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/ab/4cdb0fa3db045434df8c692c2704d6/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/1fffb548fa4e10c9ec207fcbade05d/aih-tih-sc-176637-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/4cdb0fa3db045434df8c692c2704d6/.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-176637-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-176637-R1_B23WHYVLT4_1.md.bam --METRICS_FILE aih-tih-sc-176637-R1_B23WHYVLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
08:14:51.883 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 08:14:51 GMT 2026] MarkDuplicates --INPUT aih-tih-sc-176637-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-176637-R1_B23WHYVLT4_1.md.bam --METRICS_FILE aih-tih-sc-176637-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 08:14:51 GMT 2026] Executing as ?@nf-ab4cdb0fa3db045434df8c692c2704d6-3990e-hfbzw 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 08:14:51 MarkDuplicates Start of doWork freeMemory: 105492256; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 08:14:51 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 08:14:51 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 08:14:58 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:2,502,327
INFO 2026-06-08 08:14:58 MarkDuplicates Tracking 3782 as yet unmatched pairs. 54 records in RAM.
INFO 2026-06-08 08:15:00 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: chr1:11,127,721
INFO 2026-06-08 08:15:00 MarkDuplicates Tracking 7371 as yet unmatched pairs. 111 records in RAM.
INFO 2026-06-08 08:15:02 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: chr1:17,656,557
INFO 2026-06-08 08:15:02 MarkDuplicates Tracking 10570 as yet unmatched pairs. 120 records in RAM.
INFO 2026-06-08 08:15:05 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 2s. Last read position: chr1:21,855,316
INFO 2026-06-08 08:15:05 MarkDuplicates Tracking 14555 as yet unmatched pairs. 552 records in RAM.
INFO 2026-06-08 08:15:08 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: chr1:24,670,176
INFO 2026-06-08 08:15:08 MarkDuplicates Tracking 17434 as yet unmatched pairs. 83 records in RAM.
INFO 2026-06-08 08:15:10 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr1:28,581,627
INFO 2026-06-08 08:15:10 MarkDuplicates Tracking 20814 as yet unmatched pairs. 39 records in RAM.
INFO 2026-06-08 08:15:12 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 2s. Last read position: chr1:32,657,487
INFO 2026-06-08 08:15:12 MarkDuplicates Tracking 25347 as yet unmatched pairs. 1154 records in RAM.
INFO 2026-06-08 08:15:15 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 2s. Last read position: chr1:36,286,594
INFO 2026-06-08 08:15:15 MarkDuplicates Tracking 28373 as yet unmatched pairs. 782 records in RAM.
INFO 2026-06-08 08:15:17 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 2s. Last read position: chr1:39,452,770
INFO 2026-06-08 08:15:17 MarkDuplicates Tracking 31132 as yet unmatched pairs. 337 records in RAM.
INFO 2026-06-08 08:15:20 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 2s. Last read position: chr1:43,171,479
INFO 2026-06-08 08:15:20 MarkDuplicates Tracking 34537 as yet unmatched pairs. 525 records in RAM.
INFO 2026-06-08 08:15:22 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 2s. Last read position: chr1:45,515,788
INFO 2026-06-08 08:15:22 MarkDuplicates Tracking 41874 as yet unmatched pairs. 4327 records in RAM.
INFO 2026-06-08 08:15:24 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 2s. Last read position: chr1:51,878,451
INFO 2026-06-08 08:15:24 MarkDuplicates Tracking 41295 as yet unmatched pairs. 491 records in RAM.
INFO 2026-06-08 08:15:26 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 2s. Last read position: chr1:59,512,392
INFO 2026-06-08 08:15:26 MarkDuplicates Tracking 44447 as yet unmatched pairs. 201 records in RAM.
INFO 2026-06-08 08:15:29 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 2s. Last read position: chr1:78,627,893
INFO 2026-06-08 08:15:29 MarkDuplicates Tracking 48070 as yet unmatched pairs. 759 records in RAM.
INFO 2026-06-08 08:15:32 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 2s. Last read position: chr1:94,174,443
INFO 2026-06-08 08:15:32 MarkDuplicates Tracking 51142 as yet unmatched pairs. 628 records in RAM.
INFO 2026-06-08 08:15:34 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 2s. Last read position: chr1:109,194,585
INFO 2026-06-08 08:15:34 MarkDuplicates Tracking 54008 as yet unmatched pairs. 644 records in RAM.
INFO 2026-06-08 08:15:36 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chr1:113,100,235
INFO 2026-06-08 08:15:36 MarkDuplicates Tracking 56957 as yet unmatched pairs. 280 records in RAM.
INFO 2026-06-08 08:15:38 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 2s. Last read position: chr1:117,942,510
INFO 2026-06-08 08:15:38 MarkDuplicates Tracking 59917 as yet unmatched pairs. 193 records in RAM.
INFO 2026-06-08 08:15:40 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 1s. Last read position: chr1:119,968,142
INFO 2026-06-08 08:15:40 MarkDuplicates Tracking 65166 as yet unmatched pairs. 2161 records in RAM.
INFO 2026-06-08 08:15:43 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 3s. Last read position: chr1:145,400,537
INFO 2026-06-08 08:15:43 MarkDuplicates Tracking 65086 as yet unmatched pairs. 408 records in RAM.
INFO 2026-06-08 08:15:46 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 2s. Last read position: chr1:146,865,728
INFO 2026-06-08 08:15:46 MarkDuplicates Tracking 66382 as yet unmatched pairs. 123 records in RAM.
INFO 2026-06-08 08:15:47 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 1s. Last read position: chr1:148,598,593
INFO 2026-06-08 08:15:47 MarkDuplicates Tracking 68057 as yet unmatched pairs. 624 records in RAM.
INFO 2026-06-08 08:15:49 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 1s. Last read position: chr1:149,923,927
INFO 2026-06-08 08:15:49 MarkDuplicates Tracking 69381 as yet unmatched pairs. 343 records in RAM.
INFO 2026-06-08 08:15:51 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 1s. Last read position: chr1:150,852,776
INFO 2026-06-08 08:15:51 MarkDuplicates Tracking 72545 as yet unmatched pairs. 394 records in RAM.
INFO 2026-06-08 08:15:53 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 1s. Last read position: chr1:152,213,752
INFO 2026-06-08 08:15:53 MarkDuplicates Tracking 75644 as yet unmatched pairs. 179 records in RAM.
INFO 2026-06-08 08:15:55 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 1s. Last read position: chr1:152,350,969
INFO 2026-06-08 08:15:55 MarkDuplicates Tracking 78577 as yet unmatched pairs. 827 records in RAM.
INFO 2026-06-08 08:15:57 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 1s. Last read position: chr1:154,172,908
INFO 2026-06-08 08:15:57 MarkDuplicates Tracking 84177 as yet unmatched pairs. 3334 records in RAM.
INFO 2026-06-08 08:15:58 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 1s. Last read position: chr1:155,062,261
INFO 2026-06-08 08:15:58 MarkDuplicates Tracking 84355 as yet unmatched pairs. 354 records in RAM.
INFO 2026-06-08 08:16:00 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 1s. Last read position: chr1:155,415,811
INFO 2026-06-08 08:16:00 MarkDuplicates Tracking 87025 as yet unmatched pairs. 266 records in RAM.
INFO 2026-06-08 08:16:03 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 2s. Last read position: chr1:156,137,185
INFO 2026-06-08 08:16:03 MarkDuplicates Tracking 93048 as yet unmatched pairs. 2830 records in RAM.
INFO 2026-06-08 08:16:05 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 2s. Last read position: chr1:158,177,212
INFO 2026-06-08 08:16:05 MarkDuplicates Tracking 93626 as yet unmatched pairs. 73 records in RAM.
INFO 2026-06-08 08:16:07 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 1s. Last read position: chr1:161,213,881
INFO 2026-06-08 08:16:07 MarkDuplicates Tracking 97599 as yet unmatched pairs. 738 records in RAM.
INFO 2026-06-08 08:16:09 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 1s. Last read position: chr1:169,130,068
INFO 2026-06-08 08:16:09 MarkDuplicates Tracking 103033 as yet unmatched pairs. 3013 records in RAM.
INFO 2026-06-08 08:16:11 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 1s. Last read position: chr1:178,902,056
INFO 2026-06-08 08:16:11 MarkDuplicates Tracking 103418 as yet unmatched pairs. 411 records in RAM.
INFO 2026-06-08 08:16:13 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 1s. Last read position: chr1:184,541,895
INFO 2026-06-08 08:16:13 MarkDuplicates Tracking 106937 as yet unmatched pairs. 723 records in RAM.
INFO 2026-06-08 08:16:15 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 1s. Last read position: chr1:192,578,275
INFO 2026-06-08 08:16:15 MarkDuplicates Tracking 109619 as yet unmatched pairs. 671 records in RAM.
INFO 2026-06-08 08:16:17 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 1s. Last read position: chr1:202,001,689
INFO 2026-06-08 08:16:17 MarkDuplicates Tracking 112798 as yet unmatched pairs. 623 records in RAM.
INFO 2026-06-08 08:16:19 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 2s. Last read position: chr1:204,137,126
INFO 2026-06-08 08:16:19 MarkDuplicates Tracking 115461 as yet unmatched pairs. 175 records in RAM.
INFO 2026-06-08 08:16:21 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 1s. Last read position: chr1:207,757,586
INFO 2026-06-08 08:16:21 MarkDuplicates Tracking 120245 as yet unmatched pairs. 1759 records in RAM.
INFO 2026-06-08 08:16:23 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 2s. Last read position: chr1:220,796,668
INFO 2026-06-08 08:16:23 MarkDuplicates Tracking 121522 as yet unmatched pairs. 81 records in RAM.
INFO 2026-06-08 08:16:26 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 3s. Last read position: chr1:226,065,756
INFO 2026-06-08 08:16:26 MarkDuplicates Tracking 125346 as yet unmatched pairs. 893 records in RAM.
INFO 2026-06-08 08:16:29 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 2s. Last read position: chr1:230,958,262
INFO 2026-06-08 08:16:29 MarkDuplicates Tracking 128147 as yet unmatched pairs. 79 records in RAM.
INFO 2026-06-08 08:16:31 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 2s. Last read position: chr1:236,826,882
INFO 2026-06-08 08:16:31 MarkDuplicates Tracking 131678 as yet unmatched pairs. 274 records in RAM.
INFO 2026-06-08 08:16:34 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 3s. Last read position: chr2:271,901
INFO 2026-06-08 08:16:34 MarkDuplicates Tracking 135313 as yet unmatched pairs. 132812 records in RAM.
INFO 2026-06-08 08:16:36 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 2s. Last read position: chr2:20,203,181
INFO 2026-06-08 08:16:36 MarkDuplicates Tracking 141037 as yet unmatched pairs. 138434 records in RAM.
INFO 2026-06-08 08:16:39 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 2s. Last read position: chr2:27,036,563
INFO 2026-06-08 08:16:39 MarkDuplicates Tracking 141205 as yet unmatched pairs. 138550 records in RAM.
INFO 2026-06-08 08:16:41 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 2s. Last read position: chr2:32,515,611
INFO 2026-06-08 08:16:41 MarkDuplicates Tracking 144364 as yet unmatched pairs. 141668 records in RAM.
INFO 2026-06-08 08:16:43 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,264
INFO 2026-06-08 08:16:43 MarkDuplicates Tracking 291838 as yet unmatched pairs. 132807 records in RAM.
INFO 2026-06-08 08:16:46 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,264
INFO 2026-06-08 08:16:46 MarkDuplicates Tracking 940276 as yet unmatched pairs. 93231 records in RAM.
INFO 2026-06-08 08:16:48 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,406
INFO 2026-06-08 08:16:48 MarkDuplicates Tracking 1048270 as yet unmatched pairs. 86594 records in RAM.
INFO 2026-06-08 08:16:49 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 1s. Last read position: chr2:36,916,108
INFO 2026-06-08 08:16:49 MarkDuplicates Tracking 1117516 as yet unmatched pairs. 82022 records in RAM.
INFO 2026-06-08 08:16:51 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 1s. Last read position: chr2:44,320,299
INFO 2026-06-08 08:16:51 MarkDuplicates Tracking 1114237 as yet unmatched pairs. 78669 records in RAM.
INFO 2026-06-08 08:16:53 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 2s. Last read position: chr2:55,335,152
INFO 2026-06-08 08:16:53 MarkDuplicates Tracking 1111922 as yet unmatched pairs. 76262 records in RAM.
INFO 2026-06-08 08:16:55 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 2s. Last read position: chr2:69,326,094
INFO 2026-06-08 08:16:55 MarkDuplicates Tracking 1108894 as yet unmatched pairs. 73145 records in RAM.
INFO 2026-06-08 08:16:57 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 1s. Last read position: chr2:74,371,106
INFO 2026-06-08 08:16:57 MarkDuplicates Tracking 1105634 as yet unmatched pairs. 69804 records in RAM.
INFO 2026-06-08 08:16:59 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 2s. Last read position: chr2:86,969,008
INFO 2026-06-08 08:16:59 MarkDuplicates Tracking 1102319 as yet unmatched pairs. 66413 records in RAM.
INFO 2026-06-08 08:17:01 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 1s. Last read position: chr2:97,218,996
INFO 2026-06-08 08:17:01 MarkDuplicates Tracking 1099932 as yet unmatched pairs. 63968 records in RAM.
INFO 2026-06-08 08:17:03 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 1s. Last read position: chr2:107,872,337
INFO 2026-06-08 08:17:03 MarkDuplicates Tracking 1097062 as yet unmatched pairs. 60989 records in RAM.
INFO 2026-06-08 08:17:05 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 1s. Last read position: chr2:110,534,163
INFO 2026-06-08 08:17:05 MarkDuplicates Tracking 1095032 as yet unmatched pairs. 58928 records in RAM.
INFO 2026-06-08 08:17:07 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 2s. Last read position: chr2:119,679,232
INFO 2026-06-08 08:17:07 MarkDuplicates Tracking 1093189 as yet unmatched pairs. 57035 records in RAM.
INFO 2026-06-08 08:17:09 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 1s. Last read position: chr2:131,532,760
INFO 2026-06-08 08:17:09 MarkDuplicates Tracking 1091033 as yet unmatched pairs. 54806 records in RAM.
INFO 2026-06-08 08:17:11 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 1s. Last read position: chr2:144,400,075
INFO 2026-06-08 08:17:11 MarkDuplicates Tracking 1087994 as yet unmatched pairs. 51642 records in RAM.
INFO 2026-06-08 08:17:13 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 2s. Last read position: chr2:168,561,211
INFO 2026-06-08 08:17:13 MarkDuplicates Tracking 1086612 as yet unmatched pairs. 50169 records in RAM.
INFO 2026-06-08 08:17:15 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 2s. Last read position: chr2:170,961,679
INFO 2026-06-08 08:17:15 MarkDuplicates Tracking 1082286 as yet unmatched pairs. 45785 records in RAM.
INFO 2026-06-08 08:17:17 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 1s. Last read position: chr2:178,611,502
INFO 2026-06-08 08:17:17 MarkDuplicates Tracking 1079285 as yet unmatched pairs. 42711 records in RAM.
INFO 2026-06-08 08:17:19 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 2s. Last read position: chr2:182,756,389
INFO 2026-06-08 08:17:19 MarkDuplicates Tracking 1076998 as yet unmatched pairs. 40364 records in RAM.
INFO 2026-06-08 08:17:21 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 2s. Last read position: chr2:189,034,916
INFO 2026-06-08 08:17:21 MarkDuplicates Tracking 1072882 as yet unmatched pairs. 36181 records in RAM.
INFO 2026-06-08 08:17:24 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 2s. Last read position: chr2:197,453,626
INFO 2026-06-08 08:17:24 MarkDuplicates Tracking 1069831 as yet unmatched pairs. 33064 records in RAM.
INFO 2026-06-08 08:17:27 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 2s. Last read position: chr2:206,004,523
INFO 2026-06-08 08:17:27 MarkDuplicates Tracking 1066879 as yet unmatched pairs. 30064 records in RAM.
INFO 2026-06-08 08:17:29 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 2s. Last read position: chr2:215,349,143
INFO 2026-06-08 08:17:29 MarkDuplicates Tracking 1064510 as yet unmatched pairs. 27610 records in RAM.
INFO 2026-06-08 08:17:31 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 2s. Last read position: chr2:215,373,410
INFO 2026-06-08 08:17:31 MarkDuplicates Tracking 1073174 as yet unmatched pairs. 36245 records in RAM.
INFO 2026-06-08 08:17:34 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 2s. Last read position: chr2:215,384,899
INFO 2026-06-08 08:17:34 MarkDuplicates Tracking 1064358 as yet unmatched pairs. 27398 records in RAM.
INFO 2026-06-08 08:17:36 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 2s. Last read position: chr2:215,406,467
INFO 2026-06-08 08:17:36 MarkDuplicates Tracking 1063926 as yet unmatched pairs. 26941 records in RAM.
INFO 2026-06-08 08:17:38 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 2s. Last read position: chr2:215,424,266
INFO 2026-06-08 08:17:38 MarkDuplicates Tracking 1061442 as yet unmatched pairs. 24442 records in RAM.
INFO 2026-06-08 08:17:40 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 2s. Last read position: chr2:217,890,987
INFO 2026-06-08 08:17:40 MarkDuplicates Tracking 1049693 as yet unmatched pairs. 12659 records in RAM.
INFO 2026-06-08 08:17:43 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 2s. Last read position: chr2:222,624,319
INFO 2026-06-08 08:17:43 MarkDuplicates Tracking 1046006 as yet unmatched pairs. 8920 records in RAM.
INFO 2026-06-08 08:17:45 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 2s. Last read position: chr2:232,662,802
INFO 2026-06-08 08:17:45 MarkDuplicates Tracking 1043179 as yet unmatched pairs. 6019 records in RAM.
INFO 2026-06-08 08:17:47 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 1s. Last read position: chr2:237,396,748
INFO 2026-06-08 08:17:47 MarkDuplicates Tracking 1040523 as yet unmatched pairs. 3306 records in RAM.
INFO 2026-06-08 08:17:49 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 2s. Last read position: chr3:5,215,849
INFO 2026-06-08 08:17:49 MarkDuplicates Tracking 1036228 as yet unmatched pairs. 55465 records in RAM.
INFO 2026-06-08 08:17:52 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 2s. Last read position: chr3:12,935,530
INFO 2026-06-08 08:17:52 MarkDuplicates Tracking 1033001 as yet unmatched pairs. 52182 records in RAM.
INFO 2026-06-08 08:17:54 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 1s. Last read position: chr3:31,533,293
INFO 2026-06-08 08:17:54 MarkDuplicates Tracking 1030661 as yet unmatched pairs. 49754 records in RAM.
INFO 2026-06-08 08:17:56 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 1s. Last read position: chr3:40,461,968
INFO 2026-06-08 08:17:56 MarkDuplicates Tracking 1027761 as yet unmatched pairs. 46797 records in RAM.
INFO 2026-06-08 08:17:58 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 2s. Last read position: chr3:47,122,395
INFO 2026-06-08 08:17:58 MarkDuplicates Tracking 1024128 as yet unmatched pairs. 43100 records in RAM.
INFO 2026-06-08 08:18:00 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 2s. Last read position: chr3:49,014,122
INFO 2026-06-08 08:18:00 MarkDuplicates Tracking 1020728 as yet unmatched pairs. 39676 records in RAM.
INFO 2026-06-08 08:18:02 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 2s. Last read position: chr3:50,117,095
INFO 2026-06-08 08:18:02 MarkDuplicates Tracking 1017192 as yet unmatched pairs. 36071 records in RAM.
INFO 2026-06-08 08:18:05 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 2s. Last read position: chr3:52,694,039
INFO 2026-06-08 08:18:05 MarkDuplicates Tracking 1013828 as yet unmatched pairs. 32667 records in RAM.
INFO 2026-06-08 08:18:07 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 1s. Last read position: chr3:64,013,495
INFO 2026-06-08 08:18:07 MarkDuplicates Tracking 1010798 as yet unmatched pairs. 29590 records in RAM.
INFO 2026-06-08 08:18:09 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 2s. Last read position: chr3:100,728,750
INFO 2026-06-08 08:18:09 MarkDuplicates Tracking 1010310 as yet unmatched pairs. 29029 records in RAM.
INFO 2026-06-08 08:18:11 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 2s. Last read position: chr3:114,308,235
INFO 2026-06-08 08:18:11 MarkDuplicates Tracking 1004916 as yet unmatched pairs. 23557 records in RAM.
INFO 2026-06-08 08:18:13 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 1s. Last read position: chr3:123,620,238
INFO 2026-06-08 08:18:13 MarkDuplicates Tracking 1001985 as yet unmatched pairs. 20563 records in RAM.
INFO 2026-06-08 08:18:15 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 2s. Last read position: chr3:129,439,745
INFO 2026-06-08 08:18:15 MarkDuplicates Tracking 998544 as yet unmatched pairs. 17036 records in RAM.
INFO 2026-06-08 08:18:18 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 2s. Last read position: chr3:141,576,999
INFO 2026-06-08 08:18:18 MarkDuplicates Tracking 995561 as yet unmatched pairs. 13996 records in RAM.
INFO 2026-06-08 08:18:20 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 1s. Last read position: chr3:158,666,640
INFO 2026-06-08 08:18:20 MarkDuplicates Tracking 992636 as yet unmatched pairs. 10999 records in RAM.
INFO 2026-06-08 08:18:22 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 2s. Last read position: chr3:183,508,169
INFO 2026-06-08 08:18:22 MarkDuplicates Tracking 989471 as yet unmatched pairs. 7785 records in RAM.
INFO 2026-06-08 08:18:24 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 2s. Last read position: chr3:188,760,175
INFO 2026-06-08 08:18:24 MarkDuplicates Tracking 987405 as yet unmatched pairs. 5682 records in RAM.
INFO 2026-06-08 08:18:26 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 2s. Last read position: chr3:195,725,783
INFO 2026-06-08 08:18:26 MarkDuplicates Tracking 984174 as yet unmatched pairs. 2387 records in RAM.
INFO 2026-06-08 08:18:29 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 2s. Last read position: chr4:1,023,681
INFO 2026-06-08 08:18:29 MarkDuplicates Tracking 980827 as yet unmatched pairs. 34721 records in RAM.
INFO 2026-06-08 08:18:31 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 2s. Last read position: chr4:4,434,813
INFO 2026-06-08 08:18:31 MarkDuplicates Tracking 977393 as yet unmatched pairs. 31205 records in RAM.
INFO 2026-06-08 08:18:34 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 2s. Last read position: chr4:20,712,783
INFO 2026-06-08 08:18:34 MarkDuplicates Tracking 973967 as yet unmatched pairs. 27724 records in RAM.
INFO 2026-06-08 08:18:36 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 2s. Last read position: chr4:48,548,544
INFO 2026-06-08 08:18:36 MarkDuplicates Tracking 971170 as yet unmatched pairs. 24857 records in RAM.
INFO 2026-06-08 08:18:38 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 2s. Last read position: chr4:68,337,604
INFO 2026-06-08 08:18:38 MarkDuplicates Tracking 968524 as yet unmatched pairs. 22158 records in RAM.
INFO 2026-06-08 08:18:40 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 2s. Last read position: chr4:77,058,607
INFO 2026-06-08 08:18:40 MarkDuplicates Tracking 966174 as yet unmatched pairs. 19751 records in RAM.
INFO 2026-06-08 08:18:42 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 2s. Last read position: chr4:87,612,460
INFO 2026-06-08 08:18:42 MarkDuplicates Tracking 962390 as yet unmatched pairs. 15908 records in RAM.
INFO 2026-06-08 08:18:44 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 2s. Last read position: chr4:105,693,376
INFO 2026-06-08 08:18:44 MarkDuplicates Tracking 959343 as yet unmatched pairs. 12778 records in RAM.
INFO 2026-06-08 08:18:46 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 2s. Last read position: chr4:124,669,449
INFO 2026-06-08 08:18:46 MarkDuplicates Tracking 956664 as yet unmatched pairs. 10051 records in RAM.
INFO 2026-06-08 08:18:49 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 2s. Last read position: chr4:143,439,641
INFO 2026-06-08 08:18:49 MarkDuplicates Tracking 953563 as yet unmatched pairs. 6895 records in RAM.
INFO 2026-06-08 08:18:51 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 2s. Last read position: chr4:158,131,008
INFO 2026-06-08 08:18:51 MarkDuplicates Tracking 951258 as yet unmatched pairs. 4536 records in RAM.
INFO 2026-06-08 08:18:53 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 2s. Last read position: chr4:185,190,274
INFO 2026-06-08 08:18:53 MarkDuplicates Tracking 947641 as yet unmatched pairs. 837 records in RAM.
INFO 2026-06-08 08:18:57 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 3s. Last read position: chr5:14,419,857
INFO 2026-06-08 08:18:57 MarkDuplicates Tracking 945163 as yet unmatched pairs. 54582 records in RAM.
INFO 2026-06-08 08:19:00 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 2s. Last read position: chr5:36,975,968
INFO 2026-06-08 08:19:00 MarkDuplicates Tracking 941517 as yet unmatched pairs. 50885 records in RAM.
INFO 2026-06-08 08:19:02 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 2s. Last read position: chr5:54,518,593
INFO 2026-06-08 08:19:02 MarkDuplicates Tracking 938751 as yet unmatched pairs. 48019 records in RAM.
INFO 2026-06-08 08:19:04 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 2s. Last read position: chr5:69,119,446
INFO 2026-06-08 08:19:04 MarkDuplicates Tracking 935875 as yet unmatched pairs. 45064 records in RAM.
INFO 2026-06-08 08:19:07 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 2s. Last read position: chr5:74,725,739
INFO 2026-06-08 08:19:07 MarkDuplicates Tracking 933653 as yet unmatched pairs. 42800 records in RAM.
INFO 2026-06-08 08:19:09 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 2s. Last read position: chr5:83,519,849
INFO 2026-06-08 08:19:09 MarkDuplicates Tracking 931536 as yet unmatched pairs. 40625 records in RAM.
INFO 2026-06-08 08:19:11 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 2s. Last read position: chr5:98,889,191
INFO 2026-06-08 08:19:11 MarkDuplicates Tracking 928099 as yet unmatched pairs. 37133 records in RAM.
INFO 2026-06-08 08:19:13 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 2s. Last read position: chr5:132,343,780
INFO 2026-06-08 08:19:13 MarkDuplicates Tracking 924831 as yet unmatched pairs. 33797 records in RAM.
INFO 2026-06-08 08:19:15 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 2s. Last read position: chr5:138,571,019
INFO 2026-06-08 08:19:15 MarkDuplicates Tracking 922374 as yet unmatched pairs. 31304 records in RAM.
INFO 2026-06-08 08:19:17 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 1s. Last read position: chr5:141,421,741
INFO 2026-06-08 08:19:17 MarkDuplicates Tracking 918686 as yet unmatched pairs. 27588 records in RAM.
INFO 2026-06-08 08:19:19 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 2s. Last read position: chr5:150,123,094
INFO 2026-06-08 08:19:19 MarkDuplicates Tracking 915788 as yet unmatched pairs. 24659 records in RAM.
INFO 2026-06-08 08:19:21 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 2s. Last read position: chr5:150,404,681
INFO 2026-06-08 08:19:21 MarkDuplicates Tracking 929531 as yet unmatched pairs. 38388 records in RAM.
INFO 2026-06-08 08:19:24 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 2s. Last read position: chr5:150,412,659
INFO 2026-06-08 08:19:24 MarkDuplicates Tracking 907980 as yet unmatched pairs. 16810 records in RAM.
INFO 2026-06-08 08:19:25 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 1s. Last read position: chr5:157,086,100
INFO 2026-06-08 08:19:25 MarkDuplicates Tracking 905104 as yet unmatched pairs. 13891 records in RAM.
INFO 2026-06-08 08:19:28 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 2s. Last read position: chr5:171,400,175
INFO 2026-06-08 08:19:28 MarkDuplicates Tracking 909866 as yet unmatched pairs. 18599 records in RAM.
INFO 2026-06-08 08:19:30 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 2s. Last read position: chr5:177,238,415
INFO 2026-06-08 08:19:30 MarkDuplicates Tracking 898965 as yet unmatched pairs. 7655 records in RAM.
INFO 2026-06-08 08:19:32 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 1s. Last read position: chr5:179,765,972
INFO 2026-06-08 08:19:32 MarkDuplicates Tracking 896162 as yet unmatched pairs. 4787 records in RAM.
INFO 2026-06-08 08:19:34 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 2s. Last read position: chr5:180,792,192
INFO 2026-06-08 08:19:34 MarkDuplicates Tracking 892464 as yet unmatched pairs. 1044 records in RAM.
INFO 2026-06-08 08:19:38 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 3s. Last read position: chr6:7,568,513
INFO 2026-06-08 08:19:38 MarkDuplicates Tracking 889526 as yet unmatched pairs. 66336 records in RAM.
INFO 2026-06-08 08:19:40 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 2s. Last read position: chr6:24,658,558
INFO 2026-06-08 08:19:40 MarkDuplicates Tracking 886126 as yet unmatched pairs. 62884 records in RAM.
INFO 2026-06-08 08:19:42 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 2s. Last read position: chr6:29,828,074
INFO 2026-06-08 08:19:42 MarkDuplicates Tracking 882920 as yet unmatched pairs. 59622 records in RAM.
INFO 2026-06-08 08:19:45 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 2s. Last read position: chr6:30,894,620
INFO 2026-06-08 08:19:45 MarkDuplicates Tracking 880195 as yet unmatched pairs. 56872 records in RAM.
INFO 2026-06-08 08:19:47 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 2s. Last read position: chr6:31,639,088
INFO 2026-06-08 08:19:47 MarkDuplicates Tracking 876452 as yet unmatched pairs. 53106 records in RAM.
INFO 2026-06-08 08:19:49 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 1s. Last read position: chr6:31,829,134
INFO 2026-06-08 08:19:49 MarkDuplicates Tracking 874976 as yet unmatched pairs. 51606 records in RAM.
INFO 2026-06-08 08:19:52 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 2s. Last read position: chr6:32,062,290
INFO 2026-06-08 08:19:52 MarkDuplicates Tracking 871858 as yet unmatched pairs. 48462 records in RAM.
INFO 2026-06-08 08:19:54 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 2s. Last read position: chr6:33,069,127
INFO 2026-06-08 08:19:54 MarkDuplicates Tracking 868827 as yet unmatched pairs. 45394 records in RAM.
INFO 2026-06-08 08:19:57 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 2s. Last read position: chr6:34,247,797
INFO 2026-06-08 08:19:57 MarkDuplicates Tracking 864658 as yet unmatched pairs. 41202 records in RAM.
INFO 2026-06-08 08:19:59 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 2s. Last read position: chr6:41,638,743
INFO 2026-06-08 08:19:59 MarkDuplicates Tracking 861419 as yet unmatched pairs. 37900 records in RAM.
INFO 2026-06-08 08:20:01 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 1s. Last read position: chr6:44,232,364
INFO 2026-06-08 08:20:01 MarkDuplicates Tracking 859299 as yet unmatched pairs. 35749 records in RAM.
INFO 2026-06-08 08:20:04 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 2s. Last read position: chr6:56,615,784
INFO 2026-06-08 08:20:04 MarkDuplicates Tracking 855553 as yet unmatched pairs. 31888 records in RAM.
INFO 2026-06-08 08:20:06 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 2s. Last read position: chr6:78,983,063
INFO 2026-06-08 08:20:06 MarkDuplicates Tracking 852510 as yet unmatched pairs. 28819 records in RAM.
INFO 2026-06-08 08:20:09 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 2s. Last read position: chr6:107,929,454
INFO 2026-06-08 08:20:09 MarkDuplicates Tracking 849890 as yet unmatched pairs. 26150 records in RAM.
INFO 2026-06-08 08:20:11 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 2s. Last read position: chr6:127,286,168
INFO 2026-06-08 08:20:11 MarkDuplicates Tracking 847085 as yet unmatched pairs. 23280 records in RAM.
INFO 2026-06-08 08:20:13 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 2s. Last read position: chr6:136,791,825
INFO 2026-06-08 08:20:13 MarkDuplicates Tracking 843825 as yet unmatched pairs. 19957 records in RAM.
INFO 2026-06-08 08:20:16 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 2s. Last read position: chr6:148,543,881
INFO 2026-06-08 08:20:16 MarkDuplicates Tracking 841088 as yet unmatched pairs. 17149 records in RAM.
INFO 2026-06-08 08:20:18 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 2s. Last read position: chr6:151,808,042
INFO 2026-06-08 08:20:18 MarkDuplicates Tracking 841749 as yet unmatched pairs. 17758 records in RAM.
INFO 2026-06-08 08:20:20 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 2s. Last read position: chr6:151,944,284
INFO 2026-06-08 08:20:20 MarkDuplicates Tracking 843796 as yet unmatched pairs. 19749 records in RAM.
INFO 2026-06-08 08:20:22 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 2s. Last read position: chr6:158,084,050
INFO 2026-06-08 08:20:22 MarkDuplicates Tracking 830947 as yet unmatched pairs. 6805 records in RAM.
INFO 2026-06-08 08:20:24 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 2s. Last read position: chr6:160,991,870
INFO 2026-06-08 08:20:24 MarkDuplicates Tracking 827400 as yet unmatched pairs. 3226 records in RAM.
INFO 2026-06-08 08:20:26 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 2s. Last read position: chr6:170,583,736
INFO 2026-06-08 08:20:26 MarkDuplicates Tracking 824359 as yet unmatched pairs. 153 records in RAM.
INFO 2026-06-08 08:20:29 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 2s. Last read position: chr7:5,398,973
INFO 2026-06-08 08:20:29 MarkDuplicates Tracking 820346 as yet unmatched pairs. 56940 records in RAM.
INFO 2026-06-08 08:20:31 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 2s. Last read position: chr7:6,466,114
INFO 2026-06-08 08:20:31 MarkDuplicates Tracking 817343 as yet unmatched pairs. 53892 records in RAM.
INFO 2026-06-08 08:20:33 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 1s. Last read position: chr7:22,813,089
INFO 2026-06-08 08:20:33 MarkDuplicates Tracking 814754 as yet unmatched pairs. 51253 records in RAM.
INFO 2026-06-08 08:20:36 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 2s. Last read position: chr7:33,096,568
INFO 2026-06-08 08:20:36 MarkDuplicates Tracking 810887 as yet unmatched pairs. 47326 records in RAM.
INFO 2026-06-08 08:20:39 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 2s. Last read position: chr7:44,056,834
INFO 2026-06-08 08:20:39 MarkDuplicates Tracking 808546 as yet unmatched pairs. 44941 records in RAM.
INFO 2026-06-08 08:20:41 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 2s. Last read position: chr7:45,083,887
INFO 2026-06-08 08:20:41 MarkDuplicates Tracking 804540 as yet unmatched pairs. 40894 records in RAM.
INFO 2026-06-08 08:20:43 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 2s. Last read position: chr7:70,790,232
INFO 2026-06-08 08:20:43 MarkDuplicates Tracking 801864 as yet unmatched pairs. 38131 records in RAM.
INFO 2026-06-08 08:20:45 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 2s. Last read position: chr7:74,736,653
INFO 2026-06-08 08:20:45 MarkDuplicates Tracking 799325 as yet unmatched pairs. 35571 records in RAM.
INFO 2026-06-08 08:20:47 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 1s. Last read position: chr7:76,302,977
INFO 2026-06-08 08:20:47 MarkDuplicates Tracking 804506 as yet unmatched pairs. 40733 records in RAM.
INFO 2026-06-08 08:20:49 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 2s. Last read position: chr7:88,210,902
INFO 2026-06-08 08:20:49 MarkDuplicates Tracking 793950 as yet unmatched pairs. 30143 records in RAM.
INFO 2026-06-08 08:20:52 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 2s. Last read position: chr7:94,394,937
INFO 2026-06-08 08:20:52 MarkDuplicates Tracking 793202 as yet unmatched pairs. 29360 records in RAM.
INFO 2026-06-08 08:20:54 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 2s. Last read position: chr7:94,663,888
INFO 2026-06-08 08:20:54 MarkDuplicates Tracking 791282 as yet unmatched pairs. 27393 records in RAM.
INFO 2026-06-08 08:20:57 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 2s. Last read position: chr7:100,089,730
INFO 2026-06-08 08:20:57 MarkDuplicates Tracking 784562 as yet unmatched pairs. 20644 records in RAM.
INFO 2026-06-08 08:20:59 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 1s. Last read position: chr7:102,544,868
INFO 2026-06-08 08:20:59 MarkDuplicates Tracking 781516 as yet unmatched pairs. 17558 records in RAM.
INFO 2026-06-08 08:21:01 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 1s. Last read position: chr7:111,977,167
INFO 2026-06-08 08:21:01 MarkDuplicates Tracking 779148 as yet unmatched pairs. 15148 records in RAM.
INFO 2026-06-08 08:21:03 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:06:09s. Time for last 1,000,000: 2s. Last read position: chr7:128,608,170
INFO 2026-06-08 08:21:03 MarkDuplicates Tracking 776529 as yet unmatched pairs. 12475 records in RAM.
INFO 2026-06-08 08:21:05 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 2s. Last read position: chr7:138,881,467
INFO 2026-06-08 08:21:05 MarkDuplicates Tracking 773206 as yet unmatched pairs. 9118 records in RAM.
INFO 2026-06-08 08:21:07 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 2s. Last read position: chr7:143,858,829
INFO 2026-06-08 08:21:07 MarkDuplicates Tracking 770276 as yet unmatched pairs. 6133 records in RAM.
INFO 2026-06-08 08:21:09 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 2s. Last read position: chr7:151,240,456
INFO 2026-06-08 08:21:09 MarkDuplicates Tracking 766580 as yet unmatched pairs. 2398 records in RAM.
INFO 2026-06-08 08:21:12 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 2s. Last read position: chr8:11,808,749
INFO 2026-06-08 08:21:12 MarkDuplicates Tracking 764323 as yet unmatched pairs. 71293 records in RAM.
INFO 2026-06-08 08:21:14 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 2s. Last read position: chr8:22,513,304
INFO 2026-06-08 08:21:14 MarkDuplicates Tracking 760717 as yet unmatched pairs. 67631 records in RAM.
INFO 2026-06-08 08:21:17 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 2s. Last read position: chr8:30,544,458
INFO 2026-06-08 08:21:17 MarkDuplicates Tracking 759261 as yet unmatched pairs. 66143 records in RAM.
INFO 2026-06-08 08:21:19 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 2s. Last read position: chr8:38,329,707
INFO 2026-06-08 08:21:19 MarkDuplicates Tracking 755448 as yet unmatched pairs. 62312 records in RAM.
INFO 2026-06-08 08:21:21 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 2s. Last read position: chr8:42,838,087
INFO 2026-06-08 08:21:21 MarkDuplicates Tracking 750533 as yet unmatched pairs. 57361 records in RAM.
INFO 2026-06-08 08:21:23 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 2s. Last read position: chr8:63,017,527
INFO 2026-06-08 08:21:23 MarkDuplicates Tracking 747588 as yet unmatched pairs. 54366 records in RAM.
INFO 2026-06-08 08:21:26 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 2s. Last read position: chr8:70,156,361
INFO 2026-06-08 08:21:26 MarkDuplicates Tracking 745179 as yet unmatched pairs. 51914 records in RAM.
INFO 2026-06-08 08:21:28 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 2s. Last read position: chr8:86,369,010
INFO 2026-06-08 08:21:28 MarkDuplicates Tracking 745011 as yet unmatched pairs. 51720 records in RAM.
INFO 2026-06-08 08:21:30 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 2s. Last read position: chr8:94,665,053
INFO 2026-06-08 08:21:30 MarkDuplicates Tracking 739369 as yet unmatched pairs. 46053 records in RAM.
INFO 2026-06-08 08:21:32 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 2s. Last read position: chr8:99,878,256
INFO 2026-06-08 08:21:32 MarkDuplicates Tracking 749103 as yet unmatched pairs. 55737 records in RAM.
INFO 2026-06-08 08:21:35 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 2s. Last read position: chr8:100,948,789
INFO 2026-06-08 08:21:35 MarkDuplicates Tracking 733340 as yet unmatched pairs. 39926 records in RAM.
INFO 2026-06-08 08:21:37 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 2s. Last read position: chr8:115,587,502
INFO 2026-06-08 08:21:37 MarkDuplicates Tracking 731003 as yet unmatched pairs. 37528 records in RAM.
INFO 2026-06-08 08:21:39 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 2s. Last read position: chr8:123,030,696
INFO 2026-06-08 08:21:39 MarkDuplicates Tracking 727817 as yet unmatched pairs. 34296 records in RAM.
INFO 2026-06-08 08:21:42 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 2s. Last read position: chr8:125,073,313
INFO 2026-06-08 08:21:42 MarkDuplicates Tracking 724452 as yet unmatched pairs. 30885 records in RAM.
INFO 2026-06-08 08:21:44 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 2s. Last read position: chr8:133,475,765
INFO 2026-06-08 08:21:44 MarkDuplicates Tracking 722380 as yet unmatched pairs. 28753 records in RAM.
INFO 2026-06-08 08:21:47 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 2s. Last read position: chr8:143,536,292
INFO 2026-06-08 08:21:47 MarkDuplicates Tracking 716887 as yet unmatched pairs. 23209 records in RAM.
INFO 2026-06-08 08:21:49 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 2s. Last read position: chr8:143,817,136
INFO 2026-06-08 08:21:49 MarkDuplicates Tracking 713208 as yet unmatched pairs. 19492 records in RAM.
INFO 2026-06-08 08:21:50 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 1s. Last read position: chr8:143,860,435
INFO 2026-06-08 08:21:50 MarkDuplicates Tracking 712310 as yet unmatched pairs. 18585 records in RAM.
INFO 2026-06-08 08:21:52 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 1s. Last read position: chr8:143,863,086
INFO 2026-06-08 08:21:52 MarkDuplicates Tracking 713873 as yet unmatched pairs. 20144 records in RAM.
INFO 2026-06-08 08:21:53 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 1s. Last read position: chr8:143,866,192
INFO 2026-06-08 08:21:53 MarkDuplicates Tracking 708631 as yet unmatched pairs. 14895 records in RAM.
INFO 2026-06-08 08:21:55 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 1s. Last read position: chr8:143,919,987
INFO 2026-06-08 08:21:55 MarkDuplicates Tracking 706136 as yet unmatched pairs. 12377 records in RAM.
INFO 2026-06-08 08:21:57 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:07:03s. Time for last 1,000,000: 1s. Last read position: chr8:143,991,789
INFO 2026-06-08 08:21:57 MarkDuplicates Tracking 704646 as yet unmatched pairs. 10849 records in RAM.
INFO 2026-06-08 08:21:59 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 2s. Last read position: chr8:144,423,737
INFO 2026-06-08 08:21:59 MarkDuplicates Tracking 697772 as yet unmatched pairs. 3924 records in RAM.
INFO 2026-06-08 08:22:02 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 2s. Last read position: chr9:2,058,343
INFO 2026-06-08 08:22:02 MarkDuplicates Tracking 693547 as yet unmatched pairs. 43052 records in RAM.
INFO 2026-06-08 08:22:04 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 2s. Last read position: chr9:19,288,628
INFO 2026-06-08 08:22:04 MarkDuplicates Tracking 691038 as yet unmatched pairs. 40463 records in RAM.
INFO 2026-06-08 08:22:06 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:07:12s. Time for last 1,000,000: 2s. Last read position: chr9:34,660,375
INFO 2026-06-08 08:22:06 MarkDuplicates Tracking 687297 as yet unmatched pairs. 36686 records in RAM.
INFO 2026-06-08 08:22:08 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:07:14s. Time for last 1,000,000: 2s. Last read position: chr9:37,126,655
INFO 2026-06-08 08:22:08 MarkDuplicates Tracking 683891 as yet unmatched pairs. 33249 records in RAM.
INFO 2026-06-08 08:22:11 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:07:17s. Time for last 1,000,000: 2s. Last read position: chr9:83,663,933
INFO 2026-06-08 08:22:11 MarkDuplicates Tracking 681462 as yet unmatched pairs. 30769 records in RAM.
INFO 2026-06-08 08:22:13 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:07:19s. Time for last 1,000,000: 2s. Last read position: chr9:93,308,605
INFO 2026-06-08 08:22:13 MarkDuplicates Tracking 678287 as yet unmatched pairs. 27556 records in RAM.
INFO 2026-06-08 08:22:15 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:07:21s. Time for last 1,000,000: 2s. Last read position: chr9:105,525,731
INFO 2026-06-08 08:22:15 MarkDuplicates Tracking 675286 as yet unmatched pairs. 24480 records in RAM.
INFO 2026-06-08 08:22:17 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:07:23s. Time for last 1,000,000: 2s. Last read position: chr9:114,504,443
INFO 2026-06-08 08:22:17 MarkDuplicates Tracking 672231 as yet unmatched pairs. 21377 records in RAM.
INFO 2026-06-08 08:22:20 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:07:25s. Time for last 1,000,000: 2s. Last read position: chr9:124,998,328
INFO 2026-06-08 08:22:20 MarkDuplicates Tracking 668856 as yet unmatched pairs. 17944 records in RAM.
INFO 2026-06-08 08:22:22 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:07:28s. Time for last 1,000,000: 2s. Last read position: chr9:128,322,863
INFO 2026-06-08 08:22:22 MarkDuplicates Tracking 665579 as yet unmatched pairs. 14648 records in RAM.
INFO 2026-06-08 08:22:24 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:07:30s. Time for last 1,000,000: 1s. Last read position: chr9:130,863,018
INFO 2026-06-08 08:22:24 MarkDuplicates Tracking 662548 as yet unmatched pairs. 11570 records in RAM.
INFO 2026-06-08 08:22:26 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:07:32s. Time for last 1,000,000: 2s. Last read position: chr9:134,048,257
INFO 2026-06-08 08:22:26 MarkDuplicates Tracking 659016 as yet unmatched pairs. 7993 records in RAM.
INFO 2026-06-08 08:22:28 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:07:34s. Time for last 1,000,000: 2s. Last read position: chr9:136,807,981
INFO 2026-06-08 08:22:28 MarkDuplicates Tracking 655141 as yet unmatched pairs. 4082 records in RAM.
INFO 2026-06-08 08:22:30 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:07:36s. Time for last 1,000,000: 2s. Last read position: chr9:138,243,662
INFO 2026-06-08 08:22:30 MarkDuplicates Tracking 651105 as yet unmatched pairs. 26 records in RAM.
INFO 2026-06-08 08:22:33 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:07:39s. Time for last 1,000,000: 2s. Last read position: chr10:8,073,871
INFO 2026-06-08 08:22:33 MarkDuplicates Tracking 648591 as yet unmatched pairs. 32473 records in RAM.
INFO 2026-06-08 08:22:35 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:07:41s. Time for last 1,000,000: 2s. Last read position: chr10:24,543,563
INFO 2026-06-08 08:22:35 MarkDuplicates Tracking 645089 as yet unmatched pairs. 28896 records in RAM.
INFO 2026-06-08 08:22:38 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:07:44s. Time for last 1,000,000: 2s. Last read position: chr10:32,018,536
INFO 2026-06-08 08:22:38 MarkDuplicates Tracking 645157 as yet unmatched pairs. 28921 records in RAM.
INFO 2026-06-08 08:22:40 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:07:46s. Time for last 1,000,000: 2s. Last read position: chr10:38,055,315
INFO 2026-06-08 08:22:40 MarkDuplicates Tracking 639501 as yet unmatched pairs. 23237 records in RAM.
INFO 2026-06-08 08:22:42 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:07:48s. Time for last 1,000,000: 2s. Last read position: chr10:50,125,382
INFO 2026-06-08 08:22:42 MarkDuplicates Tracking 636771 as yet unmatched pairs. 20463 records in RAM.
INFO 2026-06-08 08:22:44 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:07:50s. Time for last 1,000,000: 2s. Last read position: chr10:71,834,372
INFO 2026-06-08 08:22:44 MarkDuplicates Tracking 634856 as yet unmatched pairs. 18501 records in RAM.
INFO 2026-06-08 08:22:46 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:07:52s. Time for last 1,000,000: 2s. Last read position: chr10:84,141,574
INFO 2026-06-08 08:22:46 MarkDuplicates Tracking 630712 as yet unmatched pairs. 14315 records in RAM.
INFO 2026-06-08 08:22:48 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:07:54s. Time for last 1,000,000: 2s. Last read position: chr10:94,356,565
INFO 2026-06-08 08:22:48 MarkDuplicates Tracking 627523 as yet unmatched pairs. 11100 records in RAM.
INFO 2026-06-08 08:22:51 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:07:57s. Time for last 1,000,000: 2s. Last read position: chr10:101,798,067
INFO 2026-06-08 08:22:51 MarkDuplicates Tracking 624672 as yet unmatched pairs. 8224 records in RAM.
INFO 2026-06-08 08:22:53 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:07:59s. Time for last 1,000,000: 2s. Last read position: chr10:114,162,851
INFO 2026-06-08 08:22:53 MarkDuplicates Tracking 621165 as yet unmatched pairs. 4687 records in RAM.
INFO 2026-06-08 08:22:56 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:08:02s. Time for last 1,000,000: 2s. Last read position: chr10:124,681,952
INFO 2026-06-08 08:22:56 MarkDuplicates Tracking 618176 as yet unmatched pairs. 1662 records in RAM.
INFO 2026-06-08 08:22:59 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 3s. Last read position: chr11:408,178
INFO 2026-06-08 08:22:59 MarkDuplicates Tracking 614926 as yet unmatched pairs. 66236 records in RAM.
INFO 2026-06-08 08:23:01 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:08:07s. Time for last 1,000,000: 2s. Last read position: chr11:1,761,344
INFO 2026-06-08 08:23:01 MarkDuplicates Tracking 615260 as yet unmatched pairs. 66550 records in RAM.
INFO 2026-06-08 08:23:04 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:08:10s. Time for last 1,000,000: 2s. Last read position: chr11:8,683,245
INFO 2026-06-08 08:23:04 MarkDuplicates Tracking 607829 as yet unmatched pairs. 59088 records in RAM.
INFO 2026-06-08 08:23:06 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:08:12s. Time for last 1,000,000: 2s. Last read position: chr11:17,301,843
INFO 2026-06-08 08:23:06 MarkDuplicates Tracking 605289 as yet unmatched pairs. 56513 records in RAM.
INFO 2026-06-08 08:23:08 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:08:14s. Time for last 1,000,000: 1s. Last read position: chr11:34,099,354
INFO 2026-06-08 08:23:08 MarkDuplicates Tracking 602016 as yet unmatched pairs. 53209 records in RAM.
INFO 2026-06-08 08:23:11 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:08:17s. Time for last 1,000,000: 2s. Last read position: chr11:46,428,621
INFO 2026-06-08 08:23:11 MarkDuplicates Tracking 598003 as yet unmatched pairs. 49175 records in RAM.
INFO 2026-06-08 08:23:13 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 1s. Last read position: chr11:57,407,706
INFO 2026-06-08 08:23:13 MarkDuplicates Tracking 594777 as yet unmatched pairs. 45928 records in RAM.
INFO 2026-06-08 08:23:15 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 2s. Last read position: chr11:61,303,942
INFO 2026-06-08 08:23:15 MarkDuplicates Tracking 591833 as yet unmatched pairs. 42963 records in RAM.
INFO 2026-06-08 08:23:17 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 2s. Last read position: chr11:62,521,038
INFO 2026-06-08 08:23:17 MarkDuplicates Tracking 590404 as yet unmatched pairs. 41511 records in RAM.
INFO 2026-06-08 08:23:20 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:08:26s. Time for last 1,000,000: 2s. Last read position: chr11:62,529,723
INFO 2026-06-08 08:23:20 MarkDuplicates Tracking 589635 as yet unmatched pairs. 40733 records in RAM.
INFO 2026-06-08 08:23:22 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:08:28s. Time for last 1,000,000: 2s. Last read position: chr11:62,801,957
INFO 2026-06-08 08:23:22 MarkDuplicates Tracking 583429 as yet unmatched pairs. 34508 records in RAM.
INFO 2026-06-08 08:23:25 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:08:31s. Time for last 1,000,000: 2s. Last read position: chr11:65,117,512
INFO 2026-06-08 08:23:25 MarkDuplicates Tracking 579294 as yet unmatched pairs. 30355 records in RAM.
INFO 2026-06-08 08:23:27 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:08:33s. Time for last 1,000,000: 2s. Last read position: chr11:65,920,593
INFO 2026-06-08 08:23:27 MarkDuplicates Tracking 575891 as yet unmatched pairs. 26850 records in RAM.
INFO 2026-06-08 08:23:29 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 2s. Last read position: chr11:67,663,201
INFO 2026-06-08 08:23:29 MarkDuplicates Tracking 572018 as yet unmatched pairs. 22954 records in RAM.
INFO 2026-06-08 08:23:31 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 2s. Last read position: chr11:70,435,584
INFO 2026-06-08 08:23:31 MarkDuplicates Tracking 568544 as yet unmatched pairs. 19464 records in RAM.
INFO 2026-06-08 08:23:34 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 2s. Last read position: chr11:73,873,317
INFO 2026-06-08 08:23:34 MarkDuplicates Tracking 564597 as yet unmatched pairs. 15488 records in RAM.
INFO 2026-06-08 08:23:36 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:08:42s. Time for last 1,000,000: 2s. Last read position: chr11:83,168,846
INFO 2026-06-08 08:23:36 MarkDuplicates Tracking 561395 as yet unmatched pairs. 12263 records in RAM.
INFO 2026-06-08 08:23:38 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:08:44s. Time for last 1,000,000: 2s. Last read position: chr11:108,227,834
INFO 2026-06-08 08:23:38 MarkDuplicates Tracking 558986 as yet unmatched pairs. 9808 records in RAM.
INFO 2026-06-08 08:23:40 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:08:46s. Time for last 1,000,000: 2s. Last read position: chr11:118,755,422
INFO 2026-06-08 08:23:40 MarkDuplicates Tracking 555824 as yet unmatched pairs. 6604 records in RAM.
INFO 2026-06-08 08:23:42 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 2s. Last read position: chr11:125,608,180
INFO 2026-06-08 08:23:42 MarkDuplicates Tracking 552709 as yet unmatched pairs. 3454 records in RAM.
INFO 2026-06-08 08:23:46 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:08:52s. Time for last 1,000,000: 3s. Last read position: chr12:307,528
INFO 2026-06-08 08:23:46 MarkDuplicates Tracking 549572 as yet unmatched pairs. 65111 records in RAM.
INFO 2026-06-08 08:23:48 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 2s. Last read position: chr12:6,330,892
INFO 2026-06-08 08:23:48 MarkDuplicates Tracking 546543 as yet unmatched pairs. 62059 records in RAM.
INFO 2026-06-08 08:23:50 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:08:56s. Time for last 1,000,000: 2s. Last read position: chr12:7,070,236
INFO 2026-06-08 08:23:50 MarkDuplicates Tracking 543506 as yet unmatched pairs. 59000 records in RAM.
INFO 2026-06-08 08:23:52 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:08:58s. Time for last 1,000,000: 2s. Last read position: chr12:11,869,712
INFO 2026-06-08 08:23:52 MarkDuplicates Tracking 540840 as yet unmatched pairs. 56312 records in RAM.
INFO 2026-06-08 08:23:54 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:09:00s. Time for last 1,000,000: 2s. Last read position: chr12:21,474,883
INFO 2026-06-08 08:23:54 MarkDuplicates Tracking 536932 as yet unmatched pairs. 52380 records in RAM.
INFO 2026-06-08 08:23:57 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:09:02s. Time for last 1,000,000: 2s. Last read position: chr12:45,849,702
INFO 2026-06-08 08:23:57 MarkDuplicates Tracking 534436 as yet unmatched pairs. 49850 records in RAM.
INFO 2026-06-08 08:23:59 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 2s. Last read position: chr12:49,043,667
INFO 2026-06-08 08:23:59 MarkDuplicates Tracking 530971 as yet unmatched pairs. 46344 records in RAM.
INFO 2026-06-08 08:24:01 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:09:07s. Time for last 1,000,000: 2s. Last read position: chr12:50,994,548
INFO 2026-06-08 08:24:01 MarkDuplicates Tracking 528181 as yet unmatched pairs. 43542 records in RAM.
INFO 2026-06-08 08:24:03 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:09:09s. Time for last 1,000,000: 2s. Last read position: chr12:53,060,459
INFO 2026-06-08 08:24:03 MarkDuplicates Tracking 525002 as yet unmatched pairs. 40346 records in RAM.
INFO 2026-06-08 08:24:06 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:09:12s. Time for last 1,000,000: 2s. Last read position: chr12:54,283,861
INFO 2026-06-08 08:24:06 MarkDuplicates Tracking 524273 as yet unmatched pairs. 39583 records in RAM.
INFO 2026-06-08 08:24:08 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 2s. Last read position: chr12:56,160,645
INFO 2026-06-08 08:24:08 MarkDuplicates Tracking 521763 as yet unmatched pairs. 37059 records in RAM.
INFO 2026-06-08 08:24:10 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 2s. Last read position: chr12:57,098,516
INFO 2026-06-08 08:24:10 MarkDuplicates Tracking 517304 as yet unmatched pairs. 32589 records in RAM.
INFO 2026-06-08 08:24:13 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:09:19s. Time for last 1,000,000: 2s. Last read position: chr12:57,295,416
INFO 2026-06-08 08:24:13 MarkDuplicates Tracking 512759 as yet unmatched pairs. 28028 records in RAM.
INFO 2026-06-08 08:25:34 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:10:40s. Time for last 1,000,000: 81s. Last read position: chr12:64,481,948
INFO 2026-06-08 08:25:34 MarkDuplicates Tracking 509251 as yet unmatched pairs. 24510 records in RAM.
INFO 2026-06-08 08:25:36 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:10:42s. Time for last 1,000,000: 2s. Last read position: chr12:69,597,696
INFO 2026-06-08 08:25:36 MarkDuplicates Tracking 507586 as yet unmatched pairs. 22810 records in RAM.
INFO 2026-06-08 08:25:38 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:10:44s. Time for last 1,000,000: 2s. Last read position: chr12:91,146,179
INFO 2026-06-08 08:25:38 MarkDuplicates Tracking 505364 as yet unmatched pairs. 20567 records in RAM.
INFO 2026-06-08 08:25:40 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 2s. Last read position: chr12:103,796,920
INFO 2026-06-08 08:25:40 MarkDuplicates Tracking 500719 as yet unmatched pairs. 15889 records in RAM.
INFO 2026-06-08 08:25:43 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:10:49s. Time for last 1,000,000: 2s. Last read position: chr12:110,346,022
INFO 2026-06-08 08:25:43 MarkDuplicates Tracking 497686 as yet unmatched pairs. 12830 records in RAM.
INFO 2026-06-08 08:25:45 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:10:51s. Time for last 1,000,000: 2s. Last read position: chr12:114,671,990
INFO 2026-06-08 08:25:45 MarkDuplicates Tracking 494404 as yet unmatched pairs. 9517 records in RAM.
INFO 2026-06-08 08:25:48 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:10:54s. Time for last 1,000,000: 2s. Last read position: chr12:121,430,288
INFO 2026-06-08 08:25:48 MarkDuplicates Tracking 491141 as yet unmatched pairs. 6233 records in RAM.
INFO 2026-06-08 08:25:50 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:10:56s. Time for last 1,000,000: 2s. Last read position: chr12:124,795,206
INFO 2026-06-08 08:25:50 MarkDuplicates Tracking 487815 as yet unmatched pairs. 2890 records in RAM.
INFO 2026-06-08 08:25:53 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 2s. Last read position: chr13:20,051,451
INFO 2026-06-08 08:25:53 MarkDuplicates Tracking 484836 as yet unmatched pairs. 15844 records in RAM.
INFO 2026-06-08 08:25:55 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:11:01s. Time for last 1,000,000: 2s. Last read position: chr13:37,008,808
INFO 2026-06-08 08:25:55 MarkDuplicates Tracking 481629 as yet unmatched pairs. 12611 records in RAM.
INFO 2026-06-08 08:25:57 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:11:03s. Time for last 1,000,000: 2s. Last read position: chr13:48,086,409
INFO 2026-06-08 08:25:57 MarkDuplicates Tracking 478921 as yet unmatched pairs. 9890 records in RAM.
INFO 2026-06-08 08:25:59 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:11:05s. Time for last 1,000,000: 2s. Last read position: chr13:77,177,898
INFO 2026-06-08 08:25:59 MarkDuplicates Tracking 475903 as yet unmatched pairs. 6830 records in RAM.
INFO 2026-06-08 08:26:02 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:11:08s. Time for last 1,000,000: 2s. Last read position: chr13:110,162,339
INFO 2026-06-08 08:26:02 MarkDuplicates Tracking 473139 as yet unmatched pairs. 4025 records in RAM.
INFO 2026-06-08 08:26:05 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:11:11s. Time for last 1,000,000: 3s. Last read position: chr14:20,451,958
INFO 2026-06-08 08:26:05 MarkDuplicates Tracking 468996 as yet unmatched pairs. 42313 records in RAM.
INFO 2026-06-08 08:26:07 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:11:13s. Time for last 1,000,000: 2s. Last read position: chr14:23,079,933
INFO 2026-06-08 08:26:07 MarkDuplicates Tracking 466481 as yet unmatched pairs. 39764 records in RAM.
INFO 2026-06-08 08:26:09 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:11:15s. Time for last 1,000,000: 2s. Last read position: chr14:24,373,833
INFO 2026-06-08 08:26:09 MarkDuplicates Tracking 462345 as yet unmatched pairs. 35616 records in RAM.
INFO 2026-06-08 08:26:12 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:11:18s. Time for last 1,000,000: 2s. Last read position: chr14:35,762,733
INFO 2026-06-08 08:26:12 MarkDuplicates Tracking 459862 as yet unmatched pairs. 33108 records in RAM.
INFO 2026-06-08 08:26:14 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:11:20s. Time for last 1,000,000: 2s. Last read position: chr14:50,297,856
INFO 2026-06-08 08:26:14 MarkDuplicates Tracking 456335 as yet unmatched pairs. 29494 records in RAM.
INFO 2026-06-08 08:26:16 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:11:22s. Time for last 1,000,000: 2s. Last read position: chr14:57,283,112
INFO 2026-06-08 08:26:16 MarkDuplicates Tracking 453614 as yet unmatched pairs. 26751 records in RAM.
INFO 2026-06-08 08:26:19 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:11:24s. Time for last 1,000,000: 2s. Last read position: chr14:65,076,612
INFO 2026-06-08 08:26:19 MarkDuplicates Tracking 450416 as yet unmatched pairs. 23545 records in RAM.
INFO 2026-06-08 08:26:21 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:11:27s. Time for last 1,000,000: 2s. Last read position: chr14:73,896,314
INFO 2026-06-08 08:26:21 MarkDuplicates Tracking 447368 as yet unmatched pairs. 20459 records in RAM.
INFO 2026-06-08 08:26:23 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:11:29s. Time for last 1,000,000: 2s. Last read position: chr14:88,601,948
INFO 2026-06-08 08:26:23 MarkDuplicates Tracking 444116 as yet unmatched pairs. 17182 records in RAM.
INFO 2026-06-08 08:26:26 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:11:32s. Time for last 1,000,000: 2s. Last read position: chr14:96,303,179
INFO 2026-06-08 08:26:26 MarkDuplicates Tracking 441035 as yet unmatched pairs. 14073 records in RAM.
INFO 2026-06-08 08:26:28 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:11:34s. Time for last 1,000,000: 2s. Last read position: chr14:103,339,235
INFO 2026-06-08 08:26:28 MarkDuplicates Tracking 437913 as yet unmatched pairs. 10925 records in RAM.
INFO 2026-06-08 08:26:30 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:11:36s. Time for last 1,000,000: 2s. Last read position: chr14:105,625,932
INFO 2026-06-08 08:26:30 MarkDuplicates Tracking 434779 as yet unmatched pairs. 7776 records in RAM.
INFO 2026-06-08 08:26:32 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:11:38s. Time for last 1,000,000: 1s. Last read position: chr14:105,742,997
INFO 2026-06-08 08:26:32 MarkDuplicates Tracking 434087 as yet unmatched pairs. 7079 records in RAM.
INFO 2026-06-08 08:26:34 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:11:40s. Time for last 1,000,000: 1s. Last read position: chr14:105,855,137
INFO 2026-06-08 08:26:34 MarkDuplicates Tracking 441020 as yet unmatched pairs. 14000 records in RAM.
INFO 2026-06-08 08:26:36 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:11:42s. Time for last 1,000,000: 2s. Last read position: chr15:22,866,389
INFO 2026-06-08 08:26:36 MarkDuplicates Tracking 426910 as yet unmatched pairs. 35702 records in RAM.
INFO 2026-06-08 08:26:39 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:11:44s. Time for last 1,000,000: 2s. Last read position: chr15:34,529,735
INFO 2026-06-08 08:26:39 MarkDuplicates Tracking 423922 as yet unmatched pairs. 32704 records in RAM.
INFO 2026-06-08 08:26:41 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:11:47s. Time for last 1,000,000: 2s. Last read position: chr15:41,736,261
INFO 2026-06-08 08:26:41 MarkDuplicates Tracking 421353 as yet unmatched pairs. 30104 records in RAM.
INFO 2026-06-08 08:26:43 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:11:49s. Time for last 1,000,000: 2s. Last read position: chr15:43,771,112
INFO 2026-06-08 08:26:43 MarkDuplicates Tracking 419151 as yet unmatched pairs. 27887 records in RAM.
INFO 2026-06-08 08:26:45 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:11:51s. Time for last 1,000,000: 2s. Last read position: chr15:48,515,526
INFO 2026-06-08 08:26:45 MarkDuplicates Tracking 414970 as yet unmatched pairs. 23690 records in RAM.
INFO 2026-06-08 08:26:47 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:11:53s. Time for last 1,000,000: 2s. Last read position: chr15:57,231,232
INFO 2026-06-08 08:26:47 MarkDuplicates Tracking 414008 as yet unmatched pairs. 22702 records in RAM.
INFO 2026-06-08 08:26:50 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:11:55s. Time for last 1,000,000: 2s. Last read position: chr15:63,674,652
INFO 2026-06-08 08:26:50 MarkDuplicates Tracking 408871 as yet unmatched pairs. 17549 records in RAM.
INFO 2026-06-08 08:26:52 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:11:58s. Time for last 1,000,000: 2s. Last read position: chr15:68,317,323
INFO 2026-06-08 08:26:52 MarkDuplicates Tracking 405615 as yet unmatched pairs. 14278 records in RAM.
INFO 2026-06-08 08:26:55 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:12:01s. Time for last 1,000,000: 2s. Last read position: chr15:74,035,733
INFO 2026-06-08 08:26:55 MarkDuplicates Tracking 403470 as yet unmatched pairs. 12097 records in RAM.
INFO 2026-06-08 08:26:57 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:12:03s. Time for last 1,000,000: 2s. Last read position: chr15:78,886,142
INFO 2026-06-08 08:26:57 MarkDuplicates Tracking 399547 as yet unmatched pairs. 8153 records in RAM.
INFO 2026-06-08 08:26:59 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:12:05s. Time for last 1,000,000: 2s. Last read position: chr15:89,665,603
INFO 2026-06-08 08:26:59 MarkDuplicates Tracking 396159 as yet unmatched pairs. 4735 records in RAM.
INFO 2026-06-08 08:27:02 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:12:07s. Time for last 1,000,000: 2s. Last read position: chr15:98,896,787
INFO 2026-06-08 08:27:02 MarkDuplicates Tracking 393653 as yet unmatched pairs. 2212 records in RAM.
INFO 2026-06-08 08:27:04 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:12:10s. Time for last 1,000,000: 2s. Last read position: chr16:669,552
INFO 2026-06-08 08:27:04 MarkDuplicates Tracking 389572 as yet unmatched pairs. 59279 records in RAM.
INFO 2026-06-08 08:27:07 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:12:13s. Time for last 1,000,000: 3s. Last read position: chr16:1,698,898
INFO 2026-06-08 08:27:07 MarkDuplicates Tracking 385336 as yet unmatched pairs. 55037 records in RAM.
INFO 2026-06-08 08:27:10 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:12:16s. Time for last 1,000,000: 2s. Last read position: chr16:2,519,538
INFO 2026-06-08 08:27:10 MarkDuplicates Tracking 384069 as yet unmatched pairs. 53754 records in RAM.
INFO 2026-06-08 08:27:13 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:12:19s. Time for last 1,000,000: 2s. Last read position: chr16:3,290,334
INFO 2026-06-08 08:27:13 MarkDuplicates Tracking 377732 as yet unmatched pairs. 47404 records in RAM.
INFO 2026-06-08 08:27:16 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:12:21s. Time for last 1,000,000: 2s. Last read position: chr16:10,481,980
INFO 2026-06-08 08:27:16 MarkDuplicates Tracking 374181 as yet unmatched pairs. 43829 records in RAM.
INFO 2026-06-08 08:27:18 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:12:24s. Time for last 1,000,000: 2s. Last read position: chr16:14,868,589
INFO 2026-06-08 08:27:18 MarkDuplicates Tracking 371691 as yet unmatched pairs. 41329 records in RAM.
INFO 2026-06-08 08:27:20 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:12:26s. Time for last 1,000,000: 1s. Last read position: chr16:16,285,363
INFO 2026-06-08 08:27:20 MarkDuplicates Tracking 369195 as yet unmatched pairs. 38825 records in RAM.
INFO 2026-06-08 08:27:22 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:12:28s. Time for last 1,000,000: 1s. Last read position: chr16:18,417,390
INFO 2026-06-08 08:27:22 MarkDuplicates Tracking 367983 as yet unmatched pairs. 37612 records in RAM.
INFO 2026-06-08 08:27:24 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:12:30s. Time for last 1,000,000: 1s. Last read position: chr16:21,405,035
INFO 2026-06-08 08:27:24 MarkDuplicates Tracking 366183 as yet unmatched pairs. 35809 records in RAM.
INFO 2026-06-08 08:27:26 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:12:32s. Time for last 1,000,000: 1s. Last read position: chr16:21,887,596
INFO 2026-06-08 08:27:26 MarkDuplicates Tracking 365298 as yet unmatched pairs. 34917 records in RAM.
INFO 2026-06-08 08:27:27 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:12:33s. Time for last 1,000,000: 1s. Last read position: chr16:22,535,334
INFO 2026-06-08 08:27:27 MarkDuplicates Tracking 363702 as yet unmatched pairs. 33317 records in RAM.
INFO 2026-06-08 08:27:30 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:12:36s. Time for last 1,000,000: 2s. Last read position: chr16:28,495,259
INFO 2026-06-08 08:27:30 MarkDuplicates Tracking 361107 as yet unmatched pairs. 30707 records in RAM.
INFO 2026-06-08 08:27:32 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:12:37s. Time for last 1,000,000: 1s. Last read position: chr16:29,483,834
INFO 2026-06-08 08:27:32 MarkDuplicates Tracking 361047 as yet unmatched pairs. 30642 records in RAM.
INFO 2026-06-08 08:27:34 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:12:40s. Time for last 1,000,000: 2s. Last read position: chr16:30,069,500
INFO 2026-06-08 08:27:34 MarkDuplicates Tracking 359270 as yet unmatched pairs. 28853 records in RAM.
INFO 2026-06-08 08:27:36 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:12:42s. Time for last 1,000,000: 1s. Last read position: chr16:30,555,346
INFO 2026-06-08 08:27:36 MarkDuplicates Tracking 354185 as yet unmatched pairs. 23759 records in RAM.
INFO 2026-06-08 08:27:39 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:12:45s. Time for last 1,000,000: 2s. Last read position: chr16:31,189,730
INFO 2026-06-08 08:27:39 MarkDuplicates Tracking 353013 as yet unmatched pairs. 22575 records in RAM.
INFO 2026-06-08 08:27:41 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:12:47s. Time for last 1,000,000: 2s. Last read position: chr16:53,324,477
INFO 2026-06-08 08:27:41 MarkDuplicates Tracking 347804 as yet unmatched pairs. 17339 records in RAM.
INFO 2026-06-08 08:27:43 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:12:49s. Time for last 1,000,000: 2s. Last read position: chr16:58,718,277
INFO 2026-06-08 08:27:43 MarkDuplicates Tracking 344578 as yet unmatched pairs. 14093 records in RAM.
INFO 2026-06-08 08:27:45 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:12:51s. Time for last 1,000,000: 2s. Last read position: chr16:68,819,353
INFO 2026-06-08 08:27:45 MarkDuplicates Tracking 341616 as yet unmatched pairs. 11100 records in RAM.
INFO 2026-06-08 08:27:48 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:12:53s. Time for last 1,000,000: 2s. Last read position: chr16:71,789,381
INFO 2026-06-08 08:27:48 MarkDuplicates Tracking 338190 as yet unmatched pairs. 7667 records in RAM.
INFO 2026-06-08 08:27:50 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:12:55s. Time for last 1,000,000: 2s. Last read position: chr16:85,634,094
INFO 2026-06-08 08:27:50 MarkDuplicates Tracking 334581 as yet unmatched pairs. 4039 records in RAM.
INFO 2026-06-08 08:27:52 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:12:58s. Time for last 1,000,000: 2s. Last read position: chr16:89,898,624
INFO 2026-06-08 08:27:52 MarkDuplicates Tracking 331210 as yet unmatched pairs. 653 records in RAM.
INFO 2026-06-08 08:27:56 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:13:02s. Time for last 1,000,000: 4s. Last read position: chr17:2,371,260
INFO 2026-06-08 08:27:56 MarkDuplicates Tracking 327650 as yet unmatched pairs. 123285 records in RAM.
INFO 2026-06-08 08:27:59 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:13:05s. Time for last 1,000,000: 3s. Last read position: chr17:5,559,234
INFO 2026-06-08 08:27:59 MarkDuplicates Tracking 323972 as yet unmatched pairs. 119598 records in RAM.
INFO 2026-06-08 08:28:01 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:13:07s. Time for last 1,000,000: 2s. Last read position: chr17:7,700,802
INFO 2026-06-08 08:28:01 MarkDuplicates Tracking 320770 as yet unmatched pairs. 116390 records in RAM.
INFO 2026-06-08 08:28:03 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:13:09s. Time for last 1,000,000: 2s. Last read position: chr17:16,422,672
INFO 2026-06-08 08:28:03 MarkDuplicates Tracking 317638 as yet unmatched pairs. 113249 records in RAM.
INFO 2026-06-08 08:28:05 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:13:11s. Time for last 1,000,000: 2s. Last read position: chr17:21,184,434
INFO 2026-06-08 08:28:05 MarkDuplicates Tracking 314509 as yet unmatched pairs. 110110 records in RAM.
INFO 2026-06-08 08:28:08 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:13:14s. Time for last 1,000,000: 2s. Last read position: chr17:29,287,561
INFO 2026-06-08 08:28:08 MarkDuplicates Tracking 311467 as yet unmatched pairs. 107059 records in RAM.
INFO 2026-06-08 08:28:10 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:13:16s. Time for last 1,000,000: 2s. Last read position: chr17:35,258,813
INFO 2026-06-08 08:28:10 MarkDuplicates Tracking 308289 as yet unmatched pairs. 103871 records in RAM.
INFO 2026-06-08 08:28:12 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:13:18s. Time for last 1,000,000: 2s. Last read position: chr17:37,978,868
INFO 2026-06-08 08:28:12 MarkDuplicates Tracking 305188 as yet unmatched pairs. 100766 records in RAM.
INFO 2026-06-08 08:28:14 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:13:20s. Time for last 1,000,000: 1s. Last read position: chr17:39,700,157
INFO 2026-06-08 08:28:14 MarkDuplicates Tracking 303137 as yet unmatched pairs. 98712 records in RAM.
INFO 2026-06-08 08:28:16 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:13:22s. Time for last 1,000,000: 2s. Last read position: chr17:39,723,536
INFO 2026-06-08 08:28:16 MarkDuplicates Tracking 306226 as yet unmatched pairs. 101792 records in RAM.
INFO 2026-06-08 08:28:19 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:13:24s. Time for last 1,000,000: 2s. Last read position: chr17:40,404,208
INFO 2026-06-08 08:28:19 MarkDuplicates Tracking 295265 as yet unmatched pairs. 90819 records in RAM.
INFO 2026-06-08 08:28:21 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:13:27s. Time for last 1,000,000: 2s. Last read position: chr17:41,769,476
INFO 2026-06-08 08:28:21 MarkDuplicates Tracking 292308 as yet unmatched pairs. 87857 records in RAM.
INFO 2026-06-08 08:28:24 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:13:30s. Time for last 1,000,000: 2s. Last read position: chr17:42,818,544
INFO 2026-06-08 08:28:24 MarkDuplicates Tracking 288234 as yet unmatched pairs. 83775 records in RAM.
INFO 2026-06-08 08:28:26 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:13:32s. Time for last 1,000,000: 2s. Last read position: chr17:45,081,655
INFO 2026-06-08 08:28:26 MarkDuplicates Tracking 284645 as yet unmatched pairs. 80178 records in RAM.
INFO 2026-06-08 08:28:28 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:13:34s. Time for last 1,000,000: 2s. Last read position: chr17:47,839,524
INFO 2026-06-08 08:28:28 MarkDuplicates Tracking 282096 as yet unmatched pairs. 77628 records in RAM.
INFO 2026-06-08 08:28:30 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:13:36s. Time for last 1,000,000: 2s. Last read position: chr17:50,185,591
INFO 2026-06-08 08:28:30 MarkDuplicates Tracking 284244 as yet unmatched pairs. 79766 records in RAM.
INFO 2026-06-08 08:28:33 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:13:39s. Time for last 1,000,000: 2s. Last read position: chr17:50,187,516
INFO 2026-06-08 08:28:33 MarkDuplicates Tracking 294965 as yet unmatched pairs. 90483 records in RAM.
INFO 2026-06-08 08:28:35 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:13:41s. Time for last 1,000,000: 2s. Last read position: chr17:50,189,241
INFO 2026-06-08 08:28:35 MarkDuplicates Tracking 289467 as yet unmatched pairs. 84982 records in RAM.
INFO 2026-06-08 08:28:37 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:13:43s. Time for last 1,000,000: 2s. Last read position: chr17:50,190,836
INFO 2026-06-08 08:28:37 MarkDuplicates Tracking 281022 as yet unmatched pairs. 76518 records in RAM.
INFO 2026-06-08 08:28:40 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:13:46s. Time for last 1,000,000: 2s. Last read position: chr17:50,193,988
INFO 2026-06-08 08:28:40 MarkDuplicates Tracking 289466 as yet unmatched pairs. 84960 records in RAM.
INFO 2026-06-08 08:28:43 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:13:49s. Time for last 1,000,000: 3s. Last read position: chr17:50,195,270
INFO 2026-06-08 08:28:43 MarkDuplicates Tracking 282883 as yet unmatched pairs. 78373 records in RAM.
INFO 2026-06-08 08:28:45 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:13:51s. Time for last 1,000,000: 2s. Last read position: chr17:50,196,642
INFO 2026-06-08 08:28:45 MarkDuplicates Tracking 291640 as yet unmatched pairs. 87103 records in RAM.
INFO 2026-06-08 08:28:47 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:13:53s. Time for last 1,000,000: 2s. Last read position: chr17:50,199,577
INFO 2026-06-08 08:28:47 MarkDuplicates Tracking 264082 as yet unmatched pairs. 59539 records in RAM.
INFO 2026-06-08 08:28:49 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:13:55s. Time for last 1,000,000: 2s. Last read position: chr17:51,168,295
INFO 2026-06-08 08:28:49 MarkDuplicates Tracking 252361 as yet unmatched pairs. 47817 records in RAM.
INFO 2026-06-08 08:28:52 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:13:57s. Time for last 1,000,000: 2s. Last read position: chr17:59,574,229
INFO 2026-06-08 08:28:52 MarkDuplicates Tracking 247174 as yet unmatched pairs. 42611 records in RAM.
INFO 2026-06-08 08:28:54 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:14:00s. Time for last 1,000,000: 2s. Last read position: chr17:59,679,467
INFO 2026-06-08 08:28:54 MarkDuplicates Tracking 253090 as yet unmatched pairs. 48520 records in RAM.
INFO 2026-06-08 08:28:56 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:14:02s. Time for last 1,000,000: 2s. Last read position: chr17:60,391,947
INFO 2026-06-08 08:28:56 MarkDuplicates Tracking 240610 as yet unmatched pairs. 35999 records in RAM.
INFO 2026-06-08 08:28:58 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:14:04s. Time for last 1,000,000: 1s. Last read position: chr17:64,329,702
INFO 2026-06-08 08:28:58 MarkDuplicates Tracking 238604 as yet unmatched pairs. 33986 records in RAM.
INFO 2026-06-08 08:29:00 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:14:06s. Time for last 1,000,000: 2s. Last read position: chr17:67,964,333
INFO 2026-06-08 08:29:00 MarkDuplicates Tracking 235046 as yet unmatched pairs. 30423 records in RAM.
INFO 2026-06-08 08:29:03 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:14:08s. Time for last 1,000,000: 2s. Last read position: chr17:73,205,582
INFO 2026-06-08 08:29:03 MarkDuplicates Tracking 232010 as yet unmatched pairs. 27375 records in RAM.
INFO 2026-06-08 08:29:05 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:14:11s. Time for last 1,000,000: 2s. Last read position: chr17:75,501,093
INFO 2026-06-08 08:29:05 MarkDuplicates Tracking 228351 as yet unmatched pairs. 23704 records in RAM.
INFO 2026-06-08 08:29:07 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:14:13s. Time for last 1,000,000: 2s. Last read position: chr17:76,387,019
INFO 2026-06-08 08:29:07 MarkDuplicates Tracking 224608 as yet unmatched pairs. 19948 records in RAM.
INFO 2026-06-08 08:29:10 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:14:16s. Time for last 1,000,000: 2s. Last read position: chr17:78,972,089
INFO 2026-06-08 08:29:10 MarkDuplicates Tracking 222472 as yet unmatched pairs. 17803 records in RAM.
INFO 2026-06-08 08:29:12 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:14:18s. Time for last 1,000,000: 2s. Last read position: chr17:80,337,992
INFO 2026-06-08 08:29:12 MarkDuplicates Tracking 218547 as yet unmatched pairs. 13869 records in RAM.
INFO 2026-06-08 08:29:14 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:14:20s. Time for last 1,000,000: 2s. Last read position: chr17:81,512,263
INFO 2026-06-08 08:29:14 MarkDuplicates Tracking 214143 as yet unmatched pairs. 9456 records in RAM.
INFO 2026-06-08 08:29:17 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:14:23s. Time for last 1,000,000: 2s. Last read position: chr17:82,016,986
INFO 2026-06-08 08:29:17 MarkDuplicates Tracking 211499 as yet unmatched pairs. 6795 records in RAM.
INFO 2026-06-08 08:29:19 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:14:25s. Time for last 1,000,000: 2s. Last read position: chr17:82,265,487
INFO 2026-06-08 08:29:19 MarkDuplicates Tracking 206134 as yet unmatched pairs. 1416 records in RAM.
INFO 2026-06-08 08:29:21 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:14:27s. Time for last 1,000,000: 2s. Last read position: chr18:8,824,929
INFO 2026-06-08 08:29:21 MarkDuplicates Tracking 202798 as yet unmatched pairs. 13112 records in RAM.
INFO 2026-06-08 08:29:24 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:14:29s. Time for last 1,000,000: 2s. Last read position: chr18:26,018,215
INFO 2026-06-08 08:29:24 MarkDuplicates Tracking 200540 as yet unmatched pairs. 10847 records in RAM.
INFO 2026-06-08 08:29:26 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:14:32s. Time for last 1,000,000: 2s. Last read position: chr18:36,123,499
INFO 2026-06-08 08:29:26 MarkDuplicates Tracking 205424 as yet unmatched pairs. 15727 records in RAM.
INFO 2026-06-08 08:29:29 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:14:34s. Time for last 1,000,000: 2s. Last read position: chr18:49,954,422
INFO 2026-06-08 08:29:29 MarkDuplicates Tracking 193966 as yet unmatched pairs. 4255 records in RAM.
INFO 2026-06-08 08:29:31 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:14:37s. Time for last 1,000,000: 2s. Last read position: chr18:74,634,683
INFO 2026-06-08 08:29:31 MarkDuplicates Tracking 190562 as yet unmatched pairs. 839 records in RAM.
INFO 2026-06-08 08:29:34 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:14:39s. Time for last 1,000,000: 2s. Last read position: chr19:1,105,781
INFO 2026-06-08 08:29:34 MarkDuplicates Tracking 188905 as yet unmatched pairs. 76440 records in RAM.
INFO 2026-06-08 08:29:36 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:14:42s. Time for last 1,000,000: 2s. Last read position: chr19:2,476,590
INFO 2026-06-08 08:29:36 MarkDuplicates Tracking 182767 as yet unmatched pairs. 70296 records in RAM.
INFO 2026-06-08 08:29:38 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:14:44s. Time for last 1,000,000: 2s. Last read position: chr19:4,839,398
INFO 2026-06-08 08:29:38 MarkDuplicates Tracking 178920 as yet unmatched pairs. 66440 records in RAM.
INFO 2026-06-08 08:29:40 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:14:46s. Time for last 1,000,000: 2s. Last read position: chr19:7,459,907
INFO 2026-06-08 08:29:40 MarkDuplicates Tracking 175327 as yet unmatched pairs. 62841 records in RAM.
INFO 2026-06-08 08:29:42 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:14:48s. Time for last 1,000,000: 1s. Last read position: chr19:10,368,402
INFO 2026-06-08 08:29:42 MarkDuplicates Tracking 171843 as yet unmatched pairs. 59352 records in RAM.
INFO 2026-06-08 08:29:44 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:14:50s. Time for last 1,000,000: 2s. Last read position: chr19:12,273,163
INFO 2026-06-08 08:29:44 MarkDuplicates Tracking 168365 as yet unmatched pairs. 55870 records in RAM.
INFO 2026-06-08 08:29:46 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:14:52s. Time for last 1,000,000: 2s. Last read position: chr19:14,464,104
INFO 2026-06-08 08:29:46 MarkDuplicates Tracking 164693 as yet unmatched pairs. 52190 records in RAM.
INFO 2026-06-08 08:29:49 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:14:54s. Time for last 1,000,000: 2s. Last read position: chr19:16,157,376
INFO 2026-06-08 08:29:49 MarkDuplicates Tracking 161007 as yet unmatched pairs. 48502 records in RAM.
INFO 2026-06-08 08:29:51 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:14:57s. Time for last 1,000,000: 2s. Last read position: chr19:18,435,362
INFO 2026-06-08 08:29:51 MarkDuplicates Tracking 157065 as yet unmatched pairs. 44545 records in RAM.
INFO 2026-06-08 08:29:53 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:14:59s. Time for last 1,000,000: 2s. Last read position: chr19:31,277,029
INFO 2026-06-08 08:29:53 MarkDuplicates Tracking 153279 as yet unmatched pairs. 40752 records in RAM.
INFO 2026-06-08 08:29:56 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:15:02s. Time for last 1,000,000: 2s. Last read position: chr19:35,745,639
INFO 2026-06-08 08:29:56 MarkDuplicates Tracking 149566 as yet unmatched pairs. 37036 records in RAM.
INFO 2026-06-08 08:29:58 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:15:04s. Time for last 1,000,000: 2s. Last read position: chr19:38,836,679
INFO 2026-06-08 08:29:58 MarkDuplicates Tracking 146783 as yet unmatched pairs. 34247 records in RAM.
INFO 2026-06-08 08:30:00 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:15:06s. Time for last 1,000,000: 2s. Last read position: chr19:40,366,608
INFO 2026-06-08 08:30:00 MarkDuplicates Tracking 143919 as yet unmatched pairs. 31375 records in RAM.
INFO 2026-06-08 08:30:02 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:15:08s. Time for last 1,000,000: 2s. Last read position: chr19:42,274,393
INFO 2026-06-08 08:30:02 MarkDuplicates Tracking 139357 as yet unmatched pairs. 26812 records in RAM.
INFO 2026-06-08 08:30:05 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:15:10s. Time for last 1,000,000: 2s. Last read position: chr19:44,985,252
INFO 2026-06-08 08:30:05 MarkDuplicates Tracking 135276 as yet unmatched pairs. 22728 records in RAM.
INFO 2026-06-08 08:30:07 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:15:13s. Time for last 1,000,000: 2s. Last read position: chr19:47,275,211
INFO 2026-06-08 08:30:07 MarkDuplicates Tracking 131375 as yet unmatched pairs. 18816 records in RAM.
INFO 2026-06-08 08:30:09 MarkDuplicates Read 368,000,000 records. Elapsed time: 00:15:15s. Time for last 1,000,000: 2s. Last read position: chr19:49,168,693
INFO 2026-06-08 08:30:09 MarkDuplicates Tracking 127683 as yet unmatched pairs. 15119 records in RAM.
INFO 2026-06-08 08:30:11 MarkDuplicates Read 369,000,000 records. Elapsed time: 00:15:17s. Time for last 1,000,000: 2s. Last read position: chr19:50,278,117
INFO 2026-06-08 08:30:11 MarkDuplicates Tracking 123725 as yet unmatched pairs. 11161 records in RAM.
INFO 2026-06-08 08:30:13 MarkDuplicates Read 370,000,000 records. Elapsed time: 00:15:19s. Time for last 1,000,000: 2s. Last read position: chr19:54,256,097
INFO 2026-06-08 08:30:13 MarkDuplicates Tracking 120600 as yet unmatched pairs. 8026 records in RAM.
INFO 2026-06-08 08:30:16 MarkDuplicates Read 371,000,000 records. Elapsed time: 00:15:22s. Time for last 1,000,000: 2s. Last read position: chr19:57,291,340
INFO 2026-06-08 08:30:16 MarkDuplicates Tracking 117312 as yet unmatched pairs. 4736 records in RAM.
INFO 2026-06-08 08:30:20 MarkDuplicates Read 372,000,000 records. Elapsed time: 00:15:25s. Time for last 1,000,000: 3s. Last read position: chr19:58,067,210
INFO 2026-06-08 08:30:20 MarkDuplicates Tracking 114348 as yet unmatched pairs. 1772 records in RAM.
INFO 2026-06-08 08:30:22 MarkDuplicates Read 373,000,000 records. Elapsed time: 00:15:28s. Time for last 1,000,000: 2s. Last read position: chr20:3,017,842
INFO 2026-06-08 08:30:22 MarkDuplicates Tracking 110917 as yet unmatched pairs. 34158 records in RAM.
INFO 2026-06-08 08:30:25 MarkDuplicates Read 374,000,000 records. Elapsed time: 00:15:30s. Time for last 1,000,000: 2s. Last read position: chr20:17,636,609
INFO 2026-06-08 08:30:25 MarkDuplicates Tracking 107815 as yet unmatched pairs. 31054 records in RAM.
INFO 2026-06-08 08:30:27 MarkDuplicates Read 375,000,000 records. Elapsed time: 00:15:33s. Time for last 1,000,000: 2s. Last read position: chr20:32,136,123
INFO 2026-06-08 08:30:27 MarkDuplicates Tracking 104458 as yet unmatched pairs. 27688 records in RAM.
INFO 2026-06-08 08:30:29 MarkDuplicates Read 376,000,000 records. Elapsed time: 00:15:35s. Time for last 1,000,000: 2s. Last read position: chr20:35,557,030
INFO 2026-06-08 08:30:29 MarkDuplicates Tracking 102882 as yet unmatched pairs. 26110 records in RAM.
INFO 2026-06-08 08:30:31 MarkDuplicates Read 377,000,000 records. Elapsed time: 00:15:37s. Time for last 1,000,000: 2s. Last read position: chr20:38,499,623
INFO 2026-06-08 08:30:31 MarkDuplicates Tracking 98599 as yet unmatched pairs. 21817 records in RAM.
INFO 2026-06-08 08:30:34 MarkDuplicates Read 378,000,000 records. Elapsed time: 00:15:40s. Time for last 1,000,000: 2s. Last read position: chr20:45,335,847
INFO 2026-06-08 08:30:34 MarkDuplicates Tracking 95695 as yet unmatched pairs. 18912 records in RAM.
INFO 2026-06-08 08:30:36 MarkDuplicates Read 379,000,000 records. Elapsed time: 00:15:42s. Time for last 1,000,000: 2s. Last read position: chr20:49,084,050
INFO 2026-06-08 08:30:36 MarkDuplicates Tracking 91717 as yet unmatched pairs. 14930 records in RAM.
INFO 2026-06-08 08:30:39 MarkDuplicates Read 380,000,000 records. Elapsed time: 00:15:45s. Time for last 1,000,000: 2s. Last read position: chr20:54,028,475
INFO 2026-06-08 08:30:39 MarkDuplicates Tracking 88962 as yet unmatched pairs. 12172 records in RAM.
INFO 2026-06-08 08:30:41 MarkDuplicates Read 381,000,000 records. Elapsed time: 00:15:47s. Time for last 1,000,000: 2s. Last read position: chr20:62,136,860
INFO 2026-06-08 08:30:41 MarkDuplicates Tracking 85031 as yet unmatched pairs. 8236 records in RAM.
INFO 2026-06-08 08:30:43 MarkDuplicates Read 382,000,000 records. Elapsed time: 00:15:49s. Time for last 1,000,000: 2s. Last read position: chr20:63,520,802
INFO 2026-06-08 08:30:43 MarkDuplicates Tracking 82652 as yet unmatched pairs. 5845 records in RAM.
INFO 2026-06-08 08:30:45 MarkDuplicates Read 383,000,000 records. Elapsed time: 00:15:51s. Time for last 1,000,000: 2s. Last read position: chr21:5,134,102
INFO 2026-06-08 08:30:45 MarkDuplicates Tracking 76751 as yet unmatched pairs. 12827 records in RAM.
INFO 2026-06-08 08:30:47 MarkDuplicates Read 384,000,000 records. Elapsed time: 00:15:53s. Time for last 1,000,000: 1s. Last read position: chr21:29,327,131
INFO 2026-06-08 08:30:47 MarkDuplicates Tracking 74977 as yet unmatched pairs. 11052 records in RAM.
INFO 2026-06-08 08:30:49 MarkDuplicates Read 385,000,000 records. Elapsed time: 00:15:55s. Time for last 1,000,000: 2s. Last read position: chr21:37,160,806
INFO 2026-06-08 08:30:49 MarkDuplicates Tracking 72967 as yet unmatched pairs. 9037 records in RAM.
INFO 2026-06-08 08:30:52 MarkDuplicates Read 386,000,000 records. Elapsed time: 00:15:57s. Time for last 1,000,000: 2s. Last read position: chr21:44,128,306
INFO 2026-06-08 08:30:52 MarkDuplicates Tracking 68264 as yet unmatched pairs. 4328 records in RAM.
INFO 2026-06-08 08:30:54 MarkDuplicates Read 387,000,000 records. Elapsed time: 00:16:00s. Time for last 1,000,000: 2s. Last read position: chr21:46,273,439
INFO 2026-06-08 08:30:54 MarkDuplicates Tracking 64761 as yet unmatched pairs. 818 records in RAM.
INFO 2026-06-08 08:30:57 MarkDuplicates Read 388,000,000 records. Elapsed time: 00:16:03s. Time for last 1,000,000: 2s. Last read position: chr22:21,962,464
INFO 2026-06-08 08:30:57 MarkDuplicates Tracking 61055 as yet unmatched pairs. 23819 records in RAM.
INFO 2026-06-08 08:30:59 MarkDuplicates Read 389,000,000 records. Elapsed time: 00:16:05s. Time for last 1,000,000: 2s. Last read position: chr22:28,163,314
INFO 2026-06-08 08:30:59 MarkDuplicates Tracking 57577 as yet unmatched pairs. 20340 records in RAM.
INFO 2026-06-08 08:31:01 MarkDuplicates Read 390,000,000 records. Elapsed time: 00:16:07s. Time for last 1,000,000: 2s. Last read position: chr22:30,607,329
INFO 2026-06-08 08:31:01 MarkDuplicates Tracking 54438 as yet unmatched pairs. 17201 records in RAM.
INFO 2026-06-08 08:31:04 MarkDuplicates Read 391,000,000 records. Elapsed time: 00:16:10s. Time for last 1,000,000: 2s. Last read position: chr22:36,348,961
INFO 2026-06-08 08:31:04 MarkDuplicates Tracking 51593 as yet unmatched pairs. 14347 records in RAM.
INFO 2026-06-08 08:31:06 MarkDuplicates Read 392,000,000 records. Elapsed time: 00:16:12s. Time for last 1,000,000: 2s. Last read position: chr22:39,521,804
INFO 2026-06-08 08:31:06 MarkDuplicates Tracking 48592 as yet unmatched pairs. 11343 records in RAM.
INFO 2026-06-08 08:31:09 MarkDuplicates Read 393,000,000 records. Elapsed time: 00:16:15s. Time for last 1,000,000: 2s. Last read position: chr22:43,127,717
INFO 2026-06-08 08:31:09 MarkDuplicates Tracking 43950 as yet unmatched pairs. 6695 records in RAM.
INFO 2026-06-08 08:31:11 MarkDuplicates Read 394,000,000 records. Elapsed time: 00:16:17s. Time for last 1,000,000: 2s. Last read position: chr22:50,255,114
INFO 2026-06-08 08:31:11 MarkDuplicates Tracking 39776 as yet unmatched pairs. 2520 records in RAM.
INFO 2026-06-08 08:31:14 MarkDuplicates Read 395,000,000 records. Elapsed time: 00:16:20s. Time for last 1,000,000: 2s. Last read position: chrX:3,317,744
INFO 2026-06-08 08:31:14 MarkDuplicates Tracking 36061 as yet unmatched pairs. 32362 records in RAM.
INFO 2026-06-08 08:31:16 MarkDuplicates Read 396,000,000 records. Elapsed time: 00:16:22s. Time for last 1,000,000: 2s. Last read position: chrX:23,675,068
INFO 2026-06-08 08:31:16 MarkDuplicates Tracking 33048 as yet unmatched pairs. 29348 records in RAM.
INFO 2026-06-08 08:31:18 MarkDuplicates Read 397,000,000 records. Elapsed time: 00:16:24s. Time for last 1,000,000: 2s. Last read position: chrX:41,346,555
INFO 2026-06-08 08:31:18 MarkDuplicates Tracking 30504 as yet unmatched pairs. 26803 records in RAM.
INFO 2026-06-08 08:31:20 MarkDuplicates Read 398,000,000 records. Elapsed time: 00:16:26s. Time for last 1,000,000: 2s. Last read position: chrX:48,989,700
INFO 2026-06-08 08:31:20 MarkDuplicates Tracking 26431 as yet unmatched pairs. 22730 records in RAM.
INFO 2026-06-08 08:31:23 MarkDuplicates Read 399,000,000 records. Elapsed time: 00:16:29s. Time for last 1,000,000: 2s. Last read position: chrX:53,634,280
INFO 2026-06-08 08:31:23 MarkDuplicates Tracking 23161 as yet unmatched pairs. 19460 records in RAM.
INFO 2026-06-08 08:31:25 MarkDuplicates Read 400,000,000 records. Elapsed time: 00:16:31s. Time for last 1,000,000: 2s. Last read position: chrX:71,123,203
INFO 2026-06-08 08:31:25 MarkDuplicates Tracking 19947 as yet unmatched pairs. 16243 records in RAM.
INFO 2026-06-08 08:31:27 MarkDuplicates Read 401,000,000 records. Elapsed time: 00:16:33s. Time for last 1,000,000: 2s. Last read position: chrX:77,683,759
INFO 2026-06-08 08:31:27 MarkDuplicates Tracking 17520 as yet unmatched pairs. 13815 records in RAM.
INFO 2026-06-08 08:31:30 MarkDuplicates Read 402,000,000 records. Elapsed time: 00:16:35s. Time for last 1,000,000: 2s. Last read position: chrX:111,226,766
INFO 2026-06-08 08:31:30 MarkDuplicates Tracking 13883 as yet unmatched pairs. 10178 records in RAM.
INFO 2026-06-08 08:31:32 MarkDuplicates Read 403,000,000 records. Elapsed time: 00:16:38s. Time for last 1,000,000: 2s. Last read position: chrX:133,661,779
INFO 2026-06-08 08:31:32 MarkDuplicates Tracking 11101 as yet unmatched pairs. 7395 records in RAM.
INFO 2026-06-08 08:31:34 MarkDuplicates Read 404,000,000 records. Elapsed time: 00:16:40s. Time for last 1,000,000: 2s. Last read position: chrX:153,954,196
INFO 2026-06-08 08:31:34 MarkDuplicates Tracking 7878 as yet unmatched pairs. 4171 records in RAM.
INFO 2026-06-08 08:31:37 MarkDuplicates Read 405,000,000 records. Elapsed time: 00:16:43s. Time for last 1,000,000: 2s. Last read position: chrX:154,837,669
INFO 2026-06-08 08:31:37 MarkDuplicates Tracking 4100 as yet unmatched pairs. 393 records in RAM.
INFO 2026-06-08 08:31:38 MarkDuplicates Read 406,000,000 records. Elapsed time: 00:16:44s. Time for last 1,000,000: 1s. Last read position: KI270733.1:133,599
INFO 2026-06-08 08:31:38 MarkDuplicates Tracking 222 as yet unmatched pairs. 195 records in RAM.
INFO 2026-06-08 08:31:39 MarkDuplicates Read 406203300 records. 0 pairs never matched.
INFO 2026-06-08 08:32:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 36193877744; totalMemory: 51673825280; maxMemory: 63585648640
INFO 2026-06-08 08:32:42 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:32:54 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:33:19 OpticalDuplicateFinder Large duplicate set. size = 1057
INFO 2026-06-08 08:33:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,291
INFO 2026-06-08 08:33:19 OpticalDuplicateFinder Large duplicate set. size = 1571
INFO 2026-06-08 08:33:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,201
INFO 2026-06-08 08:33:24 OpticalDuplicateFinder Large duplicate set. size = 1088
INFO 2026-06-08 08:33:24 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:5,992
INFO 2026-06-08 08:33:36 OpticalDuplicateFinder Large duplicate set. size = 1131
INFO 2026-06-08 08:33:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:5,102
INFO 2026-06-08 08:33:36 OpticalDuplicateFinder Large duplicate set. size = 1136
INFO 2026-06-08 08:33:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,008
INFO 2026-06-08 08:33:36 OpticalDuplicateFinder Large duplicate set. size = 1599
INFO 2026-06-08 08:33:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-21,117
INFO 2026-06-08 08:33:36 OpticalDuplicateFinder Large duplicate set. size = 1078
INFO 2026-06-08 08:33:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,818
INFO 2026-06-08 08:33:37 OpticalDuplicateFinder Large duplicate set. size = 1108
INFO 2026-06-08 08:33:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,621
INFO 2026-06-08 08:33:37 OpticalDuplicateFinder Large duplicate set. size = 1056
INFO 2026-06-08 08:33:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:1,372
INFO 2026-06-08 08:33:37 OpticalDuplicateFinder Large duplicate set. size = 1254
INFO 2026-06-08 08:33:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:6,525
INFO 2026-06-08 08:33:37 OpticalDuplicateFinder Large duplicate set. size = 1241
INFO 2026-06-08 08:33:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:15,190
INFO 2026-06-08 08:33:37 OpticalDuplicateFinder Large duplicate set. size = 1077
INFO 2026-06-08 08:33:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,473
INFO 2026-06-08 08:33:42 MarkDuplicates Traversing fragment information and detecting duplicates.
WARNING 2026-06-08 08:33:42 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
INFO 2026-06-08 08:34:46 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:34:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300690272; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-08 08:34:55 MarkDuplicates Marking 166030141 records as duplicates.
INFO 2026-06-08 08:34:55 MarkDuplicates Found 17740450 optical duplicate clusters.
INFO 2026-06-08 08:34:55 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 08:35:24 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:28s. Time for last 10,000,000: 28s. Last read position: chr1:43,171,479
INFO 2026-06-08 08:35:52 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:57s. Time for last 10,000,000: 28s. Last read position: chr1:145,400,537
INFO 2026-06-08 08:36:22 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:27s. Time for last 10,000,000: 30s. Last read position: chr1:156,137,185
INFO 2026-06-08 08:36:51 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:55s. Time for last 10,000,000: 28s. Last read position: chr1:220,796,668
INFO 2026-06-08 08:37:20 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:02:24s. Time for last 10,000,000: 28s. Last read position: chr2:32,916,406
INFO 2026-06-08 08:37:46 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:50s. Time for last 10,000,000: 25s. Last read position: chr2:119,679,232
INFO 2026-06-08 08:38:13 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:03:17s. Time for last 10,000,000: 26s. Last read position: chr2:215,349,143
INFO 2026-06-08 08:38:41 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:03:45s. Time for last 10,000,000: 28s. Last read position: chr3:12,935,530
INFO 2026-06-08 08:39:08 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:04:12s. Time for last 10,000,000: 26s. Last read position: chr3:123,620,238
INFO 2026-06-08 08:39:35 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:04:39s. Time for last 10,000,000: 27s. Last read position: chr4:48,548,544
INFO 2026-06-08 08:40:02 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:05:06s. Time for last 10,000,000: 26s. Last read position: chr5:36,975,968
INFO 2026-06-08 08:40:30 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:05:34s. Time for last 10,000,000: 27s. Last read position: chr5:150,404,681
INFO 2026-06-08 08:40:56 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:06:00s. Time for last 10,000,000: 26s. Last read position: chr6:30,894,620
INFO 2026-06-08 08:41:25 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:06:29s. Time for last 10,000,000: 28s. Last read position: chr6:107,929,454
INFO 2026-06-08 08:41:49 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:06:53s. Time for last 10,000,000: 24s. Last read position: chr7:6,466,114
INFO 2026-06-08 08:42:14 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:07:18s. Time for last 10,000,000: 24s. Last read position: chr7:94,663,888
INFO 2026-06-08 08:42:35 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:07:39s. Time for last 10,000,000: 21s. Last read position: chr8:30,544,458
INFO 2026-06-08 08:42:56 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:08:00s. Time for last 10,000,000: 20s. Last read position: chr8:123,030,696
INFO 2026-06-08 08:43:16 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:08:21s. Time for last 10,000,000: 20s. Last read position: chr8:144,423,737
INFO 2026-06-08 08:43:38 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:08:42s. Time for last 10,000,000: 21s. Last read position: chr9:128,322,863
INFO 2026-06-08 08:44:00 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:09:04s. Time for last 10,000,000: 22s. Last read position: chr10:71,834,372
INFO 2026-06-08 08:44:21 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:09:26s. Time for last 10,000,000: 21s. Last read position: chr11:34,099,354
INFO 2026-06-08 08:44:42 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:09:46s. Time for last 10,000,000: 20s. Last read position: chr11:70,435,584
INFO 2026-06-08 08:45:03 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:10:07s. Time for last 10,000,000: 20s. Last read position: chr12:21,474,883
INFO 2026-06-08 08:45:24 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:10:28s. Time for last 10,000,000: 21s. Last read position: chr12:69,597,696
INFO 2026-06-08 08:45:47 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:10:51s. Time for last 10,000,000: 22s. Last read position: chr13:77,177,898
INFO 2026-06-08 08:46:12 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:11:16s. Time for last 10,000,000: 24s. Last read position: chr14:88,601,948
INFO 2026-06-08 08:46:36 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:11:40s. Time for last 10,000,000: 24s. Last read position: chr15:48,515,526
INFO 2026-06-08 08:47:04 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:12:09s. Time for last 10,000,000: 28s. Last read position: chr16:2,519,538
INFO 2026-06-08 08:47:33 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:12:37s. Time for last 10,000,000: 28s. Last read position: chr16:29,483,834
INFO 2026-06-08 08:48:02 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:13:07s. Time for last 10,000,000: 29s. Last read position: chr17:2,371,260
INFO 2026-06-08 08:48:30 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:13:35s. Time for last 10,000,000: 28s. Last read position: chr17:40,404,208
INFO 2026-06-08 08:48:59 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:14:04s. Time for last 10,000,000: 28s. Last read position: chr17:50,195,270
INFO 2026-06-08 08:49:27 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:14:31s. Time for last 10,000,000: 27s. Last read position: chr17:75,501,093
INFO 2026-06-08 08:49:55 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:14:59s. Time for last 10,000,000: 28s. Last read position: chr18:49,954,422
INFO 2026-06-08 08:50:23 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:15:27s. Time for last 10,000,000: 28s. Last read position: chr19:18,435,362
INFO 2026-06-08 08:50:51 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:15:55s. Time for last 10,000,000: 27s. Last read position: chr19:54,256,097
INFO 2026-06-08 08:51:19 MarkDuplicates Written 380,000,000 records. Elapsed time: 00:16:23s. Time for last 10,000,000: 28s. Last read position: chr20:54,028,475
INFO 2026-06-08 08:51:47 MarkDuplicates Written 390,000,000 records. Elapsed time: 00:16:51s. Time for last 10,000,000: 28s. Last read position: chr22:30,607,329
INFO 2026-06-08 08:52:15 MarkDuplicates Written 400,000,000 records. Elapsed time: 00:17:19s. Time for last 10,000,000: 28s. Last read position: chrX:71,123,203
INFO 2026-06-08 08:52:43 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:52:43 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:52:43 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:52:43 MarkDuplicates Before output close freeMemory: 37313885536; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-08 08:52:43 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:52:43 MarkDuplicates After output close freeMemory: 203853152; totalMemory: 234881024; maxMemory: 63585648640
[Mon Jun 08 08:52:43 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 37.87 minutes.
Runtime.totalMemory()=234881024
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory