read position: chr2:74,214,125
INFO 2026-06-08 08:17:57 MarkDuplicates Tracking 853434 as yet unmatched pairs. 44947 records in RAM.
INFO 2026-06-08 08:17:59 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 1s. Last read position: chr2:86,981,157
INFO 2026-06-08 08:17:59 MarkDuplicates Tracking 850765 as yet unmatched pairs. 42272 records in RAM.
INFO 2026-06-08 08:18:01 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 2s. Last read position: chr2:97,585,383
INFO 2026-06-08 08:18:01 MarkDuplicates Tracking 848704 as yet unmatched pairs. 40199 records in RAM.
INFO 2026-06-08 08:18:03 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 1s. Last read position: chr2:106,426,037
INFO 2026-06-08 08:18:03 MarkDuplicates Tracking 846507 as yet unmatched pairs. 37996 records in RAM.
INFO 2026-06-08 08:18:04 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 1s. Last read position: chr2:108,766,986
INFO 2026-06-08 08:18:04 MarkDuplicates Tracking 844967 as yet unmatched pairs. 36456 records in RAM.
INFO 2026-06-08 08:18:06 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 1s. Last read position: chr2:110,547,216
INFO 2026-06-08 08:18:06 MarkDuplicates Tracking 843670 as yet unmatched pairs. 35159 records in RAM.
INFO 2026-06-08 08:18:08 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 1s. Last read position: chr2:121,281,192
INFO 2026-06-08 08:18:08 MarkDuplicates Tracking 841849 as yet unmatched pairs. 33336 records in RAM.
INFO 2026-06-08 08:18:09 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 1s. Last read position: chr2:136,115,172
INFO 2026-06-08 08:18:09 MarkDuplicates Tracking 840823 as yet unmatched pairs. 32308 records in RAM.
INFO 2026-06-08 08:18:11 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 1s. Last read position: chr2:159,780,044
INFO 2026-06-08 08:18:11 MarkDuplicates Tracking 837158 as yet unmatched pairs. 28634 records in RAM.
INFO 2026-06-08 08:18:13 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 2s. Last read position: chr2:174,435,770
INFO 2026-06-08 08:18:13 MarkDuplicates Tracking 834839 as yet unmatched pairs. 26308 records in RAM.
INFO 2026-06-08 08:18:15 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 1s. Last read position: chr2:181,916,126
INFO 2026-06-08 08:18:15 MarkDuplicates Tracking 832782 as yet unmatched pairs. 24245 records in RAM.
INFO 2026-06-08 08:18:17 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 1s. Last read position: chr2:190,880,858
INFO 2026-06-08 08:18:17 MarkDuplicates Tracking 830052 as yet unmatched pairs. 21506 records in RAM.
INFO 2026-06-08 08:18:19 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 2s. Last read position: chr2:201,633,343
INFO 2026-06-08 08:18:19 MarkDuplicates Tracking 827654 as yet unmatched pairs. 19082 records in RAM.
INFO 2026-06-08 08:18:21 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 2s. Last read position: chr2:215,361,536
INFO 2026-06-08 08:18:21 MarkDuplicates Tracking 826671 as yet unmatched pairs. 18094 records in RAM.
INFO 2026-06-08 08:18:23 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 1s. Last read position: chr2:215,422,155
INFO 2026-06-08 08:18:23 MarkDuplicates Tracking 823795 as yet unmatched pairs. 15217 records in RAM.
INFO 2026-06-08 08:18:25 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 2s. Last read position: chr2:217,848,158
INFO 2026-06-08 08:18:25 MarkDuplicates Tracking 821600 as yet unmatched pairs. 13019 records in RAM.
INFO 2026-06-08 08:18:27 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 1s. Last read position: chr2:219,420,304
INFO 2026-06-08 08:18:27 MarkDuplicates Tracking 818868 as yet unmatched pairs. 10280 records in RAM.
INFO 2026-06-08 08:18:29 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 2s. Last read position: chr2:229,799,282
INFO 2026-06-08 08:18:29 MarkDuplicates Tracking 815789 as yet unmatched pairs. 7197 records in RAM.
INFO 2026-06-08 08:18:31 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 2s. Last read position: chr2:237,324,655
INFO 2026-06-08 08:18:31 MarkDuplicates Tracking 813485 as yet unmatched pairs. 4885 records in RAM.
INFO 2026-06-08 08:18:33 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 1s. Last read position: chr2:240,741,315
INFO 2026-06-08 08:18:33 MarkDuplicates Tracking 810479 as yet unmatched pairs. 1873 records in RAM.
INFO 2026-06-08 08:18:36 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 2s. Last read position: chr3:4,982,855
INFO 2026-06-08 08:18:36 MarkDuplicates Tracking 808175 as yet unmatched pairs. 55089 records in RAM.
INFO 2026-06-08 08:18:38 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 2s. Last read position: chr3:12,840,208
INFO 2026-06-08 08:18:38 MarkDuplicates Tracking 805365 as yet unmatched pairs. 52274 records in RAM.
INFO 2026-06-08 08:18:40 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr3:29,401,802
INFO 2026-06-08 08:18:40 MarkDuplicates Tracking 803030 as yet unmatched pairs. 49938 records in RAM.
INFO 2026-06-08 08:18:42 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 2s. Last read position: chr3:39,143,517
INFO 2026-06-08 08:18:42 MarkDuplicates Tracking 800478 as yet unmatched pairs. 47384 records in RAM.
INFO 2026-06-08 08:18:44 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 1s. Last read position: chr3:45,595,316
INFO 2026-06-08 08:18:44 MarkDuplicates Tracking 798174 as yet unmatched pairs. 45068 records in RAM.
INFO 2026-06-08 08:18:46 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 1s. Last read position: chr3:46,456,325
INFO 2026-06-08 08:18:46 MarkDuplicates Tracking 797676 as yet unmatched pairs. 44570 records in RAM.
INFO 2026-06-08 08:18:48 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 2s. Last read position: chr3:47,916,565
INFO 2026-06-08 08:18:48 MarkDuplicates Tracking 793522 as yet unmatched pairs. 40400 records in RAM.
INFO 2026-06-08 08:18:50 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 1s. Last read position: chr3:49,016,617
INFO 2026-06-08 08:18:50 MarkDuplicates Tracking 790254 as yet unmatched pairs. 37120 records in RAM.
INFO 2026-06-08 08:18:51 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 1s. Last read position: chr3:50,110,601
INFO 2026-06-08 08:18:51 MarkDuplicates Tracking 787778 as yet unmatched pairs. 34639 records in RAM.
INFO 2026-06-08 08:18:53 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 1s. Last read position: chr3:52,513,751
INFO 2026-06-08 08:18:53 MarkDuplicates Tracking 785476 as yet unmatched pairs. 32336 records in RAM.
INFO 2026-06-08 08:18:55 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 1s. Last read position: chr3:58,123,382
INFO 2026-06-08 08:18:55 MarkDuplicates Tracking 782853 as yet unmatched pairs. 29702 records in RAM.
INFO 2026-06-08 08:18:57 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 1s. Last read position: chr3:72,757,314
INFO 2026-06-08 08:18:57 MarkDuplicates Tracking 780182 as yet unmatched pairs. 27021 records in RAM.
INFO 2026-06-08 08:18:58 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 1s. Last read position: chr3:101,682,477
INFO 2026-06-08 08:18:58 MarkDuplicates Tracking 779154 as yet unmatched pairs. 25977 records in RAM.
INFO 2026-06-08 08:19:00 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 2s. Last read position: chr3:114,380,254
INFO 2026-06-08 08:19:00 MarkDuplicates Tracking 775943 as yet unmatched pairs. 22756 records in RAM.
INFO 2026-06-08 08:19:02 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 1s. Last read position: chr3:123,614,333
INFO 2026-06-08 08:19:02 MarkDuplicates Tracking 773959 as yet unmatched pairs. 20768 records in RAM.
INFO 2026-06-08 08:19:04 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 1s. Last read position: chr3:128,620,412
INFO 2026-06-08 08:19:04 MarkDuplicates Tracking 770966 as yet unmatched pairs. 17773 records in RAM.
INFO 2026-06-08 08:19:07 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 2s. Last read position: chr3:132,682,663
INFO 2026-06-08 08:19:07 MarkDuplicates Tracking 768270 as yet unmatched pairs. 15067 records in RAM.
INFO 2026-06-08 08:19:08 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 1s. Last read position: chr3:146,196,662
INFO 2026-06-08 08:19:08 MarkDuplicates Tracking 765812 as yet unmatched pairs. 12583 records in RAM.
INFO 2026-06-08 08:19:10 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 1s. Last read position: chr3:158,805,463
INFO 2026-06-08 08:19:10 MarkDuplicates Tracking 763770 as yet unmatched pairs. 10540 records in RAM.
INFO 2026-06-08 08:19:12 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 1s. Last read position: chr3:179,604,864
INFO 2026-06-08 08:19:12 MarkDuplicates Tracking 761544 as yet unmatched pairs. 8310 records in RAM.
INFO 2026-06-08 08:19:14 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 1s. Last read position: chr3:184,710,913
INFO 2026-06-08 08:19:14 MarkDuplicates Tracking 759044 as yet unmatched pairs. 5804 records in RAM.
INFO 2026-06-08 08:19:15 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 1s. Last read position: chr3:188,866,320
INFO 2026-06-08 08:19:15 MarkDuplicates Tracking 758266 as yet unmatched pairs. 5025 records in RAM.
INFO 2026-06-08 08:19:18 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 2s. Last read position: chr3:195,786,073
INFO 2026-06-08 08:19:18 MarkDuplicates Tracking 755318 as yet unmatched pairs. 2075 records in RAM.
INFO 2026-06-08 08:19:20 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 2s. Last read position: chr4:1,167,539
INFO 2026-06-08 08:19:20 MarkDuplicates Tracking 753236 as yet unmatched pairs. 31726 records in RAM.
INFO 2026-06-08 08:19:22 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 1s. Last read position: chr4:4,274,689
INFO 2026-06-08 08:19:22 MarkDuplicates Tracking 749322 as yet unmatched pairs. 27805 records in RAM.
INFO 2026-06-08 08:19:25 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 2s. Last read position: chr4:17,803,695
INFO 2026-06-08 08:19:25 MarkDuplicates Tracking 747262 as yet unmatched pairs. 25745 records in RAM.
INFO 2026-06-08 08:19:27 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 1s. Last read position: chr4:40,122,150
INFO 2026-06-08 08:19:27 MarkDuplicates Tracking 744426 as yet unmatched pairs. 22902 records in RAM.
INFO 2026-06-08 08:19:28 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 1s. Last read position: chr4:56,930,864
INFO 2026-06-08 08:19:28 MarkDuplicates Tracking 742051 as yet unmatched pairs. 20515 records in RAM.
INFO 2026-06-08 08:19:30 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 1s. Last read position: chr4:76,174,220
INFO 2026-06-08 08:19:30 MarkDuplicates Tracking 739798 as yet unmatched pairs. 18255 records in RAM.
INFO 2026-06-08 08:19:32 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 1s. Last read position: chr4:86,016,071
INFO 2026-06-08 08:19:32 MarkDuplicates Tracking 737421 as yet unmatched pairs. 15867 records in RAM.
INFO 2026-06-08 08:19:34 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 1s. Last read position: chr4:94,662,485
INFO 2026-06-08 08:19:34 MarkDuplicates Tracking 736214 as yet unmatched pairs. 14659 records in RAM.
INFO 2026-06-08 08:19:36 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 1s. Last read position: chr4:110,476,626
INFO 2026-06-08 08:19:36 MarkDuplicates Tracking 732584 as yet unmatched pairs. 11018 records in RAM.
INFO 2026-06-08 08:19:38 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 1s. Last read position: chr4:119,565,401
INFO 2026-06-08 08:19:38 MarkDuplicates Tracking 730544 as yet unmatched pairs. 8978 records in RAM.
INFO 2026-06-08 08:19:39 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 1s. Last read position: chr4:140,668,980
INFO 2026-06-08 08:19:39 MarkDuplicates Tracking 728120 as yet unmatched pairs. 6550 records in RAM.
INFO 2026-06-08 08:19:41 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 1s. Last read position: chr4:153,270,427
INFO 2026-06-08 08:19:41 MarkDuplicates Tracking 726184 as yet unmatched pairs. 4603 records in RAM.
INFO 2026-06-08 08:19:43 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 1s. Last read position: chr4:173,388,548
INFO 2026-06-08 08:19:43 MarkDuplicates Tracking 723483 as yet unmatched pairs. 1902 records in RAM.
INFO 2026-06-08 08:19:45 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 2s. Last read position: chr5:1,501,567
INFO 2026-06-08 08:19:45 MarkDuplicates Tracking 721049 as yet unmatched pairs. 45199 records in RAM.
INFO 2026-06-08 08:19:48 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 2s. Last read position: chr5:14,482,608
INFO 2026-06-08 08:19:48 MarkDuplicates Tracking 718647 as yet unmatched pairs. 42787 records in RAM.
INFO 2026-06-08 08:19:49 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 1s. Last read position: chr5:37,058,992
INFO 2026-06-08 08:19:49 MarkDuplicates Tracking 716211 as yet unmatched pairs. 40341 records in RAM.
INFO 2026-06-08 08:19:51 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 1s. Last read position: chr5:55,322,421
INFO 2026-06-08 08:19:51 MarkDuplicates Tracking 713934 as yet unmatched pairs. 38057 records in RAM.
INFO 2026-06-08 08:19:53 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 1s. Last read position: chr5:69,121,786
INFO 2026-06-08 08:19:53 MarkDuplicates Tracking 711461 as yet unmatched pairs. 35577 records in RAM.
INFO 2026-06-08 08:19:55 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 1s. Last read position: chr5:74,636,115
INFO 2026-06-08 08:19:55 MarkDuplicates Tracking 709734 as yet unmatched pairs. 33848 records in RAM.
INFO 2026-06-08 08:19:56 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 1s. Last read position: chr5:83,580,292
INFO 2026-06-08 08:19:56 MarkDuplicates Tracking 707493 as yet unmatched pairs. 31600 records in RAM.
INFO 2026-06-08 08:19:58 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 1s. Last read position: chr5:108,798,212
INFO 2026-06-08 08:19:58 MarkDuplicates Tracking 705111 as yet unmatched pairs. 29210 records in RAM.
INFO 2026-06-08 08:20:00 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 1s. Last read position: chr5:128,152,743
INFO 2026-06-08 08:20:00 MarkDuplicates Tracking 703074 as yet unmatched pairs. 27172 records in RAM.
INFO 2026-06-08 08:20:02 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 1s. Last read position: chr5:136,062,663
INFO 2026-06-08 08:20:02 MarkDuplicates Tracking 700522 as yet unmatched pairs. 24613 records in RAM.
INFO 2026-06-08 08:20:03 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 1s. Last read position: chr5:140,528,493
INFO 2026-06-08 08:20:03 MarkDuplicates Tracking 698417 as yet unmatched pairs. 22487 records in RAM.
INFO 2026-06-08 08:20:06 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 2s. Last read position: chr5:141,645,121
INFO 2026-06-08 08:20:06 MarkDuplicates Tracking 695710 as yet unmatched pairs. 19777 records in RAM.
INFO 2026-06-08 08:20:08 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 2s. Last read position: chr5:150,120,932
INFO 2026-06-08 08:20:08 MarkDuplicates Tracking 694268 as yet unmatched pairs. 18329 records in RAM.
INFO 2026-06-08 08:20:10 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 2s. Last read position: chr5:150,403,300
INFO 2026-06-08 08:20:10 MarkDuplicates Tracking 695809 as yet unmatched pairs. 19869 records in RAM.
INFO 2026-06-08 08:20:12 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 2s. Last read position: chr5:150,649,651
INFO 2026-06-08 08:20:12 MarkDuplicates Tracking 688379 as yet unmatched pairs. 12439 records in RAM.
INFO 2026-06-08 08:20:14 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 2s. Last read position: chr5:163,454,015
INFO 2026-06-08 08:20:14 MarkDuplicates Tracking 685534 as yet unmatched pairs. 9588 records in RAM.
INFO 2026-06-08 08:20:16 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 1s. Last read position: chr5:171,407,709
INFO 2026-06-08 08:20:16 MarkDuplicates Tracking 690316 as yet unmatched pairs. 14369 records in RAM.
INFO 2026-06-08 08:20:18 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 1s. Last read position: chr5:177,491,746
INFO 2026-06-08 08:20:18 MarkDuplicates Tracking 680796 as yet unmatched pairs. 4845 records in RAM.
INFO 2026-06-08 08:20:20 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 1s. Last read position: chr5:179,824,214
INFO 2026-06-08 08:20:20 MarkDuplicates Tracking 679194 as yet unmatched pairs. 3243 records in RAM.
INFO 2026-06-08 08:20:22 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 2s. Last read position: chr6:3,224,848
INFO 2026-06-08 08:20:22 MarkDuplicates Tracking 675424 as yet unmatched pairs. 45653 records in RAM.
INFO 2026-06-08 08:20:24 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 1s. Last read position: chr6:12,123,646
INFO 2026-06-08 08:20:24 MarkDuplicates Tracking 672750 as yet unmatched pairs. 42974 records in RAM.
INFO 2026-06-08 08:20:26 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 1s. Last read position: chr6:26,940,445
INFO 2026-06-08 08:20:26 MarkDuplicates Tracking 670281 as yet unmatched pairs. 40504 records in RAM.
INFO 2026-06-08 08:20:28 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 1s. Last read position: chr6:30,896,793
INFO 2026-06-08 08:20:28 MarkDuplicates Tracking 668054 as yet unmatched pairs. 38270 records in RAM.
INFO 2026-06-08 08:20:30 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 1s. Last read position: chr6:31,728,992
INFO 2026-06-08 08:20:30 MarkDuplicates Tracking 665439 as yet unmatched pairs. 35655 records in RAM.
INFO 2026-06-08 08:20:31 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 1s. Last read position: chr6:31,993,602
INFO 2026-06-08 08:20:31 MarkDuplicates Tracking 663724 as yet unmatched pairs. 33931 records in RAM.
INFO 2026-06-08 08:20:33 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 1s. Last read position: chr6:32,554,742
INFO 2026-06-08 08:20:33 MarkDuplicates Tracking 661453 as yet unmatched pairs. 31658 records in RAM.
INFO 2026-06-08 08:20:35 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 1s. Last read position: chr6:33,313,295
INFO 2026-06-08 08:20:35 MarkDuplicates Tracking 659850 as yet unmatched pairs. 30051 records in RAM.
INFO 2026-06-08 08:20:36 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 1s. Last read position: chr6:35,874,231
INFO 2026-06-08 08:20:36 MarkDuplicates Tracking 656239 as yet unmatched pairs. 26433 records in RAM.
INFO 2026-06-08 08:20:38 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 2s. Last read position: chr6:43,049,488
INFO 2026-06-08 08:20:38 MarkDuplicates Tracking 653737 as yet unmatched pairs. 23925 records in RAM.
INFO 2026-06-08 08:20:40 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 1s. Last read position: chr6:53,013,844
INFO 2026-06-08 08:20:40 MarkDuplicates Tracking 651159 as yet unmatched pairs. 21340 records in RAM.
INFO 2026-06-08 08:20:42 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 1s. Last read position: chr6:75,175,286
INFO 2026-06-08 08:20:42 MarkDuplicates Tracking 648877 as yet unmatched pairs. 19058 records in RAM.
INFO 2026-06-08 08:20:44 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr6:89,693,123
INFO 2026-06-08 08:20:44 MarkDuplicates Tracking 646724 as yet unmatched pairs. 16900 records in RAM.
INFO 2026-06-08 08:20:46 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 2s. Last read position: chr6:109,506,488
INFO 2026-06-08 08:20:46 MarkDuplicates Tracking 644284 as yet unmatched pairs. 14459 records in RAM.
INFO 2026-06-08 08:20:48 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 1s. Last read position: chr6:127,976,922
INFO 2026-06-08 08:20:48 MarkDuplicates Tracking 641900 as yet unmatched pairs. 12066 records in RAM.
INFO 2026-06-08 08:20:50 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 2s. Last read position: chr6:138,291,731
INFO 2026-06-08 08:20:50 MarkDuplicates Tracking 639456 as yet unmatched pairs. 9605 records in RAM.
INFO 2026-06-08 08:20:52 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 2s. Last read position: chr6:149,378,880
INFO 2026-06-08 08:20:52 MarkDuplicates Tracking 637523 as yet unmatched pairs. 7664 records in RAM.
INFO 2026-06-08 08:20:54 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 1s. Last read position: chr6:154,832,693
INFO 2026-06-08 08:20:54 MarkDuplicates Tracking 634774 as yet unmatched pairs. 4913 records in RAM.
INFO 2026-06-08 08:20:55 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 1s. Last read position: chr6:160,060,591
INFO 2026-06-08 08:20:55 MarkDuplicates Tracking 632098 as yet unmatched pairs. 2236 records in RAM.
INFO 2026-06-08 08:20:58 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 2s. Last read position: chr7:1,438,157
INFO 2026-06-08 08:20:58 MarkDuplicates Tracking 629445 as yet unmatched pairs. 44896 records in RAM.
INFO 2026-06-08 08:21:00 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 1s. Last read position: chr7:5,389,088
INFO 2026-06-08 08:21:00 MarkDuplicates Tracking 626375 as yet unmatched pairs. 41820 records in RAM.
INFO 2026-06-08 08:21:02 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 1s. Last read position: chr7:6,508,144
INFO 2026-06-08 08:21:02 MarkDuplicates Tracking 623778 as yet unmatched pairs. 39221 records in RAM.
INFO 2026-06-08 08:21:03 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 1s. Last read position: chr7:26,371,915
INFO 2026-06-08 08:21:03 MarkDuplicates Tracking 621429 as yet unmatched pairs. 36863 records in RAM.
INFO 2026-06-08 08:21:05 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 1s. Last read position: chr7:43,878,791
INFO 2026-06-08 08:21:05 MarkDuplicates Tracking 618990 as yet unmatched pairs. 34423 records in RAM.
INFO 2026-06-08 08:21:07 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 1s. Last read position: chr7:55,019,119
INFO 2026-06-08 08:21:07 MarkDuplicates Tracking 616638 as yet unmatched pairs. 32064 records in RAM.
INFO 2026-06-08 08:21:08 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 1s. Last read position: chr7:72,950,081
INFO 2026-06-08 08:21:08 MarkDuplicates Tracking 614343 as yet unmatched pairs. 29768 records in RAM.
INFO 2026-06-08 08:21:10 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 1s. Last read position: chr7:75,148,624
INFO 2026-06-08 08:21:10 MarkDuplicates Tracking 612496 as yet unmatched pairs. 27921 records in RAM.
INFO 2026-06-08 08:21:12 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 1s. Last read position: chr7:77,253,743
INFO 2026-06-08 08:21:12 MarkDuplicates Tracking 610581 as yet unmatched pairs. 26000 records in RAM.
INFO 2026-06-08 08:21:13 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 1s. Last read position: chr7:92,084,914
INFO 2026-06-08 08:21:13 MarkDuplicates Tracking 608747 as yet unmatched pairs. 24165 records in RAM.
INFO 2026-06-08 08:21:15 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 1s. Last read position: chr7:98,921,759
INFO 2026-06-08 08:21:15 MarkDuplicates Tracking 605972 as yet unmatched pairs. 21383 records in RAM.
INFO 2026-06-08 08:21:17 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 1s. Last read position: chr7:100,572,546
INFO 2026-06-08 08:21:17 MarkDuplicates Tracking 603676 as yet unmatched pairs. 19085 records in RAM.
INFO 2026-06-08 08:21:19 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 1s. Last read position: chr7:101,001,661
INFO 2026-06-08 08:21:19 MarkDuplicates Tracking 601540 as yet unmatched pairs. 16932 records in RAM.
INFO 2026-06-08 08:21:20 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 1s. Last read position: chr7:106,097,689
INFO 2026-06-08 08:21:20 MarkDuplicates Tracking 599789 as yet unmatched pairs. 15173 records in RAM.
INFO 2026-06-08 08:21:22 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 1s. Last read position: chr7:127,652,318
INFO 2026-06-08 08:21:22 MarkDuplicates Tracking 598405 as yet unmatched pairs. 13780 records in RAM.
INFO 2026-06-08 08:21:24 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 2s. Last read position: chr7:128,947,149
INFO 2026-06-08 08:21:24 MarkDuplicates Tracking 594773 as yet unmatched pairs. 10144 records in RAM.
INFO 2026-06-08 08:21:26 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 1s. Last read position: chr7:137,928,150
INFO 2026-06-08 08:21:26 MarkDuplicates Tracking 593501 as yet unmatched pairs. 8872 records in RAM.
INFO 2026-06-08 08:21:28 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 1s. Last read position: chr7:142,801,118
INFO 2026-06-08 08:21:28 MarkDuplicates Tracking 590357 as yet unmatched pairs. 5728 records in RAM.
INFO 2026-06-08 08:21:30 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 2s. Last read position: chr7:150,371,633
INFO 2026-06-08 08:21:30 MarkDuplicates Tracking 588060 as yet unmatched pairs. 3429 records in RAM.
INFO 2026-06-08 08:21:32 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 1s. Last read position: chr7:156,688,166
INFO 2026-06-08 08:21:32 MarkDuplicates Tracking 585406 as yet unmatched pairs. 761 records in RAM.
INFO 2026-06-08 08:21:34 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 1s. Last read position: chr8:17,753,812
INFO 2026-06-08 08:21:34 MarkDuplicates Tracking 583092 as yet unmatched pairs. 34893 records in RAM.
INFO 2026-06-08 08:21:36 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 1s. Last read position: chr8:23,679,794
INFO 2026-06-08 08:21:36 MarkDuplicates Tracking 581246 as yet unmatched pairs. 33043 records in RAM.
INFO 2026-06-08 08:21:37 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 1s. Last read position: chr8:30,799,729
INFO 2026-06-08 08:21:37 MarkDuplicates Tracking 577993 as yet unmatched pairs. 29790 records in RAM.
INFO 2026-06-08 08:21:39 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 1s. Last read position: chr8:38,788,762
INFO 2026-06-08 08:21:39 MarkDuplicates Tracking 577333 as yet unmatched pairs. 29122 records in RAM.
INFO 2026-06-08 08:21:41 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 1s. Last read position: chr8:47,737,488
INFO 2026-06-08 08:21:41 MarkDuplicates Tracking 573498 as yet unmatched pairs. 25286 records in RAM.
INFO 2026-06-08 08:21:43 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 1s. Last read position: chr8:67,059,238
INFO 2026-06-08 08:21:43 MarkDuplicates Tracking 570416 as yet unmatched pairs. 22196 records in RAM.
INFO 2026-06-08 08:21:45 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 1s. Last read position: chr8:80,499,595
INFO 2026-06-08 08:21:45 MarkDuplicates Tracking 568041 as yet unmatched pairs. 19820 records in RAM.
INFO 2026-06-08 08:21:46 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 1s. Last read position: chr8:99,121,372
INFO 2026-06-08 08:21:46 MarkDuplicates Tracking 566118 as yet unmatched pairs. 17893 records in RAM.
INFO 2026-06-08 08:21:48 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 1s. Last read position: chr8:102,651,572
INFO 2026-06-08 08:21:48 MarkDuplicates Tracking 563271 as yet unmatched pairs. 15045 records in RAM.
INFO 2026-06-08 08:21:50 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 2s. Last read position: chr8:124,487,299
INFO 2026-06-08 08:21:50 MarkDuplicates Tracking 560837 as yet unmatched pairs. 12604 records in RAM.
INFO 2026-06-08 08:21:52 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 1s. Last read position: chr8:140,300,584
INFO 2026-06-08 08:21:52 MarkDuplicates Tracking 558301 as yet unmatched pairs. 10063 records in RAM.
INFO 2026-06-08 08:21:54 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 1s. Last read position: chr8:143,858,299
INFO 2026-06-08 08:21:54 MarkDuplicates Tracking 555363 as yet unmatched pairs. 7124 records in RAM.
INFO 2026-06-08 08:21:55 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 1s. Last read position: chr8:143,864,383
INFO 2026-06-08 08:21:55 MarkDuplicates Tracking 554368 as yet unmatched pairs. 6129 records in RAM.
INFO 2026-06-08 08:21:57 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 1s. Last read position: chr8:143,927,910
INFO 2026-06-08 08:21:57 MarkDuplicates Tracking 552122 as yet unmatched pairs. 3882 records in RAM.
INFO 2026-06-08 08:21:58 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 1s. Last read position: chr8:144,526,981
INFO 2026-06-08 08:21:58 MarkDuplicates Tracking 548797 as yet unmatched pairs. 552 records in RAM.
INFO 2026-06-08 08:22:01 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:05:43s. Time for last 1,000,000: 2s. Last read position: chr9:14,088,203
INFO 2026-06-08 08:22:01 MarkDuplicates Tracking 547835 as yet unmatched pairs. 39051 records in RAM.
INFO 2026-06-08 08:22:03 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 1s. Last read position: chr9:32,544,093
INFO 2026-06-08 08:22:03 MarkDuplicates Tracking 544202 as yet unmatched pairs. 35415 records in RAM.
INFO 2026-06-08 08:22:05 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 1s. Last read position: chr9:35,685,437
INFO 2026-06-08 08:22:05 MarkDuplicates Tracking 541806 as yet unmatched pairs. 33017 records in RAM.
INFO 2026-06-08 08:22:07 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 1s. Last read position: chr9:65,894,735
INFO 2026-06-08 08:22:07 MarkDuplicates Tracking 539114 as yet unmatched pairs. 30320 records in RAM.
INFO 2026-06-08 08:22:09 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 2s. Last read position: chr9:83,972,094
INFO 2026-06-08 08:22:09 MarkDuplicates Tracking 537076 as yet unmatched pairs. 28282 records in RAM.
INFO 2026-06-08 08:22:11 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 1s. Last read position: chr9:93,257,109
INFO 2026-06-08 08:22:11 MarkDuplicates Tracking 534429 as yet unmatched pairs. 25634 records in RAM.
INFO 2026-06-08 08:22:13 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 1s. Last read position: chr9:99,227,923
INFO 2026-06-08 08:22:13 MarkDuplicates Tracking 532026 as yet unmatched pairs. 23227 records in RAM.
INFO 2026-06-08 08:22:14 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 1s. Last read position: chr9:112,470,439
INFO 2026-06-08 08:22:14 MarkDuplicates Tracking 529232 as yet unmatched pairs. 20429 records in RAM.
INFO 2026-06-08 08:22:16 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 1s. Last read position: chr9:120,905,069
INFO 2026-06-08 08:22:16 MarkDuplicates Tracking 526566 as yet unmatched pairs. 17755 records in RAM.
INFO 2026-06-08 08:22:18 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 1s. Last read position: chr9:127,397,503
INFO 2026-06-08 08:22:18 MarkDuplicates Tracking 524010 as yet unmatched pairs. 15198 records in RAM.
INFO 2026-06-08 08:22:20 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 1s. Last read position: chr9:128,693,920
INFO 2026-06-08 08:22:20 MarkDuplicates Tracking 521502 as yet unmatched pairs. 12687 records in RAM.
INFO 2026-06-08 08:22:22 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 1s. Last read position: chr9:130,884,567
INFO 2026-06-08 08:22:22 MarkDuplicates Tracking 519157 as yet unmatched pairs. 10333 records in RAM.
INFO 2026-06-08 08:22:24 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 1s. Last read position: chr9:133,349,937
INFO 2026-06-08 08:22:24 MarkDuplicates Tracking 516959 as yet unmatched pairs. 8132 records in RAM.
INFO 2026-06-08 08:22:25 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 1s. Last read position: chr9:136,475,934
INFO 2026-06-08 08:22:25 MarkDuplicates Tracking 514039 as yet unmatched pairs. 5209 records in RAM.
INFO 2026-06-08 08:22:27 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:06:09s. Time for last 1,000,000: 1s. Last read position: chr9:137,169,079
INFO 2026-06-08 08:22:27 MarkDuplicates Tracking 510909 as yet unmatched pairs. 2078 records in RAM.
INFO 2026-06-08 08:22:29 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 2s. Last read position: chr10:5,748,814
INFO 2026-06-08 08:22:29 MarkDuplicates Tracking 507937 as yet unmatched pairs. 31793 records in RAM.
INFO 2026-06-08 08:22:31 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 1s. Last read position: chr10:21,173,765
INFO 2026-06-08 08:22:31 MarkDuplicates Tracking 505378 as yet unmatched pairs. 29231 records in RAM.
INFO 2026-06-08 08:22:33 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 2s. Last read position: chr10:32,011,474
INFO 2026-06-08 08:22:33 MarkDuplicates Tracking 503393 as yet unmatched pairs. 27244 records in RAM.
INFO 2026-06-08 08:22:34 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:06:16s. Time for last 1,000,000: 1s. Last read position: chr10:38,115,231
INFO 2026-06-08 08:22:34 MarkDuplicates Tracking 500668 as yet unmatched pairs. 24513 records in RAM.
INFO 2026-06-08 08:22:36 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 1s. Last read position: chr10:46,837,380
INFO 2026-06-08 08:22:36 MarkDuplicates Tracking 498860 as yet unmatched pairs. 22705 records in RAM.
INFO 2026-06-08 08:22:39 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 2s. Last read position: chr10:62,000,043
INFO 2026-06-08 08:22:39 MarkDuplicates Tracking 496931 as yet unmatched pairs. 20772 records in RAM.
INFO 2026-06-08 08:22:41 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 2s. Last read position: chr10:73,030,280
INFO 2026-06-08 08:22:41 MarkDuplicates Tracking 494374 as yet unmatched pairs. 18209 records in RAM.
INFO 2026-06-08 08:22:43 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 1s. Last read position: chr10:77,819,240
INFO 2026-06-08 08:22:43 MarkDuplicates Tracking 492064 as yet unmatched pairs. 15894 records in RAM.
INFO 2026-06-08 08:22:44 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 1s. Last read position: chr10:87,952,130
INFO 2026-06-08 08:22:44 MarkDuplicates Tracking 490045 as yet unmatched pairs. 13870 records in RAM.
INFO 2026-06-08 08:22:46 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 1s. Last read position: chr10:95,397,274
INFO 2026-06-08 08:22:46 MarkDuplicates Tracking 487472 as yet unmatched pairs. 11296 records in RAM.
INFO 2026-06-08 08:22:48 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:06:30s. Time for last 1,000,000: 1s. Last read position: chr10:100,961,840
INFO 2026-06-08 08:22:48 MarkDuplicates Tracking 484627 as yet unmatched pairs. 8450 records in RAM.
INFO 2026-06-08 08:22:50 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 1s. Last read position: chr10:104,008,241
INFO 2026-06-08 08:22:50 MarkDuplicates Tracking 482100 as yet unmatched pairs. 5922 records in RAM.
INFO 2026-06-08 08:22:52 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 1s. Last read position: chr10:119,070,890
INFO 2026-06-08 08:22:52 MarkDuplicates Tracking 479886 as yet unmatched pairs. 3708 records in RAM.
INFO 2026-06-08 08:22:53 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:06:35s. Time for last 1,000,000: 1s. Last read position: chr10:127,280,275
INFO 2026-06-08 08:22:53 MarkDuplicates Tracking 477452 as yet unmatched pairs. 1272 records in RAM.
INFO 2026-06-08 08:22:55 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 2s. Last read position: chr11:494,953
INFO 2026-06-08 08:22:55 MarkDuplicates Tracking 474794 as yet unmatched pairs. 56739 records in RAM.
INFO 2026-06-08 08:22:57 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 1s. Last read position: chr11:2,402,720
INFO 2026-06-08 08:22:57 MarkDuplicates Tracking 471932 as yet unmatched pairs. 53876 records in RAM.
INFO 2026-06-08 08:22:59 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 1s. Last read position: chr11:6,682,218
INFO 2026-06-08 08:22:59 MarkDuplicates Tracking 469206 as yet unmatched pairs. 51145 records in RAM.
INFO 2026-06-08 08:23:01 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 1s. Last read position: chr11:10,802,126
INFO 2026-06-08 08:23:01 MarkDuplicates Tracking 467248 as yet unmatched pairs. 49182 records in RAM.
INFO 2026-06-08 08:23:03 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 2s. Last read position: chr11:19,984,179
INFO 2026-06-08 08:23:03 MarkDuplicates Tracking 464294 as yet unmatched pairs. 46222 records in RAM.
INFO 2026-06-08 08:23:06 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 2s. Last read position: chr11:44,083,700
INFO 2026-06-08 08:23:06 MarkDuplicates Tracking 462089 as yet unmatched pairs. 44010 records in RAM.
INFO 2026-06-08 08:23:08 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 2s. Last read position: chr11:47,425,203
INFO 2026-06-08 08:23:08 MarkDuplicates Tracking 459506 as yet unmatched pairs. 41424 records in RAM.
INFO 2026-06-08 08:23:10 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 1s. Last read position: chr11:59,181,949
INFO 2026-06-08 08:23:10 MarkDuplicates Tracking 456906 as yet unmatched pairs. 38823 records in RAM.
INFO 2026-06-08 08:23:11 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 1s. Last read position: chr11:62,519,737
INFO 2026-06-08 08:23:11 MarkDuplicates Tracking 455001 as yet unmatched pairs. 36912 records in RAM.
INFO 2026-06-08 08:23:13 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 1s. Last read position: chr11:62,533,391
INFO 2026-06-08 08:23:13 MarkDuplicates Tracking 452849 as yet unmatched pairs. 34760 records in RAM.
INFO 2026-06-08 08:23:15 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:06:57s. Time for last 1,000,000: 1s. Last read position: chr11:64,194,204
INFO 2026-06-08 08:23:15 MarkDuplicates Tracking 449744 as yet unmatched pairs. 31649 records in RAM.
INFO 2026-06-08 08:23:17 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 1s. Last read position: chr11:65,376,920
INFO 2026-06-08 08:23:17 MarkDuplicates Tracking 447054 as yet unmatched pairs. 28956 records in RAM.
INFO 2026-06-08 08:23:19 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 1s. Last read position: chr11:65,868,536
INFO 2026-06-08 08:23:19 MarkDuplicates Tracking 444453 as yet unmatched pairs. 26355 records in RAM.
INFO 2026-06-08 08:23:20 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 1s. Last read position: chr11:67,352,719
INFO 2026-06-08 08:23:20 MarkDuplicates Tracking 442052 as yet unmatched pairs. 23954 records in RAM.
INFO 2026-06-08 08:23:22 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:07:04s. Time for last 1,000,000: 1s. Last read position: chr11:69,643,885
INFO 2026-06-08 08:23:22 MarkDuplicates Tracking 439689 as yet unmatched pairs. 21590 records in RAM.
INFO 2026-06-08 08:23:24 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 1s. Last read position: chr11:72,238,137
INFO 2026-06-08 08:23:24 MarkDuplicates Tracking 436149 as yet unmatched pairs. 18050 records in RAM.
INFO 2026-06-08 08:23:26 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 1s. Last read position: chr11:76,796,181
INFO 2026-06-08 08:23:26 MarkDuplicates Tracking 433729 as yet unmatched pairs. 15627 records in RAM.
INFO 2026-06-08 08:23:28 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 1s. Last read position: chr11:95,129,376
INFO 2026-06-08 08:23:28 MarkDuplicates Tracking 431473 as yet unmatched pairs. 13363 records in RAM.
INFO 2026-06-08 08:23:29 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:07:11s. Time for last 1,000,000: 1s. Last read position: chr11:110,164,505
INFO 2026-06-08 08:23:29 MarkDuplicates Tracking 428905 as yet unmatched pairs. 10793 records in RAM.
INFO 2026-06-08 08:23:31 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 1s. Last read position: chr11:117,190,659
INFO 2026-06-08 08:23:31 MarkDuplicates Tracking 426412 as yet unmatched pairs. 8300 records in RAM.
INFO 2026-06-08 08:23:33 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:07:15s. Time for last 1,000,000: 1s. Last read position: chr11:118,900,003
INFO 2026-06-08 08:23:33 MarkDuplicates Tracking 424131 as yet unmatched pairs. 6019 records in RAM.
INFO 2026-06-08 08:23:35 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:07:17s. Time for last 1,000,000: 1s. Last read position: chr11:123,430,873
INFO 2026-06-08 08:23:35 MarkDuplicates Tracking 421469 as yet unmatched pairs. 3351 records in RAM.
INFO 2026-06-08 08:23:37 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:07:19s. Time for last 1,000,000: 2s. Last read position: chr11:134,176,327
INFO 2026-06-08 08:23:37 MarkDuplicates Tracking 419477 as yet unmatched pairs. 1358 records in RAM.
INFO 2026-06-08 08:23:40 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:07:22s. Time for last 1,000,000: 2s. Last read position: chr12:3,011,017
INFO 2026-06-08 08:23:40 MarkDuplicates Tracking 416534 as yet unmatched pairs. 50449 records in RAM.
INFO 2026-06-08 08:23:42 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:07:24s. Time for last 1,000,000: 1s. Last read position: chr12:6,936,726
INFO 2026-06-08 08:23:42 MarkDuplicates Tracking 414101 as yet unmatched pairs. 48014 records in RAM.
INFO 2026-06-08 08:23:44 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:07:26s. Time for last 1,000,000: 2s. Last read position: chr12:9,072,779
INFO 2026-06-08 08:23:44 MarkDuplicates Tracking 411997 as yet unmatched pairs. 45909 records in RAM.
INFO 2026-06-08 08:23:45 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 1s. Last read position: chr12:14,460,709
INFO 2026-06-08 08:23:45 MarkDuplicates Tracking 409456 as yet unmatched pairs. 43367 records in RAM.
INFO 2026-06-08 08:23:47 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:07:29s. Time for last 1,000,000: 1s. Last read position: chr12:30,729,011
INFO 2026-06-08 08:23:47 MarkDuplicates Tracking 406543 as yet unmatched pairs. 40451 records in RAM.
INFO 2026-06-08 08:23:49 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:07:31s. Time for last 1,000,000: 1s. Last read position: chr12:48,693,410
INFO 2026-06-08 08:23:49 MarkDuplicates Tracking 404219 as yet unmatched pairs. 38126 records in RAM.
INFO 2026-06-08 08:23:51 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:07:33s. Time for last 1,000,000: 1s. Last read position: chr12:49,651,977
INFO 2026-06-08 08:23:51 MarkDuplicates Tracking 401663 as yet unmatched pairs. 35567 records in RAM.
INFO 2026-06-08 08:23:52 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:07:34s. Time for last 1,000,000: 1s. Last read position: chr12:53,021,813
INFO 2026-06-08 08:23:52 MarkDuplicates Tracking 399575 as yet unmatched pairs. 33478 records in RAM.
INFO 2026-06-08 08:23:54 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:07:36s. Time for last 1,000,000: 1s. Last read position: chr12:54,281,482
INFO 2026-06-08 08:23:54 MarkDuplicates Tracking 398256 as yet unmatched pairs. 32159 records in RAM.
INFO 2026-06-08 08:23:56 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:07:38s. Time for last 1,000,000: 1s. Last read position: chr12:56,159,699
INFO 2026-06-08 08:23:56 MarkDuplicates Tracking 395238 as yet unmatched pairs. 29133 records in RAM.
INFO 2026-06-08 08:23:57 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:07:39s. Time for last 1,000,000: 1s. Last read position: chr12:56,720,461
INFO 2026-06-08 08:23:57 MarkDuplicates Tracking 392554 as yet unmatched pairs. 26449 records in RAM.
INFO 2026-06-08 08:23:59 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:07:41s. Time for last 1,000,000: 1s. Last read position: chr12:57,256,064
INFO 2026-06-08 08:23:59 MarkDuplicates Tracking 389599 as yet unmatched pairs. 23494 records in RAM.
INFO 2026-06-08 08:24:02 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:07:44s. Time for last 1,000,000: 2s. Last read position: chr12:66,138,060
INFO 2026-06-08 08:24:02 MarkDuplicates Tracking 387516 as yet unmatched pairs. 21410 records in RAM.
INFO 2026-06-08 08:24:04 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:07:46s. Time for last 1,000,000: 2s. Last read position: chr12:79,872,811
INFO 2026-06-08 08:24:04 MarkDuplicates Tracking 385134 as yet unmatched pairs. 19028 records in RAM.
INFO 2026-06-08 08:24:06 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:07:48s. Time for last 1,000,000: 1s. Last read position: chr12:101,395,610
INFO 2026-06-08 08:24:06 MarkDuplicates Tracking 382927 as yet unmatched pairs. 16819 records in RAM.
INFO 2026-06-08 08:24:08 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:07:50s. Time for last 1,000,000: 2s. Last read position: chr12:108,623,751
INFO 2026-06-08 08:24:08 MarkDuplicates Tracking 380400 as yet unmatched pairs. 14287 records in RAM.
INFO 2026-06-08 08:24:10 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:07:52s. Time for last 1,000,000: 2s. Last read position: chr12:112,190,821
INFO 2026-06-08 08:24:10 MarkDuplicates Tracking 377661 as yet unmatched pairs. 11548 records in RAM.
INFO 2026-06-08 08:24:12 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:07:54s. Time for last 1,000,000: 2s. Last read position: chr12:117,174,319
INFO 2026-06-08 08:24:12 MarkDuplicates Tracking 374958 as yet unmatched pairs. 8838 records in RAM.
INFO 2026-06-08 08:24:14 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:07:56s. Time for last 1,000,000: 1s. Last read position: chr12:121,814,411
INFO 2026-06-08 08:24:14 MarkDuplicates Tracking 372351 as yet unmatched pairs. 6225 records in RAM.
INFO 2026-06-08 08:25:17 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:08:59s. Time for last 1,000,000: 62s. Last read position: chr12:124,336,989
INFO 2026-06-08 08:25:17 MarkDuplicates Tracking 370249 as yet unmatched pairs. 4123 records in RAM.
INFO 2026-06-08 08:25:19 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:09:01s. Time for last 1,000,000: 1s. Last read position: chr12:132,661,006
INFO 2026-06-08 08:25:19 MarkDuplicates Tracking 367012 as yet unmatched pairs. 877 records in RAM.
INFO 2026-06-08 08:25:21 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:09:03s. Time for last 1,000,000: 2s. Last read position: chr13:24,290,827
INFO 2026-06-08 08:25:21 MarkDuplicates Tracking 364547 as yet unmatched pairs. 13617 records in RAM.
INFO 2026-06-08 08:25:23 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 1s. Last read position: chr13:37,590,527
INFO 2026-06-08 08:25:23 MarkDuplicates Tracking 362278 as yet unmatched pairs. 11343 records in RAM.
INFO 2026-06-08 08:25:24 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:09:06s. Time for last 1,000,000: 1s. Last read position: chr13:46,011,418
INFO 2026-06-08 08:25:24 MarkDuplicates Tracking 359788 as yet unmatched pairs. 8849 records in RAM.
INFO 2026-06-08 08:25:26 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 1s. Last read position: chr13:75,526,512
INFO 2026-06-08 08:25:26 MarkDuplicates Tracking 357971 as yet unmatched pairs. 7032 records in RAM.
INFO 2026-06-08 08:25:28 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:09:10s. Time for last 1,000,000: 1s. Last read position: chr13:99,254,948
INFO 2026-06-08 08:25:28 MarkDuplicates Tracking 355390 as yet unmatched pairs. 4443 records in RAM.
INFO 2026-06-08 08:25:30 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:09:12s. Time for last 1,000,000: 1s. Last read position: chr13:111,115,641
INFO 2026-06-08 08:25:30 MarkDuplicates Tracking 352413 as yet unmatched pairs. 1464 records in RAM.
INFO 2026-06-08 08:25:32 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 2s. Last read position: chr14:21,078,371
INFO 2026-06-08 08:25:32 MarkDuplicates Tracking 350103 as yet unmatched pairs. 30298 records in RAM.
INFO 2026-06-08 08:25:34 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 1s. Last read position: chr14:23,953,847
INFO 2026-06-08 08:25:34 MarkDuplicates Tracking 347592 as yet unmatched pairs. 27787 records in RAM.
INFO 2026-06-08 08:25:36 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:09:18s. Time for last 1,000,000: 2s. Last read position: chr14:31,309,155
INFO 2026-06-08 08:25:36 MarkDuplicates Tracking 344821 as yet unmatched pairs. 25016 records in RAM.
INFO 2026-06-08 08:25:38 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 1s. Last read position: chr14:49,586,740
INFO 2026-06-08 08:25:38 MarkDuplicates Tracking 342405 as yet unmatched pairs. 22594 records in RAM.
INFO 2026-06-08 08:25:39 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:09:21s. Time for last 1,000,000: 1s. Last read position: chr14:58,208,966
INFO 2026-06-08 08:25:39 MarkDuplicates Tracking 340044 as yet unmatched pairs. 20226 records in RAM.
INFO 2026-06-08 08:25:41 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:09:23s. Time for last 1,000,000: 1s. Last read position: chr14:67,320,244
INFO 2026-06-08 08:25:41 MarkDuplicates Tracking 337742 as yet unmatched pairs. 17922 records in RAM.
INFO 2026-06-08 08:25:43 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 1s. Last read position: chr14:73,217,223
INFO 2026-06-08 08:25:43 MarkDuplicates Tracking 335298 as yet unmatched pairs. 15464 records in RAM.
INFO 2026-06-08 08:25:45 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:09:27s. Time for last 1,000,000: 1s. Last read position: chr14:76,763,081
INFO 2026-06-08 08:25:45 MarkDuplicates Tracking 332755 as yet unmatched pairs. 12919 records in RAM.
INFO 2026-06-08 08:25:46 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:09:28s. Time for last 1,000,000: 1s. Last read position: chr14:93,183,180
INFO 2026-06-08 08:25:46 MarkDuplicates Tracking 330207 as yet unmatched pairs. 10371 records in RAM.
INFO 2026-06-08 08:25:48 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:09:30s. Time for last 1,000,000: 1s. Last read position: chr14:100,360,600
INFO 2026-06-08 08:25:48 MarkDuplicates Tracking 327700 as yet unmatched pairs. 7862 records in RAM.
INFO 2026-06-08 08:25:50 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:09:32s. Time for last 1,000,000: 1s. Last read position: chr14:103,521,289
INFO 2026-06-08 08:25:50 MarkDuplicates Tracking 325052 as yet unmatched pairs. 5211 records in RAM.
INFO 2026-06-08 08:25:52 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:09:34s. Time for last 1,000,000: 1s. Last read position: chr14:105,625,066
INFO 2026-06-08 08:25:52 MarkDuplicates Tracking 322448 as yet unmatched pairs. 2606 records in RAM.
INFO 2026-06-08 08:25:53 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 1s. Last read position: chr14:105,742,909
INFO 2026-06-08 08:25:53 MarkDuplicates Tracking 322434 as yet unmatched pairs. 2592 records in RAM.
INFO 2026-06-08 08:25:55 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 2s. Last read position: chr15:28,641,179
INFO 2026-06-08 08:25:55 MarkDuplicates Tracking 318455 as yet unmatched pairs. 28002 records in RAM.
INFO 2026-06-08 08:25:57 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:09:39s. Time for last 1,000,000: 1s. Last read position: chr15:37,098,018
INFO 2026-06-08 08:25:57 MarkDuplicates Tracking 316699 as yet unmatched pairs. 26246 records in RAM.
INFO 2026-06-08 08:25:58 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:09:40s. Time for last 1,000,000: 1s. Last read position: chr15:42,187,292
INFO 2026-06-08 08:25:58 MarkDuplicates Tracking 314080 as yet unmatched pairs. 23625 records in RAM.
INFO 2026-06-08 08:26:01 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:09:42s. Time for last 1,000,000: 2s. Last read position: chr15:44,521,368
INFO 2026-06-08 08:26:01 MarkDuplicates Tracking 311742 as yet unmatched pairs. 21286 records in RAM.
INFO 2026-06-08 08:26:03 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:09:45s. Time for last 1,000,000: 2s. Last read position: chr15:52,552,054
INFO 2026-06-08 08:26:03 MarkDuplicates Tracking 309263 as yet unmatched pairs. 18806 records in RAM.
INFO 2026-06-08 08:26:04 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:09:46s. Time for last 1,000,000: 1s. Last read position: chr15:61,927,205
INFO 2026-06-08 08:26:04 MarkDuplicates Tracking 306934 as yet unmatched pairs. 16475 records in RAM.
INFO 2026-06-08 08:26:06 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:09:48s. Time for last 1,000,000: 1s. Last read position: chr15:65,043,155
INFO 2026-06-08 08:26:06 MarkDuplicates Tracking 304370 as yet unmatched pairs. 13908 records in RAM.
INFO 2026-06-08 08:26:08 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:09:50s. Time for last 1,000,000: 2s. Last read position: chr15:71,994,550
INFO 2026-06-08 08:26:08 MarkDuplicates Tracking 302109 as yet unmatched pairs. 11643 records in RAM.
INFO 2026-06-08 08:26:10 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:09:52s. Time for last 1,000,000: 1s. Last read position: chr15:75,338,670
INFO 2026-06-08 08:26:10 MarkDuplicates Tracking 299135 as yet unmatched pairs. 8668 records in RAM.
INFO 2026-06-08 08:26:11 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:09:53s. Time for last 1,000,000: 1s. Last read position: chr15:82,536,773
INFO 2026-06-08 08:26:11 MarkDuplicates Tracking 297981 as yet unmatched pairs. 7501 records in RAM.
INFO 2026-06-08 08:26:13 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:09:55s. Time for last 1,000,000: 1s. Last read position: chr15:89,912,705
INFO 2026-06-08 08:26:13 MarkDuplicates Tracking 294514 as yet unmatched pairs. 4034 records in RAM.
INFO 2026-06-08 08:26:15 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:09:57s. Time for last 1,000,000: 1s. Last read position: chr15:99,130,630
INFO 2026-06-08 08:26:15 MarkDuplicates Tracking 292581 as yet unmatched pairs. 2100 records in RAM.
INFO 2026-06-08 08:26:17 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 2s. Last read position: chr16:547,335
INFO 2026-06-08 08:26:17 MarkDuplicates Tracking 289504 as yet unmatched pairs. 52440 records in RAM.
INFO 2026-06-08 08:26:19 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:10:01s. Time for last 1,000,000: 1s. Last read position: chr16:1,775,568
INFO 2026-06-08 08:26:19 MarkDuplicates Tracking 286254 as yet unmatched pairs. 49189 records in RAM.
INFO 2026-06-08 08:26:20 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:10:02s. Time for last 1,000,000: 1s. Last read position: chr16:2,519,294
INFO 2026-06-08 08:26:20 MarkDuplicates Tracking 283179 as yet unmatched pairs. 46114 records in RAM.
INFO 2026-06-08 08:26:22 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:10:04s. Time for last 1,000,000: 1s. Last read position: chr16:3,300,133
INFO 2026-06-08 08:26:22 MarkDuplicates Tracking 280688 as yet unmatched pairs. 43620 records in RAM.
INFO 2026-06-08 08:26:24 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 2s. Last read position: chr16:9,116,778
INFO 2026-06-08 08:26:24 MarkDuplicates Tracking 278022 as yet unmatched pairs. 40954 records in RAM.
INFO 2026-06-08 08:26:26 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:10:08s. Time for last 1,000,000: 2s. Last read position: chr16:14,895,081
INFO 2026-06-08 08:26:26 MarkDuplicates Tracking 276020 as yet unmatched pairs. 38952 records in RAM.
INFO 2026-06-08 08:26:28 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:10:10s. Time for last 1,000,000: 1s. Last read position: chr16:15,136,936
INFO 2026-06-08 08:26:28 MarkDuplicates Tracking 274549 as yet unmatched pairs. 37481 records in RAM.
INFO 2026-06-08 08:26:30 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 1s. Last read position: chr16:15,735,453
INFO 2026-06-08 08:26:30 MarkDuplicates Tracking 273160 as yet unmatched pairs. 36084 records in RAM.
INFO 2026-06-08 08:26:32 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:10:14s. Time for last 1,000,000: 1s. Last read position: chr16:16,007,951
INFO 2026-06-08 08:26:32 MarkDuplicates Tracking 269801 as yet unmatched pairs. 32723 records in RAM.
INFO 2026-06-08 08:26:33 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:10:15s. Time for last 1,000,000: 1s. Last read position: chr16:16,361,179
INFO 2026-06-08 08:26:33 MarkDuplicates Tracking 269283 as yet unmatched pairs. 32205 records in RAM.
INFO 2026-06-08 08:26:34 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:10:16s. Time for last 1,000,000: 1s. Last read position: chr16:18,381,981
INFO 2026-06-08 08:26:34 MarkDuplicates Tracking 268834 as yet unmatched pairs. 31755 records in RAM.
INFO 2026-06-08 08:26:36 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:10:18s. Time for last 1,000,000: 1s. Last read position: chr16:20,920,176
INFO 2026-06-08 08:26:36 MarkDuplicates Tracking 266052 as yet unmatched pairs. 28973 records in RAM.
INFO 2026-06-08 08:26:37 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:10:19s. Time for last 1,000,000: 1s. Last read position: chr16:21,834,675
INFO 2026-06-08 08:26:37 MarkDuplicates Tracking 264935 as yet unmatched pairs. 27855 records in RAM.
INFO 2026-06-08 08:26:38 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:10:20s. Time for last 1,000,000: 1s. Last read position: chr16:22,482,609
INFO 2026-06-08 08:26:38 MarkDuplicates Tracking 263973 as yet unmatched pairs. 26893 records in RAM.
INFO 2026-06-08 08:26:40 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:10:22s. Time for last 1,000,000: 1s. Last read position: chr16:24,553,539
INFO 2026-06-08 08:26:40 MarkDuplicates Tracking 263178 as yet unmatched pairs. 26098 records in RAM.
INFO 2026-06-08 08:26:41 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:10:23s. Time for last 1,000,000: 1s. Last read position: chr16:28,832,231
INFO 2026-06-08 08:26:41 MarkDuplicates Tracking 262168 as yet unmatched pairs. 25084 records in RAM.
INFO 2026-06-08 08:26:43 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:10:25s. Time for last 1,000,000: 1s. Last read position: chr16:29,485,789
INFO 2026-06-08 08:26:43 MarkDuplicates Tracking 260258 as yet unmatched pairs. 23174 records in RAM.
INFO 2026-06-08 08:26:44 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 1s. Last read position: chr16:30,224,524
INFO 2026-06-08 08:26:44 MarkDuplicates Tracking 258326 as yet unmatched pairs. 21242 records in RAM.
INFO 2026-06-08 08:26:46 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:10:28s. Time for last 1,000,000: 1s. Last read position: chr16:30,765,483
INFO 2026-06-08 08:26:46 MarkDuplicates Tracking 255901 as yet unmatched pairs. 18816 records in RAM.
INFO 2026-06-08 08:26:48 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:10:30s. Time for last 1,000,000: 2s. Last read position: chr16:48,261,424
INFO 2026-06-08 08:26:48 MarkDuplicates Tracking 253440 as yet unmatched pairs. 16355 records in RAM.
INFO 2026-06-08 08:26:50 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:10:32s. Time for last 1,000,000: 1s. Last read position: chr16:56,932,235
INFO 2026-06-08 08:26:50 MarkDuplicates Tracking 250896 as yet unmatched pairs. 13808 records in RAM.
INFO 2026-06-08 08:26:52 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:10:34s. Time for last 1,000,000: 2s. Last read position: chr16:67,282,538
INFO 2026-06-08 08:26:52 MarkDuplicates Tracking 247980 as yet unmatched pairs. 10892 records in RAM.
INFO 2026-06-08 08:26:53 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:10:35s. Time for last 1,000,000: 1s. Last read position: chr16:69,757,639
INFO 2026-06-08 08:26:53 MarkDuplicates Tracking 245515 as yet unmatched pairs. 8427 records in RAM.
INFO 2026-06-08 08:26:56 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:10:38s. Time for last 1,000,000: 2s. Last read position: chr16:74,456,688
INFO 2026-06-08 08:26:56 MarkDuplicates Tracking 243300 as yet unmatched pairs. 6212 records in RAM.
INFO 2026-06-08 08:26:57 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:10:39s. Time for last 1,000,000: 1s. Last read position: chr16:86,511,334
INFO 2026-06-08 08:26:57 MarkDuplicates Tracking 240692 as yet unmatched pairs. 3603 records in RAM.
INFO 2026-06-08 08:26:59 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:10:41s. Time for last 1,000,000: 1s. Last read position: chr16:89,646,635
INFO 2026-06-08 08:26:59 MarkDuplicates Tracking 237872 as yet unmatched pairs. 783 records in RAM.
INFO 2026-06-08 08:27:01 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:10:43s. Time for last 1,000,000: 2s. Last read position: chr17:1,726,311
INFO 2026-06-08 08:27:01 MarkDuplicates Tracking 235199 as yet unmatched pairs. 63990 records in RAM.
INFO 2026-06-08 08:27:03 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:10:45s. Time for last 1,000,000: 1s. Last read position: chr17:4,893,434
INFO 2026-06-08 08:27:03 MarkDuplicates Tracking 232452 as yet unmatched pairs. 61243 records in RAM.
INFO 2026-06-08 08:27:05 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:10:47s. Time for last 1,000,000: 1s. Last read position: chr17:7,417,191
INFO 2026-06-08 08:27:05 MarkDuplicates Tracking 229954 as yet unmatched pairs. 58744 records in RAM.
INFO 2026-06-08 08:27:07 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:10:49s. Time for last 1,000,000: 1s. Last read position: chr17:8,142,344
INFO 2026-06-08 08:27:07 MarkDuplicates Tracking 227669 as yet unmatched pairs. 56459 records in RAM.
INFO 2026-06-08 08:27:09 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:10:50s. Time for last 1,000,000: 1s. Last read position: chr17:16,382,350
INFO 2026-06-08 08:27:09 MarkDuplicates Tracking 225213 as yet unmatched pairs. 54002 records in RAM.
INFO 2026-06-08 08:27:10 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:10:52s. Time for last 1,000,000: 1s. Last read position: chr17:19,381,020
INFO 2026-06-08 08:27:10 MarkDuplicates Tracking 222514 as yet unmatched pairs. 51300 records in RAM.
INFO 2026-06-08 08:27:12 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:10:54s. Time for last 1,000,000: 2s. Last read position: chr17:28,906,947
INFO 2026-06-08 08:27:12 MarkDuplicates Tracking 220331 as yet unmatched pairs. 49117 records in RAM.
INFO 2026-06-08 08:27:14 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:10:56s. Time for last 1,000,000: 2s. Last read position: chr17:32,473,872
INFO 2026-06-08 08:27:14 MarkDuplicates Tracking 217889 as yet unmatched pairs. 46673 records in RAM.
INFO 2026-06-08 08:27:16 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 1s. Last read position: chr17:37,330,262
INFO 2026-06-08 08:27:16 MarkDuplicates Tracking 216236 as yet unmatched pairs. 45020 records in RAM.
INFO 2026-06-08 08:27:18 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:11:00s. Time for last 1,000,000: 1s. Last read position: chr17:39,201,211
INFO 2026-06-08 08:27:18 MarkDuplicates Tracking 214476 as yet unmatched pairs. 43260 records in RAM.
INFO 2026-06-08 08:27:19 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:11:01s. Time for last 1,000,000: 1s. Last read position: chr17:40,096,488
INFO 2026-06-08 08:27:19 MarkDuplicates Tracking 211345 as yet unmatched pairs. 40129 records in RAM.
INFO 2026-06-08 08:27:21 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:11:03s. Time for last 1,000,000: 1s. Last read position: chr17:42,315,762
INFO 2026-06-08 08:27:21 MarkDuplicates Tracking 210127 as yet unmatched pairs. 38911 records in RAM.
INFO 2026-06-08 08:27:23 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:11:05s. Time for last 1,000,000: 1s. Last read position: chr17:44,212,414
INFO 2026-06-08 08:27:23 MarkDuplicates Tracking 206370 as yet unmatched pairs. 35149 records in RAM.
INFO 2026-06-08 08:27:24 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:11:06s. Time for last 1,000,000: 1s. Last read position: chr17:46,570,755
INFO 2026-06-08 08:27:24 MarkDuplicates Tracking 204250 as yet unmatched pairs. 33028 records in RAM.
INFO 2026-06-08 08:27:26 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:11:08s. Time for last 1,000,000: 1s. Last read position: chr17:50,075,687
INFO 2026-06-08 08:27:26 MarkDuplicates Tracking 201912 as yet unmatched pairs. 30689 records in RAM.
INFO 2026-06-08 08:27:28 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:11:10s. Time for last 1,000,000: 2s. Last read position: chr17:50,190,049
INFO 2026-06-08 08:27:28 MarkDuplicates Tracking 202857 as yet unmatched pairs. 31630 records in RAM.
INFO 2026-06-08 08:27:30 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:11:12s. Time for last 1,000,000: 1s. Last read position: chr17:50,196,508
INFO 2026-06-08 08:27:30 MarkDuplicates Tracking 199825 as yet unmatched pairs. 28597 records in RAM.
INFO 2026-06-08 08:27:32 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:11:14s. Time for last 1,000,000: 1s. Last read position: chr17:57,106,836
INFO 2026-06-08 08:27:32 MarkDuplicates Tracking 194027 as yet unmatched pairs. 22799 records in RAM.
INFO 2026-06-08 08:27:33 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:11:15s. Time for last 1,000,000: 1s. Last read position: chr17:59,685,657
INFO 2026-06-08 08:27:33 MarkDuplicates Tracking 192679 as yet unmatched pairs. 21451 records in RAM.
INFO 2026-06-08 08:27:35 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:11:17s. Time for last 1,000,000: 1s. Last read position: chr17:64,499,800
INFO 2026-06-08 08:27:35 MarkDuplicates Tracking 189661 as yet unmatched pairs. 18433 records in RAM.
INFO 2026-06-08 08:27:38 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:11:20s. Time for last 1,000,000: 2s. Last read position: chr17:68,527,878
INFO 2026-06-08 08:27:38 MarkDuplicates Tracking 187413 as yet unmatched pairs. 16185 records in RAM.
INFO 2026-06-08 08:27:40 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:11:22s. Time for last 1,000,000: 2s. Last read position: chr17:75,619,905
INFO 2026-06-08 08:27:40 MarkDuplicates Tracking 184326 as yet unmatched pairs. 13098 records in RAM.
INFO 2026-06-08 08:27:41 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:11:23s. Time for last 1,000,000: 1s. Last read position: chr17:78,117,830
INFO 2026-06-08 08:27:41 MarkDuplicates Tracking 181726 as yet unmatched pairs. 10498 records in RAM.
INFO 2026-06-08 08:27:43 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:11:25s. Time for last 1,000,000: 1s. Last read position: chr17:80,346,877
INFO 2026-06-08 08:27:43 MarkDuplicates Tracking 179113 as yet unmatched pairs. 7885 records in RAM.
INFO 2026-06-08 08:27:45 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:11:27s. Time for last 1,000,000: 1s. Last read position: chr17:81,868,392
INFO 2026-06-08 08:27:45 MarkDuplicates Tracking 177383 as yet unmatched pairs. 6154 records in RAM.
INFO 2026-06-08 08:27:47 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:11:29s. Time for last 1,000,000: 1s. Last read position: chr17:82,090,963
INFO 2026-06-08 08:27:47 MarkDuplicates Tracking 173572 as yet unmatched pairs. 2343 records in RAM.
INFO 2026-06-08 08:27:48 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:11:30s. Time for last 1,000,000: 1s. Last read position: chr18:6,824,904
INFO 2026-06-08 08:27:48 MarkDuplicates Tracking 170390 as yet unmatched pairs. 9215 records in RAM.
INFO 2026-06-08 08:27:50 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:11:32s. Time for last 1,000,000: 1s. Last read position: chr18:26,018,363
INFO 2026-06-08 08:27:50 MarkDuplicates Tracking 168306 as yet unmatched pairs. 7125 records in RAM.
INFO 2026-06-08 08:27:52 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:11:34s. Time for last 1,000,000: 1s. Last read position: chr18:48,761,410
INFO 2026-06-08 08:27:52 MarkDuplicates Tracking 165894 as yet unmatched pairs. 4711 records in RAM.
INFO 2026-06-08 08:27:54 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:11:36s. Time for last 1,000,000: 1s. Last read position: chr18:62,221,224
INFO 2026-06-08 08:27:54 MarkDuplicates Tracking 164010 as yet unmatched pairs. 2826 records in RAM.
INFO 2026-06-08 08:27:56 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:11:38s. Time for last 1,000,000: 2s. Last read position: chr19:621,668
INFO 2026-06-08 08:27:56 MarkDuplicates Tracking 160721 as yet unmatched pairs. 68533 records in RAM.
INFO 2026-06-08 08:27:58 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:11:40s. Time for last 1,000,000: 2s. Last read position: chr19:1,440,031
INFO 2026-06-08 08:27:58 MarkDuplicates Tracking 159069 as yet unmatched pairs. 66881 records in RAM.
INFO 2026-06-08 08:28:00 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:11:42s. Time for last 1,000,000: 2s. Last read position: chr19:3,054,026
INFO 2026-06-08 08:28:00 MarkDuplicates Tracking 155113 as yet unmatched pairs. 62925 records in RAM.
INFO 2026-06-08 08:28:02 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:11:44s. Time for last 1,000,000: 1s. Last read position: chr19:5,119,747
INFO 2026-06-08 08:28:02 MarkDuplicates Tracking 151784 as yet unmatched pairs. 59596 records in RAM.
INFO 2026-06-08 08:28:04 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:11:46s. Time for last 1,000,000: 1s. Last read position: chr19:6,710,995
INFO 2026-06-08 08:28:04 MarkDuplicates Tracking 149043 as yet unmatched pairs. 56853 records in RAM.
INFO 2026-06-08 08:28:06 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:11:48s. Time for last 1,000,000: 1s. Last read position: chr19:8,938,848
INFO 2026-06-08 08:28:06 MarkDuplicates Tracking 146083 as yet unmatched pairs. 53891 records in RAM.
INFO 2026-06-08 08:28:08 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:11:50s. Time for last 1,000,000: 1s. Last read position: chr19:11,105,173
INFO 2026-06-08 08:28:08 MarkDuplicates Tracking 143418 as yet unmatched pairs. 51225 records in RAM.
INFO 2026-06-08 08:28:09 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:11:51s. Time for last 1,000,000: 1s. Last read position: chr19:12,878,740
INFO 2026-06-08 08:28:09 MarkDuplicates Tracking 140845 as yet unmatched pairs. 48652 records in RAM.
INFO 2026-06-08 08:28:11 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:11:53s. Time for last 1,000,000: 1s. Last read position: chr19:15,110,600
INFO 2026-06-08 08:28:11 MarkDuplicates Tracking 138129 as yet unmatched pairs. 45936 records in RAM.
INFO 2026-06-08 08:28:13 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:11:55s. Time for last 1,000,000: 1s. Last read position: chr19:16,325,872
INFO 2026-06-08 08:28:13 MarkDuplicates Tracking 135531 as yet unmatched pairs. 43338 records in RAM.
INFO 2026-06-08 08:28:14 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:11:56s. Time for last 1,000,000: 1s. Last read position: chr19:18,265,546
INFO 2026-06-08 08:28:14 MarkDuplicates Tracking 132598 as yet unmatched pairs. 40404 records in RAM.
INFO 2026-06-08 08:28:16 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:11:58s. Time for last 1,000,000: 1s. Last read position: chr19:21,034,119
INFO 2026-06-08 08:28:16 MarkDuplicates Tracking 129805 as yet unmatched pairs. 37611 records in RAM.
INFO 2026-06-08 08:28:18 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:12:00s. Time for last 1,000,000: 1s. Last read position: chr19:35,546,682
INFO 2026-06-08 08:28:18 MarkDuplicates Tracking 126902 as yet unmatched pairs. 34706 records in RAM.
INFO 2026-06-08 08:28:20 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:12:02s. Time for last 1,000,000: 2s. Last read position: chr19:38,624,090
INFO 2026-06-08 08:28:20 MarkDuplicates Tracking 124486 as yet unmatched pairs. 32290 records in RAM.
INFO 2026-06-08 08:28:21 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:12:03s. Time for last 1,000,000: 1s. Last read position: chr19:39,918,444
INFO 2026-06-08 08:28:21 MarkDuplicates Tracking 121645 as yet unmatched pairs. 29449 records in RAM.
INFO 2026-06-08 08:28:24 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:12:06s. Time for last 1,000,000: 2s. Last read position: chr19:41,276,272
INFO 2026-06-08 08:28:24 MarkDuplicates Tracking 119062 as yet unmatched pairs. 26865 records in RAM.
INFO 2026-06-08 08:28:26 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:12:08s. Time for last 1,000,000: 2s. Last read position: chr19:42,292,370
INFO 2026-06-08 08:28:26 MarkDuplicates Tracking 116648 as yet unmatched pairs. 24451 records in RAM.
INFO 2026-06-08 08:28:28 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:12:10s. Time for last 1,000,000: 1s. Last read position: chr19:45,140,536
INFO 2026-06-08 08:28:28 MarkDuplicates Tracking 113257 as yet unmatched pairs. 21057 records in RAM.
INFO 2026-06-08 08:28:29 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:12:11s. Time for last 1,000,000: 1s. Last read position: chr19:47,069,150
INFO 2026-06-08 08:28:29 MarkDuplicates Tracking 110603 as yet unmatched pairs. 18403 records in RAM.
INFO 2026-06-08 08:28:31 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:12:13s. Time for last 1,000,000: 1s. Last read position: chr19:49,104,716
INFO 2026-06-08 08:28:31 MarkDuplicates Tracking 108068 as yet unmatched pairs. 15866 records in RAM.
INFO 2026-06-08 08:28:33 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:12:15s. Time for last 1,000,000: 1s. Last read position: chr19:49,800,015
INFO 2026-06-08 08:28:33 MarkDuplicates Tracking 104879 as yet unmatched pairs. 12677 records in RAM.
INFO 2026-06-08 08:28:35 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:12:17s. Time for last 1,000,000: 1s. Last read position: chr19:50,858,419
INFO 2026-06-08 08:28:35 MarkDuplicates Tracking 105456 as yet unmatched pairs. 13254 records in RAM.
INFO 2026-06-08 08:28:36 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:12:18s. Time for last 1,000,000: 1s. Last read position: chr19:51,965,869
INFO 2026-06-08 08:28:36 MarkDuplicates Tracking 99752 as yet unmatched pairs. 7550 records in RAM.
INFO 2026-06-08 08:28:38 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:12:20s. Time for last 1,000,000: 1s. Last read position: chr19:54,455,408
INFO 2026-06-08 08:28:38 MarkDuplicates Tracking 97588 as yet unmatched pairs. 5384 records in RAM.
INFO 2026-06-08 08:28:40 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:12:22s. Time for last 1,000,000: 1s. Last read position: chr19:57,253,181
INFO 2026-06-08 08:28:40 MarkDuplicates Tracking 94580 as yet unmatched pairs. 2376 records in RAM.
INFO 2026-06-08 08:28:42 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:12:24s. Time for last 1,000,000: 2s. Last read position: chr20:489,877
INFO 2026-06-08 08:28:42 MarkDuplicates Tracking 92238 as yet unmatched pairs. 22367 records in RAM.
INFO 2026-06-08 08:28:44 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:12:26s. Time for last 1,000,000: 2s. Last read position: chr20:10,646,995
INFO 2026-06-08 08:28:44 MarkDuplicates Tracking 89439 as yet unmatched pairs. 19568 records in RAM.
INFO 2026-06-08 08:28:46 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:12:28s. Time for last 1,000,000: 2s. Last read position: chr20:25,277,273
INFO 2026-06-08 08:28:46 MarkDuplicates Tracking 87150 as yet unmatched pairs. 17279 records in RAM.
INFO 2026-06-08 08:28:49 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:12:31s. Time for last 1,000,000: 2s. Last read position: chr20:35,269,793
INFO 2026-06-08 08:28:49 MarkDuplicates Tracking 84424 as yet unmatched pairs. 14553 records in RAM.
INFO 2026-06-08 08:28:50 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:12:32s. Time for last 1,000,000: 1s. Last read position: chr20:38,011,893
INFO 2026-06-08 08:28:50 MarkDuplicates Tracking 82049 as yet unmatched pairs. 12177 records in RAM.
INFO 2026-06-08 08:28:52 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:12:34s. Time for last 1,000,000: 1s. Last read position: chr20:45,327,326
INFO 2026-06-08 08:28:52 MarkDuplicates Tracking 79945 as yet unmatched pairs. 10073 records in RAM.
INFO 2026-06-08 08:28:54 MarkDuplicates Read 368,000,000 records. Elapsed time: 00:12:36s. Time for last 1,000,000: 1s. Last read position: chr20:50,191,549
INFO 2026-06-08 08:28:54 MarkDuplicates Tracking 76786 as yet unmatched pairs. 6914 records in RAM.
INFO 2026-06-08 08:28:56 MarkDuplicates Read 369,000,000 records. Elapsed time: 00:12:38s. Time for last 1,000,000: 1s. Last read position: chr20:59,001,493
INFO 2026-06-08 08:28:56 MarkDuplicates Tracking 74195 as yet unmatched pairs. 4323 records in RAM.
INFO 2026-06-08 08:28:58 MarkDuplicates Read 370,000,000 records. Elapsed time: 00:12:40s. Time for last 1,000,000: 1s. Last read position: chr20:63,560,309
INFO 2026-06-08 08:28:58 MarkDuplicates Tracking 71373 as yet unmatched pairs. 1501 records in RAM.
INFO 2026-06-08 08:28:59 MarkDuplicates Read 371,000,000 records. Elapsed time: 00:12:41s. Time for last 1,000,000: 1s. Last read position: chr21:8,390,877
INFO 2026-06-08 08:28:59 MarkDuplicates Tracking 69155 as yet unmatched pairs. 13747 records in RAM.
INFO 2026-06-08 08:29:01 MarkDuplicates Read 372,000,000 records. Elapsed time: 00:12:43s. Time for last 1,000,000: 1s. Last read position: chr21:32,319,329
INFO 2026-06-08 08:29:01 MarkDuplicates Tracking 67101 as yet unmatched pairs. 11692 records in RAM.
INFO 2026-06-08 08:29:03 MarkDuplicates Read 373,000,000 records. Elapsed time: 00:12:45s. Time for last 1,000,000: 1s. Last read position: chr21:37,088,208
INFO 2026-06-08 08:29:03 MarkDuplicates Tracking 64585 as yet unmatched pairs. 9176 records in RAM.
INFO 2026-06-08 08:29:05 MarkDuplicates Read 374,000,000 records. Elapsed time: 00:12:47s. Time for last 1,000,000: 1s. Last read position: chr21:41,468,453
INFO 2026-06-08 08:29:05 MarkDuplicates Tracking 64552 as yet unmatched pairs. 9143 records in RAM.
INFO 2026-06-08 08:29:06 MarkDuplicates Read 375,000,000 records. Elapsed time: 00:12:48s. Time for last 1,000,000: 1s. Last read position: chr21:44,228,350
INFO 2026-06-08 08:29:06 MarkDuplicates Tracking 59455 as yet unmatched pairs. 4046 records in RAM.
INFO 2026-06-08 08:29:08 MarkDuplicates Read 376,000,000 records. Elapsed time: 00:12:50s. Time for last 1,000,000: 1s. Last read position: chr21:46,129,280
INFO 2026-06-08 08:29:08 MarkDuplicates Tracking 56949 as yet unmatched pairs. 1539 records in RAM.
INFO 2026-06-08 08:29:10 MarkDuplicates Read 377,000,000 records. Elapsed time: 00:12:52s. Time for last 1,000,000: 1s. Last read position: chr22:19,977,506
INFO 2026-06-08 08:29:10 MarkDuplicates Tracking 54045 as yet unmatched pairs. 23734 records in RAM.
INFO 2026-06-08 08:29:12 MarkDuplicates Read 378,000,000 records. Elapsed time: 00:12:54s. Time for last 1,000,000: 1s. Last read position: chr22:23,400,343
INFO 2026-06-08 08:29:12 MarkDuplicates Tracking 51547 as yet unmatched pairs. 21236 records in RAM.
INFO 2026-06-08 08:29:13 MarkDuplicates Read 379,000,000 records. Elapsed time: 00:12:55s. Time for last 1,000,000: 1s. Last read position: chr22:28,797,076
INFO 2026-06-08 08:29:13 MarkDuplicates Tracking 49854 as yet unmatched pairs. 19543 records in RAM.
INFO 2026-06-08 08:29:15 MarkDuplicates Read 380,000,000 records. Elapsed time: 00:12:57s. Time for last 1,000,000: 1s. Last read position: chr22:30,581,021
INFO 2026-06-08 08:29:15 MarkDuplicates Tracking 46658 as yet unmatched pairs. 16347 records in RAM.
INFO 2026-06-08 08:29:17 MarkDuplicates Read 381,000,000 records. Elapsed time: 00:12:59s. Time for last 1,000,000: 1s. Last read position: chr22:36,294,947
INFO 2026-06-08 08:29:17 MarkDuplicates Tracking 44127 as yet unmatched pairs. 13816 records in RAM.
INFO 2026-06-08 08:29:18 MarkDuplicates Read 382,000,000 records. Elapsed time: 00:13:00s. Time for last 1,000,000: 1s. Last read position: chr22:38,481,414
INFO 2026-06-08 08:29:18 MarkDuplicates Tracking 41182 as yet unmatched pairs. 10871 records in RAM.
INFO 2026-06-08 08:29:20 MarkDuplicates Read 383,000,000 records. Elapsed time: 00:13:02s. Time for last 1,000,000: 1s. Last read position: chr22:40,967,874
INFO 2026-06-08 08:29:20 MarkDuplicates Tracking 39074 as yet unmatched pairs. 8763 records in RAM.
INFO 2026-06-08 08:29:23 MarkDuplicates Read 384,000,000 records. Elapsed time: 00:13:05s. Time for last 1,000,000: 2s. Last read position: chr22:42,823,656
INFO 2026-06-08 08:29:23 MarkDuplicates Tracking 36427 as yet unmatched pairs. 6116 records in RAM.
INFO 2026-06-08 08:29:25 MarkDuplicates Read 385,000,000 records. Elapsed time: 00:13:07s. Time for last 1,000,000: 2s. Last read position: chr22:50,248,117
INFO 2026-06-08 08:29:25 MarkDuplicates Tracking 33240 as yet unmatched pairs. 2929 records in RAM.
INFO 2026-06-08 08:29:27 MarkDuplicates Read 386,000,000 records. Elapsed time: 00:13:09s. Time for last 1,000,000: 2s. Last read position: chrX:1,600,865
INFO 2026-06-08 08:29:27 MarkDuplicates Tracking 29945 as yet unmatched pairs. 26876 records in RAM.
INFO 2026-06-08 08:29:29 MarkDuplicates Read 387,000,000 records. Elapsed time: 00:13:11s. Time for last 1,000,000: 1s. Last read position: chrX:20,200,679
INFO 2026-06-08 08:29:29 MarkDuplicates Tracking 27744 as yet unmatched pairs. 24674 records in RAM.
INFO 2026-06-08 08:29:31 MarkDuplicates Read 388,000,000 records. Elapsed time: 00:13:13s. Time for last 1,000,000: 1s. Last read position: chrX:41,342,628
INFO 2026-06-08 08:29:31 MarkDuplicates Tracking 25352 as yet unmatched pairs. 22282 records in RAM.
INFO 2026-06-08 08:29:32 MarkDuplicates Read 389,000,000 records. Elapsed time: 00:13:14s. Time for last 1,000,000: 1s. Last read position: chrX:48,917,818
INFO 2026-06-08 08:29:32 MarkDuplicates Tracking 22629 as yet unmatched pairs. 19559 records in RAM.
INFO 2026-06-08 08:29:34 MarkDuplicates Read 390,000,000 records. Elapsed time: 00:13:16s. Time for last 1,000,000: 1s. Last read position: chrX:53,617,015
INFO 2026-06-08 08:29:34 MarkDuplicates Tracking 20433 as yet unmatched pairs. 17363 records in RAM.
INFO 2026-06-08 08:29:36 MarkDuplicates Read 391,000,000 records. Elapsed time: 00:13:18s. Time for last 1,000,000: 1s. Last read position: chrX:71,299,995
INFO 2026-06-08 08:29:36 MarkDuplicates Tracking 18005 as yet unmatched pairs. 14935 records in RAM.
INFO 2026-06-08 08:29:37 MarkDuplicates Read 392,000,000 records. Elapsed time: 00:13:19s. Time for last 1,000,000: 1s. Last read position: chrX:78,015,844
INFO 2026-06-08 08:29:37 MarkDuplicates Tracking 15378 as yet unmatched pairs. 12308 records in RAM.
INFO 2026-06-08 08:29:39 MarkDuplicates Read 393,000,000 records. Elapsed time: 00:13:21s. Time for last 1,000,000: 1s. Last read position: chrX:111,518,903
INFO 2026-06-08 08:29:39 MarkDuplicates Tracking 13139 as yet unmatched pairs. 10069 records in RAM.
INFO 2026-06-08 08:29:41 MarkDuplicates Read 394,000,000 records. Elapsed time: 00:13:23s. Time for last 1,000,000: 1s. Last read position: chrX:135,579,824
INFO 2026-06-08 08:29:41 MarkDuplicates Tracking 10875 as yet unmatched pairs. 7805 records in RAM.
INFO 2026-06-08 08:29:43 MarkDuplicates Read 395,000,000 records. Elapsed time: 00:13:25s. Time for last 1,000,000: 1s. Last read position: chrX:153,959,988
INFO 2026-06-08 08:29:43 MarkDuplicates Tracking 8664 as yet unmatched pairs. 5594 records in RAM.
INFO 2026-06-08 08:29:44 MarkDuplicates Read 396,000,000 records. Elapsed time: 00:13:26s. Time for last 1,000,000: 1s. Last read position: chrX:154,361,398
INFO 2026-06-08 08:29:44 MarkDuplicates Tracking 7505 as yet unmatched pairs. 4435 records in RAM.
INFO 2026-06-08 08:29:46 MarkDuplicates Read 397,000,000 records. Elapsed time: 00:13:28s. Time for last 1,000,000: 1s. Last read position: chrX:155,514,177
INFO 2026-06-08 08:29:46 MarkDuplicates Tracking 3124 as yet unmatched pairs. 54 records in RAM.
INFO 2026-06-08 08:29:47 MarkDuplicates Read 398,000,000 records. Elapsed time: 00:13:29s. Time for last 1,000,000: 1s. Last read position: KI270733.1:132,323
INFO 2026-06-08 08:29:47 MarkDuplicates Tracking 1379 as yet unmatched pairs. 1365 records in RAM.
INFO 2026-06-08 08:29:48 MarkDuplicates Read 398327360 records. 0 pairs never matched.
INFO 2026-06-08 08:30:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 35345066736; totalMemory: 50465865728; maxMemory: 63585648640
INFO 2026-06-08 08:30:28 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:30:43 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:31:03 OpticalDuplicateFinder Large duplicate set. size = 1066
INFO 2026-06-08 08:31:03 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:1,712
INFO 2026-06-08 08:31:24 MarkDuplicates Traversing fragment information and detecting duplicates.
WARNING 2026-06-08 08:31:24 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
INFO 2026-06-08 08:32:06 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:32:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 34516402576; totalMemory: 50465865728; maxMemory: 63585648640
INFO 2026-06-08 08:32:15 MarkDuplicates Marking 230308622 records as duplicates.
INFO 2026-06-08 08:32:15 MarkDuplicates Found 6458836 optical duplicate clusters.
INFO 2026-06-08 08:32:15 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 08:32:32 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:16s. Time for last 10,000,000: 16s. Last read position: chr1:36,466,456
INFO 2026-06-08 08:32:48 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:32s. Time for last 10,000,000: 16s. Last read position: chr1:120,814,840
INFO 2026-06-08 08:33:04 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:49s. Time for last 10,000,000: 16s. Last read position: chr1:186,347,353
INFO 2026-06-08 08:33:21 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:05s. Time for last 10,000,000: 16s. Last read position: chr2:32,468,669
INFO 2026-06-08 08:33:37 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:21s. Time for last 10,000,000: 16s. Last read position: chr2:97,585,383
INFO 2026-06-08 08:33:53 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:37s. Time for last 10,000,000: 16s. Last read position: chr2:201,633,343
INFO 2026-06-08 08:34:09 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:01:54s. Time for last 10,000,000: 16s. Last read position: chr3:29,401,802
INFO 2026-06-08 08:34:26 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:10s. Time for last 10,000,000: 16s. Last read position: chr3:101,682,477
INFO 2026-06-08 08:34:42 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:27s. Time for last 10,000,000: 16s. Last read position: chr3:195,786,073
INFO 2026-06-08 08:34:58 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:43s. Time for last 10,000,000: 16s. Last read position: chr4:119,565,401
INFO 2026-06-08 08:35:15 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:02:59s. Time for last 10,000,000: 16s. Last read position: chr5:83,580,292
INFO 2026-06-08 08:35:31 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:16s. Time for last 10,000,000: 16s. Last read position: chr5:171,407,709
INFO 2026-06-08 08:35:48 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:33s. Time for last 10,000,000: 16s. Last read position: chr6:33,313,295
INFO 2026-06-08 08:36:05 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:03:49s. Time for last 10,000,000: 16s. Last read position: chr6:154,832,693
INFO 2026-06-08 08:36:21 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:04:06s. Time for last 10,000,000: 16s. Last read position: chr7:77,253,743
INFO 2026-06-08 08:36:38 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:22s. Time for last 10,000,000: 16s. Last read position: chr7:150,371,633
INFO 2026-06-08 08:36:54 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:04:39s. Time for last 10,000,000: 16s. Last read position: chr8:102,651,572
INFO 2026-06-08 08:37:11 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:04:55s. Time for last 10,000,000: 16s. Last read position: chr9:65,894,735
INFO 2026-06-08 08:37:27 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:05:12s. Time for last 10,000,000: 16s. Last read position: chr9:136,475,934
INFO 2026-06-08 08:37:44 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:05:28s. Time for last 10,000,000: 16s. Last read position: chr10:87,952,130
INFO 2026-06-08 08:38:00 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:05:45s. Time for last 10,000,000: 16s. Last read position: chr11:19,984,179
INFO 2026-06-08 08:38:16 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:06:01s. Time for last 10,000,000: 16s. Last read position: chr11:69,643,885
INFO 2026-06-08 08:38:33 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:06:17s. Time for last 10,000,000: 16s. Last read position: chr12:6,936,726
INFO 2026-06-08 08:38:49 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:06:34s. Time for last 10,000,000: 16s. Last read position: chr12:57,256,064
INFO 2026-06-08 08:39:06 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:06:50s. Time for last 10,000,000: 16s. Last read position: chr13:24,290,827
INFO 2026-06-08 08:39:23 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:07:07s. Time for last 10,000,000: 16s. Last read position: chr14:58,208,966
INFO 2026-06-08 08:39:40 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:07:24s. Time for last 10,000,000: 16s. Last read position: chr15:37,098,018
INFO 2026-06-08 08:39:56 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:07:41s. Time for last 10,000,000: 16s. Last read position: chr15:99,130,630
INFO 2026-06-08 08:40:13 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:07:58s. Time for last 10,000,000: 16s. Last read position: chr16:16,361,179
INFO 2026-06-08 08:40:30 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:08:14s. Time for last 10,000,000: 16s. Last read position: chr16:48,261,424
INFO 2026-06-08 08:40:47 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:08:32s. Time for last 10,000,000: 17s. Last read position: chr17:8,142,344
INFO 2026-06-08 08:41:04 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:08:48s. Time for last 10,000,000: 16s. Last read position: chr17:46,570,755
INFO 2026-06-08 08:41:21 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:09:05s. Time for last 10,000,000: 16s. Last read position: chr17:80,346,877
INFO 2026-06-08 08:41:38 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:09:22s. Time for last 10,000,000: 16s. Last read position: chr19:5,119,747
INFO 2026-06-08 08:41:55 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:09:39s. Time for last 10,000,000: 17s. Last read position: chr19:38,624,090
INFO 2026-06-08 08:42:12 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:09:56s. Time for last 10,000,000: 17s. Last read position: chr19:54,455,408
INFO 2026-06-08 08:42:29 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:10:13s. Time for last 10,000,000: 16s. Last read position: chr20:63,560,309
INFO 2026-06-08 08:42:45 MarkDuplicates Written 380,000,000 records. Elapsed time: 00:10:30s. Time for last 10,000,000: 16s. Last read position: chr22:30,581,021
INFO 2026-06-08 08:43:02 MarkDuplicates Written 390,000,000 records. Elapsed time: 00:10:46s. Time for last 10,000,000: 16s. Last read position: chrX:53,617,015
INFO 2026-06-08 08:43:20 MarkDuplicates Written 400,000,000 records. Elapsed time: 00:11:05s. Time for last 10,000,000: 18s. Last read position: */*
INFO 2026-06-08 08:43:23 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:43:23 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:43:23 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:43:23 MarkDuplicates Before output close freeMemory: 12180915928; totalMemory: 50465865728; maxMemory: 63585648640
INFO 2026-06-08 08:43:23 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:43:23 MarkDuplicates After output close freeMemory: 204593328; totalMemory: 234881024; maxMemory: 63585648640
[Mon Jun 08 08:43:23 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 27.12 minutes.
Runtime.totalMemory()=234881024
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory