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/72/f21c7fb9fa70d1e7d38ae3f44fb9dd/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/a04e6b1a84269c72052322ee552dca/aih-tih-sc-5ef3cb-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/f21c7fb9fa70d1e7d38ae3f44fb9dd/.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 aih-tih-sc-5ef3cb-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-5ef3cb-R1_B23WHYVLT4_1.md.bam --METRICS_FILE aih-tih-sc-5ef3cb-R1_B23WHYVLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
09:31:02.686 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 09:31:02 GMT 2026] MarkDuplicates --INPUT aih-tih-sc-5ef3cb-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-5ef3cb-R1_B23WHYVLT4_1.md.bam --METRICS_FILE aih-tih-sc-5ef3cb-R1_B23WHYVLT4_1.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 09:31:02 GMT 2026] Executing as ?@nf-72f21c7fb9fa70d1e7d38ae3f44fb9dd-4e003-v65xm 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 09:31:02 MarkDuplicates Start of doWork freeMemory: 105826856; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 09:31:02 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 09:31:02 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 09:31:06 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:1,342,130
INFO 2026-06-08 09:31:06 MarkDuplicates Tracking 3075 as yet unmatched pairs. 341 records in RAM.
INFO 2026-06-08 09:31:08 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 2s. Last read position: chr1:1,754,612
INFO 2026-06-08 09:31:08 MarkDuplicates Tracking 6304 as yet unmatched pairs. 788 records in RAM.
INFO 2026-06-08 09:31:10 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: chr1:6,461,362
INFO 2026-06-08 09:31:10 MarkDuplicates Tracking 9236 as yet unmatched pairs. 253 records in RAM.
INFO 2026-06-08 09:31:12 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 1s. Last read position: chr1:9,717,017
INFO 2026-06-08 09:31:12 MarkDuplicates Tracking 13430 as yet unmatched pairs. 1388 records in RAM.
INFO 2026-06-08 09:31:14 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 2s. Last read position: chr1:11,676,907
INFO 2026-06-08 09:31:14 MarkDuplicates Tracking 15391 as yet unmatched pairs. 148 records in RAM.
INFO 2026-06-08 09:31:16 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: chr1:13,778,768
INFO 2026-06-08 09:31:16 MarkDuplicates Tracking 18747 as yet unmatched pairs. 259 records in RAM.
INFO 2026-06-08 09:31:18 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: chr1:15,935,831
INFO 2026-06-08 09:31:18 MarkDuplicates Tracking 21651 as yet unmatched pairs. 401 records in RAM.
INFO 2026-06-08 09:31:21 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 3s. Last read position: chr1:17,420,766
INFO 2026-06-08 09:31:21 MarkDuplicates Tracking 24565 as yet unmatched pairs. 149 records in RAM.
INFO 2026-06-08 09:31:23 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: chr1:19,978,057
INFO 2026-06-08 09:31:23 MarkDuplicates Tracking 27404 as yet unmatched pairs. 27 records in RAM.
INFO 2026-06-08 09:31:25 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 2s. Last read position: chr1:22,638,838
INFO 2026-06-08 09:31:25 MarkDuplicates Tracking 41865 as yet unmatched pairs. 11649 records in RAM.
INFO 2026-06-08 09:31:26 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: chr1:22,660,866
INFO 2026-06-08 09:31:26 MarkDuplicates Tracking 35837 as yet unmatched pairs. 2735 records in RAM.
INFO 2026-06-08 09:31:28 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: chr1:25,829,543
INFO 2026-06-08 09:31:28 MarkDuplicates Tracking 36254 as yet unmatched pairs. 213 records in RAM.
INFO 2026-06-08 09:31:30 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 2s. Last read position: chr1:26,994,309
INFO 2026-06-08 09:31:30 MarkDuplicates Tracking 39191 as yet unmatched pairs. 34 records in RAM.
INFO 2026-06-08 09:31:32 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 1s. Last read position: chr1:27,882,857
INFO 2026-06-08 09:31:32 MarkDuplicates Tracking 45160 as yet unmatched pairs. 2285 records in RAM.
INFO 2026-06-08 09:31:33 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 1s. Last read position: chr1:31,059,226
INFO 2026-06-08 09:31:33 MarkDuplicates Tracking 46045 as yet unmatched pairs. 324 records in RAM.
INFO 2026-06-08 09:31:35 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 1s. Last read position: chr1:35,189,307
INFO 2026-06-08 09:31:35 MarkDuplicates Tracking 50285 as yet unmatched pairs. 1594 records in RAM.
INFO 2026-06-08 09:31:37 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 2s. Last read position: chr1:36,178,711
INFO 2026-06-08 09:31:37 MarkDuplicates Tracking 52244 as yet unmatched pairs. 402 records in RAM.
INFO 2026-06-08 09:31:39 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 1s. Last read position: chr1:39,295,830
INFO 2026-06-08 09:31:39 MarkDuplicates Tracking 55334 as yet unmatched pairs. 580 records in RAM.
INFO 2026-06-08 09:31:40 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 1s. Last read position: chr1:40,059,447
INFO 2026-06-08 09:31:40 MarkDuplicates Tracking 57374 as yet unmatched pairs. 183 records in RAM.
INFO 2026-06-08 09:31:42 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 1s. Last read position: chr1:43,403,179
INFO 2026-06-08 09:31:42 MarkDuplicates Tracking 60566 as yet unmatched pairs. 459 records in RAM.
INFO 2026-06-08 09:31:45 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 2s. Last read position: chr1:45,327,967
INFO 2026-06-08 09:31:45 MarkDuplicates Tracking 63338 as yet unmatched pairs. 124 records in RAM.
INFO 2026-06-08 09:31:47 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 2s. Last read position: chr1:52,489,002
INFO 2026-06-08 09:31:47 MarkDuplicates Tracking 66048 as yet unmatched pairs. 156 records in RAM.
INFO 2026-06-08 09:31:49 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 1s. Last read position: chr1:67,425,079
INFO 2026-06-08 09:31:49 MarkDuplicates Tracking 68560 as yet unmatched pairs. 66 records in RAM.
INFO 2026-06-08 09:31:50 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 1s. Last read position: chr1:89,112,549
INFO 2026-06-08 09:31:50 MarkDuplicates Tracking 71626 as yet unmatched pairs. 531 records in RAM.
INFO 2026-06-08 09:31:52 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 1s. Last read position: chr1:101,239,616
INFO 2026-06-08 09:31:52 MarkDuplicates Tracking 73825 as yet unmatched pairs. 215 records in RAM.
INFO 2026-06-08 09:31:54 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 1s. Last read position: chr1:111,448,722
INFO 2026-06-08 09:31:54 MarkDuplicates Tracking 76624 as yet unmatched pairs. 201 records in RAM.
INFO 2026-06-08 09:31:55 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 1s. Last read position: chr1:114,548,520
INFO 2026-06-08 09:31:55 MarkDuplicates Tracking 79241 as yet unmatched pairs. 17 records in RAM.
INFO 2026-06-08 09:31:57 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 1s. Last read position: chr1:119,925,608
INFO 2026-06-08 09:31:57 MarkDuplicates Tracking 84877 as yet unmatched pairs. 2796 records in RAM.
INFO 2026-06-08 09:31:59 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 1s. Last read position: chr1:120,435,954
INFO 2026-06-08 09:31:59 MarkDuplicates Tracking 84942 as yet unmatched pairs. 39 records in RAM.
INFO 2026-06-08 09:32:00 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 1s. Last read position: chr1:121,280,845
INFO 2026-06-08 09:32:00 MarkDuplicates Tracking 87006 as yet unmatched pairs. 1033 records in RAM.
INFO 2026-06-08 09:32:01 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 1s. Last read position: chr1:145,750,466
INFO 2026-06-08 09:32:01 MarkDuplicates Tracking 87178 as yet unmatched pairs. 93 records in RAM.
INFO 2026-06-08 09:32:03 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 2s. Last read position: chr1:146,140,540
INFO 2026-06-08 09:32:03 MarkDuplicates Tracking 89079 as yet unmatched pairs. 858 records in RAM.
INFO 2026-06-08 09:32:05 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 1s. Last read position: chr1:148,108,601
INFO 2026-06-08 09:32:05 MarkDuplicates Tracking 89765 as yet unmatched pairs. 172 records in RAM.
INFO 2026-06-08 09:32:06 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 1s. Last read position: chr1:148,571,005
INFO 2026-06-08 09:32:06 MarkDuplicates Tracking 90399 as yet unmatched pairs. 195 records in RAM.
INFO 2026-06-08 09:32:08 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 1s. Last read position: chr1:148,981,231
INFO 2026-06-08 09:32:08 MarkDuplicates Tracking 91659 as yet unmatched pairs. 350 records in RAM.
INFO 2026-06-08 09:32:09 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 1s. Last read position: chr1:149,480,162
INFO 2026-06-08 09:32:09 MarkDuplicates Tracking 94171 as yet unmatched pairs. 1903 records in RAM.
INFO 2026-06-08 09:32:10 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 1s. Last read position: chr1:150,364,656
INFO 2026-06-08 09:32:10 MarkDuplicates Tracking 94222 as yet unmatched pairs. 25 records in RAM.
INFO 2026-06-08 09:32:12 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 1s. Last read position: chr1:150,944,980
INFO 2026-06-08 09:32:12 MarkDuplicates Tracking 97541 as yet unmatched pairs. 286 records in RAM.
INFO 2026-06-08 09:32:13 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 1s. Last read position: chr1:153,638,355
INFO 2026-06-08 09:32:13 MarkDuplicates Tracking 100982 as yet unmatched pairs. 1160 records in RAM.
INFO 2026-06-08 09:32:15 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 1s. Last read position: chr1:154,157,515
INFO 2026-06-08 09:32:15 MarkDuplicates Tracking 106443 as yet unmatched pairs. 3596 records in RAM.
INFO 2026-06-08 09:32:16 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 1s. Last read position: chr1:154,182,999
INFO 2026-06-08 09:32:16 MarkDuplicates Tracking 110002 as yet unmatched pairs. 4294 records in RAM.
INFO 2026-06-08 09:32:18 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 1s. Last read position: chr1:154,970,240
INFO 2026-06-08 09:32:18 MarkDuplicates Tracking 108831 as yet unmatched pairs. 527 records in RAM.
INFO 2026-06-08 09:32:19 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 1s. Last read position: chr1:155,675,049
INFO 2026-06-08 09:32:19 MarkDuplicates Tracking 111498 as yet unmatched pairs. 576 records in RAM.
INFO 2026-06-08 09:32:21 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 2s. Last read position: chr1:156,135,934
INFO 2026-06-08 09:32:21 MarkDuplicates Tracking 116078 as yet unmatched pairs. 1801 records in RAM.
INFO 2026-06-08 09:32:25 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 3s. Last read position: chr1:158,180,925
INFO 2026-06-08 09:32:25 MarkDuplicates Tracking 117842 as yet unmatched pairs. 408 records in RAM.
INFO 2026-06-08 09:32:26 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 1s. Last read position: chr1:160,548,215
INFO 2026-06-08 09:32:26 MarkDuplicates Tracking 120894 as yet unmatched pairs. 848 records in RAM.
INFO 2026-06-08 09:32:28 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 1s. Last read position: chr1:161,542,425
INFO 2026-06-08 09:32:28 MarkDuplicates Tracking 125275 as yet unmatched pairs. 2559 records in RAM.
INFO 2026-06-08 09:32:29 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 1s. Last read position: chr1:161,750,194
INFO 2026-06-08 09:32:29 MarkDuplicates Tracking 124715 as yet unmatched pairs. 39 records in RAM.
INFO 2026-06-08 09:32:31 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 1s. Last read position: chr1:171,545,574
INFO 2026-06-08 09:32:31 MarkDuplicates Tracking 127711 as yet unmatched pairs. 104 records in RAM.
INFO 2026-06-08 09:32:33 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 1s. Last read position: chr1:180,155,047
INFO 2026-06-08 09:32:33 MarkDuplicates Tracking 130747 as yet unmatched pairs. 605 records in RAM.
INFO 2026-06-08 09:32:34 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 1s. Last read position: chr1:182,390,613
INFO 2026-06-08 09:32:34 MarkDuplicates Tracking 135457 as yet unmatched pairs. 2097 records in RAM.
INFO 2026-06-08 09:32:36 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 1s. Last read position: chr1:186,323,726
INFO 2026-06-08 09:32:36 MarkDuplicates Tracking 137295 as yet unmatched pairs. 1108 records in RAM.
INFO 2026-06-08 09:32:38 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 2s. Last read position: chr1:198,731,706
INFO 2026-06-08 09:32:38 MarkDuplicates Tracking 140974 as yet unmatched pairs. 2477 records in RAM.
INFO 2026-06-08 09:32:41 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 2s. Last read position: chr1:203,007,716
INFO 2026-06-08 09:32:41 MarkDuplicates Tracking 141686 as yet unmatched pairs. 276 records in RAM.
INFO 2026-06-08 09:32:42 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 1s. Last read position: chr1:206,436,979
INFO 2026-06-08 09:32:42 MarkDuplicates Tracking 144256 as yet unmatched pairs. 763 records in RAM.
INFO 2026-06-08 09:32:44 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 1s. Last read position: chr1:211,783,342
INFO 2026-06-08 09:32:44 MarkDuplicates Tracking 146261 as yet unmatched pairs. 30 records in RAM.
INFO 2026-06-08 09:32:45 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 1s. Last read position: chr1:224,434,232
INFO 2026-06-08 09:32:45 MarkDuplicates Tracking 151466 as yet unmatched pairs. 2550 records in RAM.
INFO 2026-06-08 09:32:46 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 1s. Last read position: chr1:228,394,701
INFO 2026-06-08 09:32:46 MarkDuplicates Tracking 152141 as yet unmatched pairs. 175 records in RAM.
INFO 2026-06-08 09:32:48 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 1s. Last read position: chr1:235,135,747
INFO 2026-06-08 09:32:48 MarkDuplicates Tracking 156017 as yet unmatched pairs. 271 records in RAM.
INFO 2026-06-08 09:32:50 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 1s. Last read position: chr1:244,862,693
INFO 2026-06-08 09:32:50 MarkDuplicates Tracking 159277 as yet unmatched pairs. 641 records in RAM.
INFO 2026-06-08 09:32:52 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 2s. Last read position: chr2:8,793,936
INFO 2026-06-08 09:32:52 MarkDuplicates Tracking 161932 as yet unmatched pairs. 161583 records in RAM.
INFO 2026-06-08 09:32:54 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 1s. Last read position: chr2:24,208,230
INFO 2026-06-08 09:32:54 MarkDuplicates Tracking 165025 as yet unmatched pairs. 164672 records in RAM.
INFO 2026-06-08 09:32:56 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 1s. Last read position: chr2:27,342,836
INFO 2026-06-08 09:32:56 MarkDuplicates Tracking 167603 as yet unmatched pairs. 167245 records in RAM.
INFO 2026-06-08 09:32:59 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 3s. Last read position: chr2:32,415,120
INFO 2026-06-08 09:32:59 MarkDuplicates Tracking 170413 as yet unmatched pairs. 170052 records in RAM.
INFO 2026-06-08 09:33:01 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,259
INFO 2026-06-08 09:33:01 MarkDuplicates Tracking 260380 as yet unmatched pairs. 166755 records in RAM.
INFO 2026-06-08 09:33:03 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,264
INFO 2026-06-08 09:33:03 MarkDuplicates Tracking 677048 as yet unmatched pairs. 149412 records in RAM.
INFO 2026-06-08 09:33:05 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,265
INFO 2026-06-08 09:33:05 MarkDuplicates Tracking 1301911 as yet unmatched pairs. 123889 records in RAM.
INFO 2026-06-08 09:33:06 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,406
INFO 2026-06-08 09:33:06 MarkDuplicates Tracking 1418262 as yet unmatched pairs. 118534 records in RAM.
INFO 2026-06-08 09:33:07 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,406
INFO 2026-06-08 09:33:07 MarkDuplicates Tracking 1422923 as yet unmatched pairs. 118364 records in RAM.
INFO 2026-06-08 09:33:09 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 1s. Last read position: chr2:37,645,914
INFO 2026-06-08 09:33:09 MarkDuplicates Tracking 1531513 as yet unmatched pairs. 112794 records in RAM.
INFO 2026-06-08 09:33:10 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 1s. Last read position: chr2:42,295,210
INFO 2026-06-08 09:33:10 MarkDuplicates Tracking 1536340 as yet unmatched pairs. 117616 records in RAM.
INFO 2026-06-08 09:33:13 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 2s. Last read position: chr2:44,201,840
INFO 2026-06-08 09:33:13 MarkDuplicates Tracking 1526210 as yet unmatched pairs. 107484 records in RAM.
INFO 2026-06-08 09:33:15 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 1s. Last read position: chr2:55,050,176
INFO 2026-06-08 09:33:15 MarkDuplicates Tracking 1523484 as yet unmatched pairs. 104755 records in RAM.
INFO 2026-06-08 09:33:16 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 1s. Last read position: chr2:60,921,955
INFO 2026-06-08 09:33:16 MarkDuplicates Tracking 1521149 as yet unmatched pairs. 102420 records in RAM.
INFO 2026-06-08 09:33:18 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 1s. Last read position: chr2:69,465,405
INFO 2026-06-08 09:33:18 MarkDuplicates Tracking 1518725 as yet unmatched pairs. 99978 records in RAM.
INFO 2026-06-08 09:33:19 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 1s. Last read position: chr2:73,386,051
INFO 2026-06-08 09:33:19 MarkDuplicates Tracking 1515083 as yet unmatched pairs. 96334 records in RAM.
INFO 2026-06-08 09:33:21 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 1s. Last read position: chr2:74,527,758
INFO 2026-06-08 09:33:21 MarkDuplicates Tracking 1512897 as yet unmatched pairs. 94143 records in RAM.
INFO 2026-06-08 09:33:22 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 1s. Last read position: chr2:86,510,455
INFO 2026-06-08 09:33:22 MarkDuplicates Tracking 1509567 as yet unmatched pairs. 90812 records in RAM.
INFO 2026-06-08 09:33:24 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 1s. Last read position: chr2:87,785,085
INFO 2026-06-08 09:33:24 MarkDuplicates Tracking 1508814 as yet unmatched pairs. 90049 records in RAM.
INFO 2026-06-08 09:33:25 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 1s. Last read position: chr2:96,551,350
INFO 2026-06-08 09:33:25 MarkDuplicates Tracking 1506760 as yet unmatched pairs. 87995 records in RAM.
INFO 2026-06-08 09:33:27 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 1s. Last read position: chr2:99,360,501
INFO 2026-06-08 09:33:27 MarkDuplicates Tracking 1503019 as yet unmatched pairs. 84253 records in RAM.
INFO 2026-06-08 09:33:29 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 1s. Last read position: chr2:108,729,179
INFO 2026-06-08 09:33:29 MarkDuplicates Tracking 1501510 as yet unmatched pairs. 82730 records in RAM.
INFO 2026-06-08 09:33:31 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 2s. Last read position: chr2:109,824,513
INFO 2026-06-08 09:33:31 MarkDuplicates Tracking 1499001 as yet unmatched pairs. 80217 records in RAM.
INFO 2026-06-08 09:33:32 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 1s. Last read position: chr2:112,250,227
INFO 2026-06-08 09:33:32 MarkDuplicates Tracking 1497667 as yet unmatched pairs. 78879 records in RAM.
INFO 2026-06-08 09:33:33 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 1s. Last read position: chr2:113,890,166
INFO 2026-06-08 09:33:33 MarkDuplicates Tracking 1497222 as yet unmatched pairs. 78434 records in RAM.
INFO 2026-06-08 09:33:35 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 1s. Last read position: chr2:119,257,531
INFO 2026-06-08 09:33:35 MarkDuplicates Tracking 1493280 as yet unmatched pairs. 74491 records in RAM.
INFO 2026-06-08 09:33:37 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 1s. Last read position: chr2:131,520,142
INFO 2026-06-08 09:33:37 MarkDuplicates Tracking 1490761 as yet unmatched pairs. 71967 records in RAM.
INFO 2026-06-08 09:33:38 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 1s. Last read position: chr2:144,404,836
INFO 2026-06-08 09:33:38 MarkDuplicates Tracking 1489530 as yet unmatched pairs. 70708 records in RAM.
INFO 2026-06-08 09:33:40 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 1s. Last read position: chr2:156,330,124
INFO 2026-06-08 09:33:40 MarkDuplicates Tracking 1485093 as yet unmatched pairs. 66266 records in RAM.
INFO 2026-06-08 09:33:41 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 1s. Last read position: chr2:170,079,922
INFO 2026-06-08 09:33:41 MarkDuplicates Tracking 1482681 as yet unmatched pairs. 63847 records in RAM.
INFO 2026-06-08 09:33:43 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 1s. Last read position: chr2:178,546,724
INFO 2026-06-08 09:33:43 MarkDuplicates Tracking 1479901 as yet unmatched pairs. 61066 records in RAM.
INFO 2026-06-08 09:33:44 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 1s. Last read position: chr2:189,761,420
INFO 2026-06-08 09:33:44 MarkDuplicates Tracking 1477527 as yet unmatched pairs. 58688 records in RAM.
INFO 2026-06-08 09:33:46 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 1s. Last read position: chr2:200,571,536
INFO 2026-06-08 09:33:46 MarkDuplicates Tracking 1474745 as yet unmatched pairs. 55894 records in RAM.
INFO 2026-06-08 09:33:47 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 1s. Last read position: chr2:203,867,954
INFO 2026-06-08 09:33:47 MarkDuplicates Tracking 1472339 as yet unmatched pairs. 53476 records in RAM.
INFO 2026-06-08 09:33:49 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 1s. Last read position: chr2:215,361,613
INFO 2026-06-08 09:33:49 MarkDuplicates Tracking 1485813 as yet unmatched pairs. 66949 records in RAM.
INFO 2026-06-08 09:33:51 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 1s. Last read position: chr2:215,365,587
INFO 2026-06-08 09:33:51 MarkDuplicates Tracking 1480239 as yet unmatched pairs. 61373 records in RAM.
INFO 2026-06-08 09:33:52 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 1s. Last read position: chr2:215,372,177
INFO 2026-06-08 09:33:52 MarkDuplicates Tracking 1492643 as yet unmatched pairs. 73777 records in RAM.
INFO 2026-06-08 09:33:54 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 1s. Last read position: chr2:215,375,629
INFO 2026-06-08 09:33:54 MarkDuplicates Tracking 1484279 as yet unmatched pairs. 65412 records in RAM.
INFO 2026-06-08 09:33:56 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 1s. Last read position: chr2:215,379,202
INFO 2026-06-08 09:33:56 MarkDuplicates Tracking 1479498 as yet unmatched pairs. 60631 records in RAM.
INFO 2026-06-08 09:33:57 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 1s. Last read position: chr2:215,384,170
INFO 2026-06-08 09:33:57 MarkDuplicates Tracking 1467553 as yet unmatched pairs. 48686 records in RAM.
INFO 2026-06-08 09:34:00 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 2s. Last read position: chr2:215,394,696
INFO 2026-06-08 09:34:00 MarkDuplicates Tracking 1468432 as yet unmatched pairs. 49565 records in RAM.
INFO 2026-06-08 09:34:02 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 2s. Last read position: chr2:215,406,247
INFO 2026-06-08 09:34:02 MarkDuplicates Tracking 1470780 as yet unmatched pairs. 51908 records in RAM.
INFO 2026-06-08 09:34:04 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 1s. Last read position: chr2:215,408,403
INFO 2026-06-08 09:34:04 MarkDuplicates Tracking 1471099 as yet unmatched pairs. 52227 records in RAM.
INFO 2026-06-08 09:34:06 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 1s. Last read position: chr2:215,419,353
INFO 2026-06-08 09:34:06 MarkDuplicates Tracking 1450036 as yet unmatched pairs. 31163 records in RAM.
INFO 2026-06-08 09:34:07 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 1s. Last read position: chr2:215,425,107
INFO 2026-06-08 09:34:07 MarkDuplicates Tracking 1462034 as yet unmatched pairs. 43153 records in RAM.
INFO 2026-06-08 09:34:09 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 1s. Last read position: chr2:215,428,323
INFO 2026-06-08 09:34:09 MarkDuplicates Tracking 1465337 as yet unmatched pairs. 46456 records in RAM.
INFO 2026-06-08 09:34:10 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 1s. Last read position: chr2:215,433,363
INFO 2026-06-08 09:34:10 MarkDuplicates Tracking 1459575 as yet unmatched pairs. 40671 records in RAM.
INFO 2026-06-08 09:34:12 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 1s. Last read position: chr2:217,809,812
INFO 2026-06-08 09:34:12 MarkDuplicates Tracking 1436434 as yet unmatched pairs. 17520 records in RAM.
INFO 2026-06-08 09:34:14 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 1s. Last read position: chr2:218,391,458
INFO 2026-06-08 09:34:14 MarkDuplicates Tracking 1435085 as yet unmatched pairs. 16171 records in RAM.
INFO 2026-06-08 09:34:15 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 1s. Last read position: chr2:219,220,708
INFO 2026-06-08 09:34:15 MarkDuplicates Tracking 1430414 as yet unmatched pairs. 11500 records in RAM.
INFO 2026-06-08 09:34:16 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 1s. Last read position: chr2:227,551,956
INFO 2026-06-08 09:34:16 MarkDuplicates Tracking 1429500 as yet unmatched pairs. 10544 records in RAM.
INFO 2026-06-08 09:34:18 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 1s. Last read position: chr2:232,238,590
INFO 2026-06-08 09:34:18 MarkDuplicates Tracking 1425292 as yet unmatched pairs. 6334 records in RAM.
INFO 2026-06-08 09:34:20 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 1s. Last read position: chr2:238,061,060
INFO 2026-06-08 09:34:20 MarkDuplicates Tracking 1422649 as yet unmatched pairs. 3691 records in RAM.
INFO 2026-06-08 09:34:21 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 1s. Last read position: chr2:241,685,826
INFO 2026-06-08 09:34:21 MarkDuplicates Tracking 1419341 as yet unmatched pairs. 371 records in RAM.
INFO 2026-06-08 09:34:23 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 2s. Last read position: chr3:9,834,739
INFO 2026-06-08 09:34:23 MarkDuplicates Tracking 1416826 as yet unmatched pairs. 82456 records in RAM.
INFO 2026-06-08 09:34:25 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 1s. Last read position: chr3:12,920,471
INFO 2026-06-08 09:34:25 MarkDuplicates Tracking 1413938 as yet unmatched pairs. 79562 records in RAM.
INFO 2026-06-08 09:34:26 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: chr3:18,349,244
INFO 2026-06-08 09:34:26 MarkDuplicates Tracking 1410757 as yet unmatched pairs. 76376 records in RAM.
INFO 2026-06-08 09:34:28 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 1s. Last read position: chr3:33,684,408
INFO 2026-06-08 09:34:28 MarkDuplicates Tracking 1407954 as yet unmatched pairs. 73565 records in RAM.
INFO 2026-06-08 09:34:29 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 1s. Last read position: chr3:40,423,867
INFO 2026-06-08 09:34:29 MarkDuplicates Tracking 1404633 as yet unmatched pairs. 70235 records in RAM.
INFO 2026-06-08 09:34:32 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 2s. Last read position: chr3:45,966,372
INFO 2026-06-08 09:34:32 MarkDuplicates Tracking 1402198 as yet unmatched pairs. 67793 records in RAM.
INFO 2026-06-08 09:34:33 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 1s. Last read position: chr3:47,101,544
INFO 2026-06-08 09:34:33 MarkDuplicates Tracking 1398686 as yet unmatched pairs. 64281 records in RAM.
INFO 2026-06-08 09:34:35 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 1s. Last read position: chr3:48,609,193
INFO 2026-06-08 09:34:35 MarkDuplicates Tracking 1395739 as yet unmatched pairs. 61330 records in RAM.
INFO 2026-06-08 09:34:37 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 1s. Last read position: chr3:49,335,584
INFO 2026-06-08 09:34:37 MarkDuplicates Tracking 1392722 as yet unmatched pairs. 58309 records in RAM.
INFO 2026-06-08 09:34:38 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 1s. Last read position: chr3:50,276,658
INFO 2026-06-08 09:34:38 MarkDuplicates Tracking 1389909 as yet unmatched pairs. 55495 records in RAM.
INFO 2026-06-08 09:34:41 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 2s. Last read position: chr3:52,375,300
INFO 2026-06-08 09:34:41 MarkDuplicates Tracking 1387224 as yet unmatched pairs. 52804 records in RAM.
INFO 2026-06-08 09:34:42 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 1s. Last read position: chr3:52,503,785
INFO 2026-06-08 09:34:42 MarkDuplicates Tracking 1387706 as yet unmatched pairs. 53285 records in RAM.
INFO 2026-06-08 09:34:44 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 1s. Last read position: chr3:52,511,680
INFO 2026-06-08 09:34:44 MarkDuplicates Tracking 1392901 as yet unmatched pairs. 58480 records in RAM.
INFO 2026-06-08 09:34:46 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 1s. Last read position: chr3:52,517,364
INFO 2026-06-08 09:34:46 MarkDuplicates Tracking 1388481 as yet unmatched pairs. 54048 records in RAM.
INFO 2026-06-08 09:34:48 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 1s. Last read position: chr3:52,522,889
INFO 2026-06-08 09:34:48 MarkDuplicates Tracking 1376817 as yet unmatched pairs. 42383 records in RAM.
INFO 2026-06-08 09:34:49 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 1s. Last read position: chr3:57,679,700
INFO 2026-06-08 09:34:49 MarkDuplicates Tracking 1370412 as yet unmatched pairs. 35978 records in RAM.
INFO 2026-06-08 09:34:51 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 1s. Last read position: chr3:70,965,889
INFO 2026-06-08 09:34:51 MarkDuplicates Tracking 1367942 as yet unmatched pairs. 33504 records in RAM.
INFO 2026-06-08 09:34:52 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 1s. Last read position: chr3:105,547,216
INFO 2026-06-08 09:34:52 MarkDuplicates Tracking 1365396 as yet unmatched pairs. 30951 records in RAM.
INFO 2026-06-08 09:34:54 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 1s. Last read position: chr3:121,694,326
INFO 2026-06-08 09:34:54 MarkDuplicates Tracking 1363069 as yet unmatched pairs. 28621 records in RAM.
INFO 2026-06-08 09:34:56 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 1s. Last read position: chr3:125,594,684
INFO 2026-06-08 09:34:56 MarkDuplicates Tracking 1360132 as yet unmatched pairs. 25677 records in RAM.
INFO 2026-06-08 09:34:57 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 1s. Last read position: chr3:129,437,723
INFO 2026-06-08 09:34:57 MarkDuplicates Tracking 1356977 as yet unmatched pairs. 22500 records in RAM.
INFO 2026-06-08 09:34:59 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 1s. Last read position: chr3:136,151,608
INFO 2026-06-08 09:34:59 MarkDuplicates Tracking 1353587 as yet unmatched pairs. 19109 records in RAM.
INFO 2026-06-08 09:35:00 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 1s. Last read position: chr3:150,762,794
INFO 2026-06-08 09:35:00 MarkDuplicates Tracking 1350820 as yet unmatched pairs. 16340 records in RAM.
INFO 2026-06-08 09:35:02 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 1s. Last read position: chr3:170,178,788
INFO 2026-06-08 09:35:02 MarkDuplicates Tracking 1348446 as yet unmatched pairs. 13957 records in RAM.
INFO 2026-06-08 09:35:03 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 1s. Last read position: chr3:184,141,898
INFO 2026-06-08 09:35:03 MarkDuplicates Tracking 1345043 as yet unmatched pairs. 10554 records in RAM.
INFO 2026-06-08 09:35:05 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 1s. Last read position: chr3:186,060,316
INFO 2026-06-08 09:35:05 MarkDuplicates Tracking 1342607 as yet unmatched pairs. 8107 records in RAM.
INFO 2026-06-08 09:35:06 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 1s. Last read position: chr3:194,431,002
INFO 2026-06-08 09:35:06 MarkDuplicates Tracking 1340421 as yet unmatched pairs. 5919 records in RAM.
INFO 2026-06-08 09:35:08 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 1s. Last read position: chr3:195,909,087
INFO 2026-06-08 09:35:08 MarkDuplicates Tracking 1337163 as yet unmatched pairs. 2656 records in RAM.
INFO 2026-06-08 09:35:10 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 1s. Last read position: chr4:678,953
INFO 2026-06-08 09:35:10 MarkDuplicates Tracking 1334530 as yet unmatched pairs. 36797 records in RAM.
INFO 2026-06-08 09:35:11 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 1s. Last read position: chr4:1,727,964
INFO 2026-06-08 09:35:11 MarkDuplicates Tracking 1331309 as yet unmatched pairs. 33570 records in RAM.
INFO 2026-06-08 09:35:13 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 1s. Last read position: chr4:2,833,745
INFO 2026-06-08 09:35:13 MarkDuplicates Tracking 1329300 as yet unmatched pairs. 31561 records in RAM.
INFO 2026-06-08 09:35:15 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 1s. Last read position: chr4:6,871,643
INFO 2026-06-08 09:35:15 MarkDuplicates Tracking 1324586 as yet unmatched pairs. 26843 records in RAM.
INFO 2026-06-08 09:35:16 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 1s. Last read position: chr4:13,604,830
INFO 2026-06-08 09:35:16 MarkDuplicates Tracking 1321899 as yet unmatched pairs. 24143 records in RAM.
INFO 2026-06-08 09:35:18 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 1s. Last read position: chr4:37,649,324
INFO 2026-06-08 09:35:18 MarkDuplicates Tracking 1319116 as yet unmatched pairs. 21351 records in RAM.
INFO 2026-06-08 09:35:21 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 2s. Last read position: chr4:48,851,874
INFO 2026-06-08 09:35:21 MarkDuplicates Tracking 1316120 as yet unmatched pairs. 18352 records in RAM.
INFO 2026-06-08 09:35:22 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 1s. Last read position: chr4:75,491,903
INFO 2026-06-08 09:35:22 MarkDuplicates Tracking 1313081 as yet unmatched pairs. 15310 records in RAM.
INFO 2026-06-08 09:35:24 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 1s. Last read position: chr4:82,995,972
INFO 2026-06-08 09:35:24 MarkDuplicates Tracking 1310270 as yet unmatched pairs. 12494 records in RAM.
INFO 2026-06-08 09:35:25 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 1s. Last read position: chr4:99,816,867
INFO 2026-06-08 09:35:25 MarkDuplicates Tracking 1307932 as yet unmatched pairs. 10153 records in RAM.
INFO 2026-06-08 09:35:27 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 1s. Last read position: chr4:118,731,274
INFO 2026-06-08 09:35:27 MarkDuplicates Tracking 1304800 as yet unmatched pairs. 6983 records in RAM.
INFO 2026-06-08 09:35:29 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 1s. Last read position: chr4:143,547,944
INFO 2026-06-08 09:35:29 MarkDuplicates Tracking 1302241 as yet unmatched pairs. 4424 records in RAM.
INFO 2026-06-08 09:35:30 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr4:165,278,914
INFO 2026-06-08 09:35:30 MarkDuplicates Tracking 1300544 as yet unmatched pairs. 2705 records in RAM.
INFO 2026-06-08 09:35:33 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 2s. Last read position: chr5:864,460
INFO 2026-06-08 09:35:33 MarkDuplicates Tracking 1297396 as yet unmatched pairs. 71976 records in RAM.
INFO 2026-06-08 09:35:34 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 1s. Last read position: chr5:14,290,791
INFO 2026-06-08 09:35:34 MarkDuplicates Tracking 1295516 as yet unmatched pairs. 70079 records in RAM.
INFO 2026-06-08 09:35:36 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 1s. Last read position: chr5:14,711,172
INFO 2026-06-08 09:35:36 MarkDuplicates Tracking 1291617 as yet unmatched pairs. 66171 records in RAM.
INFO 2026-06-08 09:35:37 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 1s. Last read position: chr5:39,153,471
INFO 2026-06-08 09:35:37 MarkDuplicates Tracking 1289891 as yet unmatched pairs. 64434 records in RAM.
INFO 2026-06-08 09:35:39 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 1s. Last read position: chr5:55,414,194
INFO 2026-06-08 09:35:39 MarkDuplicates Tracking 1286052 as yet unmatched pairs. 60593 records in RAM.
INFO 2026-06-08 09:35:40 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 1s. Last read position: chr5:68,280,935
INFO 2026-06-08 09:35:40 MarkDuplicates Tracking 1283834 as yet unmatched pairs. 58373 records in RAM.
INFO 2026-06-08 09:35:42 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 1s. Last read position: chr5:75,596,580
INFO 2026-06-08 09:35:42 MarkDuplicates Tracking 1281836 as yet unmatched pairs. 56366 records in RAM.
INFO 2026-06-08 09:35:44 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 2s. Last read position: chr5:83,521,839
INFO 2026-06-08 09:35:44 MarkDuplicates Tracking 1280622 as yet unmatched pairs. 55137 records in RAM.
INFO 2026-06-08 09:35:46 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 1s. Last read position: chr5:96,729,619
INFO 2026-06-08 09:35:46 MarkDuplicates Tracking 1276834 as yet unmatched pairs. 51348 records in RAM.
INFO 2026-06-08 09:35:48 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 1s. Last read position: chr5:119,071,532
INFO 2026-06-08 09:35:48 MarkDuplicates Tracking 1274924 as yet unmatched pairs. 49435 records in RAM.
INFO 2026-06-08 09:35:49 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 1s. Last read position: chr5:134,142,830
INFO 2026-06-08 09:35:49 MarkDuplicates Tracking 1271789 as yet unmatched pairs. 46296 records in RAM.
INFO 2026-06-08 09:35:51 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 1s. Last read position: chr5:138,467,445
INFO 2026-06-08 09:35:51 MarkDuplicates Tracking 1269000 as yet unmatched pairs. 43504 records in RAM.
INFO 2026-06-08 09:35:53 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 1s. Last read position: chr5:140,631,890
INFO 2026-06-08 09:35:53 MarkDuplicates Tracking 1269962 as yet unmatched pairs. 44357 records in RAM.
INFO 2026-06-08 09:35:55 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 2s. Last read position: chr5:141,642,937
INFO 2026-06-08 09:35:55 MarkDuplicates Tracking 1263082 as yet unmatched pairs. 37477 records in RAM.
INFO 2026-06-08 09:35:57 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 1s. Last read position: chr5:150,010,240
INFO 2026-06-08 09:35:57 MarkDuplicates Tracking 1260665 as yet unmatched pairs. 35052 records in RAM.
INFO 2026-06-08 09:35:58 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 1s. Last read position: chr5:150,402,223
INFO 2026-06-08 09:35:58 MarkDuplicates Tracking 1285520 as yet unmatched pairs. 59907 records in RAM.
INFO 2026-06-08 09:36:00 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 1s. Last read position: chr5:150,405,109
INFO 2026-06-08 09:36:00 MarkDuplicates Tracking 1273430 as yet unmatched pairs. 47817 records in RAM.
INFO 2026-06-08 09:36:01 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 1s. Last read position: chr5:150,407,152
INFO 2026-06-08 09:36:01 MarkDuplicates Tracking 1269250 as yet unmatched pairs. 43637 records in RAM.
INFO 2026-06-08 09:36:03 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 1s. Last read position: chr5:151,803,946
INFO 2026-06-08 09:36:03 MarkDuplicates Tracking 1248586 as yet unmatched pairs. 22973 records in RAM.
INFO 2026-06-08 09:36:05 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 1s. Last read position: chr5:169,598,550
INFO 2026-06-08 09:36:05 MarkDuplicates Tracking 1245089 as yet unmatched pairs. 19471 records in RAM.
INFO 2026-06-08 09:36:06 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 1s. Last read position: chr5:172,061,252
INFO 2026-06-08 09:36:06 MarkDuplicates Tracking 1242708 as yet unmatched pairs. 17087 records in RAM.
INFO 2026-06-08 09:36:08 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 1s. Last read position: chr5:176,532,091
INFO 2026-06-08 09:36:08 MarkDuplicates Tracking 1240148 as yet unmatched pairs. 14520 records in RAM.
INFO 2026-06-08 09:36:10 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 1s. Last read position: chr5:177,436,506
INFO 2026-06-08 09:36:10 MarkDuplicates Tracking 1236682 as yet unmatched pairs. 11053 records in RAM.
INFO 2026-06-08 09:36:11 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 1s. Last read position: chr5:179,272,918
INFO 2026-06-08 09:36:11 MarkDuplicates Tracking 1233064 as yet unmatched pairs. 7433 records in RAM.
INFO 2026-06-08 09:36:13 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr5:179,823,906
INFO 2026-06-08 09:36:13 MarkDuplicates Tracking 1235596 as yet unmatched pairs. 9955 records in RAM.
INFO 2026-06-08 09:36:14 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 1s. Last read position: chr5:181,260,021
INFO 2026-06-08 09:36:14 MarkDuplicates Tracking 1225900 as yet unmatched pairs. 239 records in RAM.
INFO 2026-06-08 09:36:17 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 2s. Last read position: chr6:7,229,583
INFO 2026-06-08 09:36:17 MarkDuplicates Tracking 1224434 as yet unmatched pairs. 75247 records in RAM.
INFO 2026-06-08 09:36:19 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 2s. Last read position: chr6:7,888,756
INFO 2026-06-08 09:36:19 MarkDuplicates Tracking 1219466 as yet unmatched pairs. 70278 records in RAM.
INFO 2026-06-08 09:36:21 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 1s. Last read position: chr6:18,052,486
INFO 2026-06-08 09:36:21 MarkDuplicates Tracking 1216738 as yet unmatched pairs. 67543 records in RAM.
INFO 2026-06-08 09:36:23 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 1s. Last read position: chr6:27,838,658
INFO 2026-06-08 09:36:23 MarkDuplicates Tracking 1214368 as yet unmatched pairs. 65171 records in RAM.
INFO 2026-06-08 09:36:24 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:05:20s. Time for last 1,000,000: 1s. Last read position: chr6:30,335,882
INFO 2026-06-08 09:36:24 MarkDuplicates Tracking 1211636 as yet unmatched pairs. 62436 records in RAM.
INFO 2026-06-08 09:36:26 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 1s. Last read position: chr6:30,730,160
INFO 2026-06-08 09:36:26 MarkDuplicates Tracking 1208991 as yet unmatched pairs. 59791 records in RAM.
INFO 2026-06-08 09:36:27 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 1s. Last read position: chr6:31,355,442
INFO 2026-06-08 09:36:27 MarkDuplicates Tracking 1209830 as yet unmatched pairs. 60628 records in RAM.
INFO 2026-06-08 09:36:29 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 1s. Last read position: chr6:31,635,719
INFO 2026-06-08 09:36:29 MarkDuplicates Tracking 1202805 as yet unmatched pairs. 53580 records in RAM.
INFO 2026-06-08 09:36:30 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 1s. Last read position: chr6:31,951,782
INFO 2026-06-08 09:36:30 MarkDuplicates Tracking 1200258 as yet unmatched pairs. 51032 records in RAM.
INFO 2026-06-08 09:36:31 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 1s. Last read position: chr6:32,580,755
INFO 2026-06-08 09:36:31 MarkDuplicates Tracking 1198948 as yet unmatched pairs. 49718 records in RAM.
INFO 2026-06-08 09:36:33 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 1s. Last read position: chr6:32,979,977
INFO 2026-06-08 09:36:33 MarkDuplicates Tracking 1196520 as yet unmatched pairs. 47289 records in RAM.
INFO 2026-06-08 09:36:34 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 1s. Last read position: chr6:33,412,530
INFO 2026-06-08 09:36:34 MarkDuplicates Tracking 1193634 as yet unmatched pairs. 44394 records in RAM.
INFO 2026-06-08 09:36:37 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 2s. Last read position: chr6:35,294,471
INFO 2026-06-08 09:36:37 MarkDuplicates Tracking 1188504 as yet unmatched pairs. 39260 records in RAM.
INFO 2026-06-08 09:36:38 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 1s. Last read position: chr6:37,170,772
INFO 2026-06-08 09:36:38 MarkDuplicates Tracking 1186008 as yet unmatched pairs. 36756 records in RAM.
INFO 2026-06-08 09:36:40 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 1s. Last read position: chr6:43,043,423
INFO 2026-06-08 09:36:40 MarkDuplicates Tracking 1182165 as yet unmatched pairs. 32883 records in RAM.
INFO 2026-06-08 09:36:42 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 2s. Last read position: chr6:45,547,051
INFO 2026-06-08 09:36:42 MarkDuplicates Tracking 1179116 as yet unmatched pairs. 29820 records in RAM.
INFO 2026-06-08 09:36:44 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 1s. Last read position: chr6:73,452,082
INFO 2026-06-08 09:36:44 MarkDuplicates Tracking 1176741 as yet unmatched pairs. 27429 records in RAM.
INFO 2026-06-08 09:36:45 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 1s. Last read position: chr6:89,080,918
INFO 2026-06-08 09:36:45 MarkDuplicates Tracking 1174538 as yet unmatched pairs. 25226 records in RAM.
INFO 2026-06-08 09:36:46 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 1s. Last read position: chr6:107,906,522
INFO 2026-06-08 09:36:46 MarkDuplicates Tracking 1171168 as yet unmatched pairs. 21853 records in RAM.
INFO 2026-06-08 09:36:48 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 1s. Last read position: chr6:113,860,496
INFO 2026-06-08 09:36:48 MarkDuplicates Tracking 1168004 as yet unmatched pairs. 18675 records in RAM.
INFO 2026-06-08 09:36:50 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 1s. Last read position: chr6:130,955,994
INFO 2026-06-08 09:36:50 MarkDuplicates Tracking 1165130 as yet unmatched pairs. 15797 records in RAM.
INFO 2026-06-08 09:36:51 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 1s. Last read position: chr6:139,167,077
INFO 2026-06-08 09:36:51 MarkDuplicates Tracking 1162911 as yet unmatched pairs. 13573 records in RAM.
INFO 2026-06-08 09:36:53 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 1s. Last read position: chr6:149,379,025
INFO 2026-06-08 09:36:53 MarkDuplicates Tracking 1161018 as yet unmatched pairs. 11672 records in RAM.
INFO 2026-06-08 09:36:54 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 1s. Last read position: chr6:157,885,051
INFO 2026-06-08 09:36:54 MarkDuplicates Tracking 1157543 as yet unmatched pairs. 8192 records in RAM.
INFO 2026-06-08 09:36:56 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 2s. Last read position: chr6:158,785,534
INFO 2026-06-08 09:36:56 MarkDuplicates Tracking 1157684 as yet unmatched pairs. 8333 records in RAM.
INFO 2026-06-08 09:36:58 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 1s. Last read position: chr6:163,478,780
INFO 2026-06-08 09:36:58 MarkDuplicates Tracking 1152530 as yet unmatched pairs. 3178 records in RAM.
INFO 2026-06-08 09:37:00 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 2s. Last read position: chr7:193,454
INFO 2026-06-08 09:37:00 MarkDuplicates Tracking 1150515 as yet unmatched pairs. 80631 records in RAM.
INFO 2026-06-08 09:37:02 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 1s. Last read position: chr7:2,263,211
INFO 2026-06-08 09:37:02 MarkDuplicates Tracking 1144966 as yet unmatched pairs. 75075 records in RAM.
INFO 2026-06-08 09:37:03 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 1s. Last read position: chr7:2,652,204
INFO 2026-06-08 09:37:03 MarkDuplicates Tracking 1142416 as yet unmatched pairs. 72525 records in RAM.
INFO 2026-06-08 09:37:05 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 1s. Last read position: chr7:5,362,667
INFO 2026-06-08 09:37:05 MarkDuplicates Tracking 1137969 as yet unmatched pairs. 68077 records in RAM.
INFO 2026-06-08 09:37:06 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 1s. Last read position: chr7:5,528,492
INFO 2026-06-08 09:37:06 MarkDuplicates Tracking 1138813 as yet unmatched pairs. 68919 records in RAM.
INFO 2026-06-08 09:37:08 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 1s. Last read position: chr7:6,591,779
INFO 2026-06-08 09:37:08 MarkDuplicates Tracking 1131025 as yet unmatched pairs. 61107 records in RAM.
INFO 2026-06-08 09:37:10 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 1s. Last read position: chr7:26,197,677
INFO 2026-06-08 09:37:10 MarkDuplicates Tracking 1129920 as yet unmatched pairs. 59997 records in RAM.
INFO 2026-06-08 09:37:11 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 1s. Last read position: chr7:39,951,401
INFO 2026-06-08 09:37:11 MarkDuplicates Tracking 1125441 as yet unmatched pairs. 55516 records in RAM.
INFO 2026-06-08 09:37:13 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:06:09s. Time for last 1,000,000: 1s. Last read position: chr7:44,763,400
INFO 2026-06-08 09:37:13 MarkDuplicates Tracking 1122931 as yet unmatched pairs. 53001 records in RAM.
INFO 2026-06-08 09:37:15 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 1s. Last read position: chr7:48,094,810
INFO 2026-06-08 09:37:15 MarkDuplicates Tracking 1119196 as yet unmatched pairs. 49266 records in RAM.
INFO 2026-06-08 09:37:16 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 1s. Last read position: chr7:72,925,492
INFO 2026-06-08 09:37:16 MarkDuplicates Tracking 1117394 as yet unmatched pairs. 47445 records in RAM.
INFO 2026-06-08 09:37:18 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 1s. Last read position: chr7:73,594,278
INFO 2026-06-08 09:37:18 MarkDuplicates Tracking 1116621 as yet unmatched pairs. 46670 records in RAM.
INFO 2026-06-08 09:37:19 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 1s. Last read position: chr7:75,209,447
INFO 2026-06-08 09:37:19 MarkDuplicates Tracking 1112618 as yet unmatched pairs. 42665 records in RAM.
INFO 2026-06-08 09:37:21 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:06:16s. Time for last 1,000,000: 1s. Last read position: chr7:76,540,246
INFO 2026-06-08 09:37:21 MarkDuplicates Tracking 1110100 as yet unmatched pairs. 40146 records in RAM.
INFO 2026-06-08 09:37:22 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 1s. Last read position: chr7:92,052,932
INFO 2026-06-08 09:37:22 MarkDuplicates Tracking 1108413 as yet unmatched pairs. 38457 records in RAM.
INFO 2026-06-08 09:37:25 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 2s. Last read position: chr7:98,291,107
INFO 2026-06-08 09:37:25 MarkDuplicates Tracking 1106430 as yet unmatched pairs. 36473 records in RAM.
INFO 2026-06-08 09:37:26 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 1s. Last read position: chr7:100,098,277
INFO 2026-06-08 09:37:26 MarkDuplicates Tracking 1102465 as yet unmatched pairs. 32508 records in RAM.
INFO 2026-06-08 09:37:28 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 1s. Last read position: chr7:100,575,897
INFO 2026-06-08 09:37:28 MarkDuplicates Tracking 1101279 as yet unmatched pairs. 31321 records in RAM.
INFO 2026-06-08 09:37:29 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 1s. Last read position: chr7:101,087,914
INFO 2026-06-08 09:37:29 MarkDuplicates Tracking 1096509 as yet unmatched pairs. 26550 records in RAM.
INFO 2026-06-08 09:37:31 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 1s. Last read position: chr7:102,555,886
INFO 2026-06-08 09:37:31 MarkDuplicates Tracking 1093958 as yet unmatched pairs. 23999 records in RAM.
INFO 2026-06-08 09:37:32 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 1s. Last read position: chr7:105,112,302
INFO 2026-06-08 09:37:32 MarkDuplicates Tracking 1092366 as yet unmatched pairs. 22396 records in RAM.
INFO 2026-06-08 09:37:34 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 1s. Last read position: chr7:123,692,618
INFO 2026-06-08 09:37:34 MarkDuplicates Tracking 1089770 as yet unmatched pairs. 19793 records in RAM.
INFO 2026-06-08 09:37:35 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:06:31s. Time for last 1,000,000: 1s. Last read position: chr7:128,946,503
INFO 2026-06-08 09:37:35 MarkDuplicates Tracking 1087334 as yet unmatched pairs. 17349 records in RAM.
INFO 2026-06-08 09:37:37 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 1s. Last read position: chr7:139,079,806
INFO 2026-06-08 09:37:37 MarkDuplicates Tracking 1085237 as yet unmatched pairs. 15250 records in RAM.
INFO 2026-06-08 09:37:38 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 1s. Last read position: chr7:141,927,364
INFO 2026-06-08 09:37:38 MarkDuplicates Tracking 1081105 as yet unmatched pairs. 11106 records in RAM.
INFO 2026-06-08 09:37:40 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 2s. Last read position: chr7:144,285,730
INFO 2026-06-08 09:37:40 MarkDuplicates Tracking 1078825 as yet unmatched pairs. 8814 records in RAM.
INFO 2026-06-08 09:37:42 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 1s. Last read position: chr7:151,040,495
INFO 2026-06-08 09:37:42 MarkDuplicates Tracking 1075929 as yet unmatched pairs. 5916 records in RAM.
INFO 2026-06-08 09:37:43 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 1s. Last read position: chr7:152,187,732
INFO 2026-06-08 09:37:43 MarkDuplicates Tracking 1073172 as yet unmatched pairs. 3158 records in RAM.
INFO 2026-06-08 09:37:45 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 1s. Last read position: chr8:687,623
INFO 2026-06-08 09:37:45 MarkDuplicates Tracking 1070068 as yet unmatched pairs. 55160 records in RAM.
INFO 2026-06-08 09:37:48 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:06:44s. Time for last 1,000,000: 3s. Last read position: chr8:11,852,520
INFO 2026-06-08 09:37:48 MarkDuplicates Tracking 1069255 as yet unmatched pairs. 54347 records in RAM.
INFO 2026-06-08 09:37:50 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:06:46s. Time for last 1,000,000: 1s. Last read position: chr8:21,974,396
INFO 2026-06-08 09:37:50 MarkDuplicates Tracking 1064355 as yet unmatched pairs. 49439 records in RAM.
INFO 2026-06-08 09:37:51 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:06:47s. Time for last 1,000,000: 1s. Last read position: chr8:22,619,254
INFO 2026-06-08 09:37:51 MarkDuplicates Tracking 1062926 as yet unmatched pairs. 48003 records in RAM.
INFO 2026-06-08 09:37:53 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 1s. Last read position: chr8:27,310,856
INFO 2026-06-08 09:37:53 MarkDuplicates Tracking 1058887 as yet unmatched pairs. 43964 records in RAM.
INFO 2026-06-08 09:37:54 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 1s. Last read position: chr8:38,329,575
INFO 2026-06-08 09:37:54 MarkDuplicates Tracking 1056189 as yet unmatched pairs. 41266 records in RAM.
INFO 2026-06-08 09:37:56 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 1s. Last read position: chr8:41,612,149
INFO 2026-06-08 09:37:56 MarkDuplicates Tracking 1053796 as yet unmatched pairs. 38868 records in RAM.
INFO 2026-06-08 09:37:58 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 2s. Last read position: chr8:52,657,318
INFO 2026-06-08 09:37:58 MarkDuplicates Tracking 1050357 as yet unmatched pairs. 35428 records in RAM.
INFO 2026-06-08 09:38:00 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 1s. Last read position: chr8:70,121,351
INFO 2026-06-08 09:38:00 MarkDuplicates Tracking 1048138 as yet unmatched pairs. 33207 records in RAM.
INFO 2026-06-08 09:38:01 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:06:57s. Time for last 1,000,000: 1s. Last read position: chr8:94,871,893
INFO 2026-06-08 09:38:01 MarkDuplicates Tracking 1045039 as yet unmatched pairs. 30105 records in RAM.
INFO 2026-06-08 09:38:03 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 1s. Last read position: chr8:102,650,097
INFO 2026-06-08 09:38:03 MarkDuplicates Tracking 1042667 as yet unmatched pairs. 27733 records in RAM.
INFO 2026-06-08 09:38:05 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:07:00s. Time for last 1,000,000: 1s. Last read position: chr8:124,553,477
INFO 2026-06-08 09:38:05 MarkDuplicates Tracking 1042339 as yet unmatched pairs. 27397 records in RAM.
INFO 2026-06-08 09:38:06 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 1s. Last read position: chr8:130,354,344
INFO 2026-06-08 09:38:06 MarkDuplicates Tracking 1036897 as yet unmatched pairs. 21950 records in RAM.
INFO 2026-06-08 09:38:08 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:07:04s. Time for last 1,000,000: 1s. Last read position: chr8:143,021,685
INFO 2026-06-08 09:38:08 MarkDuplicates Tracking 1033927 as yet unmatched pairs. 18980 records in RAM.
INFO 2026-06-08 09:38:09 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 1s. Last read position: chr8:143,862,194
INFO 2026-06-08 09:38:09 MarkDuplicates Tracking 1030675 as yet unmatched pairs. 15722 records in RAM.
INFO 2026-06-08 09:38:11 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:07:07s. Time for last 1,000,000: 1s. Last read position: chr8:143,920,287
INFO 2026-06-08 09:38:11 MarkDuplicates Tracking 1029504 as yet unmatched pairs. 14551 records in RAM.
INFO 2026-06-08 09:38:13 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:07:09s. Time for last 1,000,000: 1s. Last read position: chr8:143,925,091
INFO 2026-06-08 09:38:13 MarkDuplicates Tracking 1028299 as yet unmatched pairs. 13345 records in RAM.
INFO 2026-06-08 09:39:11 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:08:07s. Time for last 1,000,000: 57s. Last read position: chr8:143,985,507
INFO 2026-06-08 09:39:11 MarkDuplicates Tracking 1019628 as yet unmatched pairs. 4673 records in RAM.
INFO 2026-06-08 09:39:12 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:08:08s. Time for last 1,000,000: 1s. Last read position: chr8:144,497,240
INFO 2026-06-08 09:39:12 MarkDuplicates Tracking 1016262 as yet unmatched pairs. 1303 records in RAM.
INFO 2026-06-08 09:39:14 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:08:10s. Time for last 1,000,000: 1s. Last read position: chr9:5,072,582
INFO 2026-06-08 09:39:14 MarkDuplicates Tracking 1013598 as yet unmatched pairs. 56982 records in RAM.
INFO 2026-06-08 09:39:16 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:08:12s. Time for last 1,000,000: 1s. Last read position: chr9:32,488,036
INFO 2026-06-08 09:39:16 MarkDuplicates Tracking 1010773 as yet unmatched pairs. 54145 records in RAM.
INFO 2026-06-08 09:39:17 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:08:13s. Time for last 1,000,000: 1s. Last read position: chr9:35,106,375
INFO 2026-06-08 09:39:17 MarkDuplicates Tracking 1007909 as yet unmatched pairs. 51272 records in RAM.
INFO 2026-06-08 09:39:19 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:08:15s. Time for last 1,000,000: 1s. Last read position: chr9:36,835,411
INFO 2026-06-08 09:39:19 MarkDuplicates Tracking 1004369 as yet unmatched pairs. 47712 records in RAM.
INFO 2026-06-08 09:39:20 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 1s. Last read position: chr9:79,391,282
INFO 2026-06-08 09:39:20 MarkDuplicates Tracking 1001881 as yet unmatched pairs. 45220 records in RAM.
INFO 2026-06-08 09:39:22 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:08:17s. Time for last 1,000,000: 1s. Last read position: chr9:87,731,041
INFO 2026-06-08 09:39:22 MarkDuplicates Tracking 1002010 as yet unmatched pairs. 45349 records in RAM.
INFO 2026-06-08 09:39:23 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 1s. Last read position: chr9:93,660,422
INFO 2026-06-08 09:39:23 MarkDuplicates Tracking 996452 as yet unmatched pairs. 39789 records in RAM.
INFO 2026-06-08 09:39:25 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 1s. Last read position: chr9:104,799,935
INFO 2026-06-08 09:39:25 MarkDuplicates Tracking 994261 as yet unmatched pairs. 37596 records in RAM.
INFO 2026-06-08 09:39:27 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 1s. Last read position: chr9:112,124,416
INFO 2026-06-08 09:39:27 MarkDuplicates Tracking 990744 as yet unmatched pairs. 34055 records in RAM.
INFO 2026-06-08 09:39:29 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 1s. Last read position: chr9:114,377,140
INFO 2026-06-08 09:39:29 MarkDuplicates Tracking 989278 as yet unmatched pairs. 32589 records in RAM.
INFO 2026-06-08 09:39:30 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:08:26s. Time for last 1,000,000: 1s. Last read position: chr9:121,321,352
INFO 2026-06-08 09:39:30 MarkDuplicates Tracking 985397 as yet unmatched pairs. 28706 records in RAM.
INFO 2026-06-08 09:39:32 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:08:28s. Time for last 1,000,000: 1s. Last read position: chr9:127,516,841
INFO 2026-06-08 09:39:32 MarkDuplicates Tracking 982651 as yet unmatched pairs. 25960 records in RAM.
INFO 2026-06-08 09:39:33 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 1s. Last read position: chr9:128,185,592
INFO 2026-06-08 09:39:33 MarkDuplicates Tracking 979249 as yet unmatched pairs. 22555 records in RAM.
INFO 2026-06-08 09:39:35 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:08:31s. Time for last 1,000,000: 1s. Last read position: chr9:129,900,016
INFO 2026-06-08 09:39:35 MarkDuplicates Tracking 976171 as yet unmatched pairs. 19476 records in RAM.
INFO 2026-06-08 09:39:36 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 1s. Last read position: chr9:131,483,332
INFO 2026-06-08 09:39:36 MarkDuplicates Tracking 973670 as yet unmatched pairs. 16975 records in RAM.
INFO 2026-06-08 09:39:38 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 1s. Last read position: chr9:133,108,168
INFO 2026-06-08 09:39:38 MarkDuplicates Tracking 971519 as yet unmatched pairs. 14816 records in RAM.
INFO 2026-06-08 09:39:39 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 1s. Last read position: chr9:134,916,410
INFO 2026-06-08 09:39:39 MarkDuplicates Tracking 968064 as yet unmatched pairs. 11360 records in RAM.
INFO 2026-06-08 09:39:41 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 1s. Last read position: chr9:136,508,104
INFO 2026-06-08 09:39:41 MarkDuplicates Tracking 964289 as yet unmatched pairs. 7576 records in RAM.
INFO 2026-06-08 09:39:43 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:08:38s. Time for last 1,000,000: 1s. Last read position: chr9:137,024,178
INFO 2026-06-08 09:39:43 MarkDuplicates Tracking 960925 as yet unmatched pairs. 4210 records in RAM.
INFO 2026-06-08 09:39:44 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 1s. Last read position: chr9:137,834,504
INFO 2026-06-08 09:39:44 MarkDuplicates Tracking 957172 as yet unmatched pairs. 457 records in RAM.
INFO 2026-06-08 09:39:46 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:08:42s. Time for last 1,000,000: 2s. Last read position: chr10:6,108,643
INFO 2026-06-08 09:39:46 MarkDuplicates Tracking 954031 as yet unmatched pairs. 47965 records in RAM.
INFO 2026-06-08 09:39:48 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:08:43s. Time for last 1,000,000: 1s. Last read position: chr10:12,087,583
INFO 2026-06-08 09:39:48 MarkDuplicates Tracking 951013 as yet unmatched pairs. 44935 records in RAM.
INFO 2026-06-08 09:39:49 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:08:45s. Time for last 1,000,000: 1s. Last read position: chr10:24,585,623
INFO 2026-06-08 09:39:49 MarkDuplicates Tracking 948173 as yet unmatched pairs. 42086 records in RAM.
INFO 2026-06-08 09:39:51 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:08:47s. Time for last 1,000,000: 1s. Last read position: chr10:32,031,224
INFO 2026-06-08 09:39:51 MarkDuplicates Tracking 945963 as yet unmatched pairs. 39872 records in RAM.
INFO 2026-06-08 09:39:52 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 1s. Last read position: chr10:45,428,589
INFO 2026-06-08 09:39:52 MarkDuplicates Tracking 943463 as yet unmatched pairs. 37354 records in RAM.
INFO 2026-06-08 09:39:54 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 1s. Last read position: chr10:48,450,877
INFO 2026-06-08 09:39:54 MarkDuplicates Tracking 940882 as yet unmatched pairs. 34764 records in RAM.
INFO 2026-06-08 09:39:55 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 1s. Last read position: chr10:62,805,145
INFO 2026-06-08 09:39:55 MarkDuplicates Tracking 938541 as yet unmatched pairs. 32421 records in RAM.
INFO 2026-06-08 09:39:57 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:08:52s. Time for last 1,000,000: 1s. Last read position: chr10:70,876,657
INFO 2026-06-08 09:39:57 MarkDuplicates Tracking 935591 as yet unmatched pairs. 29471 records in RAM.
INFO 2026-06-08 09:39:58 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 1s. Last read position: chr10:73,792,104
INFO 2026-06-08 09:39:58 MarkDuplicates Tracking 933100 as yet unmatched pairs. 26978 records in RAM.
INFO 2026-06-08 09:40:00 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:08:56s. Time for last 1,000,000: 1s. Last read position: chr10:78,040,629
INFO 2026-06-08 09:40:00 MarkDuplicates Tracking 929745 as yet unmatched pairs. 23619 records in RAM.
INFO 2026-06-08 09:40:02 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:08:57s. Time for last 1,000,000: 1s. Last read position: chr10:87,864,416
INFO 2026-06-08 09:40:02 MarkDuplicates Tracking 927635 as yet unmatched pairs. 21508 records in RAM.
INFO 2026-06-08 09:40:03 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:08:59s. Time for last 1,000,000: 1s. Last read position: chr10:95,869,543
INFO 2026-06-08 09:40:03 MarkDuplicates Tracking 924160 as yet unmatched pairs. 18024 records in RAM.
INFO 2026-06-08 09:40:07 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:09:02s. Time for last 1,000,000: 3s. Last read position: chr10:99,620,179
INFO 2026-06-08 09:40:07 MarkDuplicates Tracking 921057 as yet unmatched pairs. 14920 records in RAM.
INFO 2026-06-08 09:40:08 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:09:04s. Time for last 1,000,000: 1s. Last read position: chr10:102,138,604
INFO 2026-06-08 09:40:08 MarkDuplicates Tracking 918499 as yet unmatched pairs. 12360 records in RAM.
INFO 2026-06-08 09:40:10 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 1s. Last read position: chr10:103,438,639
INFO 2026-06-08 09:40:10 MarkDuplicates Tracking 915359 as yet unmatched pairs. 9216 records in RAM.
INFO 2026-06-08 09:40:11 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:09:07s. Time for last 1,000,000: 1s. Last read position: chr10:116,968,692
INFO 2026-06-08 09:40:11 MarkDuplicates Tracking 913596 as yet unmatched pairs. 7448 records in RAM.
INFO 2026-06-08 09:40:12 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 1s. Last read position: chr10:124,045,818
INFO 2026-06-08 09:40:12 MarkDuplicates Tracking 912663 as yet unmatched pairs. 6513 records in RAM.
INFO 2026-06-08 09:40:14 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:09:10s. Time for last 1,000,000: 1s. Last read position: chr10:133,283,983
INFO 2026-06-08 09:40:14 MarkDuplicates Tracking 907320 as yet unmatched pairs. 1164 records in RAM.
INFO 2026-06-08 09:40:16 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:09:12s. Time for last 1,000,000: 2s. Last read position: chr11:494,690
INFO 2026-06-08 09:40:16 MarkDuplicates Tracking 904145 as yet unmatched pairs. 104282 records in RAM.
INFO 2026-06-08 09:40:18 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 1s. Last read position: chr11:801,559
INFO 2026-06-08 09:40:18 MarkDuplicates Tracking 900243 as yet unmatched pairs. 100378 records in RAM.
INFO 2026-06-08 09:40:19 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:09:15s. Time for last 1,000,000: 1s. Last read position: chr11:1,243,604
INFO 2026-06-08 09:40:19 MarkDuplicates Tracking 897519 as yet unmatched pairs. 97650 records in RAM.
INFO 2026-06-08 09:40:21 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:09:17s. Time for last 1,000,000: 1s. Last read position: chr11:1,880,114
INFO 2026-06-08 09:40:21 MarkDuplicates Tracking 894435 as yet unmatched pairs. 94566 records in RAM.
INFO 2026-06-08 09:40:22 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:09:18s. Time for last 1,000,000: 1s. Last read position: chr11:5,697,259
INFO 2026-06-08 09:40:22 MarkDuplicates Tracking 890610 as yet unmatched pairs. 90721 records in RAM.
INFO 2026-06-08 09:40:24 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 1s. Last read position: chr11:9,178,998
INFO 2026-06-08 09:40:24 MarkDuplicates Tracking 887388 as yet unmatched pairs. 87490 records in RAM.
INFO 2026-06-08 09:40:26 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:09:21s. Time for last 1,000,000: 1s. Last read position: chr11:13,714,648
INFO 2026-06-08 09:40:26 MarkDuplicates Tracking 884479 as yet unmatched pairs. 84578 records in RAM.
INFO 2026-06-08 09:40:27 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:09:23s. Time for last 1,000,000: 1s. Last read position: chr11:35,139,208
INFO 2026-06-08 09:40:27 MarkDuplicates Tracking 886888 as yet unmatched pairs. 86985 records in RAM.
INFO 2026-06-08 09:40:29 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 1s. Last read position: chr11:46,376,097
INFO 2026-06-08 09:40:29 MarkDuplicates Tracking 879899 as yet unmatched pairs. 79992 records in RAM.
INFO 2026-06-08 09:40:31 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:09:27s. Time for last 1,000,000: 2s. Last read position: chr11:47,355,414
INFO 2026-06-08 09:40:31 MarkDuplicates Tracking 879923 as yet unmatched pairs. 80016 records in RAM.
INFO 2026-06-08 09:40:33 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:09:28s. Time for last 1,000,000: 1s. Last read position: chr11:47,780,355
INFO 2026-06-08 09:40:33 MarkDuplicates Tracking 872916 as yet unmatched pairs. 73003 records in RAM.
INFO 2026-06-08 09:40:34 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:09:30s. Time for last 1,000,000: 1s. Last read position: chr11:59,152,824
INFO 2026-06-08 09:40:34 MarkDuplicates Tracking 869821 as yet unmatched pairs. 69908 records in RAM.
INFO 2026-06-08 09:40:37 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:09:32s. Time for last 1,000,000: 2s. Last read position: chr11:61,303,976
INFO 2026-06-08 09:40:37 MarkDuplicates Tracking 866686 as yet unmatched pairs. 66773 records in RAM.
INFO 2026-06-08 09:40:38 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:09:34s. Time for last 1,000,000: 1s. Last read position: chr11:62,522,651
INFO 2026-06-08 09:40:38 MarkDuplicates Tracking 865054 as yet unmatched pairs. 65127 records in RAM.
INFO 2026-06-08 09:40:41 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:09:36s. Time for last 1,000,000: 2s. Last read position: chr11:62,532,139
INFO 2026-06-08 09:40:41 MarkDuplicates Tracking 862251 as yet unmatched pairs. 62323 records in RAM.
INFO 2026-06-08 09:40:42 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:09:38s. Time for last 1,000,000: 1s. Last read position: chr11:62,796,137
INFO 2026-06-08 09:40:42 MarkDuplicates Tracking 859317 as yet unmatched pairs. 59377 records in RAM.
INFO 2026-06-08 09:40:44 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:09:40s. Time for last 1,000,000: 1s. Last read position: chr11:64,262,694
INFO 2026-06-08 09:40:44 MarkDuplicates Tracking 855779 as yet unmatched pairs. 55839 records in RAM.
INFO 2026-06-08 09:40:45 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:09:41s. Time for last 1,000,000: 1s. Last read position: chr11:64,773,448
INFO 2026-06-08 09:40:45 MarkDuplicates Tracking 852854 as yet unmatched pairs. 52906 records in RAM.
INFO 2026-06-08 09:40:47 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:09:43s. Time for last 1,000,000: 1s. Last read position: chr11:65,394,270
INFO 2026-06-08 09:40:47 MarkDuplicates Tracking 849049 as yet unmatched pairs. 49101 records in RAM.
INFO 2026-06-08 09:40:49 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 1s. Last read position: chr11:65,598,351
INFO 2026-06-08 09:40:49 MarkDuplicates Tracking 845745 as yet unmatched pairs. 45790 records in RAM.
INFO 2026-06-08 09:40:50 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:09:46s. Time for last 1,000,000: 1s. Last read position: chr11:65,659,727
INFO 2026-06-08 09:40:50 MarkDuplicates Tracking 844472 as yet unmatched pairs. 44516 records in RAM.
INFO 2026-06-08 09:40:52 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:09:47s. Time for last 1,000,000: 1s. Last read position: chr11:66,475,720
INFO 2026-06-08 09:40:52 MarkDuplicates Tracking 838910 as yet unmatched pairs. 38953 records in RAM.
INFO 2026-06-08 09:40:53 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:09:49s. Time for last 1,000,000: 1s. Last read position: chr11:67,285,392
INFO 2026-06-08 09:40:53 MarkDuplicates Tracking 836020 as yet unmatched pairs. 36019 records in RAM.
INFO 2026-06-08 09:40:55 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:09:51s. Time for last 1,000,000: 1s. Last read position: chr11:68,003,668
INFO 2026-06-08 09:40:55 MarkDuplicates Tracking 833143 as yet unmatched pairs. 33142 records in RAM.
INFO 2026-06-08 09:40:56 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:09:52s. Time for last 1,000,000: 1s. Last read position: chr11:68,613,064
INFO 2026-06-08 09:40:56 MarkDuplicates Tracking 828886 as yet unmatched pairs. 28865 records in RAM.
INFO 2026-06-08 09:40:58 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:09:54s. Time for last 1,000,000: 1s. Last read position: chr11:72,013,766
INFO 2026-06-08 09:40:58 MarkDuplicates Tracking 825798 as yet unmatched pairs. 25772 records in RAM.
INFO 2026-06-08 09:41:00 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:09:55s. Time for last 1,000,000: 1s. Last read position: chr11:72,712,469
INFO 2026-06-08 09:41:00 MarkDuplicates Tracking 826974 as yet unmatched pairs. 26945 records in RAM.
INFO 2026-06-08 09:41:01 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:09:57s. Time for last 1,000,000: 1s. Last read position: chr11:75,005,461
INFO 2026-06-08 09:41:01 MarkDuplicates Tracking 819604 as yet unmatched pairs. 19563 records in RAM.
INFO 2026-06-08 09:41:03 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 1s. Last read position: chr11:82,914,729
INFO 2026-06-08 09:41:03 MarkDuplicates Tracking 816604 as yet unmatched pairs. 16553 records in RAM.
INFO 2026-06-08 09:41:04 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:10:00s. Time for last 1,000,000: 1s. Last read position: chr11:96,341,610
INFO 2026-06-08 09:41:04 MarkDuplicates Tracking 817482 as yet unmatched pairs. 17430 records in RAM.
INFO 2026-06-08 09:41:06 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:10:02s. Time for last 1,000,000: 2s. Last read position: chr11:117,098,157
INFO 2026-06-08 09:41:06 MarkDuplicates Tracking 812026 as yet unmatched pairs. 11967 records in RAM.
INFO 2026-06-08 09:41:08 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:10:04s. Time for last 1,000,000: 1s. Last read position: chr11:117,999,465
INFO 2026-06-08 09:41:08 MarkDuplicates Tracking 811853 as yet unmatched pairs. 11794 records in RAM.
INFO 2026-06-08 09:41:09 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:10:05s. Time for last 1,000,000: 1s. Last read position: chr11:119,206,296
INFO 2026-06-08 09:41:09 MarkDuplicates Tracking 805076 as yet unmatched pairs. 5017 records in RAM.
INFO 2026-06-08 09:41:11 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:10:07s. Time for last 1,000,000: 1s. Last read position: chr11:128,810,797
INFO 2026-06-08 09:41:11 MarkDuplicates Tracking 802151 as yet unmatched pairs. 2089 records in RAM.
INFO 2026-06-08 09:41:13 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 2s. Last read position: chr12:753,944
INFO 2026-06-08 09:41:13 MarkDuplicates Tracking 801260 as yet unmatched pairs. 89073 records in RAM.
INFO 2026-06-08 09:41:15 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:10:11s. Time for last 1,000,000: 1s. Last read position: chr12:6,557,047
INFO 2026-06-08 09:41:15 MarkDuplicates Tracking 796656 as yet unmatched pairs. 84468 records in RAM.
INFO 2026-06-08 09:41:17 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 1s. Last read position: chr12:6,955,374
INFO 2026-06-08 09:41:17 MarkDuplicates Tracking 796328 as yet unmatched pairs. 84129 records in RAM.
INFO 2026-06-08 09:41:18 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:10:14s. Time for last 1,000,000: 1s. Last read position: chr12:7,495,302
INFO 2026-06-08 09:41:18 MarkDuplicates Tracking 793505 as yet unmatched pairs. 81305 records in RAM.
INFO 2026-06-08 09:41:20 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:10:16s. Time for last 1,000,000: 1s. Last read position: chr12:9,695,642
INFO 2026-06-08 09:41:20 MarkDuplicates Tracking 789092 as yet unmatched pairs. 76891 records in RAM.
INFO 2026-06-08 09:41:21 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:10:17s. Time for last 1,000,000: 1s. Last read position: chr12:11,869,751
INFO 2026-06-08 09:41:21 MarkDuplicates Tracking 793095 as yet unmatched pairs. 80894 records in RAM.
INFO 2026-06-08 09:41:23 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:10:19s. Time for last 1,000,000: 1s. Last read position: chr12:25,090,138
INFO 2026-06-08 09:41:23 MarkDuplicates Tracking 783985 as yet unmatched pairs. 71771 records in RAM.
INFO 2026-06-08 09:41:25 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:10:20s. Time for last 1,000,000: 1s. Last read position: chr12:42,326,204
INFO 2026-06-08 09:41:25 MarkDuplicates Tracking 781691 as yet unmatched pairs. 69476 records in RAM.
INFO 2026-06-08 09:41:26 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:10:22s. Time for last 1,000,000: 1s. Last read position: chr12:49,026,728
INFO 2026-06-08 09:41:26 MarkDuplicates Tracking 779442 as yet unmatched pairs. 67226 records in RAM.
INFO 2026-06-08 09:41:28 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:10:24s. Time for last 1,000,000: 1s. Last read position: chr12:49,051,944
INFO 2026-06-08 09:41:28 MarkDuplicates Tracking 776837 as yet unmatched pairs. 64620 records in RAM.
INFO 2026-06-08 09:41:30 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 2s. Last read position: chr12:50,723,268
INFO 2026-06-08 09:41:30 MarkDuplicates Tracking 773561 as yet unmatched pairs. 61343 records in RAM.
INFO 2026-06-08 09:41:32 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:10:28s. Time for last 1,000,000: 2s. Last read position: chr12:53,306,667
INFO 2026-06-08 09:41:32 MarkDuplicates Tracking 770430 as yet unmatched pairs. 58211 records in RAM.
INFO 2026-06-08 09:41:34 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:10:30s. Time for last 1,000,000: 1s. Last read position: chr12:54,516,931
INFO 2026-06-08 09:41:34 MarkDuplicates Tracking 769087 as yet unmatched pairs. 56868 records in RAM.
INFO 2026-06-08 09:41:36 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:10:31s. Time for last 1,000,000: 1s. Last read position: chr12:56,173,766
INFO 2026-06-08 09:41:36 MarkDuplicates Tracking 765306 as yet unmatched pairs. 53086 records in RAM.