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/e6/8bbe66d59a7eace64d482eecd90ce8/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/a215a52654cec40c0e000d61ad2c83/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/8bbe66d59a7eace64d482eecd90ce8/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai
==> STAGING COMPLETE (5 inputs)
Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bam --METRICS_FILE 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
08:51:29.807 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 08:51:29 GMT 2026] MarkDuplicates --INPUT 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.md.bam --METRICS_FILE 659_bQZ-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 08:51:29 GMT 2026] Executing as ?@nf-e68bbe66d59a7eace64d482eecd90ce8-e829c-rv6tg 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 08:51:29 MarkDuplicates Start of doWork freeMemory: 105827040; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 08:51:29 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 08:51:29 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 08:51:33 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:1,354,874
INFO 2026-06-08 08:51:33 MarkDuplicates Tracking 3638 as yet unmatched pairs. 565 records in RAM.
INFO 2026-06-08 08:51:36 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: chr1:2,557,763
INFO 2026-06-08 08:51:36 MarkDuplicates Tracking 7143 as yet unmatched pairs. 912 records in RAM.
INFO 2026-06-08 08:51:38 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: chr1:7,969,380
INFO 2026-06-08 08:51:38 MarkDuplicates Tracking 10288 as yet unmatched pairs. 770 records in RAM.
INFO 2026-06-08 08:51:40 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 2s. Last read position: chr1:10,665,286
INFO 2026-06-08 08:51:40 MarkDuplicates Tracking 12635 as yet unmatched pairs. 409 records in RAM.
INFO 2026-06-08 08:51:42 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 2s. Last read position: chr1:13,779,380
INFO 2026-06-08 08:51:42 MarkDuplicates Tracking 15217 as yet unmatched pairs. 86 records in RAM.
INFO 2026-06-08 08:51:45 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 2s. Last read position: chr1:16,946,258
INFO 2026-06-08 08:51:45 MarkDuplicates Tracking 17931 as yet unmatched pairs. 111 records in RAM.
INFO 2026-06-08 08:51:47 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr1:19,308,528
INFO 2026-06-08 08:51:47 MarkDuplicates Tracking 21433 as yet unmatched pairs. 658 records in RAM.
INFO 2026-06-08 08:51:49 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: chr1:21,823,667
INFO 2026-06-08 08:51:49 MarkDuplicates Tracking 25060 as yet unmatched pairs. 1483 records in RAM.
INFO 2026-06-08 08:51:51 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 2s. Last read position: chr1:22,639,072
INFO 2026-06-08 08:51:51 MarkDuplicates Tracking 28442 as yet unmatched pairs. 1864 records in RAM.
INFO 2026-06-08 08:51:54 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 2s. Last read position: chr1:24,662,736
INFO 2026-06-08 08:51:54 MarkDuplicates Tracking 29655 as yet unmatched pairs. 499 records in RAM.
INFO 2026-06-08 08:51:55 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: chr1:26,942,913
INFO 2026-06-08 08:51:55 MarkDuplicates Tracking 32089 as yet unmatched pairs. 235 records in RAM.
INFO 2026-06-08 08:51:59 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 3s. Last read position: chr1:30,738,974
INFO 2026-06-08 08:51:59 MarkDuplicates Tracking 35798 as yet unmatched pairs. 1085 records in RAM.
INFO 2026-06-08 08:52:01 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 2s. Last read position: chr1:32,224,427
INFO 2026-06-08 08:52:01 MarkDuplicates Tracking 39844 as yet unmatched pairs. 2327 records in RAM.
INFO 2026-06-08 08:52:03 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 2s. Last read position: chr1:35,190,805
INFO 2026-06-08 08:52:03 MarkDuplicates Tracking 41579 as yet unmatched pairs. 1448 records in RAM.
INFO 2026-06-08 08:52:05 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 1s. Last read position: chr1:37,700,436
INFO 2026-06-08 08:52:05 MarkDuplicates Tracking 43364 as yet unmatched pairs. 273 records in RAM.
INFO 2026-06-08 08:52:07 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 1s. Last read position: chr1:40,161,562
INFO 2026-06-08 08:52:07 MarkDuplicates Tracking 46043 as yet unmatched pairs. 349 records in RAM.
INFO 2026-06-08 08:52:09 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 2s. Last read position: chr1:43,569,684
INFO 2026-06-08 08:52:09 MarkDuplicates Tracking 49411 as yet unmatched pairs. 886 records in RAM.
INFO 2026-06-08 08:52:11 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 1s. Last read position: chr1:45,552,527
INFO 2026-06-08 08:52:11 MarkDuplicates Tracking 52427 as yet unmatched pairs. 1156 records in RAM.
INFO 2026-06-08 08:52:13 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chr1:51,301,571
INFO 2026-06-08 08:52:13 MarkDuplicates Tracking 54264 as yet unmatched pairs. 222 records in RAM.
INFO 2026-06-08 08:52:16 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: chr1:55,061,327
INFO 2026-06-08 08:52:16 MarkDuplicates Tracking 58580 as yet unmatched pairs. 1585 records in RAM.
INFO 2026-06-08 08:52:18 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 1s. Last read position: chr1:70,354,262
INFO 2026-06-08 08:52:18 MarkDuplicates Tracking 59897 as yet unmatched pairs. 375 records in RAM.
INFO 2026-06-08 08:52:21 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 2s. Last read position: chr1:89,112,668
INFO 2026-06-08 08:52:21 MarkDuplicates Tracking 62401 as yet unmatched pairs. 436 records in RAM.
INFO 2026-06-08 08:52:23 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 2s. Last read position: chr1:101,786,319
INFO 2026-06-08 08:52:23 MarkDuplicates Tracking 64437 as yet unmatched pairs. 32 records in RAM.
INFO 2026-06-08 08:52:26 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 2s. Last read position: chr1:111,477,303
INFO 2026-06-08 08:52:26 MarkDuplicates Tracking 67114 as yet unmatched pairs. 189 records in RAM.
INFO 2026-06-08 08:52:28 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 2s. Last read position: chr1:115,663,838
INFO 2026-06-08 08:52:28 MarkDuplicates Tracking 69700 as yet unmatched pairs. 131 records in RAM.
INFO 2026-06-08 08:52:30 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 1s. Last read position: chr1:119,915,520
INFO 2026-06-08 08:52:30 MarkDuplicates Tracking 73988 as yet unmatched pairs. 1870 records in RAM.
INFO 2026-06-08 08:52:32 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 2s. Last read position: chr1:120,805,387
INFO 2026-06-08 08:52:32 MarkDuplicates Tracking 74726 as yet unmatched pairs. 117 records in RAM.
INFO 2026-06-08 08:52:33 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 1s. Last read position: chr1:147,619,437
INFO 2026-06-08 08:52:33 MarkDuplicates Tracking 76225 as yet unmatched pairs. 187 records in RAM.
INFO 2026-06-08 08:52:35 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 1s. Last read position: chr1:149,832,736
INFO 2026-06-08 08:52:35 MarkDuplicates Tracking 80448 as yet unmatched pairs. 3055 records in RAM.
INFO 2026-06-08 08:52:37 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 1s. Last read position: chr1:150,231,899
INFO 2026-06-08 08:52:37 MarkDuplicates Tracking 79372 as yet unmatched pairs. 66 records in RAM.
INFO 2026-06-08 08:52:38 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 1s. Last read position: chr1:151,315,876
INFO 2026-06-08 08:52:38 MarkDuplicates Tracking 82752 as yet unmatched pairs. 545 records in RAM.
INFO 2026-06-08 08:52:41 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 2s. Last read position: chr1:153,933,261
INFO 2026-06-08 08:52:41 MarkDuplicates Tracking 85230 as yet unmatched pairs. 427 records in RAM.
INFO 2026-06-08 08:52:43 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 1s. Last read position: chr1:154,337,470
INFO 2026-06-08 08:52:43 MarkDuplicates Tracking 87463 as yet unmatched pairs. 256 records in RAM.
INFO 2026-06-08 08:52:45 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 2s. Last read position: chr1:155,187,715
INFO 2026-06-08 08:52:45 MarkDuplicates Tracking 91626 as yet unmatched pairs. 1638 records in RAM.
INFO 2026-06-08 08:52:47 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 1s. Last read position: chr1:155,766,498
INFO 2026-06-08 08:52:47 MarkDuplicates Tracking 92463 as yet unmatched pairs. 230 records in RAM.
INFO 2026-06-08 08:52:49 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 2s. Last read position: chr1:156,136,403
INFO 2026-06-08 08:52:49 MarkDuplicates Tracking 103005 as yet unmatched pairs. 7347 records in RAM.
INFO 2026-06-08 08:52:51 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 2s. Last read position: chr1:156,800,499
INFO 2026-06-08 08:52:51 MarkDuplicates Tracking 98553 as yet unmatched pairs. 78 records in RAM.
INFO 2026-06-08 08:52:54 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 2s. Last read position: chr1:161,154,022
INFO 2026-06-08 08:52:54 MarkDuplicates Tracking 101788 as yet unmatched pairs. 538 records in RAM.
INFO 2026-06-08 08:52:57 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 2s. Last read position: chr1:165,903,182
INFO 2026-06-08 08:52:57 MarkDuplicates Tracking 104015 as yet unmatched pairs. 408 records in RAM.
INFO 2026-06-08 08:52:59 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 2s. Last read position: chr1:171,541,797
INFO 2026-06-08 08:52:59 MarkDuplicates Tracking 106956 as yet unmatched pairs. 604 records in RAM.
INFO 2026-06-08 08:53:01 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 2s. Last read position: chr1:180,197,241
INFO 2026-06-08 08:53:01 MarkDuplicates Tracking 109568 as yet unmatched pairs. 640 records in RAM.
INFO 2026-06-08 08:53:03 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 1s. Last read position: chr1:186,318,738
INFO 2026-06-08 08:53:03 MarkDuplicates Tracking 113571 as yet unmatched pairs. 1768 records in RAM.
INFO 2026-06-08 08:53:05 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 1s. Last read position: chr1:200,911,632
INFO 2026-06-08 08:53:05 MarkDuplicates Tracking 114704 as yet unmatched pairs. 441 records in RAM.
INFO 2026-06-08 08:53:07 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 1s. Last read position: chr1:202,964,611
INFO 2026-06-08 08:53:07 MarkDuplicates Tracking 117135 as yet unmatched pairs. 40 records in RAM.
INFO 2026-06-08 08:53:09 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 1s. Last read position: chr1:205,663,224
INFO 2026-06-08 08:53:09 MarkDuplicates Tracking 120245 as yet unmatched pairs. 468 records in RAM.
INFO 2026-06-08 08:53:11 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 1s. Last read position: chr1:208,043,067
INFO 2026-06-08 08:53:11 MarkDuplicates Tracking 122389 as yet unmatched pairs. 97 records in RAM.
INFO 2026-06-08 08:53:12 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 1s. Last read position: chr1:220,185,657
INFO 2026-06-08 08:53:12 MarkDuplicates Tracking 125127 as yet unmatched pairs. 131 records in RAM.
INFO 2026-06-08 08:53:14 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 1s. Last read position: chr1:225,988,186
INFO 2026-06-08 08:53:14 MarkDuplicates Tracking 127768 as yet unmatched pairs. 236 records in RAM.
INFO 2026-06-08 08:53:16 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 2s. Last read position: chr1:230,685,233
INFO 2026-06-08 08:53:16 MarkDuplicates Tracking 130660 as yet unmatched pairs. 87 records in RAM.
INFO 2026-06-08 08:53:18 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 1s. Last read position: chr1:236,552,074
INFO 2026-06-08 08:53:18 MarkDuplicates Tracking 133810 as yet unmatched pairs. 146 records in RAM.
INFO 2026-06-08 08:53:20 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 1s. Last read position: chr1:248,858,179
INFO 2026-06-08 08:53:20 MarkDuplicates Tracking 136790 as yet unmatched pairs. 422 records in RAM.
INFO 2026-06-08 08:53:23 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 2s. Last read position: chr2:10,791,821
INFO 2026-06-08 08:53:23 MarkDuplicates Tracking 139808 as yet unmatched pairs. 139086 records in RAM.
INFO 2026-06-08 08:53:25 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 1s. Last read position: chr2:24,300,124
INFO 2026-06-08 08:53:25 MarkDuplicates Tracking 142285 as yet unmatched pairs. 141544 records in RAM.
INFO 2026-06-08 08:53:27 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 1s. Last read position: chr2:27,215,361
INFO 2026-06-08 08:53:27 MarkDuplicates Tracking 145006 as yet unmatched pairs. 144258 records in RAM.
INFO 2026-06-08 08:53:29 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 1s. Last read position: chr2:32,305,552
INFO 2026-06-08 08:53:29 MarkDuplicates Tracking 147776 as yet unmatched pairs. 147009 records in RAM.
INFO 2026-06-08 08:53:32 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 3s. Last read position: chr2:32,916,262
INFO 2026-06-08 08:53:32 MarkDuplicates Tracking 217985 as yet unmatched pairs. 144151 records in RAM.
INFO 2026-06-08 08:53:35 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,264
INFO 2026-06-08 08:53:35 MarkDuplicates Tracking 860459 as yet unmatched pairs. 116270 records in RAM.
INFO 2026-06-08 08:53:37 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,406
INFO 2026-06-08 08:53:37 MarkDuplicates Tracking 1308544 as yet unmatched pairs. 96111 records in RAM.
INFO 2026-06-08 08:53:38 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,406
INFO 2026-06-08 08:53:38 MarkDuplicates Tracking 1316044 as yet unmatched pairs. 95879 records in RAM.
INFO 2026-06-08 08:53:40 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 1s. Last read position: chr2:37,237,820
INFO 2026-06-08 08:53:40 MarkDuplicates Tracking 1393222 as yet unmatched pairs. 91567 records in RAM.
INFO 2026-06-08 08:53:42 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 1s. Last read position: chr2:43,226,420
INFO 2026-06-08 08:53:42 MarkDuplicates Tracking 1390264 as yet unmatched pairs. 88590 records in RAM.
INFO 2026-06-08 08:53:45 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 2s. Last read position: chr2:47,823,225
INFO 2026-06-08 08:53:45 MarkDuplicates Tracking 1387793 as yet unmatched pairs. 86106 records in RAM.
INFO 2026-06-08 08:53:47 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 2s. Last read position: chr2:55,232,807
INFO 2026-06-08 08:53:47 MarkDuplicates Tracking 1385590 as yet unmatched pairs. 83895 records in RAM.
INFO 2026-06-08 08:53:49 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 2s. Last read position: chr2:65,069,558
INFO 2026-06-08 08:53:49 MarkDuplicates Tracking 1382602 as yet unmatched pairs. 80877 records in RAM.
INFO 2026-06-08 08:53:51 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 2s. Last read position: chr2:71,427,183
INFO 2026-06-08 08:53:51 MarkDuplicates Tracking 1380073 as yet unmatched pairs. 78327 records in RAM.
INFO 2026-06-08 08:53:54 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 2s. Last read position: chr2:74,463,231
INFO 2026-06-08 08:53:54 MarkDuplicates Tracking 1377702 as yet unmatched pairs. 75945 records in RAM.
INFO 2026-06-08 08:53:57 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 2s. Last read position: chr2:85,398,734
INFO 2026-06-08 08:53:57 MarkDuplicates Tracking 1374700 as yet unmatched pairs. 72935 records in RAM.
INFO 2026-06-08 08:53:59 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 2s. Last read position: chr2:88,857,373
INFO 2026-06-08 08:53:59 MarkDuplicates Tracking 1374800 as yet unmatched pairs. 73026 records in RAM.
INFO 2026-06-08 08:54:01 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 2s. Last read position: chr2:97,113,925
INFO 2026-06-08 08:54:01 MarkDuplicates Tracking 1369848 as yet unmatched pairs. 68066 records in RAM.
INFO 2026-06-08 08:54:04 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 2s. Last read position: chr2:102,824,103
INFO 2026-06-08 08:54:04 MarkDuplicates Tracking 1366975 as yet unmatched pairs. 65177 records in RAM.
INFO 2026-06-08 08:54:06 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 2s. Last read position: chr2:108,764,327
INFO 2026-06-08 08:54:06 MarkDuplicates Tracking 1366962 as yet unmatched pairs. 65161 records in RAM.
INFO 2026-06-08 08:54:08 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 2s. Last read position: chr2:109,824,361
INFO 2026-06-08 08:54:08 MarkDuplicates Tracking 1362815 as yet unmatched pairs. 61001 records in RAM.
INFO 2026-06-08 08:54:09 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 1s. Last read position: chr2:112,390,974
INFO 2026-06-08 08:54:09 MarkDuplicates Tracking 1361642 as yet unmatched pairs. 59815 records in RAM.
INFO 2026-06-08 08:54:12 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 2s. Last read position: chr2:126,557,369
INFO 2026-06-08 08:54:12 MarkDuplicates Tracking 1359328 as yet unmatched pairs. 57491 records in RAM.
INFO 2026-06-08 08:54:14 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 2s. Last read position: chr2:134,403,119
INFO 2026-06-08 08:54:14 MarkDuplicates Tracking 1356813 as yet unmatched pairs. 54968 records in RAM.
INFO 2026-06-08 08:54:16 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 2s. Last read position: chr2:157,770,478
INFO 2026-06-08 08:54:16 MarkDuplicates Tracking 1354373 as yet unmatched pairs. 52500 records in RAM.
INFO 2026-06-08 08:54:20 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 3s. Last read position: chr2:169,947,557
INFO 2026-06-08 08:54:20 MarkDuplicates Tracking 1351866 as yet unmatched pairs. 49968 records in RAM.
INFO 2026-06-08 08:54:23 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 2s. Last read position: chr2:177,513,826
INFO 2026-06-08 08:54:23 MarkDuplicates Tracking 1349807 as yet unmatched pairs. 47889 records in RAM.
INFO 2026-06-08 08:54:26 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 2s. Last read position: chr2:188,988,643
INFO 2026-06-08 08:54:26 MarkDuplicates Tracking 1355715 as yet unmatched pairs. 53773 records in RAM.
INFO 2026-06-08 08:54:28 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 2s. Last read position: chr2:189,006,937
INFO 2026-06-08 08:54:28 MarkDuplicates Tracking 1347758 as yet unmatched pairs. 45807 records in RAM.
INFO 2026-06-08 08:54:31 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 2s. Last read position: chr2:190,970,631
INFO 2026-06-08 08:54:31 MarkDuplicates Tracking 1341733 as yet unmatched pairs. 39771 records in RAM.
INFO 2026-06-08 08:54:33 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 2s. Last read position: chr2:200,981,700
INFO 2026-06-08 08:54:33 MarkDuplicates Tracking 1338408 as yet unmatched pairs. 36424 records in RAM.
INFO 2026-06-08 08:54:36 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 2s. Last read position: chr2:208,001,306
INFO 2026-06-08 08:54:36 MarkDuplicates Tracking 1335845 as yet unmatched pairs. 33845 records in RAM.
INFO 2026-06-08 08:54:39 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 3s. Last read position: chr2:215,370,400
INFO 2026-06-08 08:54:39 MarkDuplicates Tracking 1352493 as yet unmatched pairs. 50483 records in RAM.
INFO 2026-06-08 08:54:41 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 2s. Last read position: chr2:215,376,628
INFO 2026-06-08 08:54:41 MarkDuplicates Tracking 1344750 as yet unmatched pairs. 42739 records in RAM.
INFO 2026-06-08 08:54:43 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 2s. Last read position: chr2:215,391,634
INFO 2026-06-08 08:54:43 MarkDuplicates Tracking 1339140 as yet unmatched pairs. 37122 records in RAM.
INFO 2026-06-08 08:54:45 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 2s. Last read position: chr2:215,408,123
INFO 2026-06-08 08:54:45 MarkDuplicates Tracking 1340104 as yet unmatched pairs. 38085 records in RAM.
INFO 2026-06-08 08:54:48 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 2s. Last read position: chr2:215,425,187
INFO 2026-06-08 08:54:48 MarkDuplicates Tracking 1328919 as yet unmatched pairs. 26893 records in RAM.
INFO 2026-06-08 08:54:50 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 2s. Last read position: chr2:216,501,342
INFO 2026-06-08 08:54:50 MarkDuplicates Tracking 1321112 as yet unmatched pairs. 19079 records in RAM.
INFO 2026-06-08 08:54:52 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 2s. Last read position: chr2:218,782,320
INFO 2026-06-08 08:54:52 MarkDuplicates Tracking 1318178 as yet unmatched pairs. 16137 records in RAM.
INFO 2026-06-08 08:54:54 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 2s. Last read position: chr2:219,549,743
INFO 2026-06-08 08:54:54 MarkDuplicates Tracking 1314988 as yet unmatched pairs. 12933 records in RAM.
INFO 2026-06-08 08:54:56 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 2s. Last read position: chr2:231,146,265
INFO 2026-06-08 08:54:56 MarkDuplicates Tracking 1312732 as yet unmatched pairs. 10656 records in RAM.
INFO 2026-06-08 08:54:58 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 1s. Last read position: chr2:233,493,477
INFO 2026-06-08 08:54:58 MarkDuplicates Tracking 1310113 as yet unmatched pairs. 8018 records in RAM.
INFO 2026-06-08 08:55:00 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 2s. Last read position: chr2:237,394,855
INFO 2026-06-08 08:55:00 MarkDuplicates Tracking 1307913 as yet unmatched pairs. 5805 records in RAM.
INFO 2026-06-08 08:55:03 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 2s. Last read position: chr2:241,230,815
INFO 2026-06-08 08:55:03 MarkDuplicates Tracking 1304887 as yet unmatched pairs. 2756 records in RAM.
INFO 2026-06-08 08:55:06 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 3s. Last read position: chr3:8,549,884
INFO 2026-06-08 08:55:06 MarkDuplicates Tracking 1301211 as yet unmatched pairs. 71159 records in RAM.
INFO 2026-06-08 08:55:08 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 2s. Last read position: chr3:12,604,142
INFO 2026-06-08 08:55:08 MarkDuplicates Tracking 1300524 as yet unmatched pairs. 70446 records in RAM.
INFO 2026-06-08 08:55:11 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 2s. Last read position: chr3:20,174,760
INFO 2026-06-08 08:55:11 MarkDuplicates Tracking 1295736 as yet unmatched pairs. 65654 records in RAM.
INFO 2026-06-08 08:55:12 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 1s. Last read position: chr3:37,321,731
INFO 2026-06-08 08:55:12 MarkDuplicates Tracking 1293516 as yet unmatched pairs. 63424 records in RAM.
INFO 2026-06-08 08:55:15 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 2s. Last read position: chr3:40,462,095
INFO 2026-06-08 08:55:15 MarkDuplicates Tracking 1291463 as yet unmatched pairs. 61367 records in RAM.
INFO 2026-06-08 08:55:17 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 1s. Last read position: chr3:45,984,981
INFO 2026-06-08 08:55:17 MarkDuplicates Tracking 1287915 as yet unmatched pairs. 57800 records in RAM.
INFO 2026-06-08 08:55:19 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 2s. Last read position: chr3:47,852,705
INFO 2026-06-08 08:55:19 MarkDuplicates Tracking 1286060 as yet unmatched pairs. 55944 records in RAM.
INFO 2026-06-08 08:55:21 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 2s. Last read position: chr3:48,590,545
INFO 2026-06-08 08:55:21 MarkDuplicates Tracking 1282837 as yet unmatched pairs. 52711 records in RAM.
INFO 2026-06-08 08:55:23 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 2s. Last read position: chr3:49,122,963
INFO 2026-06-08 08:55:23 MarkDuplicates Tracking 1279379 as yet unmatched pairs. 49238 records in RAM.
INFO 2026-06-08 08:55:25 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 2s. Last read position: chr3:49,902,691
INFO 2026-06-08 08:55:25 MarkDuplicates Tracking 1277126 as yet unmatched pairs. 46982 records in RAM.
INFO 2026-06-08 08:55:27 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 2s. Last read position: chr3:51,993,889
INFO 2026-06-08 08:55:27 MarkDuplicates Tracking 1274764 as yet unmatched pairs. 44611 records in RAM.
INFO 2026-06-08 08:55:30 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 2s. Last read position: chr3:52,668,569
INFO 2026-06-08 08:55:30 MarkDuplicates Tracking 1270324 as yet unmatched pairs. 40159 records in RAM.
INFO 2026-06-08 08:55:32 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 2s. Last read position: chr3:58,121,403
INFO 2026-06-08 08:55:32 MarkDuplicates Tracking 1269645 as yet unmatched pairs. 39471 records in RAM.
INFO 2026-06-08 08:55:35 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 2s. Last read position: chr3:71,197,913
INFO 2026-06-08 08:55:35 MarkDuplicates Tracking 1265122 as yet unmatched pairs. 34941 records in RAM.
INFO 2026-06-08 08:55:37 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 2s. Last read position: chr3:101,682,801
INFO 2026-06-08 08:55:37 MarkDuplicates Tracking 1266289 as yet unmatched pairs. 36101 records in RAM.
INFO 2026-06-08 08:55:40 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 2s. Last read position: chr3:119,826,843
INFO 2026-06-08 08:55:40 MarkDuplicates Tracking 1260007 as yet unmatched pairs. 29814 records in RAM.
INFO 2026-06-08 08:55:42 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 2s. Last read position: chr3:124,769,073
INFO 2026-06-08 08:55:42 MarkDuplicates Tracking 1257819 as yet unmatched pairs. 27604 records in RAM.
INFO 2026-06-08 08:55:44 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 1s. Last read position: chr3:128,068,031
INFO 2026-06-08 08:55:44 MarkDuplicates Tracking 1256238 as yet unmatched pairs. 25988 records in RAM.
INFO 2026-06-08 08:55:46 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 1s. Last read position: chr3:131,381,880
INFO 2026-06-08 08:55:46 MarkDuplicates Tracking 1252102 as yet unmatched pairs. 21841 records in RAM.
INFO 2026-06-08 08:55:48 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 1s. Last read position: chr3:142,508,071
INFO 2026-06-08 08:55:48 MarkDuplicates Tracking 1249180 as yet unmatched pairs. 18908 records in RAM.
INFO 2026-06-08 08:55:50 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 2s. Last read position: chr3:157,150,282
INFO 2026-06-08 08:55:50 MarkDuplicates Tracking 1246755 as yet unmatched pairs. 16464 records in RAM.
INFO 2026-06-08 08:55:52 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 1s. Last read position: chr3:175,925,390
INFO 2026-06-08 08:55:52 MarkDuplicates Tracking 1243748 as yet unmatched pairs. 13421 records in RAM.
INFO 2026-06-08 08:55:54 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 1s. Last read position: chr3:184,319,691
INFO 2026-06-08 08:55:54 MarkDuplicates Tracking 1242114 as yet unmatched pairs. 11771 records in RAM.
INFO 2026-06-08 08:55:56 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 1s. Last read position: chr3:188,406,111
INFO 2026-06-08 08:55:56 MarkDuplicates Tracking 1242257 as yet unmatched pairs. 11905 records in RAM.
INFO 2026-06-08 08:55:58 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 1s. Last read position: chr3:195,765,112
INFO 2026-06-08 08:55:58 MarkDuplicates Tracking 1236590 as yet unmatched pairs. 6212 records in RAM.
INFO 2026-06-08 08:56:00 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr3:195,782,071
INFO 2026-06-08 08:56:00 MarkDuplicates Tracking 1241312 as yet unmatched pairs. 10925 records in RAM.
INFO 2026-06-08 08:56:02 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 2s. Last read position: chr3:195,786,269
INFO 2026-06-08 08:56:02 MarkDuplicates Tracking 1238670 as yet unmatched pairs. 8278 records in RAM.
INFO 2026-06-08 08:56:05 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 2s. Last read position: chr3:196,554,583
INFO 2026-06-08 08:56:05 MarkDuplicates Tracking 1231385 as yet unmatched pairs. 983 records in RAM.
INFO 2026-06-08 08:56:07 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 2s. Last read position: chr4:1,228,249
INFO 2026-06-08 08:56:07 MarkDuplicates Tracking 1229844 as yet unmatched pairs. 36764 records in RAM.
INFO 2026-06-08 08:56:09 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 1s. Last read position: chr4:2,829,950
INFO 2026-06-08 08:56:09 MarkDuplicates Tracking 1226042 as yet unmatched pairs. 32947 records in RAM.
INFO 2026-06-08 08:56:11 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 1s. Last read position: chr4:7,800,568
INFO 2026-06-08 08:56:11 MarkDuplicates Tracking 1223314 as yet unmatched pairs. 30204 records in RAM.
INFO 2026-06-08 08:56:13 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 1s. Last read position: chr4:25,156,884
INFO 2026-06-08 08:56:13 MarkDuplicates Tracking 1219948 as yet unmatched pairs. 26830 records in RAM.
INFO 2026-06-08 08:56:15 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 1s. Last read position: chr4:41,014,255
INFO 2026-06-08 08:56:15 MarkDuplicates Tracking 1217453 as yet unmatched pairs. 24315 records in RAM.
INFO 2026-06-08 08:56:17 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 1s. Last read position: chr4:56,931,087
INFO 2026-06-08 08:56:17 MarkDuplicates Tracking 1215135 as yet unmatched pairs. 21981 records in RAM.
INFO 2026-06-08 08:56:19 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 1s. Last read position: chr4:73,998,226
INFO 2026-06-08 08:56:19 MarkDuplicates Tracking 1212300 as yet unmatched pairs. 19135 records in RAM.
INFO 2026-06-08 08:56:21 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 1s. Last read position: chr4:78,604,395
INFO 2026-06-08 08:56:21 MarkDuplicates Tracking 1209227 as yet unmatched pairs. 16055 records in RAM.
INFO 2026-06-08 08:56:23 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 1s. Last read position: chr4:88,457,287
INFO 2026-06-08 08:56:23 MarkDuplicates Tracking 1206448 as yet unmatched pairs. 13264 records in RAM.
INFO 2026-06-08 08:56:25 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 1s. Last read position: chr4:108,048,742
INFO 2026-06-08 08:56:25 MarkDuplicates Tracking 1203976 as yet unmatched pairs. 10781 records in RAM.
INFO 2026-06-08 08:56:26 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 1s. Last read position: chr4:123,401,929
INFO 2026-06-08 08:56:26 MarkDuplicates Tracking 1201825 as yet unmatched pairs. 8610 records in RAM.
INFO 2026-06-08 08:56:28 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 1s. Last read position: chr4:150,315,575
INFO 2026-06-08 08:56:28 MarkDuplicates Tracking 1199683 as yet unmatched pairs. 6456 records in RAM.
INFO 2026-06-08 08:56:30 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 1s. Last read position: chr4:159,314,619
INFO 2026-06-08 08:56:30 MarkDuplicates Tracking 1196710 as yet unmatched pairs. 3471 records in RAM.
INFO 2026-06-08 08:56:32 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 1s. Last read position: chr4:186,588,495
INFO 2026-06-08 08:56:32 MarkDuplicates Tracking 1194337 as yet unmatched pairs. 1074 records in RAM.
INFO 2026-06-08 08:56:36 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 4s. Last read position: chr5:6,714,268
INFO 2026-06-08 08:56:36 MarkDuplicates Tracking 1191382 as yet unmatched pairs. 60021 records in RAM.
INFO 2026-06-08 08:56:39 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 2s. Last read position: chr5:14,487,661
INFO 2026-06-08 08:56:39 MarkDuplicates Tracking 1189087 as yet unmatched pairs. 57711 records in RAM.
INFO 2026-06-08 08:56:41 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr5:36,975,818
INFO 2026-06-08 08:56:41 MarkDuplicates Tracking 1186134 as yet unmatched pairs. 54749 records in RAM.
INFO 2026-06-08 08:56:43 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 1s. Last read position: chr5:53,658,569
INFO 2026-06-08 08:56:43 MarkDuplicates Tracking 1183874 as yet unmatched pairs. 52481 records in RAM.
INFO 2026-06-08 08:56:45 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 1s. Last read position: chr5:70,104,485
INFO 2026-06-08 08:56:45 MarkDuplicates Tracking 1181400 as yet unmatched pairs. 49981 records in RAM.
INFO 2026-06-08 08:56:46 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 1s. Last read position: chr5:76,833,122
INFO 2026-06-08 08:56:46 MarkDuplicates Tracking 1179413 as yet unmatched pairs. 47983 records in RAM.
INFO 2026-06-08 08:56:48 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 1s. Last read position: chr5:84,066,468
INFO 2026-06-08 08:56:48 MarkDuplicates Tracking 1176584 as yet unmatched pairs. 45143 records in RAM.
INFO 2026-06-08 08:56:50 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 1s. Last read position: chr5:109,847,659
INFO 2026-06-08 08:56:50 MarkDuplicates Tracking 1174289 as yet unmatched pairs. 42810 records in RAM.
INFO 2026-06-08 08:56:52 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 1s. Last read position: chr5:128,135,764
INFO 2026-06-08 08:56:52 MarkDuplicates Tracking 1172001 as yet unmatched pairs. 40512 records in RAM.
INFO 2026-06-08 08:56:54 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 1s. Last read position: chr5:134,608,478
INFO 2026-06-08 08:56:54 MarkDuplicates Tracking 1168991 as yet unmatched pairs. 37489 records in RAM.
INFO 2026-06-08 08:56:56 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 1s. Last read position: chr5:138,467,693
INFO 2026-06-08 08:56:56 MarkDuplicates Tracking 1167802 as yet unmatched pairs. 36293 records in RAM.
INFO 2026-06-08 08:56:58 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 1s. Last read position: chr5:140,538,144
INFO 2026-06-08 08:56:58 MarkDuplicates Tracking 1163853 as yet unmatched pairs. 32328 records in RAM.
INFO 2026-06-08 08:57:00 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 1s. Last read position: chr5:141,422,848
INFO 2026-06-08 08:57:00 MarkDuplicates Tracking 1161010 as yet unmatched pairs. 29484 records in RAM.
INFO 2026-06-08 08:57:02 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 2s. Last read position: chr5:147,828,041
INFO 2026-06-08 08:57:02 MarkDuplicates Tracking 1159401 as yet unmatched pairs. 27856 records in RAM.
INFO 2026-06-08 08:57:05 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 3s. Last read position: chr5:150,209,456
INFO 2026-06-08 08:57:05 MarkDuplicates Tracking 1155914 as yet unmatched pairs. 24358 records in RAM.
INFO 2026-06-08 08:57:08 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 2s. Last read position: chr5:150,405,123
INFO 2026-06-08 08:57:08 MarkDuplicates Tracking 1181696 as yet unmatched pairs. 50133 records in RAM.
INFO 2026-06-08 08:57:10 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 1s. Last read position: chr5:151,042,588
INFO 2026-06-08 08:57:10 MarkDuplicates Tracking 1151192 as yet unmatched pairs. 19626 records in RAM.
INFO 2026-06-08 08:57:11 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 1s. Last read position: chr5:157,816,775
INFO 2026-06-08 08:57:11 MarkDuplicates Tracking 1148605 as yet unmatched pairs. 17028 records in RAM.
INFO 2026-06-08 08:57:13 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 1s. Last read position: chr5:171,391,337
INFO 2026-06-08 08:57:13 MarkDuplicates Tracking 1165116 as yet unmatched pairs. 33506 records in RAM.
INFO 2026-06-08 08:57:16 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 2s. Last read position: chr5:172,362,838
INFO 2026-06-08 08:57:16 MarkDuplicates Tracking 1143463 as yet unmatched pairs. 11851 records in RAM.
INFO 2026-06-08 08:57:18 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 1s. Last read position: chr5:177,304,673
INFO 2026-06-08 08:57:18 MarkDuplicates Tracking 1141532 as yet unmatched pairs. 9913 records in RAM.
INFO 2026-06-08 08:57:20 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 1s. Last read position: chr5:179,560,044
INFO 2026-06-08 08:57:20 MarkDuplicates Tracking 1137986 as yet unmatched pairs. 6364 records in RAM.
INFO 2026-06-08 08:57:22 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 1s. Last read position: chr5:179,824,073
INFO 2026-06-08 08:57:22 MarkDuplicates Tracking 1139213 as yet unmatched pairs. 7583 records in RAM.
INFO 2026-06-08 08:57:24 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 1s. Last read position: chr5:181,241,526
INFO 2026-06-08 08:57:24 MarkDuplicates Tracking 1134517 as yet unmatched pairs. 2883 records in RAM.
INFO 2026-06-08 08:57:26 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 2s. Last read position: chr6:7,230,138
INFO 2026-06-08 08:57:26 MarkDuplicates Tracking 1130033 as yet unmatched pairs. 72243 records in RAM.
INFO 2026-06-08 08:57:28 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 2s. Last read position: chr6:13,486,700
INFO 2026-06-08 08:57:28 MarkDuplicates Tracking 1126533 as yet unmatched pairs. 68738 records in RAM.
INFO 2026-06-08 08:57:31 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 2s. Last read position: chr6:26,055,956
INFO 2026-06-08 08:57:31 MarkDuplicates Tracking 1124015 as yet unmatched pairs. 66210 records in RAM.
INFO 2026-06-08 08:57:32 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 1s. Last read position: chr6:27,146,394
INFO 2026-06-08 08:57:32 MarkDuplicates Tracking 1125218 as yet unmatched pairs. 67397 records in RAM.
INFO 2026-06-08 08:57:34 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 1s. Last read position: chr6:29,723,668
INFO 2026-06-08 08:57:34 MarkDuplicates Tracking 1119168 as yet unmatched pairs. 61346 records in RAM.
INFO 2026-06-08 08:57:36 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 1s. Last read position: chr6:30,622,893
INFO 2026-06-08 08:57:36 MarkDuplicates Tracking 1116507 as yet unmatched pairs. 58675 records in RAM.
INFO 2026-06-08 08:57:38 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 1s. Last read position: chr6:31,271,102
INFO 2026-06-08 08:57:38 MarkDuplicates Tracking 1118967 as yet unmatched pairs. 61131 records in RAM.
INFO 2026-06-08 08:57:40 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 1s. Last read position: chr6:31,643,021
INFO 2026-06-08 08:57:40 MarkDuplicates Tracking 1112761 as yet unmatched pairs. 54918 records in RAM.
INFO 2026-06-08 08:57:41 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 1s. Last read position: chr6:31,816,739
INFO 2026-06-08 08:57:41 MarkDuplicates Tracking 1109516 as yet unmatched pairs. 51672 records in RAM.
INFO 2026-06-08 08:57:43 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 1s. Last read position: chr6:31,829,306
INFO 2026-06-08 08:57:43 MarkDuplicates Tracking 1113460 as yet unmatched pairs. 55615 records in RAM.
INFO 2026-06-08 08:57:45 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 1s. Last read position: chr6:32,041,839
INFO 2026-06-08 08:57:45 MarkDuplicates Tracking 1104981 as yet unmatched pairs. 47130 records in RAM.
INFO 2026-06-08 08:57:47 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 1s. Last read position: chr6:32,853,228
INFO 2026-06-08 08:57:47 MarkDuplicates Tracking 1104910 as yet unmatched pairs. 47044 records in RAM.
INFO 2026-06-08 08:57:48 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 1s. Last read position: chr6:33,313,801
INFO 2026-06-08 08:57:48 MarkDuplicates Tracking 1099963 as yet unmatched pairs. 42096 records in RAM.
INFO 2026-06-08 08:57:50 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 1s. Last read position: chr6:34,539,291
INFO 2026-06-08 08:57:50 MarkDuplicates Tracking 1097730 as yet unmatched pairs. 39857 records in RAM.
INFO 2026-06-08 08:57:53 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 2s. Last read position: chr6:37,476,165
INFO 2026-06-08 08:57:53 MarkDuplicates Tracking 1094011 as yet unmatched pairs. 36108 records in RAM.
INFO 2026-06-08 08:57:55 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 1s. Last read position: chr6:42,886,260
INFO 2026-06-08 08:57:55 MarkDuplicates Tracking 1091483 as yet unmatched pairs. 33568 records in RAM.
INFO 2026-06-08 08:57:57 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 1s. Last read position: chr6:43,774,362
INFO 2026-06-08 08:57:57 MarkDuplicates Tracking 1089887 as yet unmatched pairs. 31961 records in RAM.
INFO 2026-06-08 08:57:58 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 1s. Last read position: chr6:52,282,780
INFO 2026-06-08 08:57:58 MarkDuplicates Tracking 1085908 as yet unmatched pairs. 27977 records in RAM.
INFO 2026-06-08 08:58:01 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:06:30s. Time for last 1,000,000: 2s. Last read position: chr6:73,781,286
INFO 2026-06-08 08:58:01 MarkDuplicates Tracking 1083264 as yet unmatched pairs. 25305 records in RAM.
INFO 2026-06-08 08:58:03 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 2s. Last read position: chr6:83,145,580
INFO 2026-06-08 08:58:03 MarkDuplicates Tracking 1080499 as yet unmatched pairs. 22525 records in RAM.
INFO 2026-06-08 08:58:05 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 1s. Last read position: chr6:100,625,324
INFO 2026-06-08 08:58:05 MarkDuplicates Tracking 1078012 as yet unmatched pairs. 20019 records in RAM.
INFO 2026-06-08 08:58:07 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:06:35s. Time for last 1,000,000: 1s. Last read position: chr6:111,331,618
INFO 2026-06-08 08:58:07 MarkDuplicates Tracking 1075422 as yet unmatched pairs. 17414 records in RAM.
INFO 2026-06-08 08:58:08 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 1s. Last read position: chr6:128,397,573
INFO 2026-06-08 08:58:08 MarkDuplicates Tracking 1073185 as yet unmatched pairs. 15163 records in RAM.
INFO 2026-06-08 08:58:10 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 1s. Last read position: chr6:137,001,935
INFO 2026-06-08 08:58:10 MarkDuplicates Tracking 1070213 as yet unmatched pairs. 12182 records in RAM.
INFO 2026-06-08 08:58:12 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 1s. Last read position: chr6:145,945,572
INFO 2026-06-08 08:58:12 MarkDuplicates Tracking 1067350 as yet unmatched pairs. 9299 records in RAM.
INFO 2026-06-08 08:58:14 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 1s. Last read position: chr6:157,206,958
INFO 2026-06-08 08:58:14 MarkDuplicates Tracking 1065274 as yet unmatched pairs. 7213 records in RAM.
INFO 2026-06-08 08:58:16 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:06:44s. Time for last 1,000,000: 1s. Last read position: chr6:159,692,661
INFO 2026-06-08 08:58:16 MarkDuplicates Tracking 1067087 as yet unmatched pairs. 9015 records in RAM.
INFO 2026-06-08 08:58:18 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:06:46s. Time for last 1,000,000: 2s. Last read position: chr6:169,225,200
INFO 2026-06-08 08:58:18 MarkDuplicates Tracking 1060831 as yet unmatched pairs. 2753 records in RAM.
INFO 2026-06-08 08:58:20 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 2s. Last read position: chr7:1,485,188
INFO 2026-06-08 08:58:20 MarkDuplicates Tracking 1056731 as yet unmatched pairs. 71939 records in RAM.
INFO 2026-06-08 08:58:22 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:06:51s. Time for last 1,000,000: 1s. Last read position: chr7:5,313,617
INFO 2026-06-08 08:58:22 MarkDuplicates Tracking 1054426 as yet unmatched pairs. 69619 records in RAM.
INFO 2026-06-08 08:58:24 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 2s. Last read position: chr7:5,528,295
INFO 2026-06-08 08:58:24 MarkDuplicates Tracking 1063789 as yet unmatched pairs. 78977 records in RAM.
INFO 2026-06-08 08:58:27 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 2s. Last read position: chr7:6,153,741
INFO 2026-06-08 08:58:27 MarkDuplicates Tracking 1047232 as yet unmatched pairs. 62413 records in RAM.
INFO 2026-06-08 08:58:29 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 2s. Last read position: chr7:16,797,694
INFO 2026-06-08 08:58:29 MarkDuplicates Tracking 1054648 as yet unmatched pairs. 69821 records in RAM.
INFO 2026-06-08 08:58:31 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:07:00s. Time for last 1,000,000: 1s. Last read position: chr7:27,458,374
INFO 2026-06-08 08:58:31 MarkDuplicates Tracking 1042323 as yet unmatched pairs. 57490 records in RAM.
INFO 2026-06-08 08:58:33 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 1s. Last read position: chr7:43,640,608
INFO 2026-06-08 08:58:33 MarkDuplicates Tracking 1039936 as yet unmatched pairs. 55097 records in RAM.
INFO 2026-06-08 08:58:35 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:07:03s. Time for last 1,000,000: 1s. Last read position: chr7:44,766,418
INFO 2026-06-08 08:58:35 MarkDuplicates Tracking 1037576 as yet unmatched pairs. 52727 records in RAM.
INFO 2026-06-08 08:58:37 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 1s. Last read position: chr7:56,102,994
INFO 2026-06-08 08:58:37 MarkDuplicates Tracking 1036410 as yet unmatched pairs. 51547 records in RAM.
INFO 2026-06-08 08:58:38 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:07:07s. Time for last 1,000,000: 1s. Last read position: chr7:73,477,151
INFO 2026-06-08 08:58:38 MarkDuplicates Tracking 1032799 as yet unmatched pairs. 47920 records in RAM.
INFO 2026-06-08 08:58:40 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:07:09s. Time for last 1,000,000: 1s. Last read position: chr7:75,019,081
INFO 2026-06-08 08:58:40 MarkDuplicates Tracking 1029591 as yet unmatched pairs. 44699 records in RAM.
INFO 2026-06-08 08:58:42 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:07:11s. Time for last 1,000,000: 1s. Last read position: chr7:76,329,789
INFO 2026-06-08 08:58:42 MarkDuplicates Tracking 1027173 as yet unmatched pairs. 42276 records in RAM.
INFO 2026-06-08 08:58:44 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 2s. Last read position: chr7:92,079,570
INFO 2026-06-08 08:58:44 MarkDuplicates Tracking 1024939 as yet unmatched pairs. 40035 records in RAM.
INFO 2026-06-08 08:58:47 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:07:15s. Time for last 1,000,000: 2s. Last read position: chr7:94,410,443
INFO 2026-06-08 08:58:47 MarkDuplicates Tracking 1029468 as yet unmatched pairs. 44562 records in RAM.
INFO 2026-06-08 08:58:49 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:07:17s. Time for last 1,000,000: 1s. Last read position: chr7:96,694,829
INFO 2026-06-08 08:58:49 MarkDuplicates Tracking 1020021 as yet unmatched pairs. 35110 records in RAM.
INFO 2026-06-08 08:58:51 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:07:19s. Time for last 1,000,000: 2s. Last read position: chr7:100,029,876
INFO 2026-06-08 08:58:51 MarkDuplicates Tracking 1016790 as yet unmatched pairs. 31851 records in RAM.
INFO 2026-06-08 08:58:53 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:07:22s. Time for last 1,000,000: 2s. Last read position: chr7:100,813,680
INFO 2026-06-08 08:58:53 MarkDuplicates Tracking 1014109 as yet unmatched pairs. 29167 records in RAM.
INFO 2026-06-08 08:58:55 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:07:24s. Time for last 1,000,000: 2s. Last read position: chr7:100,995,175
INFO 2026-06-08 08:58:55 MarkDuplicates Tracking 1011407 as yet unmatched pairs. 26460 records in RAM.
INFO 2026-06-08 08:58:57 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:07:25s. Time for last 1,000,000: 1s. Last read position: chr7:101,033,987
INFO 2026-06-08 08:58:57 MarkDuplicates Tracking 1010102 as yet unmatched pairs. 25155 records in RAM.
INFO 2026-06-08 08:58:58 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 1s. Last read position: chr7:102,582,888
INFO 2026-06-08 08:58:58 MarkDuplicates Tracking 1008485 as yet unmatched pairs. 23524 records in RAM.
INFO 2026-06-08 08:59:00 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:07:29s. Time for last 1,000,000: 1s. Last read position: chr7:107,975,744
INFO 2026-06-08 08:59:00 MarkDuplicates Tracking 1006154 as yet unmatched pairs. 21181 records in RAM.
INFO 2026-06-08 08:59:02 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:07:31s. Time for last 1,000,000: 1s. Last read position: chr7:127,686,653
INFO 2026-06-08 08:59:02 MarkDuplicates Tracking 1008927 as yet unmatched pairs. 23944 records in RAM.
INFO 2026-06-08 08:59:04 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:07:33s. Time for last 1,000,000: 1s. Last read position: chr7:128,488,098
INFO 2026-06-08 08:59:04 MarkDuplicates Tracking 1000544 as yet unmatched pairs. 15555 records in RAM.
INFO 2026-06-08 08:59:06 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:07:34s. Time for last 1,000,000: 1s. Last read position: chr7:135,643,216
INFO 2026-06-08 08:59:06 MarkDuplicates Tracking 998230 as yet unmatched pairs. 13227 records in RAM.
INFO 2026-06-08 08:59:08 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:07:36s. Time for last 1,000,000: 1s. Last read position: chr7:140,459,104
INFO 2026-06-08 08:59:08 MarkDuplicates Tracking 995636 as yet unmatched pairs. 10617 records in RAM.
INFO 2026-06-08 08:59:11 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:07:40s. Time for last 1,000,000: 3s. Last read position: chr7:144,363,326
INFO 2026-06-08 08:59:11 MarkDuplicates Tracking 992931 as yet unmatched pairs. 7900 records in RAM.
INFO 2026-06-08 08:59:13 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:07:42s. Time for last 1,000,000: 2s. Last read position: chr7:150,804,377
INFO 2026-06-08 08:59:13 MarkDuplicates Tracking 990925 as yet unmatched pairs. 5887 records in RAM.
INFO 2026-06-08 08:59:15 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:07:43s. Time for last 1,000,000: 1s. Last read position: chr7:155,297,924
INFO 2026-06-08 08:59:15 MarkDuplicates Tracking 988587 as yet unmatched pairs. 3542 records in RAM.
INFO 2026-06-08 08:59:17 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:07:46s. Time for last 1,000,000: 2s. Last read position: chr8:9,140,794
INFO 2026-06-08 08:59:17 MarkDuplicates Tracking 984058 as yet unmatched pairs. 53881 records in RAM.
INFO 2026-06-08 08:59:19 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:07:48s. Time for last 1,000,000: 1s. Last read position: chr8:19,364,150
INFO 2026-06-08 08:59:19 MarkDuplicates Tracking 981472 as yet unmatched pairs. 51282 records in RAM.
INFO 2026-06-08 08:59:21 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:07:50s. Time for last 1,000,000: 1s. Last read position: chr8:22,621,281
INFO 2026-06-08 08:59:21 MarkDuplicates Tracking 978633 as yet unmatched pairs. 48437 records in RAM.
INFO 2026-06-08 08:59:23 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:07:52s. Time for last 1,000,000: 1s. Last read position: chr8:29,186,368
INFO 2026-06-08 08:59:23 MarkDuplicates Tracking 975999 as yet unmatched pairs. 45791 records in RAM.
INFO 2026-06-08 08:59:25 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:07:54s. Time for last 1,000,000: 1s. Last read position: chr8:38,279,585
INFO 2026-06-08 08:59:25 MarkDuplicates Tracking 973297 as yet unmatched pairs. 43072 records in RAM.
INFO 2026-06-08 08:59:27 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:07:55s. Time for last 1,000,000: 1s. Last read position: chr8:41,497,578
INFO 2026-06-08 08:59:27 MarkDuplicates Tracking 970845 as yet unmatched pairs. 40616 records in RAM.
INFO 2026-06-08 08:59:29 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:07:57s. Time for last 1,000,000: 2s. Last read position: chr8:54,065,802
INFO 2026-06-08 08:59:29 MarkDuplicates Tracking 967942 as yet unmatched pairs. 37683 records in RAM.
INFO 2026-06-08 08:59:31 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:08:00s. Time for last 1,000,000: 2s. Last read position: chr8:69,603,257
INFO 2026-06-08 08:59:31 MarkDuplicates Tracking 966324 as yet unmatched pairs. 36047 records in RAM.
INFO 2026-06-08 08:59:34 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:08:02s. Time for last 1,000,000: 2s. Last read position: chr8:86,435,493
INFO 2026-06-08 08:59:34 MarkDuplicates Tracking 962712 as yet unmatched pairs. 32426 records in RAM.
INFO 2026-06-08 08:59:35 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:08:04s. Time for last 1,000,000: 1s. Last read position: chr8:99,502,926
INFO 2026-06-08 08:59:35 MarkDuplicates Tracking 960168 as yet unmatched pairs. 29866 records in RAM.
INFO 2026-06-08 08:59:37 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:08:06s. Time for last 1,000,000: 1s. Last read position: chr8:102,650,180
INFO 2026-06-08 08:59:37 MarkDuplicates Tracking 957557 as yet unmatched pairs. 27250 records in RAM.
INFO 2026-06-08 08:59:39 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:08:08s. Time for last 1,000,000: 1s. Last read position: chr8:123,768,730
INFO 2026-06-08 08:59:39 MarkDuplicates Tracking 955064 as yet unmatched pairs. 24746 records in RAM.
INFO 2026-06-08 08:59:41 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:08:10s. Time for last 1,000,000: 1s. Last read position: chr8:139,732,189
INFO 2026-06-08 08:59:41 MarkDuplicates Tracking 952070 as yet unmatched pairs. 21732 records in RAM.
INFO 2026-06-08 08:59:43 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:08:12s. Time for last 1,000,000: 1s. Last read position: chr8:143,671,977
INFO 2026-06-08 08:59:43 MarkDuplicates Tracking 948982 as yet unmatched pairs. 18631 records in RAM.
INFO 2026-06-08 08:59:45 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:08:13s. Time for last 1,000,000: 1s. Last read position: chr8:143,858,995
INFO 2026-06-08 08:59:45 MarkDuplicates Tracking 951306 as yet unmatched pairs. 20955 records in RAM.
INFO 2026-06-08 08:59:46 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:08:15s. Time for last 1,000,000: 1s. Last read position: chr8:143,861,182
INFO 2026-06-08 08:59:46 MarkDuplicates Tracking 946837 as yet unmatched pairs. 16485 records in RAM.
INFO 2026-06-08 08:59:47 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 1s. Last read position: chr8:143,862,946
INFO 2026-06-08 08:59:47 MarkDuplicates Tracking 949483 as yet unmatched pairs. 19131 records in RAM.
INFO 2026-06-08 08:59:49 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:08:18s. Time for last 1,000,000: 1s. Last read position: chr8:143,864,948
INFO 2026-06-08 08:59:49 MarkDuplicates Tracking 945296 as yet unmatched pairs. 14940 records in RAM.
INFO 2026-06-08 08:59:51 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 1s. Last read position: chr8:143,869,608
INFO 2026-06-08 08:59:51 MarkDuplicates Tracking 944240 as yet unmatched pairs. 13880 records in RAM.
INFO 2026-06-08 08:59:54 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 3s. Last read position: chr8:143,922,185
INFO 2026-06-08 08:59:54 MarkDuplicates Tracking 940094 as yet unmatched pairs. 9733 records in RAM.
INFO 2026-06-08 08:59:56 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 2s. Last read position: chr8:144,084,172
INFO 2026-06-08 08:59:56 MarkDuplicates Tracking 935447 as yet unmatched pairs. 5082 records in RAM.
INFO 2026-06-08 08:59:58 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:08:27s. Time for last 1,000,000: 1s. Last read position: chr8:144,473,155
INFO 2026-06-08 08:59:58 MarkDuplicates Tracking 933213 as yet unmatched pairs. 2844 records in RAM.
INFO 2026-06-08 09:00:00 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 2s. Last read position: chr9:6,413,474
INFO 2026-06-08 09:00:00 MarkDuplicates Tracking 929546 as yet unmatched pairs. 59703 records in RAM.
INFO 2026-06-08 09:00:02 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:08:31s. Time for last 1,000,000: 1s. Last read position: chr9:26,892,517
INFO 2026-06-08 09:00:02 MarkDuplicates Tracking 926374 as yet unmatched pairs. 56521 records in RAM.
INFO 2026-06-08 09:00:04 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:08:33s. Time for last 1,000,000: 1s. Last read position: chr9:35,059,511
INFO 2026-06-08 09:00:04 MarkDuplicates Tracking 925411 as yet unmatched pairs. 55550 records in RAM.
INFO 2026-06-08 09:00:06 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 2s. Last read position: chr9:35,737,290
INFO 2026-06-08 09:00:06 MarkDuplicates Tracking 921127 as yet unmatched pairs. 51259 records in RAM.
INFO 2026-06-08 09:00:08 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 1s. Last read position: chr9:69,249,331
INFO 2026-06-08 09:00:08 MarkDuplicates Tracking 918452 as yet unmatched pairs. 48575 records in RAM.
INFO 2026-06-08 09:00:10 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:08:39s. Time for last 1,000,000: 2s. Last read position: chr9:83,969,276
INFO 2026-06-08 09:00:10 MarkDuplicates Tracking 917354 as yet unmatched pairs. 47466 records in RAM.
INFO 2026-06-08 09:00:14 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:08:43s. Time for last 1,000,000: 3s. Last read position: chr9:92,976,313
INFO 2026-06-08 09:00:14 MarkDuplicates Tracking 913136 as yet unmatched pairs. 43245 records in RAM.
INFO 2026-06-08 09:00:16 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:08:45s. Time for last 1,000,000: 2s. Last read position: chr9:98,128,646
INFO 2026-06-08 09:00:16 MarkDuplicates Tracking 910243 as yet unmatched pairs. 40349 records in RAM.
INFO 2026-06-08 09:00:18 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:08:47s. Time for last 1,000,000: 2s. Last read position: chr9:104,822,641
INFO 2026-06-08 09:00:18 MarkDuplicates Tracking 907473 as yet unmatched pairs. 37576 records in RAM.
INFO 2026-06-08 09:00:20 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 2s. Last read position: chr9:112,268,128
INFO 2026-06-08 09:00:20 MarkDuplicates Tracking 905449 as yet unmatched pairs. 35544 records in RAM.
INFO 2026-06-08 09:00:22 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 2s. Last read position: chr9:115,073,607
INFO 2026-06-08 09:00:22 MarkDuplicates Tracking 902258 as yet unmatched pairs. 32353 records in RAM.
INFO 2026-06-08 09:01:28 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:09:57s. Time for last 1,000,000: 66s. Last read position: chr9:124,313,921
INFO 2026-06-08 09:01:28 MarkDuplicates Tracking 899384 as yet unmatched pairs. 29467 records in RAM.
INFO 2026-06-08 09:01:31 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:10:00s. Time for last 1,000,000: 2s. Last read position: chr9:127,733,473
INFO 2026-06-08 09:01:31 MarkDuplicates Tracking 896302 as yet unmatched pairs. 26372 records in RAM.
INFO 2026-06-08 09:01:33 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:10:02s. Time for last 1,000,000: 1s. Last read position: chr9:128,422,925
INFO 2026-06-08 09:01:33 MarkDuplicates Tracking 893428 as yet unmatched pairs. 23494 records in RAM.
INFO 2026-06-08 09:01:35 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:10:04s. Time for last 1,000,000: 1s. Last read position: chr9:129,098,604
INFO 2026-06-08 09:01:35 MarkDuplicates Tracking 890491 as yet unmatched pairs. 20554 records in RAM.
INFO 2026-06-08 09:01:37 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:10:05s. Time for last 1,000,000: 1s. Last read position: chr9:131,215,327
INFO 2026-06-08 09:01:37 MarkDuplicates Tracking 887449 as yet unmatched pairs. 17504 records in RAM.
INFO 2026-06-08 09:01:39 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:10:07s. Time for last 1,000,000: 1s. Last read position: chr9:133,351,260
INFO 2026-06-08 09:01:39 MarkDuplicates Tracking 885283 as yet unmatched pairs. 15327 records in RAM.
INFO 2026-06-08 09:01:40 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 1s. Last read position: chr9:134,820,153
INFO 2026-06-08 09:01:40 MarkDuplicates Tracking 884316 as yet unmatched pairs. 14353 records in RAM.
INFO 2026-06-08 09:01:42 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:10:11s. Time for last 1,000,000: 1s. Last read position: chr9:136,476,679
INFO 2026-06-08 09:01:42 MarkDuplicates Tracking 880846 as yet unmatched pairs. 10873 records in RAM.
INFO 2026-06-08 09:01:44 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:10:13s. Time for last 1,000,000: 2s. Last read position: chr9:136,993,372
INFO 2026-06-08 09:01:44 MarkDuplicates Tracking 876019 as yet unmatched pairs. 6038 records in RAM.
INFO 2026-06-08 09:01:46 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:10:15s. Time for last 1,000,000: 1s. Last read position: chr9:137,279,757
INFO 2026-06-08 09:01:46 MarkDuplicates Tracking 872140 as yet unmatched pairs. 2155 records in RAM.
INFO 2026-06-08 09:01:49 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:10:17s. Time for last 1,000,000: 2s. Last read position: chr10:5,456,889
INFO 2026-06-08 09:01:49 MarkDuplicates Tracking 868942 as yet unmatched pairs. 50480 records in RAM.
INFO 2026-06-08 09:01:50 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:10:19s. Time for last 1,000,000: 1s. Last read position: chr10:17,229,538
INFO 2026-06-08 09:01:50 MarkDuplicates Tracking 868107 as yet unmatched pairs. 49628 records in RAM.
INFO 2026-06-08 09:01:52 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:10:21s. Time for last 1,000,000: 1s. Last read position: chr10:30,029,595
INFO 2026-06-08 09:01:52 MarkDuplicates Tracking 863717 as yet unmatched pairs. 45227 records in RAM.
INFO 2026-06-08 09:01:54 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:10:22s. Time for last 1,000,000: 1s. Last read position: chr10:32,930,028
INFO 2026-06-08 09:01:54 MarkDuplicates Tracking 863881 as yet unmatched pairs. 45388 records in RAM.
INFO 2026-06-08 09:01:56 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:10:24s. Time for last 1,000,000: 1s. Last read position: chr10:46,016,545
INFO 2026-06-08 09:01:56 MarkDuplicates Tracking 862371 as yet unmatched pairs. 43868 records in RAM.
INFO 2026-06-08 09:01:57 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 1s. Last read position: chr10:62,813,569
INFO 2026-06-08 09:01:57 MarkDuplicates Tracking 856661 as yet unmatched pairs. 38147 records in RAM.
INFO 2026-06-08 09:02:00 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:10:28s. Time for last 1,000,000: 2s. Last read position: chr10:71,298,057
INFO 2026-06-08 09:02:00 MarkDuplicates Tracking 854136 as yet unmatched pairs. 35611 records in RAM.
INFO 2026-06-08 09:02:01 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:10:30s. Time for last 1,000,000: 1s. Last read position: chr10:74,114,358
INFO 2026-06-08 09:02:01 MarkDuplicates Tracking 851573 as yet unmatched pairs. 33041 records in RAM.
INFO 2026-06-08 09:02:03 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:10:32s. Time for last 1,000,000: 1s. Last read position: chr10:80,155,693
INFO 2026-06-08 09:02:03 MarkDuplicates Tracking 849329 as yet unmatched pairs. 30789 records in RAM.
INFO 2026-06-08 09:02:05 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:10:33s. Time for last 1,000,000: 1s. Last read position: chr10:87,743,388
INFO 2026-06-08 09:02:05 MarkDuplicates Tracking 846975 as yet unmatched pairs. 28422 records in RAM.
INFO 2026-06-08 09:02:07 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:10:35s. Time for last 1,000,000: 1s. Last read position: chr10:93,517,135
INFO 2026-06-08 09:02:07 MarkDuplicates Tracking 843821 as yet unmatched pairs. 25257 records in RAM.
INFO 2026-06-08 09:02:08 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:10:37s. Time for last 1,000,000: 1s. Last read position: chr10:96,750,689
INFO 2026-06-08 09:02:08 MarkDuplicates Tracking 841146 as yet unmatched pairs. 22576 records in RAM.
INFO 2026-06-08 09:02:10 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:10:39s. Time for last 1,000,000: 1s. Last read position: chr10:100,347,341
INFO 2026-06-08 09:02:10 MarkDuplicates Tracking 839104 as yet unmatched pairs. 20521 records in RAM.
INFO 2026-06-08 09:02:12 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:10:41s. Time for last 1,000,000: 1s. Last read position: chr10:102,141,518
INFO 2026-06-08 09:02:12 MarkDuplicates Tracking 837004 as yet unmatched pairs. 18419 records in RAM.
INFO 2026-06-08 09:02:14 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:10:43s. Time for last 1,000,000: 2s. Last read position: chr10:103,571,105
INFO 2026-06-08 09:02:14 MarkDuplicates Tracking 833866 as yet unmatched pairs. 15258 records in RAM.
INFO 2026-06-08 09:02:16 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:10:45s. Time for last 1,000,000: 2s. Last read position: chr10:116,954,166
INFO 2026-06-08 09:02:16 MarkDuplicates Tracking 830398 as yet unmatched pairs. 11774 records in RAM.
INFO 2026-06-08 09:02:18 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:10:47s. Time for last 1,000,000: 1s. Last read position: chr10:122,573,713
INFO 2026-06-08 09:02:18 MarkDuplicates Tracking 831369 as yet unmatched pairs. 12738 records in RAM.
INFO 2026-06-08 09:02:20 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:10:48s. Time for last 1,000,000: 1s. Last read position: chr10:122,595,359
INFO 2026-06-08 09:02:20 MarkDuplicates Tracking 833843 as yet unmatched pairs. 15212 records in RAM.
INFO 2026-06-08 09:02:21 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:10:50s. Time for last 1,000,000: 1s. Last read position: chr10:122,610,158
INFO 2026-06-08 09:02:21 MarkDuplicates Tracking 826000 as yet unmatched pairs. 7369 records in RAM.
INFO 2026-06-08 09:02:23 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:10:51s. Time for last 1,000,000: 1s. Last read position: chr10:124,789,085
INFO 2026-06-08 09:02:23 MarkDuplicates Tracking 822371 as yet unmatched pairs. 3738 records in RAM.
INFO 2026-06-08 09:02:24 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:10:53s. Time for last 1,000,000: 1s. Last read position: chr10:132,708,320
INFO 2026-06-08 09:02:24 MarkDuplicates Tracking 819736 as yet unmatched pairs. 1082 records in RAM.
INFO 2026-06-08 09:02:27 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:10:56s. Time for last 1,000,000: 2s. Last read position: chr11:397,133
INFO 2026-06-08 09:02:27 MarkDuplicates Tracking 818782 as yet unmatched pairs. 115316 records in RAM.
INFO 2026-06-08 09:02:29 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 1s. Last read position: chr11:819,776
INFO 2026-06-08 09:02:29 MarkDuplicates Tracking 814132 as yet unmatched pairs. 110659 records in RAM.
INFO 2026-06-08 09:02:31 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:10:59s. Time for last 1,000,000: 1s. Last read position: chr11:1,016,474
INFO 2026-06-08 09:02:31 MarkDuplicates Tracking 813679 as yet unmatched pairs. 110191 records in RAM.
INFO 2026-06-08 09:02:33 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:11:01s. Time for last 1,000,000: 1s. Last read position: chr11:1,017,228
INFO 2026-06-08 09:02:33 MarkDuplicates Tracking 822308 as yet unmatched pairs. 118820 records in RAM.
INFO 2026-06-08 09:02:34 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:11:03s. Time for last 1,000,000: 1s. Last read position: chr11:1,018,388
INFO 2026-06-08 09:02:34 MarkDuplicates Tracking 810958 as yet unmatched pairs. 107468 records in RAM.
INFO 2026-06-08 09:02:36 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:11:05s. Time for last 1,000,000: 2s. Last read position: chr11:1,029,585
INFO 2026-06-08 09:02:36 MarkDuplicates Tracking 810025 as yet unmatched pairs. 106518 records in RAM.
INFO 2026-06-08 09:02:39 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:11:07s. Time for last 1,000,000: 2s. Last read position: chr11:1,078,035
INFO 2026-06-08 09:02:39 MarkDuplicates Tracking 815228 as yet unmatched pairs. 111717 records in RAM.
INFO 2026-06-08 09:02:41 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:11:09s. Time for last 1,000,000: 2s. Last read position: chr11:1,082,879
INFO 2026-06-08 09:02:41 MarkDuplicates Tracking 815305 as yet unmatched pairs. 111792 records in RAM.
INFO 2026-06-08 09:02:42 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:11:11s. Time for last 1,000,000: 1s. Last read position: chr11:1,085,792
INFO 2026-06-08 09:02:42 MarkDuplicates Tracking 819335 as yet unmatched pairs. 115820 records in RAM.
INFO 2026-06-08 09:02:44 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:11:13s. Time for last 1,000,000: 1s. Last read position: chr11:1,092,851
INFO 2026-06-08 09:02:44 MarkDuplicates Tracking 799158 as yet unmatched pairs. 95634 records in RAM.
INFO 2026-06-08 09:02:46 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:11:15s. Time for last 1,000,000: 1s. Last read position: chr11:1,232,004
INFO 2026-06-08 09:02:46 MarkDuplicates Tracking 792592 as yet unmatched pairs. 89054 records in RAM.
INFO 2026-06-08 09:02:48 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:11:16s. Time for last 1,000,000: 1s. Last read position: chr11:1,243,950
INFO 2026-06-08 09:02:48 MarkDuplicates Tracking 795533 as yet unmatched pairs. 91992 records in RAM.
INFO 2026-06-08 09:02:49 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:11:18s. Time for last 1,000,000: 1s. Last read position: chr11:1,247,890
INFO 2026-06-08 09:02:49 MarkDuplicates Tracking 788959 as yet unmatched pairs. 85418 records in RAM.
INFO 2026-06-08 09:02:51 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:11:19s. Time for last 1,000,000: 1s. Last read position: chr11:1,251,432
INFO 2026-06-08 09:02:51 MarkDuplicates Tracking 787758 as yet unmatched pairs. 84217 records in RAM.
INFO 2026-06-08 09:02:53 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:11:21s. Time for last 1,000,000: 1s. Last read position: chr11:2,403,362
INFO 2026-06-08 09:02:53 MarkDuplicates Tracking 782731 as yet unmatched pairs. 79170 records in RAM.
INFO 2026-06-08 09:02:54 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:11:23s. Time for last 1,000,000: 1s. Last read position: chr11:6,479,977
INFO 2026-06-08 09:02:54 MarkDuplicates Tracking 780485 as yet unmatched pairs. 76916 records in RAM.
INFO 2026-06-08 09:02:56 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:11:25s. Time for last 1,000,000: 1s. Last read position: chr11:9,527,535
INFO 2026-06-08 09:02:56 MarkDuplicates Tracking 775908 as yet unmatched pairs. 72324 records in RAM.
INFO 2026-06-08 09:02:58 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:11:27s. Time for last 1,000,000: 1s. Last read position: chr11:16,738,812
INFO 2026-06-08 09:02:58 MarkDuplicates Tracking 773628 as yet unmatched pairs. 70034 records in RAM.
INFO 2026-06-08 09:03:00 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:11:28s. Time for last 1,000,000: 1s. Last read position: chr11:32,583,847
INFO 2026-06-08 09:03:00 MarkDuplicates Tracking 770850 as yet unmatched pairs. 67235 records in RAM.
INFO 2026-06-08 09:03:03 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:11:31s. Time for last 1,000,000: 3s. Last read position: chr11:44,126,876
INFO 2026-06-08 09:03:03 MarkDuplicates Tracking 768464 as yet unmatched pairs. 64843 records in RAM.
INFO 2026-06-08 09:03:05 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:11:33s. Time for last 1,000,000: 1s. Last read position: chr11:46,317,363
INFO 2026-06-08 09:03:05 MarkDuplicates Tracking 769791 as yet unmatched pairs. 66162 records in RAM.
INFO 2026-06-08 09:03:07 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:11:35s. Time for last 1,000,000: 1s. Last read position: chr11:47,584,361
INFO 2026-06-08 09:03:07 MarkDuplicates Tracking 763626 as yet unmatched pairs. 59996 records in RAM.
INFO 2026-06-08 09:03:08 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:11:37s. Time for last 1,000,000: 1s. Last read position: chr11:58,611,720
INFO 2026-06-08 09:03:08 MarkDuplicates Tracking 759941 as yet unmatched pairs. 56303 records in RAM.
INFO 2026-06-08 09:03:10 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:11:39s. Time for last 1,000,000: 1s. Last read position: chr11:61,231,415
INFO 2026-06-08 09:03:10 MarkDuplicates Tracking 758982 as yet unmatched pairs. 55336 records in RAM.
INFO 2026-06-08 09:03:12 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:11:40s. Time for last 1,000,000: 1s. Last read position: chr11:62,519,411
INFO 2026-06-08 09:03:12 MarkDuplicates Tracking 755461 as yet unmatched pairs. 51797 records in RAM.
INFO 2026-06-08 09:03:13 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:11:42s. Time for last 1,000,000: 1s. Last read position: chr11:62,617,038
INFO 2026-06-08 09:03:13 MarkDuplicates Tracking 752951 as yet unmatched pairs. 49283 records in RAM.
INFO 2026-06-08 09:03:15 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:11:44s. Time for last 1,000,000: 1s. Last read position: chr11:63,906,086
INFO 2026-06-08 09:03:15 MarkDuplicates Tracking 750014 as yet unmatched pairs. 46339 records in RAM.
INFO 2026-06-08 09:03:17 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:11:46s. Time for last 1,000,000: 1s. Last read position: chr11:64,742,028
INFO 2026-06-08 09:03:17 MarkDuplicates Tracking 746832 as yet unmatched pairs. 43155 records in RAM.
INFO 2026-06-08 09:03:19 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:11:48s. Time for last 1,000,000: 1s. Last read position: chr11:65,187,241
INFO 2026-06-08 09:03:19 MarkDuplicates Tracking 744454 as yet unmatched pairs. 40776 records in RAM.
INFO 2026-06-08 09:03:21 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:11:50s. Time for last 1,000,000: 1s. Last read position: chr11:65,654,728
INFO 2026-06-08 09:03:21 MarkDuplicates Tracking 743822 as yet unmatched pairs. 40117 records in RAM.
INFO 2026-06-08 09:03:22 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:11:51s. Time for last 1,000,000: 1s. Last read position: chr11:66,316,501
INFO 2026-06-08 09:03:22 MarkDuplicates Tracking 738051 as yet unmatched pairs. 34339 records in RAM.
INFO 2026-06-08 09:03:25 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:11:53s. Time for last 1,000,000: 2s. Last read position: chr11:67,401,068
INFO 2026-06-08 09:03:25 MarkDuplicates Tracking 735822 as yet unmatched pairs. 32105 records in RAM.
INFO 2026-06-08 09:03:27 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:11:56s. Time for last 1,000,000: 2s. Last read position: chr11:68,386,379
INFO 2026-06-08 09:03:27 MarkDuplicates Tracking 731766 as yet unmatched pairs. 28044 records in RAM.
INFO 2026-06-08 09:03:29 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:11:57s. Time for last 1,000,000: 1s. Last read position: chr11:71,113,334
INFO 2026-06-08 09:03:29 MarkDuplicates Tracking 728335 as yet unmatched pairs. 24606 records in RAM.
INFO 2026-06-08 09:03:31 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:11:59s. Time for last 1,000,000: 1s. Last read position: chr11:73,310,187
INFO 2026-06-08 09:03:31 MarkDuplicates Tracking 725352 as yet unmatched pairs. 21613 records in RAM.
INFO 2026-06-08 09:03:32 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:12:01s. Time for last 1,000,000: 1s. Last read position: chr11:76,542,258
INFO 2026-06-08 09:03:32 MarkDuplicates Tracking 722550 as yet unmatched pairs. 18805 records in RAM.
INFO 2026-06-08 09:03:34 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:12:03s. Time for last 1,000,000: 1s. Last read position: chr11:87,321,211
INFO 2026-06-08 09:03:34 MarkDuplicates Tracking 719757 as yet unmatched pairs. 16004 records in RAM.
INFO 2026-06-08 09:03:36 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:12:04s. Time for last 1,000,000: 1s. Last read position: chr11:105,644,579
INFO 2026-06-08 09:03:36 MarkDuplicates Tracking 717179 as yet unmatched pairs. 13408 records in RAM.
INFO 2026-06-08 09:03:37 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:12:06s. Time for last 1,000,000: 1s. Last read position: chr11:117,206,242
INFO 2026-06-08 09:03:37 MarkDuplicates Tracking 714874 as yet unmatched pairs. 11092 records in RAM.
INFO 2026-06-08 09:03:39 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:12:08s. Time for last 1,000,000: 1s. Last read position: chr11:119,018,944
INFO 2026-06-08 09:03:39 MarkDuplicates Tracking 712656 as yet unmatched pairs. 8873 records in RAM.
INFO 2026-06-08 09:03:41 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:12:10s. Time for last 1,000,000: 1s. Last read position: chr11:123,057,704
INFO 2026-06-08 09:03:41 MarkDuplicates Tracking 713494 as yet unmatched pairs. 9707 records in RAM.
INFO 2026-06-08 09:03:43 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:12:11s. Time for last 1,000,000: 1s. Last read position: chr11:126,407,340
INFO 2026-06-08 09:03:43 MarkDuplicates Tracking 707855 as yet unmatched pairs. 4059 records in RAM.
INFO 2026-06-08 09:03:45 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:12:13s. Time for last 1,000,000: 2s. Last read position: chr11:134,252,875
INFO 2026-06-08 09:03:45 MarkDuplicates Tracking 703976 as yet unmatched pairs. 169 records in RAM.
INFO 2026-06-08 09:03:47 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:12:16s. Time for last 1,000,000: 2s. Last read position: chr12:5,976,216
INFO 2026-06-08 09:03:47 MarkDuplicates Tracking 701318 as yet unmatched pairs. 80016 records in RAM.
INFO 2026-06-08 09:03:49 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:12:18s. Time for last 1,000,000: 1s. Last read position: chr12:6,591,542
INFO 2026-06-08 09:03:49 MarkDuplicates Tracking 698866 as yet unmatched pairs. 77562 records in RAM.
INFO 2026-06-08 09:03:51 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:12:19s. Time for last 1,000,000: 1s. Last read position: chr12:7,080,780
INFO 2026-06-08 09:03:51 MarkDuplicates Tracking 696577 as yet unmatched pairs. 75273 records in RAM.
INFO 2026-06-08 09:03:53 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:12:21s. Time for last 1,000,000: 1s. Last read position: chr12:11,828,426
INFO 2026-06-08 09:03:53 MarkDuplicates Tracking 693903 as yet unmatched pairs. 72588 records in RAM.
INFO 2026-06-08 09:03:55 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:12:24s. Time for last 1,000,000: 2s. Last read position: chr12:21,635,675
INFO 2026-06-08 09:03:55 MarkDuplicates Tracking 692959 as yet unmatched pairs. 71636 records in RAM.
INFO 2026-06-08 09:03:57 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:12:26s. Time for last 1,000,000: 1s. Last read position: chr12:32,792,367
INFO 2026-06-08 09:03:57 MarkDuplicates Tracking 688667 as yet unmatched pairs. 67339 records in RAM.
INFO 2026-06-08 09:03:59 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:12:28s. Time for last 1,000,000: 1s. Last read position: chr12:48,770,821
INFO 2026-06-08 09:03:59 MarkDuplicates Tracking 685907 as yet unmatched pairs. 64573 records in RAM.
INFO 2026-06-08 09:04:01 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:12:29s. Time for last 1,000,000: 1s. Last read position: chr12:49,128,446
INFO 2026-06-08 09:04:01 MarkDuplicates Tracking 687007 as yet unmatched pairs. 65662 records in RAM.
INFO 2026-06-08 09:04:02 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:12:31s. Time for last 1,000,000: 1s. Last read position: chr12:50,222,021
INFO 2026-06-08 09:04:02 MarkDuplicates Tracking 680606 as yet unmatched pairs. 59256 records in RAM.
INFO 2026-06-08 09:04:04 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:12:33s. Time for last 1,000,000: 1s. Last read position: chr12:52,058,720
INFO 2026-06-08 09:04:04 MarkDuplicates Tracking 683195 as yet unmatched pairs. 61840 records in RAM.
INFO 2026-06-08 09:04:06 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:12:35s. Time for last 1,000,000: 1s. Last read position: chr12:52,952,732
INFO 2026-06-08 09:04:06 MarkDuplicates Tracking 679963 as yet unmatched pairs. 58607 records in RAM.
INFO 2026-06-08 09:04:08 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:12:36s. Time for last 1,000,000: 1s. Last read position: chr12:53,665,285
INFO 2026-06-08 09:04:08 MarkDuplicates Tracking 677081 as yet unmatched pairs. 55717 records in RAM.
INFO 2026-06-08 09:04:09 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:12:38s. Time for last 1,000,000: 1s. Last read position: chr12:55,726,160
INFO 2026-06-08 09:04:09 MarkDuplicates Tracking 670712 as yet unmatched pairs. 49338 records in RAM.
INFO 2026-06-08 09:04:11 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:12:40s. Time for last 1,000,000: 1s. Last read position: chr12:56,252,520
INFO 2026-06-08 09:04:11 MarkDuplicates Tracking 667676 as yet unmatched pairs. 46294 records in RAM.
INFO 2026-06-08 09:04:13 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:12:41s. Time for last 1,000,000: 1s. Last read position: chr12:56,719,095
INFO 2026-06-08 09:04:13 MarkDuplicates Tracking 665615 as yet unmatched pairs. 44231 records in RAM.
INFO 2026-06-08 09:04:15 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:12:44s. Time for last 1,000,000: 2s. Last read position: chr12:57,181,273
INFO 2026-06-08 09:04:15 MarkDuplicates Tracking 662803 as yet unmatched pairs. 41413 records in RAM.
INFO 2026-06-08 09:04:18 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:12:46s. Time for last 1,000,000: 2s. Last read position: chr12:57,716,722
INFO 2026-06-08 09:04:18 MarkDuplicates Tracking 660430 as yet unmatched pairs. 39037 records in RAM.
INFO 2026-06-08 09:04:19 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:12:48s. Time for last 1,000,000: 1s. Last read position: chr12:68,828,902
INFO 2026-06-08 09:04:19 MarkDuplicates Tracking 657767 as yet unmatched pairs. 36356 records in RAM.
INFO 2026-06-08 09:04:21 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:12:50s. Time for last 1,000,000: 1s. Last read position: chr12:79,809,910
INFO 2026-06-08 09:04:21 MarkDuplicates Tracking 654824 as yet unmatched pairs. 33412 records in RAM.
INFO 2026-06-08 09:04:23 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:12:52s. Time for last 1,000,000: 1s. Last read position: chr12:95,861,254
INFO 2026-06-08 09:04:23 MarkDuplicates Tracking 653608 as yet unmatched pairs. 32191 records in RAM.
INFO 2026-06-08 09:04:25 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:12:54s. Time for last 1,000,000: 1s. Last read position: chr12:103,937,740
INFO 2026-06-08 09:04:25 MarkDuplicates Tracking 650155 as yet unmatched pairs. 28735 records in RAM.
INFO 2026-06-08 09:04:27 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:12:55s. Time for last 1,000,000: 1s. Last read position: chr12:107,741,165
INFO 2026-06-08 09:04:27 MarkDuplicates Tracking 647180 as yet unmatched pairs. 25757 records in RAM.
INFO 2026-06-08 09:04:28 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:12:57s. Time for last 1,000,000: 1s. Last read position: chr12:110,440,372
INFO 2026-06-08 09:04:28 MarkDuplicates Tracking 645046 as yet unmatched pairs. 23620 records in RAM.
INFO 2026-06-08 09:04:30 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:12:59s. Time for last 1,000,000: 1s. Last read position: chr12:112,405,904
INFO 2026-06-08 09:04:30 MarkDuplicates Tracking 644232 as yet unmatched pairs. 22801 records in RAM.
INFO 2026-06-08 09:04:32 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:13:01s. Time for last 1,000,000: 1s. Last read position: chr12:116,911,065
INFO 2026-06-08 09:04:32 MarkDuplicates Tracking 638900 as yet unmatched pairs. 17463 records in RAM.
INFO 2026-06-08 09:04:34 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:13:03s. Time for last 1,000,000: 1s. Last read position: chr12:120,198,907
INFO 2026-06-08 09:04:34 MarkDuplicates Tracking 640249 as yet unmatched pairs. 18790 records in RAM.
INFO 2026-06-08 09:04:36 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:13:04s. Time for last 1,000,000: 1s. Last read position: chr12:121,444,075
INFO 2026-06-08 09:04:36 MarkDuplicates Tracking 633225 as yet unmatched pairs. 11757 records in RAM.
INFO 2026-06-08 09:04:37 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:13:06s. Time for last 1,000,000: 1s. Last read position: chr12:122,867,405
INFO 2026-06-08 09:04:37 MarkDuplicates Tracking 630505 as yet unmatched pairs. 9030 records in RAM.
INFO 2026-06-08 09:04:39 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:13:08s. Time for last 1,000,000: 1s. Last read position: chr12:124,362,280
INFO 2026-06-08 09:04:39 MarkDuplicates Tracking 628238 as yet unmatched pairs. 6762 records in RAM.
INFO 2026-06-08 09:04:41 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:13:10s. Time for last 1,000,000: 1s. Last read position: chr12:132,021,208
INFO 2026-06-08 09:04:41 MarkDuplicates Tracking 625585 as yet unmatched pairs. 4097 records in RAM.
INFO 2026-06-08 09:04:43 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:13:12s. Time for last 1,000,000: 1s. Last read position: chr12:133,083,414
INFO 2026-06-08 09:04:43 MarkDuplicates Tracking 621839 as yet unmatched pairs. 335 records in RAM.
INFO 2026-06-08 09:04:45 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:13:14s. Time for last 1,000,000: 2s. Last read position: chr13:27,070,544
INFO 2026-06-08 09:04:45 MarkDuplicates Tracking 619200 as yet unmatched pairs. 17961 records in RAM.
INFO 2026-06-08 09:04:47 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:13:16s. Time for last 1,000,000: 1s. Last read position: chr13:37,563,338
INFO 2026-06-08 09:04:47 MarkDuplicates Tracking 618832 as yet unmatched pairs. 17593 records in RAM.
INFO 2026-06-08 09:04:49 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:13:18s. Time for last 1,000,000: 1s. Last read position: chr13:45,492,247
INFO 2026-06-08 09:04:49 MarkDuplicates Tracking 614223 as yet unmatched pairs. 12981 records in RAM.
INFO 2026-06-08 09:04:51 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:13:20s. Time for last 1,000,000: 1s. Last read position: chr13:73,062,728
INFO 2026-06-08 09:04:51 MarkDuplicates Tracking 612513 as yet unmatched pairs. 11269 records in RAM.
INFO 2026-06-08 09:04:53 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:13:21s. Time for last 1,000,000: 1s. Last read position: chr13:98,860,410
INFO 2026-06-08 09:04:53 MarkDuplicates Tracking 609018 as yet unmatched pairs. 7763 records in RAM.
INFO 2026-06-08 09:04:55 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:13:23s. Time for last 1,000,000: 1s. Last read position: chr13:110,201,436
INFO 2026-06-08 09:04:55 MarkDuplicates Tracking 607491 as yet unmatched pairs. 6235 records in RAM.
INFO 2026-06-08 09:04:56 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:13:25s. Time for last 1,000,000: 1s. Last read position: chr13:112,862,458
INFO 2026-06-08 09:04:56 MarkDuplicates Tracking 602869 as yet unmatched pairs. 1610 records in RAM.
INFO 2026-06-08 09:04:58 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:13:27s. Time for last 1,000,000: 2s. Last read position: chr14:21,090,723
INFO 2026-06-08 09:04:58 MarkDuplicates Tracking 600426 as yet unmatched pairs. 43979 records in RAM.
INFO 2026-06-08 09:05:01 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:13:29s. Time for last 1,000,000: 2s. Last read position: chr14:22,928,492
INFO 2026-06-08 09:05:01 MarkDuplicates Tracking 597833 as yet unmatched pairs. 41382 records in RAM.
INFO 2026-06-08 09:05:02 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:13:31s. Time for last 1,000,000: 1s. Last read position: chr14:24,179,818
INFO 2026-06-08 09:05:02 MarkDuplicates Tracking 594647 as yet unmatched pairs. 38192 records in RAM.
INFO 2026-06-08 09:05:04 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:13:33s. Time for last 1,000,000: 1s. Last read position: chr14:32,093,156
INFO 2026-06-08 09:05:04 MarkDuplicates Tracking 592477 as yet unmatched pairs. 36018 records in RAM.
INFO 2026-06-08 09:05:06 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:13:34s. Time for last 1,000,000: 1s. Last read position: chr14:49,621,589
INFO 2026-06-08 09:05:06 MarkDuplicates Tracking 589545 as yet unmatched pairs. 33062 records in RAM.
INFO 2026-06-08 09:05:08 MarkDuplicates Read 368,000,000 records. Elapsed time: 00:13:37s. Time for last 1,000,000: 2s. Last read position: chr14:55,271,438
INFO 2026-06-08 09:05:08 MarkDuplicates Tracking 586702 as yet unmatched pairs. 30203 records in RAM.
INFO 2026-06-08 09:05:10 MarkDuplicates Read 369,000,000 records. Elapsed time: 00:13:39s. Time for last 1,000,000: 1s. Last read position: chr14:64,400,793
INFO 2026-06-08 09:05:10 MarkDuplicates Tracking 584725 as yet unmatched pairs. 28220 records in RAM.
INFO 2026-06-08 09:05:13 MarkDuplicates Read 370,000,000 records. Elapsed time: 00:13:41s. Time for last 1,000,000: 2s. Last read position: chr14:68,890,191
INFO 2026-06-08 09:05:13 MarkDuplicates Tracking 582427 as yet unmatched pairs. 25916 records in RAM.
INFO 2026-06-08 09:05:15 MarkDuplicates Read 371,000,000 records. Elapsed time: 00:13:43s. Time for last 1,000,000: 2s. Last read position: chr14:74,060,631
INFO 2026-06-08 09:05:15 MarkDuplicates Tracking 578821 as yet unmatched pairs. 22298 records in RAM.
INFO 2026-06-08 09:05:17 MarkDuplicates Read 372,000,000 records. Elapsed time: 00:13:45s. Time for last 1,000,000: 1s. Last read position: chr14:76,779,035
INFO 2026-06-08 09:05:17 MarkDuplicates Tracking 576052 as yet unmatched pairs. 19527 records in RAM.
INFO 2026-06-08 09:05:19 MarkDuplicates Read 373,000,000 records. Elapsed time: 00:13:47s. Time for last 1,000,000: 1s. Last read position: chr14:92,652,505
INFO 2026-06-08 09:05:19 MarkDuplicates Tracking 573789 as yet unmatched pairs. 17253 records in RAM.
INFO 2026-06-08 09:05:20 MarkDuplicates Read 374,000,000 records. Elapsed time: 00:13:49s. Time for last 1,000,000: 1s. Last read position: chr14:100,106,723
INFO 2026-06-08 09:05:20 MarkDuplicates Tracking 570961 as yet unmatched pairs. 14412 records in RAM.
INFO 2026-06-08 09:05:22 MarkDuplicates Read 375,000,000 records. Elapsed time: 00:13:51s. Time for last 1,000,000: 2s. Last read position: chr14:102,084,771
INFO 2026-06-08 09:05:22 MarkDuplicates Tracking 568346 as yet unmatched pairs. 11792 records in RAM.
INFO 2026-06-08 09:05:24 MarkDuplicates Read 376,000,000 records. Elapsed time: 00:13:53s. Time for last 1,000,000: 1s. Last read position: chr14:104,711,092
INFO 2026-06-08 09:05:24 MarkDuplicates Tracking 565675 as yet unmatched pairs. 9119 records in RAM.
INFO 2026-06-08 09:05:26 MarkDuplicates Read 377,000,000 records. Elapsed time: 00:13:55s. Time for last 1,000,000: 1s. Last read position: chr14:105,250,606
INFO 2026-06-08 09:05:26 MarkDuplicates Tracking 562153 as yet unmatched pairs. 5595 records in RAM.
INFO 2026-06-08 09:05:28 MarkDuplicates Read 378,000,000 records. Elapsed time: 00:13:56s. Time for last 1,000,000: 1s. Last read position: chr14:105,707,548
INFO 2026-06-08 09:05:28 MarkDuplicates Tracking 563256 as yet unmatched pairs. 6698 records in RAM.
INFO 2026-06-08 09:05:29 MarkDuplicates Read 379,000,000 records. Elapsed time: 00:13:58s. Time for last 1,000,000: 1s. Last read position: chr14:105,742,887
INFO 2026-06-08 09:05:29 MarkDuplicates Tracking 568816 as yet unmatched pairs. 12256 records in RAM.
INFO 2026-06-08 09:05:31 MarkDuplicates Read 380,000,000 records. Elapsed time: 00:14:00s. Time for last 1,000,000: 2s. Last read position: chr15:28,213,874
INFO 2026-06-08 09:05:31 MarkDuplicates Tracking 555564 as yet unmatched pairs. 41538 records in RAM.
INFO 2026-06-08 09:05:33 MarkDuplicates Read 381,000,000 records. Elapsed time: 00:14:02s. Time for last 1,000,000: 1s. Last read position: chr15:34,084,266
INFO 2026-06-08 09:05:33 MarkDuplicates Tracking 553465 as yet unmatched pairs. 39439 records in RAM.
INFO 2026-06-08 09:05:35 MarkDuplicates Read 382,000,000 records. Elapsed time: 00:14:03s. Time for last 1,000,000: 1s. Last read position: chr15:40,266,083
INFO 2026-06-08 09:05:35 MarkDuplicates Tracking 550595 as yet unmatched pairs. 36569 records in RAM.
INFO 2026-06-08 09:05:37 MarkDuplicates Read 383,000,000 records. Elapsed time: 00:14:05s. Time for last 1,000,000: 1s. Last read position: chr15:41,811,177
INFO 2026-06-08 09:05:37 MarkDuplicates Tracking 547682 as yet unmatched pairs. 33656 records in RAM.
INFO 2026-06-08 09:05:38 MarkDuplicates Read 384,000,000 records. Elapsed time: 00:14:07s. Time for last 1,000,000: 1s. Last read position: chr15:43,763,137
INFO 2026-06-08 09:05:38 MarkDuplicates Tracking 547036 as yet unmatched pairs. 33002 records in RAM.
INFO 2026-06-08 09:05:40 MarkDuplicates Read 385,000,000 records. Elapsed time: 00:14:08s. Time for last 1,000,000: 1s. Last read position: chr15:45,414,724
INFO 2026-06-08 09:05:40 MarkDuplicates Tracking 542789 as yet unmatched pairs. 28747 records in RAM.
INFO 2026-06-08 09:05:42 MarkDuplicates Read 386,000,000 records. Elapsed time: 00:14:10s. Time for last 1,000,000: 1s. Last read position: chr15:52,608,986
INFO 2026-06-08 09:05:42 MarkDuplicates Tracking 539978 as yet unmatched pairs. 25934 records in RAM.
INFO 2026-06-08 09:05:43 MarkDuplicates Read 387,000,000 records. Elapsed time: 00:14:12s. Time for last 1,000,000: 1s. Last read position: chr15:60,357,164
INFO 2026-06-08 09:05:43 MarkDuplicates Tracking 538692 as yet unmatched pairs. 24641 records in RAM.
INFO 2026-06-08 09:05:45 MarkDuplicates Read 388,000,000 records. Elapsed time: 00:14:13s. Time for last 1,000,000: 1s. Last read position: chr15:64,072,994
INFO 2026-06-08 09:05:45 MarkDuplicates Tracking 535460 as yet unmatched pairs. 21409 records in RAM.
INFO 2026-06-08 09:05:48 MarkDuplicates Read 389,000,000 records. Elapsed time: 00:14:16s. Time for last 1,000,000: 2s. Last read position: chr15:67,181,383
INFO 2026-06-08 09:05:48 MarkDuplicates Tracking 532212 as yet unmatched pairs. 18157 records in RAM.
INFO 2026-06-08 09:05:50 MarkDuplicates Read 390,000,000 records. Elapsed time: 00:14:18s. Time for last 1,000,000: 1s. Last read position: chr15:72,752,677
INFO 2026-06-08 09:05:50 MarkDuplicates Tracking 529999 as yet unmatched pairs. 15943 records in RAM.
INFO 2026-06-08 09:05:51 MarkDuplicates Read 391,000,000 records. Elapsed time: 00:14:20s. Time for last 1,000,000: 1s. Last read position: chr15:74,908,299
INFO 2026-06-08 09:05:51 MarkDuplicates Tracking 526287 as yet unmatched pairs. 12231 records in RAM.
INFO 2026-06-08 09:05:53 MarkDuplicates Read 392,000,000 records. Elapsed time: 00:14:22s. Time for last 1,000,000: 1s. Last read position: chr15:78,293,180
INFO 2026-06-08 09:05:53 MarkDuplicates Tracking 523688 as yet unmatched pairs. 9630 records in RAM.
INFO 2026-06-08 09:05:55 MarkDuplicates Read 393,000,000 records. Elapsed time: 00:14:24s. Time for last 1,000,000: 1s. Last read position: chr15:85,064,372
INFO 2026-06-08 09:05:55 MarkDuplicates Tracking 520998 as yet unmatched pairs. 6937 records in RAM.
INFO 2026-06-08 09:05:57 MarkDuplicates Read 394,000,000 records. Elapsed time: 00:14:26s. Time for last 1,000,000: 2s. Last read position: chr15:89,893,818
INFO 2026-06-08 09:05:57 MarkDuplicates Tracking 518459 as yet unmatched pairs. 4393 records in RAM.
INFO 2026-06-08 09:05:59 MarkDuplicates Read 395,000,000 records. Elapsed time: 00:14:28s. Time for last 1,000,000: 2s. Last read position: chr15:94,318,446
INFO 2026-06-08 09:05:59 MarkDuplicates Tracking 515813 as yet unmatched pairs. 1744 records in RAM.
INFO 2026-06-08 09:06:02 MarkDuplicates Read 396,000,000 records. Elapsed time: 00:14:31s. Time for last 1,000,000: 2s. Last read position: chr16:426,561
INFO 2026-06-08 09:06:02 MarkDuplicates Tracking 513053 as yet unmatched pairs. 76605 records in RAM.
INFO 2026-06-08 09:06:04 MarkDuplicates Read 397,000,000 records. Elapsed time: 00:14:33s. Time for last 1,000,000: 2s. Last read position: chr16:1,202,340
INFO 2026-06-08 09:06:04 MarkDuplicates Tracking 509301 as yet unmatched pairs. 72849 records in RAM.
INFO 2026-06-08 09:06:06 MarkDuplicates Read 398,000,000 records. Elapsed time: 00:14:35s. Time for last 1,000,000: 1s. Last read position: chr16:1,999,556
INFO 2026-06-08 09:06:06 MarkDuplicates Tracking 506892 as yet unmatched pairs. 70438 records in RAM.
INFO 2026-06-08 09:06:08 MarkDuplicates Read 399,000,000 records. Elapsed time: 00:14:37s. Time for last 1,000,000: 2s. Last read position: chr16:2,244,409
INFO 2026-06-08 09:06:08 MarkDuplicates Tracking 503409 as yet unmatched pairs. 66954 records in RAM.
INFO 2026-06-08 09:06:11 MarkDuplicates Read 400,000,000 records. Elapsed time: 00:14:40s. Time for last 1,000,000: 2s. Last read position: chr16:2,767,360
INFO 2026-06-08 09:06:11 MarkDuplicates Tracking 501399 as yet unmatched pairs. 64940 records in RAM.
INFO 2026-06-08 09:06:13 MarkDuplicates Read 401,000,000 records. Elapsed time: 00:14:42s. Time for last 1,000,000: 2s. Last read position: chr16:3,589,072
INFO 2026-06-08 09:06:13 MarkDuplicates Tracking 496818 as yet unmatched pairs. 60351 records in RAM.
INFO 2026-06-08 09:06:15 MarkDuplicates Read 402,000,000 records. Elapsed time: 00:14:44s. Time for last 1,000,000: 2s. Last read position: chr16:8,895,091
INFO 2026-06-08 09:06:15 MarkDuplicates Tracking 494281 as yet unmatched pairs. 57812 records in RAM.
INFO 2026-06-08 09:06:17 MarkDuplicates Read 403,000,000 records. Elapsed time: 00:14:46s. Time for last 1,000,000: 2s. Last read position: chr16:14,878,794
INFO 2026-06-08 09:06:17 MarkDuplicates Tracking 491841 as yet unmatched pairs. 55366 records in RAM.
INFO 2026-06-08 09:06:19 MarkDuplicates Read 404,000,000 records. Elapsed time: 00:14:48s. Time for last 1,000,000: 1s. Last read position: chr16:15,735,518
INFO 2026-06-08 09:06:19 MarkDuplicates Tracking 489993 as yet unmatched pairs. 53518 records in RAM.
INFO 2026-06-08 09:06:20 MarkDuplicates Read 405,000,000 records. Elapsed time: 00:14:49s. Time for last 1,000,000: 1s. Last read position: chr16:16,360,825
INFO 2026-06-08 09:06:20 MarkDuplicates Tracking 488896 as yet unmatched pairs. 52421 records in RAM.
INFO 2026-06-08 09:06:22 MarkDuplicates Read 406,000,000 records. Elapsed time: 00:14:50s. Time for last 1,000,000: 1s. Last read position: chr16:18,434,696
INFO 2026-06-08 09:06:22 MarkDuplicates Tracking 487772 as yet unmatched pairs. 51297 records in RAM.
INFO 2026-06-08 09:06:24 MarkDuplicates Read 407,000,000 records. Elapsed time: 00:14:52s. Time for last 1,000,000: 1s. Last read position: chr16:20,564,674
INFO 2026-06-08 09:06:24 MarkDuplicates Tracking 484948 as yet unmatched pairs. 48472 records in RAM.
INFO 2026-06-08 09:06:25 MarkDuplicates Read 408,000,000 records. Elapsed time: 00:14:54s. Time for last 1,000,000: 1s. Last read position: chr16:21,837,170
INFO 2026-06-08 09:06:25 MarkDuplicates Tracking 483587 as yet unmatched pairs. 47109 records in RAM.
INFO 2026-06-08 09:06:27 MarkDuplicates Read 409,000,000 records. Elapsed time: 00:14:55s. Time for last 1,000,000: 1s. Last read position: chr16:22,534,983
INFO 2026-06-08 09:06:27 MarkDuplicates Tracking 483737 as yet unmatched pairs. 47259 records in RAM.
INFO 2026-06-08 09:06:28 MarkDuplicates Read 410,000,000 records. Elapsed time: 00:14:57s. Time for last 1,000,000: 1s. Last read position: chr16:28,098,541
INFO 2026-06-08 09:06:28 MarkDuplicates Tracking 480993 as yet unmatched pairs. 44515 records in RAM.
INFO 2026-06-08 09:06:30 MarkDuplicates Read 411,000,000 records. Elapsed time: 00:14:59s. Time for last 1,000,000: 1s. Last read position: chr16:28,836,674
INFO 2026-06-08 09:06:30 MarkDuplicates Tracking 479196 as yet unmatched pairs. 42710 records in RAM.
INFO 2026-06-08 09:06:32 MarkDuplicates Read 412,000,000 records. Elapsed time: 00:15:01s. Time for last 1,000,000: 1s. Last read position: chr16:29,500,077
INFO 2026-06-08 09:06:32 MarkDuplicates Tracking 477092 as yet unmatched pairs. 40604 records in RAM.
INFO 2026-06-08 09:06:34 MarkDuplicates Read 413,000,000 records. Elapsed time: 00:15:02s. Time for last 1,000,000: 1s. Last read position: chr16:30,069,299
INFO 2026-06-08 09:06:34 MarkDuplicates Tracking 476798 as yet unmatched pairs. 40310 records in RAM.
INFO 2026-06-08 09:06:36 MarkDuplicates Read 414,000,000 records. Elapsed time: 00:15:04s. Time for last 1,000,000: 1s. Last read position: chr16:30,424,459
INFO 2026-06-08 09:06:36 MarkDuplicates Tracking 472254 as yet unmatched pairs. 35766 records in RAM.
INFO 2026-06-08 09:06:38 MarkDuplicates Read 415,000,000 records. Elapsed time: 00:15:06s. Time for last 1,000,000: 2s. Last read position: chr16:31,077,690
INFO 2026-06-08 09:06:38 MarkDuplicates Tracking 468764 as yet unmatched pairs. 32275 records in RAM.
INFO 2026-06-08 09:06:39 MarkDuplicates Read 416,000,000 records. Elapsed time: 00:15:08s. Time for last 1,000,000: 1s. Last read position: chr16:31,874,123
INFO 2026-06-08 09:06:39 MarkDuplicates Tracking 465866 as yet unmatched pairs. 29375 records in RAM.
INFO 2026-06-08 09:06:41 MarkDuplicates Read 417,000,000 records. Elapsed time: 00:15:10s. Time for last 1,000,000: 2s. Last read position: chr16:55,537,598
INFO 2026-06-08 09:06:41 MarkDuplicates Tracking 463448 as yet unmatched pairs. 26949 records in RAM.
INFO 2026-06-08 09:06:43 MarkDuplicates Read 418,000,000 records. Elapsed time: 00:15:12s. Time for last 1,000,000: 2s. Last read position: chr16:57,758,846
INFO 2026-06-08 09:06:43 MarkDuplicates Tracking 460853 as yet unmatched pairs. 24351 records in RAM.
INFO 2026-06-08 09:06:45 MarkDuplicates Read 419,000,000 records. Elapsed time: 00:15:14s. Time for last 1,000,000: 1s. Last read position: chr16:67,174,656
INFO 2026-06-08 09:06:45 MarkDuplicates Tracking 458110 as yet unmatched pairs. 21607 records in RAM.
INFO 2026-06-08 09:06:47 MarkDuplicates Read 420,000,000 records. Elapsed time: 00:15:16s. Time for last 1,000,000: 1s. Last read position: chr16:68,290,451
INFO 2026-06-08 09:06:47 MarkDuplicates Tracking 454615 as yet unmatched pairs. 18110 records in RAM.
INFO 2026-06-08 09:06:49 MarkDuplicates Read 421,000,000 records. Elapsed time: 00:15:17s. Time for last 1,000,000: 1s. Last read position: chr16:70,271,839
INFO 2026-06-08 09:06:49 MarkDuplicates Tracking 451884 as yet unmatched pairs. 15372 records in RAM.
INFO 2026-06-08 09:06:50 MarkDuplicates Read 422,000,000 records. Elapsed time: 00:15:19s. Time for last 1,000,000: 1s. Last read position: chr16:74,503,713
INFO 2026-06-08 09:06:50 MarkDuplicates Tracking 450126 as yet unmatched pairs. 13614 records in RAM.
INFO 2026-06-08 09:06:53 MarkDuplicates Read 423,000,000 records. Elapsed time: 00:15:21s. Time for last 1,000,000: 2s. Last read position: chr16:84,178,940
INFO 2026-06-08 09:06:53 MarkDuplicates Tracking 446844 as yet unmatched pairs. 10329 records in RAM.
INFO 2026-06-08 09:06:55 MarkDuplicates Read 424,000,000 records. Elapsed time: 00:15:24s. Time for last 1,000,000: 2s. Last read position: chr16:88,431,694
INFO 2026-06-08 09:06:55 MarkDuplicates Tracking 443423 as yet unmatched pairs. 6907 records in RAM.
INFO 2026-06-08 09:06:59 MarkDuplicates Read 425,000,000 records. Elapsed time: 00:15:27s. Time for last 1,000,000: 3s. Last read position: chr16:89,282,531
INFO 2026-06-08 09:06:59 MarkDuplicates Tracking 440103 as yet unmatched pairs. 3581 records in RAM.
INFO 2026-06-08 09:07:02 MarkDuplicates Read 426,000,000 records. Elapsed time: 00:15:31s. Time for last 1,000,000: 3s. Last read position: chr17:521,603
INFO 2026-06-08 09:07:02 MarkDuplicates Tracking 436811 as yet unmatched pairs. 159457 records in RAM.
INFO 2026-06-08 09:07:04 MarkDuplicates Read 427,000,000 records. Elapsed time: 00:15:32s. Time for last 1,000,000: 1s. Last read position: chr17:1,673,393
INFO 2026-06-08 09:07:04 MarkDuplicates Tracking 435232 as yet unmatched pairs. 157877 records in RAM.
INFO 2026-06-08 09:07:06 MarkDuplicates Read 428,000,000 records. Elapsed time: 00:15:34s. Time for last 1,000,000: 1s. Last read position: chr17:3,884,569
INFO 2026-06-08 09:07:06 MarkDuplicates Tracking 430952 as yet unmatched pairs. 153592 records in RAM.
INFO 2026-06-08 09:07:07 MarkDuplicates Read 429,000,000 records. Elapsed time: 00:15:36s. Time for last 1,000,000: 1s. Last read position: chr17:4,893,490
INFO 2026-06-08 09:07:07 MarkDuplicates Tracking 428426 as yet unmatched pairs. 151062 records in RAM.
INFO 2026-06-08 09:07:09 MarkDuplicates Read 430,000,000 records. Elapsed time: 00:15:38s. Time for last 1,000,000: 1s. Last read position: chr17:7,219,917
INFO 2026-06-08 09:07:09 MarkDuplicates Tracking 425511 as yet unmatched pairs. 148143 records in RAM.
INFO 2026-06-08 09:07:11 MarkDuplicates Read 431,000,000 records. Elapsed time: 00:15:40s. Time for last 1,000,000: 1s. Last read position: chr17:7,499,150
INFO 2026-06-08 09:07:11 MarkDuplicates Tracking 422945 as yet unmatched pairs. 145577 records in RAM.
INFO 2026-06-08 09:07:13 MarkDuplicates Read 432,000,000 records. Elapsed time: 00:15:42s. Time for last 1,000,000: 1s. Last read position: chr17:7,855,076
INFO 2026-06-08 09:07:13 MarkDuplicates Tracking 419885 as yet unmatched pairs. 142517 records in RAM.
INFO 2026-06-08 09:07:15 MarkDuplicates Read 433,000,000 records. Elapsed time: 00:15:44s. Time for last 1,000,000: 1s. Last read position: chr17:13,015,773
INFO 2026-06-08 09:07:15 MarkDuplicates Tracking 417490 as yet unmatched pairs. 140122 records in RAM.
INFO 2026-06-08 09:07:17 MarkDuplicates Read 434,000,000 records. Elapsed time: 00:15:46s. Time for last 1,000,000: 1s. Last read position: chr17:17,495,989
INFO 2026-06-08 09:07:17 MarkDuplicates Tracking 414900 as yet unmatched pairs. 137531 records in RAM.
INFO 2026-06-08 09:07:19 MarkDuplicates Read 435,000,000 records. Elapsed time: 00:15:48s. Time for last 1,000,000: 1s. Last read position: chr17:19,332,040
INFO 2026-06-08 09:07:19 MarkDuplicates Tracking 411616 as yet unmatched pairs. 134235 records in RAM.
INFO 2026-06-08 09:07:21 MarkDuplicates Read 436,000,000 records. Elapsed time: 00:15:49s. Time for last 1,000,000: 1s. Last read position: chr17:28,631,646
INFO 2026-06-08 09:07:21 MarkDuplicates Tracking 408941 as yet unmatched pairs. 131558 records in RAM.
INFO 2026-06-08 09:07:23 MarkDuplicates Read 437,000,000 records. Elapsed time: 00:15:51s. Time for last 1,000,000: 2s. Last read position: chr17:30,249,038
INFO 2026-06-08 09:07:23 MarkDuplicates Tracking 406097 as yet unmatched pairs. 128713 records in RAM.
INFO 2026-06-08 09:07:25 MarkDuplicates Read 438,000,000 records. Elapsed time: 00:15:54s. Time for last 1,000,000: 2s. Last read position: chr17:35,353,503
INFO 2026-06-08 09:07:25 MarkDuplicates Tracking 403426 as yet unmatched pairs. 126038 records in RAM.
INFO 2026-06-08 09:07:27 MarkDuplicates Read 439,000,000 records. Elapsed time: 00:15:56s. Time for last 1,000,000: 2s. Last read position: chr17:37,934,670
INFO 2026-06-08 09:07:27 MarkDuplicates Tracking 401351 as yet unmatched pairs. 123960 records in RAM.
INFO 2026-06-08 09:07:29 MarkDuplicates Read 440,000,000 records. Elapsed time: 00:15:58s. Time for last 1,000,000: 1s. Last read position: chr17:39,201,280
INFO 2026-06-08 09:07:29 MarkDuplicates Tracking 405433 as yet unmatched pairs. 128036 records in RAM.
INFO 2026-06-08 09:07:31 MarkDuplicates Read 441,000,000 records. Elapsed time: 00:16:00s. Time for last 1,000,000: 1s. Last read position: chr17:39,725,392
INFO 2026-06-08 09:07:31 MarkDuplicates Tracking 398418 as yet unmatched pairs. 121021 records in RAM.
INFO 2026-06-08 09:07:33 MarkDuplicates Read 442,000,000 records. Elapsed time: 00:16:01s. Time for last 1,000,000: 1s. Last read position: chr17:40,496,259
INFO 2026-06-08 09:07:33 MarkDuplicates Tracking 394572 as yet unmatched pairs. 117175 records in RAM.
INFO 2026-06-08 09:07:34 MarkDuplicates Read 443,000,000 records. Elapsed time: 00:16:03s. Time for last 1,000,000: 1s. Last read position: chr17:42,023,812
INFO 2026-06-08 09:07:34 MarkDuplicates Tracking 390626 as yet unmatched pairs. 113229 records in RAM.
INFO 2026-06-08 09:07:36 MarkDuplicates Read 444,000,000 records. Elapsed time: 00:16:05s. Time for last 1,000,000: 1s. Last read position: chr17:42,998,801
INFO 2026-06-08 09:07:36 MarkDuplicates Tracking 389147 as yet unmatched pairs. 111749 records in RAM.
INFO 2026-06-08 09:07:38 MarkDuplicates Read 445,000,000 records. Elapsed time: 00:16:07s. Time for last 1,000,000: 2s. Last read position: chr17:44,397,704
INFO 2026-06-08 09:07:38 MarkDuplicates Tracking 385013 as yet unmatched pairs. 107615 records in RAM.
INFO 2026-06-08 09:07:40 MarkDuplicates Read 446,000,000 records. Elapsed time: 00:16:09s. Time for last 1,000,000: 1s. Last read position: chr17:46,549,450
INFO 2026-06-08 09:07:40 MarkDuplicates Tracking 382403 as yet unmatched pairs. 105002 records in RAM.
INFO 2026-06-08 09:07:42 MarkDuplicates Read 447,000,000 records. Elapsed time: 00:16:10s. Time for last 1,000,000: 1s. Last read position: chr17:48,894,426
INFO 2026-06-08 09:07:42 MarkDuplicates Tracking 381048 as yet unmatched pairs. 103645 records in RAM.
INFO 2026-06-08 09:07:44 MarkDuplicates Read 448,000,000 records. Elapsed time: 00:16:13s. Time for last 1,000,000: 2s. Last read position: chr17:50,185,934
INFO 2026-06-08 09:07:44 MarkDuplicates Tracking 396440 as yet unmatched pairs. 119037 records in RAM.
INFO 2026-06-08 09:07:46 MarkDuplicates Read 449,000,000 records. Elapsed time: 00:16:15s. Time for last 1,000,000: 1s. Last read position: chr17:50,187,014
INFO 2026-06-08 09:07:46 MarkDuplicates Tracking 434143 as yet unmatched pairs. 156739 records in RAM.
INFO 2026-06-08 09:07:48 MarkDuplicates Read 450,000,000 records. Elapsed time: 00:16:17s. Time for last 1,000,000: 2s. Last read position: chr17:50,187,900
INFO 2026-06-08 09:07:48 MarkDuplicates Tracking 448110 as yet unmatched pairs. 170703 records in RAM.
INFO 2026-06-08 09:07:50 MarkDuplicates Read 451,000,000 records. Elapsed time: 00:16:19s. Time for last 1,000,000: 2s. Last read position: chr17:50,188,549
INFO 2026-06-08 09:07:50 MarkDuplicates Tracking 435163 as yet unmatched pairs. 157755 records in RAM.
INFO 2026-06-08 09:07:53 MarkDuplicates Read 452,000,000 records. Elapsed time: 00:16:22s. Time for last 1,000,000: 2s. Last read position: chr17:50,188,943
INFO 2026-06-08 09:07:53 MarkDuplicates Tracking 433956 as yet unmatched pairs. 156548 records in RAM.
INFO 2026-06-08 09:07:55 MarkDuplicates Read 453,000,000 records. Elapsed time: 00:16:24s. Time for last 1,000,000: 1s. Last read position: chr17:50,189,447
INFO 2026-06-08 09:07:55 MarkDuplicates Tracking 429331 as yet unmatched pairs. 151916 records in RAM.
INFO 2026-06-08 09:07:57 MarkDuplicates Read 454,000,000 records. Elapsed time: 00:16:26s. Time for last 1,000,000: 1s. Last read position: chr17:50,189,895
INFO 2026-06-08 09:07:57 MarkDuplicates Tracking 430814 as yet unmatched pairs. 153399 records in RAM.
INFO 2026-06-08 09:07:59 MarkDuplicates Read 455,000,000 records. Elapsed time: 00:16:27s. Time for last 1,000,000: 1s. Last read position: chr17:50,190,358
INFO 2026-06-08 09:07:59 MarkDuplicates Tracking 448790 as yet unmatched pairs. 171374 records in RAM.
INFO 2026-06-08 09:08:01 MarkDuplicates Read 456,000,000 records. Elapsed time: 00:16:29s. Time for last 1,000,000: 1s. Last read position: chr17:50,191,421
INFO 2026-06-08 09:08:01 MarkDuplicates Tracking 436152 as yet unmatched pairs. 158735 records in RAM.
INFO 2026-06-08 09:08:03 MarkDuplicates Read 457,000,000 records. Elapsed time: 00:16:31s. Time for last 1,000,000: 2s. Last read position: chr17:50,192,013
INFO 2026-06-08 09:08:03 MarkDuplicates Tracking 426833 as yet unmatched pairs. 149415 records in RAM.
INFO 2026-06-08 09:08:05 MarkDuplicates Read 458,000,000 records. Elapsed time: 00:16:34s. Time for last 1,000,000: 2s. Last read position: chr17:50,192,834
INFO 2026-06-08 09:08:05 MarkDuplicates Tracking 435287 as yet unmatched pairs. 157864 records in RAM.
INFO 2026-06-08 09:08:07 MarkDuplicates Read 459,000,000 records. Elapsed time: 00:16:35s. Time for last 1,000,000: 1s. Last read position: chr17:50,194,015
INFO 2026-06-08 09:08:07 MarkDuplicates Tracking 446519 as yet unmatched pairs. 169096 records in RAM.
INFO 2026-06-08 09:08:09 MarkDuplicates Read 460,000,000 records. Elapsed time: 00:16:37s. Time for last 1,000,000: 2s. Last read position: chr17:50,194,413
INFO 2026-06-08 09:08:09 MarkDuplicates Tracking 422654 as yet unmatched pairs. 145231 records in RAM.
INFO 2026-06-08 09:08:11 MarkDuplicates Read 461,000,000 records. Elapsed time: 00:16:39s. Time for last 1,000,000: 1s. Last read position: chr17:50,195,050
INFO 2026-06-08 09:08:11 MarkDuplicates Tracking 416852 as yet unmatched pairs. 139429 records in RAM.
INFO 2026-06-08 09:08:13 MarkDuplicates Read 462,000,000 records. Elapsed time: 00:16:41s. Time for last 1,000,000: 1s. Last read position: chr17:50,195,566
INFO 2026-06-08 09:08:13 MarkDuplicates Tracking 422328 as yet unmatched pairs. 144904 records in RAM.
INFO 2026-06-08 09:08:15 MarkDuplicates Read 463,000,000 records. Elapsed time: 00:16:43s. Time for last 1,000,000: 2s. Last read position: chr17:50,196,154
INFO 2026-06-08 09:08:15 MarkDuplicates Tracking 431004 as yet unmatched pairs. 153580 records in RAM.
INFO 2026-06-08 09:08:17 MarkDuplicates Read 464,000,000 records. Elapsed time: 00:16:46s. Time for last 1,000,000: 2s. Last read position: chr17:50,196,502
INFO 2026-06-08 09:08:17 MarkDuplicates Tracking 425324 as yet unmatched pairs. 147900 records in RAM.
INFO 2026-06-08 09:08:19 MarkDuplicates Read 465,000,000 records. Elapsed time: 00:16:48s. Time for last 1,000,000: 2s. Last read position: chr17:50,197,205
INFO 2026-06-08 09:08:19 MarkDuplicates Tracking 432676 as yet unmatched pairs. 155239 records in RAM.
INFO 2026-06-08 09:08:22 MarkDuplicates Read 466,000,000 records. Elapsed time: 00:16:50s. Time for last 1,000,000: 2s. Last read position: chr17:50,198,438
INFO 2026-06-08 09:08:22 MarkDuplicates Tracking 373386 as yet unmatched pairs. 95944 records in RAM.
INFO 2026-06-08 09:08:23 MarkDuplicates Read 467,000,000 records. Elapsed time: 00:16:52s. Time for last 1,000,000: 1s. Last read position: chr17:50,199,447
INFO 2026-06-08 09:08:23 MarkDuplicates Tracking 359121 as yet unmatched pairs. 81679 records in RAM.
INFO 2026-06-08 09:08:25 MarkDuplicates Read 468,000,000 records. Elapsed time: 00:16:54s. Time for last 1,000,000: 1s. Last read position: chr17:50,551,098
INFO 2026-06-08 09:08:25 MarkDuplicates Tracking 315934 as yet unmatched pairs. 38491 records in RAM.
INFO 2026-06-08 09:08:27 MarkDuplicates Read 469,000,000 records. Elapsed time: 00:16:56s. Time for last 1,000,000: 1s. Last read position: chr17:58,347,542
INFO 2026-06-08 09:08:27 MarkDuplicates Tracking 313554 as yet unmatched pairs. 36105 records in RAM.
INFO 2026-06-08 09:08:29 MarkDuplicates Read 470,000,000 records. Elapsed time: 00:16:57s. Time for last 1,000,000: 1s. Last read position: chr17:59,685,725
INFO 2026-06-08 09:08:29 MarkDuplicates Tracking 313069 as yet unmatched pairs. 35619 records in RAM.
INFO 2026-06-08 09:08:30 MarkDuplicates Read 471,000,000 records. Elapsed time: 00:16:59s. Time for last 1,000,000: 1s. Last read position: chr17:63,834,314
INFO 2026-06-08 09:08:30 MarkDuplicates Tracking 308173 as yet unmatched pairs. 30710 records in RAM.
INFO 2026-06-08 09:08:32 MarkDuplicates Read 472,000,000 records. Elapsed time: 00:17:01s. Time for last 1,000,000: 1s. Last read position: chr17:68,515,523
INFO 2026-06-08 09:08:32 MarkDuplicates Tracking 307823 as yet unmatched pairs. 30359 records in RAM.
INFO 2026-06-08 09:08:34 MarkDuplicates Read 473,000,000 records. Elapsed time: 00:17:02s. Time for last 1,000,000: 1s. Last read position: chr17:74,959,893
INFO 2026-06-08 09:08:34 MarkDuplicates Tracking 303217 as yet unmatched pairs. 25751 records in RAM.
INFO 2026-06-08 09:08:35 MarkDuplicates Read 474,000,000 records. Elapsed time: 00:17:04s. Time for last 1,000,000: 1s. Last read position: chr17:75,651,203
INFO 2026-06-08 09:08:35 MarkDuplicates Tracking 299013 as yet unmatched pairs. 21546 records in RAM.
INFO 2026-06-08 09:08:37 MarkDuplicates Read 475,000,000 records. Elapsed time: 00:17:05s. Time for last 1,000,000: 1s. Last read position: chr17:76,391,011
INFO 2026-06-08 09:08:37 MarkDuplicates Tracking 296039 as yet unmatched pairs. 18572 records in RAM.
INFO 2026-06-08 09:08:39 MarkDuplicates Read 476,000,000 records. Elapsed time: 00:17:07s. Time for last 1,000,000: 1s. Last read position: chr17:78,814,127
INFO 2026-06-08 09:08:39 MarkDuplicates Tracking 292823 as yet unmatched pairs. 15352 records in RAM.
INFO 2026-06-08 09:08:40 MarkDuplicates Read 477,000,000 records. Elapsed time: 00:17:09s. Time for last 1,000,000: 1s. Last read position: chr17:80,332,445
INFO 2026-06-08 09:08:40 MarkDuplicates Tracking 290639 as yet unmatched pairs. 13163 records in RAM.
INFO 2026-06-08 09:08:43 MarkDuplicates Read 478,000,000 records. Elapsed time: 00:17:12s. Time for last 1,000,000: 2s. Last read position: chr17:81,510,692
INFO 2026-06-08 09:08:43 MarkDuplicates Tracking 288453 as yet unmatched pairs. 10969 records in RAM.
INFO 2026-06-08 09:08:45 MarkDuplicates Read 479,000,000 records. Elapsed time: 00:17:14s. Time for last 1,000,000: 2s. Last read position: chr17:81,847,009
INFO 2026-06-08 09:08:45 MarkDuplicates Tracking 287386 as yet unmatched pairs. 9902 records in RAM.
INFO 2026-06-08 09:08:47 MarkDuplicates Read 480,000,000 records. Elapsed time: 00:17:16s. Time for last 1,000,000: 1s. Last read position: chr17:82,083,309
INFO 2026-06-08 09:08:47 MarkDuplicates Tracking 281618 as yet unmatched pairs. 4134 records in RAM.
INFO 2026-06-08 09:08:49 MarkDuplicates Read 481,000,000 records. Elapsed time: 00:17:18s. Time for last 1,000,000: 2s. Last read position: chr17:82,923,523
INFO 2026-06-08 09:08:49 MarkDuplicates Tracking 277963 as yet unmatched pairs. 478 records in RAM.
INFO 2026-06-08 09:08:51 MarkDuplicates Read 482,000,000 records. Elapsed time: 00:17:20s. Time for last 1,000,000: 1s. Last read position: chr18:11,851,662
INFO 2026-06-08 09:08:51 MarkDuplicates Tracking 275429 as yet unmatched pairs. 11517 records in RAM.
INFO 2026-06-08 09:08:53 MarkDuplicates Read 483,000,000 records. Elapsed time: 00:17:21s. Time for last 1,000,000: 1s. Last read position: chr18:31,524,482
INFO 2026-06-08 09:08:53 MarkDuplicates Tracking 273266 as yet unmatched pairs. 9347 records in RAM.
INFO 2026-06-08 09:08:54 MarkDuplicates Read 484,000,000 records. Elapsed time: 00:17:23s. Time for last 1,000,000: 1s. Last read position: chr18:49,331,890
INFO 2026-06-08 09:08:54 MarkDuplicates Tracking 270102 as yet unmatched pairs. 6182 records in RAM.
INFO 2026-06-08 09:08:56 MarkDuplicates Read 485,000,000 records. Elapsed time: 00:17:25s. Time for last 1,000,000: 1s. Last read position: chr18:59,155,788
INFO 2026-06-08 09:08:56 MarkDuplicates Tracking 267917 as yet unmatched pairs. 3993 records in RAM.
INFO 2026-06-08 09:08:58 MarkDuplicates Read 486,000,000 records. Elapsed time: 00:17:27s. Time for last 1,000,000: 1s. Last read position: chr18:79,714,739
INFO 2026-06-08 09:08:58 MarkDuplicates Tracking 264763 as yet unmatched pairs. 834 records in RAM.
INFO 2026-06-08 09:09:02 MarkDuplicates Read 487,000,000 records. Elapsed time: 00:17:30s. Time for last 1,000,000: 3s. Last read position: chr19:758,049
INFO 2026-06-08 09:09:02 MarkDuplicates Tracking 263226 as yet unmatched pairs. 129570 records in RAM.
INFO 2026-06-08 09:09:04 MarkDuplicates Read 488,000,000 records. Elapsed time: 00:17:33s. Time for last 1,000,000: 2s. Last read position: chr19:1,112,373
INFO 2026-06-08 09:09:04 MarkDuplicates Tracking 258141 as yet unmatched pairs. 124484 records in RAM.
INFO 2026-06-08 09:09:06 MarkDuplicates Read 489,000,000 records. Elapsed time: 00:17:35s. Time for last 1,000,000: 2s. Last read position: chr19:1,483,334
INFO 2026-06-08 09:09:06 MarkDuplicates Tracking 254463 as yet unmatched pairs. 120806 records in RAM.
INFO 2026-06-08 09:09:09 MarkDuplicates Read 490,000,000 records. Elapsed time: 00:17:37s. Time for last 1,000,000: 2s. Last read position: chr19:2,226,576
INFO 2026-06-08 09:09:09 MarkDuplicates Tracking 252009 as yet unmatched pairs. 118346 records in RAM.
INFO 2026-06-08 09:09:11 MarkDuplicates Read 491,000,000 records. Elapsed time: 00:17:40s. Time for last 1,000,000: 2s. Last read position: chr19:3,532,579
INFO 2026-06-08 09:09:11 MarkDuplicates Tracking 248511 as yet unmatched pairs. 114848 records in RAM.
INFO 2026-06-08 09:09:14 MarkDuplicates Read 492,000,000 records. Elapsed time: 00:17:42s. Time for last 1,000,000: 2s. Last read position: chr19:4,446,172
INFO 2026-06-08 09:09:14 MarkDuplicates Tracking 244899 as yet unmatched pairs. 111235 records in RAM.
INFO 2026-06-08 09:09:16 MarkDuplicates Read 493,000,000 records. Elapsed time: 00:17:45s. Time for last 1,000,000: 2s. Last read position: chr19:5,719,702
INFO 2026-06-08 09:09:16 MarkDuplicates Tracking 241800 as yet unmatched pairs. 108135 records in RAM.
INFO 2026-06-08 09:09:18 MarkDuplicates Read 494,000,000 records. Elapsed time: 00:17:47s. Time for last 1,000,000: 2s. Last read position: chr19:6,532,791
INFO 2026-06-08 09:09:18 MarkDuplicates Tracking 238810 as yet unmatched pairs. 105143 records in RAM.
INFO 2026-06-08 09:09:20 MarkDuplicates Read 495,000,000 records. Elapsed time: 00:17:49s. Time for last 1,000,000: 2s. Last read position: chr19:7,682,507
INFO 2026-06-08 09:09:20 MarkDuplicates Tracking 236429 as yet unmatched pairs. 102760 records in RAM.
INFO 2026-06-08 09:09:22 MarkDuplicates Read 496,000,000 records. Elapsed time: 00:17:51s. Time for last 1,000,000: 2s. Last read position: chr19:10,092,116
INFO 2026-06-08 09:09:22 MarkDuplicates Tracking 232913 as yet unmatched pairs. 99242 records in RAM.
INFO 2026-06-08 09:10:28 MarkDuplicates Read 497,000,000 records. Elapsed time: 00:18:57s. Time for last 1,000,000: 66s. Last read position: chr19:10,683,386
INFO 2026-06-08 09:10:28 MarkDuplicates Tracking 229832 as yet unmatched pairs. 96161 records in RAM.
INFO 2026-06-08 09:11:39 MarkDuplicates Read 498,000,000 records. Elapsed time: 00:20:08s. Time for last 1,000,000: 70s. Last read position: chr19:11,252,203
INFO 2026-06-08 09:11:39 MarkDuplicates Tracking 226640 as yet unmatched pairs. 92969 records in RAM.
INFO 2026-06-08 09:11:41 MarkDuplicates Read 499,000,000 records. Elapsed time: 00:20:10s. Time for last 1,000,000: 1s. Last read position: chr19:12,792,167
INFO 2026-06-08 09:11:41 MarkDuplicates Tracking 227102 as yet unmatched pairs. 93431 records in RAM.
INFO 2026-06-08 09:11:43 MarkDuplicates Read 500,000,000 records. Elapsed time: 00:20:12s. Time for last 1,000,000: 2s. Last read position: chr19:13,919,839
INFO 2026-06-08 09:11:43 MarkDuplicates Tracking 220483 as yet unmatched pairs. 86811 records in RAM.
INFO 2026-06-08 09:11:45 MarkDuplicates Read 501,000,000 records. Elapsed time: 00:20:14s. Time for last 1,000,000: 1s. Last read position: chr19:14,516,703
INFO 2026-06-08 09:11:45 MarkDuplicates Tracking 232797 as yet unmatched pairs. 99124 records in RAM.
INFO 2026-06-08 09:11:47 MarkDuplicates Read 502,000,000 records. Elapsed time: 00:20:15s. Time for last 1,000,000: 1s. Last read position: chr19:15,239,927
INFO 2026-06-08 09:11:47 MarkDuplicates Tracking 215156 as yet unmatched pairs. 81483 records in RAM.
INFO 2026-06-08 09:11:49 MarkDuplicates Read 503,000,000 records. Elapsed time: 00:20:17s. Time for last 1,000,000: 1s. Last read position: chr19:16,568,150
INFO 2026-06-08 09:11:49 MarkDuplicates Tracking 211403 as yet unmatched pairs. 77730 records in RAM.
INFO 2026-06-08 09:11:51 MarkDuplicates Read 504,000,000 records. Elapsed time: 00:20:19s. Time for last 1,000,000: 2s. Last read position: chr19:17,861,313
INFO 2026-06-08 09:11:51 MarkDuplicates Tracking 210987 as yet unmatched pairs. 77314 records in RAM.
INFO 2026-06-08 09:11:52 MarkDuplicates Read 505,000,000 records. Elapsed time: 00:20:21s. Time for last 1,000,000: 1s. Last read position: chr19:18,539,445
INFO 2026-06-08 09:11:52 MarkDuplicates Tracking 206051 as yet unmatched pairs. 72378 records in RAM.
INFO 2026-06-08 09:11:54 MarkDuplicates Read 506,000,000 records. Elapsed time: 00:20:23s. Time for last 1,000,000: 1s. Last read position: chr19:19,635,199
INFO 2026-06-08 09:11:54 MarkDuplicates Tracking 202095 as yet unmatched pairs. 68421 records in RAM.
INFO 2026-06-08 09:11:56 MarkDuplicates Read 507,000,000 records. Elapsed time: 00:20:25s. Time for last 1,000,000: 1s. Last read position: chr19:34,409,303
INFO 2026-06-08 09:11:56 MarkDuplicates Tracking 199323 as yet unmatched pairs. 65644 records in RAM.
INFO 2026-06-08 09:11:58 MarkDuplicates Read 508,000,000 records. Elapsed time: 00:20:26s. Time for last 1,000,000: 1s. Last read position: chr19:35,729,018
INFO 2026-06-08 09:11:58 MarkDuplicates Tracking 195946 as yet unmatched pairs. 62266 records in RAM.
INFO 2026-06-08 09:11:59 MarkDuplicates Read 509,000,000 records. Elapsed time: 00:20:28s. Time for last 1,000,000: 1s. Last read position: chr19:38,327,326
INFO 2026-06-08 09:11:59 MarkDuplicates Tracking 193679 as yet unmatched pairs. 59998 records in RAM.
INFO 2026-06-08 09:12:01 MarkDuplicates Read 510,000,000 records. Elapsed time: 00:20:30s. Time for last 1,000,000: 2s. Last read position: chr19:39,175,005
INFO 2026-06-08 09:12:01 MarkDuplicates Tracking 191035 as yet unmatched pairs. 57353 records in RAM.
INFO 2026-06-08 09:12:03 MarkDuplicates Read 511,000,000 records. Elapsed time: 00:20:32s. Time for last 1,000,000: 1s. Last read position: chr19:39,867,072
INFO 2026-06-08 09:12:03 MarkDuplicates Tracking 189331 as yet unmatched pairs. 55647 records in RAM.
INFO 2026-06-08 09:12:05 MarkDuplicates Read 512,000,000 records. Elapsed time: 00:20:33s. Time for last 1,000,000: 1s. Last read position: chr19:39,886,348
INFO 2026-06-08 09:12:05 MarkDuplicates Tracking 189403 as yet unmatched pairs. 55718 records in RAM.
INFO 2026-06-08 09:12:06 MarkDuplicates Read 513,000,000 records. Elapsed time: 00:20:35s. Time for last 1,000,000: 1s. Last read position: chr19:39,901,997
INFO 2026-06-08 09:12:06 MarkDuplicates Tracking 185100 as yet unmatched pairs. 51408 records in RAM.
INFO 2026-06-08 09:12:09 MarkDuplicates Read 514,000,000 records. Elapsed time: 00:20:37s. Time for last 1,000,000: 2s. Last read position: chr19:40,233,842
INFO 2026-06-08 09:12:09 MarkDuplicates Tracking 182011 as yet unmatched pairs. 48319 records in RAM.
INFO 2026-06-08 09:12:11 MarkDuplicates Read 515,000,000 records. Elapsed time: 00:20:39s. Time for last 1,000,000: 1s. Last read position: chr19:41,305,673
INFO 2026-06-08 09:12:11 MarkDuplicates Tracking 176708 as yet unmatched pairs. 43013 records in RAM.
INFO 2026-06-08 09:12:13 MarkDuplicates Read 516,000,000 records. Elapsed time: 00:20:41s. Time for last 1,000,000: 2s. Last read position: chr19:41,904,261
INFO 2026-06-08 09:12:13 MarkDuplicates Tracking 174352 as yet unmatched pairs. 40657 records in RAM.
INFO 2026-06-08 09:12:15 MarkDuplicates Read 517,000,000 records. Elapsed time: 00:20:44s. Time for last 1,000,000: 2s. Last read position: chr19:42,293,678
INFO 2026-06-08 09:12:15 MarkDuplicates Tracking 171972 as yet unmatched pairs. 38277 records in RAM.
INFO 2026-06-08 09:12:17 MarkDuplicates Read 518,000,000 records. Elapsed time: 00:20:46s. Time for last 1,000,000: 2s. Last read position: chr19:44,793,429
INFO 2026-06-08 09:12:17 MarkDuplicates Tracking 168019 as yet unmatched pairs. 34324 records in RAM.
INFO 2026-06-08 09:12:19 MarkDuplicates Read 519,000,000 records. Elapsed time: 00:20:48s. Time for last 1,000,000: 1s. Last read position: chr19:45,525,983
INFO 2026-06-08 09:12:19 MarkDuplicates Tracking 165397 as yet unmatched pairs. 31697 records in RAM.
INFO 2026-06-08 09:12:21 MarkDuplicates Read 520,000,000 records. Elapsed time: 00:20:49s. Time for last 1,000,000: 1s. Last read position: chr19:46,787,706
INFO 2026-06-08 09:12:21 MarkDuplicates Tracking 162175 as yet unmatched pairs. 28475 records in RAM.
INFO 2026-06-08 09:12:22 MarkDuplicates Read 521,000,000 records. Elapsed time: 00:20:51s. Time for last 1,000,000: 1s. Last read position: chr19:48,472,424
INFO 2026-06-08 09:12:22 MarkDuplicates Tracking 158475 as yet unmatched pairs. 24774 records in RAM.
INFO 2026-06-08 09:12:24 MarkDuplicates Read 522,000,000 records. Elapsed time: 00:20:53s. Time for last 1,000,000: 1s. Last read position: chr19:48,974,724
INFO 2026-06-08 09:12:24 MarkDuplicates Tracking 155307 as yet unmatched pairs. 21604 records in RAM.
INFO 2026-06-08 09:12:26 MarkDuplicates Read 523,000,000 records. Elapsed time: 00:20:55s. Time for last 1,000,000: 1s. Last read position: chr19:49,497,932
INFO 2026-06-08 09:12:26 MarkDuplicates Tracking 156633 as yet unmatched pairs. 22930 records in RAM.
INFO 2026-06-08 09:12:28 MarkDuplicates Read 524,000,000 records. Elapsed time: 00:20:56s. Time for last 1,000,000: 1s. Last read position: chr19:49,863,828
INFO 2026-06-08 09:12:28 MarkDuplicates Tracking 149479 as yet unmatched pairs. 15775 records in RAM.
INFO 2026-06-08 09:12:29 MarkDuplicates Read 525,000,000 records. Elapsed time: 00:20:58s. Time for last 1,000,000: 1s. Last read position: chr19:51,994,020
INFO 2026-06-08 09:12:29 MarkDuplicates Tracking 145879 as yet unmatched pairs. 12175 records in RAM.
INFO 2026-06-08 09:12:31 MarkDuplicates Read 526,000,000 records. Elapsed time: 00:21:00s. Time for last 1,000,000: 1s. Last read position: chr19:54,201,196
INFO 2026-06-08 09:12:31 MarkDuplicates Tracking 147094 as yet unmatched pairs. 13389 records in RAM.
INFO 2026-06-08 09:12:33 MarkDuplicates Read 527,000,000 records. Elapsed time: 00:21:01s. Time for last 1,000,000: 1s. Last read position: chr19:55,242,468
INFO 2026-06-08 09:12:33 MarkDuplicates Tracking 141073 as yet unmatched pairs. 7368 records in RAM.
INFO 2026-06-08 09:12:34 MarkDuplicates Read 528,000,000 records. Elapsed time: 00:21:03s. Time for last 1,000,000: 1s. Last read position: chr19:57,212,230
INFO 2026-06-08 09:12:34 MarkDuplicates Tracking 137135 as yet unmatched pairs. 3430 records in RAM.
INFO 2026-06-08 09:12:36 MarkDuplicates Read 529,000,000 records. Elapsed time: 00:21:04s. Time for last 1,000,000: 1s. Last read position: chr19:58,550,426
INFO 2026-06-08 09:12:36 MarkDuplicates Tracking 136606 as yet unmatched pairs. 2899 records in RAM.
INFO 2026-06-08 09:12:38 MarkDuplicates Read 530,000,000 records. Elapsed time: 00:21:07s. Time for last 1,000,000: 2s. Last read position: chr20:3,200,367
INFO 2026-06-08 09:12:38 MarkDuplicates Tracking 131126 as yet unmatched pairs. 31618 records in RAM.
INFO 2026-06-08 09:12:40 MarkDuplicates Read 531,000,000 records. Elapsed time: 00:21:08s. Time for last 1,000,000: 1s. Last read position: chr20:13,801,556
INFO 2026-06-08 09:12:40 MarkDuplicates Tracking 127986 as yet unmatched pairs. 28475 records in RAM.
INFO 2026-06-08 09:12:42 MarkDuplicates Read 532,000,000 records. Elapsed time: 00:21:11s. Time for last 1,000,000: 2s. Last read position: chr20:20,601,074
INFO 2026-06-08 09:12:42 MarkDuplicates Tracking 125495 as yet unmatched pairs. 25982 records in RAM.
INFO 2026-06-08 09:12:45 MarkDuplicates Read 533,000,000 records. Elapsed time: 00:21:14s. Time for last 1,000,000: 2s. Last read position: chr20:32,228,278
INFO 2026-06-08 09:12:45 MarkDuplicates Tracking 122857 as yet unmatched pairs. 23344 records in RAM.
INFO 2026-06-08 09:12:47 MarkDuplicates Read 534,000,000 records. Elapsed time: 00:21:16s. Time for last 1,000,000: 2s. Last read position: chr20:35,174,766
INFO 2026-06-08 09:12:47 MarkDuplicates Tracking 119932 as yet unmatched pairs. 20418 records in RAM.
INFO 2026-06-08 09:12:49 MarkDuplicates Read 535,000,000 records. Elapsed time: 00:21:17s. Time for last 1,000,000: 1s. Last read position: chr20:37,230,011
INFO 2026-06-08 09:12:49 MarkDuplicates Tracking 119265 as yet unmatched pairs. 19751 records in RAM.
INFO 2026-06-08 09:12:50 MarkDuplicates Read 536,000,000 records. Elapsed time: 00:21:19s. Time for last 1,000,000: 1s. Last read position: chr20:45,174,936
INFO 2026-06-08 09:12:50 MarkDuplicates Tracking 115810 as yet unmatched pairs. 16296 records in RAM.
INFO 2026-06-08 09:12:52 MarkDuplicates Read 537,000,000 records. Elapsed time: 00:21:21s. Time for last 1,000,000: 1s. Last read position: chr20:48,652,590
INFO 2026-06-08 09:12:52 MarkDuplicates Tracking 111548 as yet unmatched pairs. 12034 records in RAM.
INFO 2026-06-08 09:12:54 MarkDuplicates Read 538,000,000 records. Elapsed time: 00:21:23s. Time for last 1,000,000: 2s. Last read position: chr20:56,517,125
INFO 2026-06-08 09:12:54 MarkDuplicates Tracking 109201 as yet unmatched pairs. 9687 records in RAM.
INFO 2026-06-08 09:12:56 MarkDuplicates Read 539,000,000 records. Elapsed time: 00:21:25s. Time for last 1,000,000: 1s. Last read position: chr20:62,323,597
INFO 2026-06-08 09:12:56 MarkDuplicates Tracking 106677 as yet unmatched pairs. 7163 records in RAM.
INFO 2026-06-08 09:12:58 MarkDuplicates Read 540,000,000 records. Elapsed time: 00:21:26s. Time for last 1,000,000: 1s. Last read position: chr20:63,521,830
INFO 2026-06-08 09:12:58 MarkDuplicates Tracking 103237 as yet unmatched pairs. 3719 records in RAM.
INFO 2026-06-08 09:13:00 MarkDuplicates Read 541,000,000 records. Elapsed time: 00:21:28s. Time for last 1,000,000: 2s. Last read position: chr21:5,147,857
INFO 2026-06-08 09:13:00 MarkDuplicates Tracking 99304 as yet unmatched pairs. 21025 records in RAM.
INFO 2026-06-08 09:13:01 MarkDuplicates Read 542,000,000 records. Elapsed time: 00:21:30s. Time for last 1,000,000: 1s. Last read position: chr21:8,443,280
INFO 2026-06-08 09:13:01 MarkDuplicates Tracking 97962 as yet unmatched pairs. 19682 records in RAM.
INFO 2026-06-08 09:13:02 MarkDuplicates Read 543,000,000 records. Elapsed time: 00:21:31s. Time for last 1,000,000: 1s. Last read position: chr21:26,468,544
INFO 2026-06-08 09:13:02 MarkDuplicates Tracking 95711 as yet unmatched pairs. 17430 records in RAM.
INFO 2026-06-08 09:13:04 MarkDuplicates Read 544,000,000 records. Elapsed time: 00:21:33s. Time for last 1,000,000: 1s. Last read position: chr21:33,660,781
INFO 2026-06-08 09:13:04 MarkDuplicates Tracking 93048 as yet unmatched pairs. 14761 records in RAM.
INFO 2026-06-08 09:13:06 MarkDuplicates Read 545,000,000 records. Elapsed time: 00:21:34s. Time for last 1,000,000: 1s. Last read position: chr21:41,168,342
INFO 2026-06-08 09:13:06 MarkDuplicates Tracking 90953 as yet unmatched pairs. 12666 records in RAM.
INFO 2026-06-08 09:13:08 MarkDuplicates Read 546,000,000 records. Elapsed time: 00:21:36s. Time for last 1,000,000: 1s. Last read position: chr21:42,362,440
INFO 2026-06-08 09:13:08 MarkDuplicates Tracking 90183 as yet unmatched pairs. 11896 records in RAM.
INFO 2026-06-08 09:13:09 MarkDuplicates Read 547,000,000 records. Elapsed time: 00:21:38s. Time for last 1,000,000: 1s. Last read position: chr21:44,861,788
INFO 2026-06-08 09:13:09 MarkDuplicates Tracking 84907 as yet unmatched pairs. 6620 records in RAM.
INFO 2026-06-08 09:13:12 MarkDuplicates Read 548,000,000 records. Elapsed time: 00:21:40s. Time for last 1,000,000: 2s. Last read position: chr21:46,112,311
INFO 2026-06-08 09:13:12 MarkDuplicates Tracking 82164 as yet unmatched pairs. 3877 records in RAM.
INFO 2026-06-08 09:13:15 MarkDuplicates Read 549,000,000 records. Elapsed time: 00:21:44s. Time for last 1,000,000: 3s. Last read position: chr22:17,727,039
INFO 2026-06-08 09:13:15 MarkDuplicates Tracking 78167 as yet unmatched pairs. 41123 records in RAM.
INFO 2026-06-08 09:13:17 MarkDuplicates Read 550,000,000 records. Elapsed time: 00:21:46s. Time for last 1,000,000: 2s. Last read position: chr22:20,584,969
INFO 2026-06-08 09:13:17 MarkDuplicates Tracking 75466 as yet unmatched pairs. 38422 records in RAM.
INFO 2026-06-08 09:13:19 MarkDuplicates Read 551,000,000 records. Elapsed time: 00:21:47s. Time for last 1,000,000: 1s. Last read position: chr22:23,310,326
INFO 2026-06-08 09:13:19 MarkDuplicates Tracking 73067 as yet unmatched pairs. 36015 records in RAM.
INFO 2026-06-08 09:13:20 MarkDuplicates Read 552,000,000 records. Elapsed time: 00:21:49s. Time for last 1,000,000: 1s. Last read position: chr22:25,170,796
INFO 2026-06-08 09:13:20 MarkDuplicates Tracking 69340 as yet unmatched pairs. 32288 records in RAM.
INFO 2026-06-08 09:13:22 MarkDuplicates Read 553,000,000 records. Elapsed time: 00:21:51s. Time for last 1,000,000: 1s. Last read position: chr22:29,299,277
INFO 2026-06-08 09:13:22 MarkDuplicates Tracking 73630 as yet unmatched pairs. 36578 records in RAM.
INFO 2026-06-08 09:13:24 MarkDuplicates Read 554,000,000 records. Elapsed time: 00:21:53s. Time for last 1,000,000: 1s. Last read position: chr22:31,126,421
INFO 2026-06-08 09:13:24 MarkDuplicates Tracking 63469 as yet unmatched pairs. 26417 records in RAM.
INFO 2026-06-08 09:13:26 MarkDuplicates Read 555,000,000 records. Elapsed time: 00:21:55s. Time for last 1,000,000: 1s. Last read position: chr22:36,285,658
INFO 2026-06-08 09:13:26 MarkDuplicates Tracking 62034 as yet unmatched pairs. 24982 records in RAM.
INFO 2026-06-08 09:13:28 MarkDuplicates Read 556,000,000 records. Elapsed time: 00:21:56s. Time for last 1,000,000: 1s. Last read position: chr22:37,495,877
INFO 2026-06-08 09:13:28 MarkDuplicates Tracking 58053 as yet unmatched pairs. 20997 records in RAM.
INFO 2026-06-08 09:13:29 MarkDuplicates Read 557,000,000 records. Elapsed time: 00:21:58s. Time for last 1,000,000: 1s. Last read position: chr22:38,294,345
INFO 2026-06-08 09:13:29 MarkDuplicates Tracking 55750 as yet unmatched pairs. 18694 records in RAM.
INFO 2026-06-08 09:13:32 MarkDuplicates Read 558,000,000 records. Elapsed time: 00:22:00s. Time for last 1,000,000: 2s. Last read position: chr22:40,300,929
INFO 2026-06-08 09:13:32 MarkDuplicates Tracking 51871 as yet unmatched pairs. 14815 records in RAM.
INFO 2026-06-08 09:13:33 MarkDuplicates Read 559,000,000 records. Elapsed time: 00:22:02s. Time for last 1,000,000: 1s. Last read position: chr22:41,833,240
INFO 2026-06-08 09:13:33 MarkDuplicates Tracking 49061 as yet unmatched pairs. 12005 records in RAM.
INFO 2026-06-08 09:13:35 MarkDuplicates Read 560,000,000 records. Elapsed time: 00:22:04s. Time for last 1,000,000: 1s. Last read position: chr22:44,802,103
INFO 2026-06-08 09:13:35 MarkDuplicates Tracking 46190 as yet unmatched pairs. 9134 records in RAM.
INFO 2026-06-08 09:13:37 MarkDuplicates Read 561,000,000 records. Elapsed time: 00:22:06s. Time for last 1,000,000: 1s. Last read position: chr22:50,193,613
INFO 2026-06-08 09:13:37 MarkDuplicates Tracking 43637 as yet unmatched pairs. 6581 records in RAM.
INFO 2026-06-08 09:13:39 MarkDuplicates Read 562,000,000 records. Elapsed time: 00:22:08s. Time for last 1,000,000: 1s. Last read position: chr22:50,464,872
INFO 2026-06-08 09:13:39 MarkDuplicates Tracking 39864 as yet unmatched pairs. 2808 records in RAM.
INFO 2026-06-08 09:13:41 MarkDuplicates Read 563,000,000 records. Elapsed time: 00:22:10s. Time for last 1,000,000: 2s. Last read position: chrX:2,720,375
INFO 2026-06-08 09:13:41 MarkDuplicates Tracking 37917 as yet unmatched pairs. 35336 records in RAM.
INFO 2026-06-08 09:13:44 MarkDuplicates Read 564,000,000 records. Elapsed time: 00:22:13s. Time for last 1,000,000: 2s. Last read position: chrX:17,099,733
INFO 2026-06-08 09:13:44 MarkDuplicates Tracking 33500 as yet unmatched pairs. 30919 records in RAM.
INFO 2026-06-08 09:13:46 MarkDuplicates Read 565,000,000 records. Elapsed time: 00:22:15s. Time for last 1,000,000: 2s. Last read position: chrX:40,062,887
INFO 2026-06-08 09:13:46 MarkDuplicates Tracking 31405 as yet unmatched pairs. 28823 records in RAM.
INFO 2026-06-08 09:13:48 MarkDuplicates Read 566,000,000 records. Elapsed time: 00:22:17s. Time for last 1,000,000: 1s. Last read position: chrX:47,144,530
INFO 2026-06-08 09:13:48 MarkDuplicates Tracking 28512 as yet unmatched pairs. 25930 records in RAM.
INFO 2026-06-08 09:13:50 MarkDuplicates Read 567,000,000 records. Elapsed time: 00:22:19s. Time for last 1,000,000: 1s. Last read position: chrX:48,903,043
INFO 2026-06-08 09:13:50 MarkDuplicates Tracking 25574 as yet unmatched pairs. 22992 records in RAM.
INFO 2026-06-08 09:13:52 MarkDuplicates Read 568,000,000 records. Elapsed time: 00:22:21s. Time for last 1,000,000: 1s. Last read position: chrX:53,266,926
INFO 2026-06-08 09:13:52 MarkDuplicates Tracking 23164 as yet unmatched pairs. 20582 records in RAM.
INFO 2026-06-08 09:13:54 MarkDuplicates Read 569,000,000 records. Elapsed time: 00:22:22s. Time for last 1,000,000: 1s. Last read position: chrX:66,172,578
INFO 2026-06-08 09:13:54 MarkDuplicates Tracking 20768 as yet unmatched pairs. 18186 records in RAM.
INFO 2026-06-08 09:13:55 MarkDuplicates Read 570,000,000 records. Elapsed time: 00:22:24s. Time for last 1,000,000: 1s. Last read position: chrX:71,564,631
INFO 2026-06-08 09:13:55 MarkDuplicates Tracking 18983 as yet unmatched pairs. 16401 records in RAM.
INFO 2026-06-08 09:13:57 MarkDuplicates Read 571,000,000 records. Elapsed time: 00:22:26s. Time for last 1,000,000: 1s. Last read position: chrX:85,864,797
INFO 2026-06-08 09:13:57 MarkDuplicates Tracking 15278 as yet unmatched pairs. 12696 records in RAM.
INFO 2026-06-08 09:13:59 MarkDuplicates Read 572,000,000 records. Elapsed time: 00:22:28s. Time for last 1,000,000: 2s. Last read position: chrX:119,236,371
INFO 2026-06-08 09:13:59 MarkDuplicates Tracking 13531 as yet unmatched pairs. 10949 records in RAM.
INFO 2026-06-08 09:14:01 MarkDuplicates Read 573,000,000 records. Elapsed time: 00:22:30s. Time for last 1,000,000: 1s. Last read position: chrX:136,511,788
INFO 2026-06-08 09:14:01 MarkDuplicates Tracking 10497 as yet unmatched pairs. 7915 records in RAM.
INFO 2026-06-08 09:14:03 MarkDuplicates Read 574,000,000 records. Elapsed time: 00:22:32s. Time for last 1,000,000: 1s. Last read position: chrX:153,952,825
INFO 2026-06-08 09:14:03 MarkDuplicates Tracking 9343 as yet unmatched pairs. 6760 records in RAM.
INFO 2026-06-08 09:14:06 MarkDuplicates Read 575,000,000 records. Elapsed time: 00:22:34s. Time for last 1,000,000: 2s. Last read position: chrX:154,370,811
INFO 2026-06-08 09:14:06 MarkDuplicates Tracking 5586 as yet unmatched pairs. 3003 records in RAM.
INFO 2026-06-08 09:14:07 MarkDuplicates Read 576,000,000 records. Elapsed time: 00:22:36s. Time for last 1,000,000: 1s. Last read position: GL000220.1:115,464
INFO 2026-06-08 09:14:07 MarkDuplicates Tracking 4529 as yet unmatched pairs. 3122 records in RAM.
INFO 2026-06-08 09:14:09 MarkDuplicates Read 577,000,000 records. Elapsed time: 00:22:37s. Time for last 1,000,000: 1s. Last read position: GL000220.1:160,284
INFO 2026-06-08 09:14:09 MarkDuplicates Tracking 1412 as yet unmatched pairs. 5 records in RAM.
INFO 2026-06-08 09:14:11 MarkDuplicates Read 577987753 records. 0 pairs never matched.
INFO 2026-06-08 09:14:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 204143336; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 09:14:40 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 09:14:45 MarkDuplicates Traversing read pair information and detecting duplicates.
WARNING 2026-06-08 09:14:45 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
INFO 2026-06-08 09:15:43 OpticalDuplicateFinder Large duplicate set. size = 1121
INFO 2026-06-08 09:15:43 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-27,136
INFO 2026-06-08 09:15:43 OpticalDuplicateFinder Large duplicate set. size = 1089
INFO 2026-06-08 09:15:43 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:14,154
INFO 2026-06-08 09:15:44 OpticalDuplicateFinder Large duplicate set. size = 1094
INFO 2026-06-08 09:15:44 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,225
INFO 2026-06-08 09:15:44 OpticalDuplicateFinder Large duplicate set. size = 1001
INFO 2026-06-08 09:15:44 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:8,467
INFO 2026-06-08 09:15:44 OpticalDuplicateFinder Large duplicate set. size = 1508
INFO 2026-06-08 09:15:45 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:5,296
INFO 2026-06-08 09:15:45 OpticalDuplicateFinder Large duplicate set. size = 1849
INFO 2026-06-08 09:15:45 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,552
INFO 2026-06-08 09:15:45 OpticalDuplicateFinder Large duplicate set. size = 1271
INFO 2026-06-08 09:15:45 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:7,124
INFO 2026-06-08 09:15:45 OpticalDuplicateFinder Large duplicate set. size = 1432
INFO 2026-06-08 09:15:45 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:17,423
INFO 2026-06-08 09:15:45 OpticalDuplicateFinder Large duplicate set. size = 1053
INFO 2026-06-08 09:15:45 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,319
INFO 2026-06-08 09:15:45 OpticalDuplicateFinder Large duplicate set. size = 1162
INFO 2026-06-08 09:15:45 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,120
INFO 2026-06-08 09:15:45 OpticalDuplicateFinder Large duplicate set. size = 1148
INFO 2026-06-08 09:15:45 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:6,364
INFO 2026-06-08 09:15:45 OpticalDuplicateFinder Large duplicate set. size = 1454
INFO 2026-06-08 09:15:45 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,627
INFO 2026-06-08 09:15:45 OpticalDuplicateFinder Large duplicate set. size = 1844
INFO 2026-06-08 09:15:45 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:6,331
INFO 2026-06-08 09:15:46 OpticalDuplicateFinder Large duplicate set. size = 1268
INFO 2026-06-08 09:15:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-25,971
INFO 2026-06-08 09:15:46 OpticalDuplicateFinder Large duplicate set. size = 1044
INFO 2026-06-08 09:15:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-27,168
INFO 2026-06-08 09:15:46 OpticalDuplicateFinder Large duplicate set. size = 1422
INFO 2026-06-08 09:15:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,465
INFO 2026-06-08 09:15:46 OpticalDuplicateFinder Large duplicate set. size = 1029
INFO 2026-06-08 09:15:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,118
INFO 2026-06-08 09:15:46 OpticalDuplicateFinder Large duplicate set. size = 1239
INFO 2026-06-08 09:15:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-14,103
INFO 2026-06-08 09:15:46 OpticalDuplicateFinder Large duplicate set. size = 2156
INFO 2026-06-08 09:15:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,180
INFO 2026-06-08 09:15:46 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,895
INFO 2026-06-08 09:15:46 OpticalDuplicateFinder Large duplicate set. size = 1357
INFO 2026-06-08 09:15:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,495
INFO 2026-06-08 09:15:46 OpticalDuplicateFinder Large duplicate set. size = 1334
INFO 2026-06-08 09:15:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:4,260
INFO 2026-06-08 09:15:46 OpticalDuplicateFinder Large duplicate set. size = 1043
INFO 2026-06-08 09:15:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:26,572
INFO 2026-06-08 09:15:46 OpticalDuplicateFinder Large duplicate set. size = 1215
INFO 2026-06-08 09:15:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,128
INFO 2026-06-08 09:15:46 OpticalDuplicateFinder Large duplicate set. size = 1466
INFO 2026-06-08 09:15:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,187
INFO 2026-06-08 09:15:47 OpticalDuplicateFinder Large duplicate set. size = 1023
INFO 2026-06-08 09:15:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,472
INFO 2026-06-08 09:15:47 OpticalDuplicateFinder Large duplicate set. size = 1080
INFO 2026-06-08 09:15:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,508
INFO 2026-06-08 09:16:19 MarkDuplicates Traversing fragment information and detecting duplicates.
WARNING 2026-06-08 09:16:19 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
INFO 2026-06-08 09:17:18 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 09:17:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 203952312; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 09:17:21 MarkDuplicates Marking 319730965 records as duplicates.
INFO 2026-06-08 09:17:21 MarkDuplicates Found 13795134 optical duplicate clusters.
INFO 2026-06-08 09:17:21 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 09:17:37 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:16s. Time for last 10,000,000: 16s. Last read position: chr1:24,662,736
INFO 2026-06-08 09:17:54 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:33s. Time for last 10,000,000: 16s. Last read position: chr1:55,061,327
INFO 2026-06-08 09:18:10 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:48s. Time for last 10,000,000: 15s. Last read position: chr1:150,231,899
INFO 2026-06-08 09:18:25 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:04s. Time for last 10,000,000: 15s. Last read position: chr1:171,541,797
INFO 2026-06-08 09:18:41 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:20s. Time for last 10,000,000: 15s. Last read position: chr1:236,552,074
INFO 2026-06-08 09:18:58 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:37s. Time for last 10,000,000: 16s. Last read position: chr2:37,237,820
INFO 2026-06-08 09:19:14 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:01:53s. Time for last 10,000,000: 16s. Last read position: chr2:102,824,103
INFO 2026-06-08 09:19:30 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:09s. Time for last 10,000,000: 16s. Last read position: chr2:189,006,937
INFO 2026-06-08 09:19:47 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:26s. Time for last 10,000,000: 16s. Last read position: chr2:218,782,320
INFO 2026-06-08 09:20:03 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:42s. Time for last 10,000,000: 16s. Last read position: chr3:40,462,095
INFO 2026-06-08 09:20:19 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:02:58s. Time for last 10,000,000: 16s. Last read position: chr3:101,682,801
INFO 2026-06-08 09:20:36 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:15s. Time for last 10,000,000: 16s. Last read position: chr3:195,765,112
INFO 2026-06-08 09:20:52 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:31s. Time for last 10,000,000: 16s. Last read position: chr4:73,998,226
INFO 2026-06-08 09:21:08 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:03:47s. Time for last 10,000,000: 16s. Last read position: chr5:36,975,818
INFO 2026-06-08 09:21:25 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:04:03s. Time for last 10,000,000: 16s. Last read position: chr5:141,422,848
INFO 2026-06-08 09:21:41 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:20s. Time for last 10,000,000: 16s. Last read position: chr5:179,824,073
INFO 2026-06-08 09:21:56 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:04:35s. Time for last 10,000,000: 15s. Last read position: chr6:31,816,739
INFO 2026-06-08 09:22:12 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:04:51s. Time for last 10,000,000: 15s. Last read position: chr6:73,781,286
INFO 2026-06-08 09:22:28 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:05:07s. Time for last 10,000,000: 16s. Last read position: chr7:1,485,188
INFO 2026-06-08 09:22:44 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:05:23s. Time for last 10,000,000: 16s. Last read position: chr7:75,019,081
INFO 2026-06-08 09:23:00 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:05:39s. Time for last 10,000,000: 16s. Last read position: chr7:107,975,744
INFO 2026-06-08 09:23:16 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:05:55s. Time for last 10,000,000: 16s. Last read position: chr8:22,621,281
INFO 2026-06-08 09:23:32 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:06:11s. Time for last 10,000,000: 15s. Last read position: chr8:139,732,189
INFO 2026-06-08 09:23:48 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:06:27s. Time for last 10,000,000: 15s. Last read position: chr9:6,413,474
INFO 2026-06-08 09:24:03 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:06:42s. Time for last 10,000,000: 15s. Last read position: chr9:115,073,607
INFO 2026-06-08 09:24:19 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:06:58s. Time for last 10,000,000: 15s. Last read position: chr9:137,279,757
INFO 2026-06-08 09:24:35 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:07:14s. Time for last 10,000,000: 16s. Last read position: chr10:87,743,388
INFO 2026-06-08 09:24:51 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:07:30s. Time for last 10,000,000: 15s. Last read position: chr10:124,789,085
INFO 2026-06-08 09:25:07 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:07:46s. Time for last 10,000,000: 15s. Last read position: chr11:1,085,792
INFO 2026-06-08 09:25:22 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:08:01s. Time for last 10,000,000: 15s. Last read position: chr11:32,583,847
INFO 2026-06-08 09:25:38 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:08:17s. Time for last 10,000,000: 15s. Last read position: chr11:65,187,241
INFO 2026-06-08 09:25:54 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:08:33s. Time for last 10,000,000: 15s. Last read position: chr11:117,206,242
INFO 2026-06-08 09:26:10 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:08:49s. Time for last 10,000,000: 15s. Last read position: chr12:32,792,367
INFO 2026-06-08 09:26:26 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:09:05s. Time for last 10,000,000: 15s. Last read position: chr12:57,181,273
INFO 2026-06-08 09:26:41 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:09:20s. Time for last 10,000,000: 15s. Last read position: chr12:120,198,907
INFO 2026-06-08 09:26:57 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:09:36s. Time for last 10,000,000: 15s. Last read position: chr13:98,860,410
INFO 2026-06-08 09:27:13 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:09:52s. Time for last 10,000,000: 16s. Last read position: chr14:68,890,191
INFO 2026-06-08 09:27:29 MarkDuplicates Written 380,000,000 records. Elapsed time: 00:10:08s. Time for last 10,000,000: 15s. Last read position: chr15:28,213,874
INFO 2026-06-08 09:27:45 MarkDuplicates Written 390,000,000 records. Elapsed time: 00:10:24s. Time for last 10,000,000: 15s. Last read position: chr15:72,752,677
INFO 2026-06-08 09:28:01 MarkDuplicates Written 400,000,000 records. Elapsed time: 00:10:40s. Time for last 10,000,000: 15s. Last read position: chr16:2,767,360
INFO 2026-06-08 09:28:16 MarkDuplicates Written 410,000,000 records. Elapsed time: 00:10:55s. Time for last 10,000,000: 15s. Last read position: chr16:28,098,541
INFO 2026-06-08 09:28:32 MarkDuplicates Written 420,000,000 records. Elapsed time: 00:11:11s. Time for last 10,000,000: 15s. Last read position: chr16:68,290,451
INFO 2026-06-08 09:28:48 MarkDuplicates Written 430,000,000 records. Elapsed time: 00:11:27s. Time for last 10,000,000: 16s. Last read position: chr17:7,219,917
INFO 2026-06-08 09:29:07 MarkDuplicates Written 440,000,000 records. Elapsed time: 00:11:46s. Time for last 10,000,000: 18s. Last read position: chr17:39,201,280
INFO 2026-06-08 09:29:29 MarkDuplicates Written 450,000,000 records. Elapsed time: 00:12:07s. Time for last 10,000,000: 21s. Last read position: chr17:50,187,900
INFO 2026-06-08 09:29:47 MarkDuplicates Written 460,000,000 records. Elapsed time: 00:12:26s. Time for last 10,000,000: 18s. Last read position: chr17:50,194,413
INFO 2026-06-08 09:30:03 MarkDuplicates Written 470,000,000 records. Elapsed time: 00:12:42s. Time for last 10,000,000: 15s. Last read position: chr17:59,685,725
INFO 2026-06-08 09:30:18 MarkDuplicates Written 480,000,000 records. Elapsed time: 00:12:57s. Time for last 10,000,000: 15s. Last read position: chr17:82,083,309
INFO 2026-06-08 09:30:34 MarkDuplicates Written 490,000,000 records. Elapsed time: 00:13:13s. Time for last 10,000,000: 15s. Last read position: chr19:2,226,576
INFO 2026-06-08 09:30:50 MarkDuplicates Written 500,000,000 records. Elapsed time: 00:13:29s. Time for last 10,000,000: 15s. Last read position: chr19:13,919,839
INFO 2026-06-08 09:31:06 MarkDuplicates Written 510,000,000 records. Elapsed time: 00:13:45s. Time for last 10,000,000: 15s. Last read position: chr19:39,175,005
INFO 2026-06-08 09:31:21 MarkDuplicates Written 520,000,000 records. Elapsed time: 00:14:00s. Time for last 10,000,000: 15s. Last read position: chr19:46,787,706
INFO 2026-06-08 09:31:38 MarkDuplicates Written 530,000,000 records. Elapsed time: 00:14:17s. Time for last 10,000,000: 16s. Last read position: chr20:3,200,367
INFO 2026-06-08 09:31:54 MarkDuplicates Written 540,000,000 records. Elapsed time: 00:14:33s. Time for last 10,000,000: 16s. Last read position: chr20:63,521,830
INFO 2026-06-08 09:32:10 MarkDuplicates Written 550,000,000 records. Elapsed time: 00:14:49s. Time for last 10,000,000: 15s. Last read position: chr22:20,584,969
INFO 2026-06-08 09:32:26 MarkDuplicates Written 560,000,000 records. Elapsed time: 00:15:05s. Time for last 10,000,000: 15s. Last read position: chr22:44,802,103
INFO 2026-06-08 09:32:42 MarkDuplicates Written 570,000,000 records. Elapsed time: 00:15:21s. Time for last 10,000,000: 15s. Last read position: chrX:71,564,631
INFO 2026-06-08 09:33:02 MarkDuplicates Written 580,000,000 records. Elapsed time: 00:15:41s. Time for last 10,000,000: 19s. Last read position: */*
INFO 2026-06-08 09:33:08 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 09:33:08 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 09:33:08 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 09:33:08 MarkDuplicates Before output close freeMemory: 203907240; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 09:33:08 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 09:33:08 MarkDuplicates After output close freeMemory: 104157304; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 09:33:08 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 41.65 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory