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/7b/4a6b6626f8f7ea903bf3a6a42ea2fa/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/4a6b6626f8f7ea903bf3a6a42ea2fa/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/ab4cba821fe861f62653a89021cb67/aih-tih-sc-3b436b-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)
Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT aih-tih-sc-3b436b-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bam --METRICS_FILE aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
19:30:34.449 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
[Wed Jun 03 19:30:34 GMT 2026] MarkDuplicates --INPUT aih-tih-sc-3b436b-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-3b436b-R1_A23YTGFLT4_1.md.bam --METRICS_FILE aih-tih-sc-3b436b-R1_A23YTGFLT4_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
[Wed Jun 03 19:30:34 GMT 2026] Executing as ?@nf-7b4a6b6626f8f7ea903bf3a6a42ea2fa-04a70-ztwpd 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 2026-06-03 19:30:34 MarkDuplicates Start of doWork freeMemory: 105828040; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-03 19:30:34 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-03 19:30:34 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-03 19:30:40 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:6,192,969
INFO 2026-06-03 19:30:40 MarkDuplicates Tracking 3334 as yet unmatched pairs. 1451 records in RAM.
INFO 2026-06-03 19:30:42 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: chr1:11,920,287
INFO 2026-06-03 19:30:42 MarkDuplicates Tracking 3984 as yet unmatched pairs. 355 records in RAM.
INFO 2026-06-03 19:30:45 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 2s. Last read position: chr1:16,585,553
INFO 2026-06-03 19:30:45 MarkDuplicates Tracking 6132 as yet unmatched pairs. 991 records in RAM.
INFO 2026-06-03 19:30:48 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 2s. Last read position: chr1:21,823,299
INFO 2026-06-03 19:30:48 MarkDuplicates Tracking 7182 as yet unmatched pairs. 394 records in RAM.
INFO 2026-06-03 19:30:50 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: chr1:23,313,657
INFO 2026-06-03 19:30:50 MarkDuplicates Tracking 9074 as yet unmatched pairs. 419 records in RAM.
INFO 2026-06-03 19:30:53 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 3s. Last read position: chr1:27,261,027
INFO 2026-06-03 19:30:53 MarkDuplicates Tracking 10525 as yet unmatched pairs. 303 records in RAM.
INFO 2026-06-03 19:30:56 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 3s. Last read position: chr1:32,302,664
INFO 2026-06-03 19:30:56 MarkDuplicates Tracking 12327 as yet unmatched pairs. 410 records in RAM.
INFO 2026-06-03 19:30:59 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 2s. Last read position: chr1:37,587,351
INFO 2026-06-03 19:30:59 MarkDuplicates Tracking 14005 as yet unmatched pairs. 403 records in RAM.
INFO 2026-06-03 19:31:01 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 2s. Last read position: chr1:42,831,002
INFO 2026-06-03 19:31:01 MarkDuplicates Tracking 15361 as yet unmatched pairs. 189 records in RAM.
INFO 2026-06-03 19:31:03 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 2s. Last read position: chr1:47,272,097
INFO 2026-06-03 19:31:03 MarkDuplicates Tracking 17031 as yet unmatched pairs. 213 records in RAM.
INFO 2026-06-03 19:31:06 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 2s. Last read position: chr1:63,629,514
INFO 2026-06-03 19:31:06 MarkDuplicates Tracking 18597 as yet unmatched pairs. 181 records in RAM.
INFO 2026-06-03 19:31:10 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 3s. Last read position: chr1:89,262,682
INFO 2026-06-03 19:31:10 MarkDuplicates Tracking 20158 as yet unmatched pairs. 255 records in RAM.
INFO 2026-06-03 19:31:13 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 3s. Last read position: chr1:109,592,124
INFO 2026-06-03 19:31:13 MarkDuplicates Tracking 21810 as yet unmatched pairs. 542 records in RAM.
INFO 2026-06-03 19:31:16 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 2s. Last read position: chr1:116,388,226
INFO 2026-06-03 19:31:16 MarkDuplicates Tracking 23636 as yet unmatched pairs. 805 records in RAM.
INFO 2026-06-03 19:31:19 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 3s. Last read position: chr1:120,454,008
INFO 2026-06-03 19:31:19 MarkDuplicates Tracking 24756 as yet unmatched pairs. 658 records in RAM.
INFO 2026-06-03 19:31:21 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: chr1:145,096,860
INFO 2026-06-03 19:31:21 MarkDuplicates Tracking 25206 as yet unmatched pairs. 361 records in RAM.
INFO 2026-06-03 19:31:24 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 2s. Last read position: chr1:146,115,998
INFO 2026-06-03 19:31:24 MarkDuplicates Tracking 25781 as yet unmatched pairs. 348 records in RAM.
INFO 2026-06-03 19:31:26 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 2s. Last read position: chr1:148,126,911
INFO 2026-06-03 19:31:26 MarkDuplicates Tracking 26550 as yet unmatched pairs. 508 records in RAM.
INFO 2026-06-03 19:31:28 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 1s. Last read position: chr1:148,679,302
INFO 2026-06-03 19:31:28 MarkDuplicates Tracking 26855 as yet unmatched pairs. 424 records in RAM.
INFO 2026-06-03 19:31:31 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 2s. Last read position: chr1:149,811,991
INFO 2026-06-03 19:31:31 MarkDuplicates Tracking 29436 as yet unmatched pairs. 2399 records in RAM.
INFO 2026-06-03 19:31:33 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 2s. Last read position: chr1:150,159,183
INFO 2026-06-03 19:31:33 MarkDuplicates Tracking 28472 as yet unmatched pairs. 258 records in RAM.
INFO 2026-06-03 19:31:37 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 3s. Last read position: chr1:153,932,768
INFO 2026-06-03 19:31:37 MarkDuplicates Tracking 29914 as yet unmatched pairs. 179 records in RAM.
INFO 2026-06-03 19:31:41 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 4s. Last read position: chr1:155,479,602
INFO 2026-06-03 19:31:41 MarkDuplicates Tracking 31638 as yet unmatched pairs. 321 records in RAM.
INFO 2026-06-03 19:31:45 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 3s. Last read position: chr1:158,845,976
INFO 2026-06-03 19:31:45 MarkDuplicates Tracking 33170 as yet unmatched pairs. 103 records in RAM.
INFO 2026-06-03 19:31:48 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 3s. Last read position: chr1:161,544,748
INFO 2026-06-03 19:31:48 MarkDuplicates Tracking 35466 as yet unmatched pairs. 788 records in RAM.
INFO 2026-06-03 19:31:50 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 2s. Last read position: chr1:174,231,269
INFO 2026-06-03 19:31:50 MarkDuplicates Tracking 36455 as yet unmatched pairs. 292 records in RAM.
INFO 2026-06-03 19:31:53 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 3s. Last read position: chr1:186,333,222
INFO 2026-06-03 19:31:53 MarkDuplicates Tracking 38535 as yet unmatched pairs. 865 records in RAM.
INFO 2026-06-03 19:31:57 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 3s. Last read position: chr1:202,741,679
INFO 2026-06-03 19:31:57 MarkDuplicates Tracking 39190 as yet unmatched pairs. 121 records in RAM.
INFO 2026-06-03 19:31:59 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 2s. Last read position: chr1:212,051,489
INFO 2026-06-03 19:31:59 MarkDuplicates Tracking 40737 as yet unmatched pairs. 177 records in RAM.
INFO 2026-06-03 19:32:02 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 3s. Last read position: chr1:226,159,276
INFO 2026-06-03 19:32:02 MarkDuplicates Tracking 42050 as yet unmatched pairs. 80 records in RAM.
INFO 2026-06-03 19:32:05 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 2s. Last read position: chr1:235,791,945
INFO 2026-06-03 19:32:05 MarkDuplicates Tracking 44087 as yet unmatched pairs. 184 records in RAM.
INFO 2026-06-03 19:32:09 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 3s. Last read position: chr2:3,388,015
INFO 2026-06-03 19:32:09 MarkDuplicates Tracking 45947 as yet unmatched pairs. 44081 records in RAM.
INFO 2026-06-03 19:32:12 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 2s. Last read position: chr2:25,743,931
INFO 2026-06-03 19:32:12 MarkDuplicates Tracking 47414 as yet unmatched pairs. 45490 records in RAM.
INFO 2026-06-03 19:32:14 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,258
INFO 2026-06-03 19:32:14 MarkDuplicates Tracking 71116 as yet unmatched pairs. 44996 records in RAM.
INFO 2026-06-03 19:32:17 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,406
INFO 2026-06-03 19:32:17 MarkDuplicates Tracking 349638 as yet unmatched pairs. 26436 records in RAM.
INFO 2026-06-03 19:32:20 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 2s. Last read position: chr2:43,995,828
INFO 2026-06-03 19:32:20 MarkDuplicates Tracking 371286 as yet unmatched pairs. 23789 records in RAM.
INFO 2026-06-03 19:32:22 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 2s. Last read position: chr2:61,380,336
INFO 2026-06-03 19:32:22 MarkDuplicates Tracking 370156 as yet unmatched pairs. 22584 records in RAM.
INFO 2026-06-03 19:32:25 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 2s. Last read position: chr2:73,847,418
INFO 2026-06-03 19:32:25 MarkDuplicates Tracking 368710 as yet unmatched pairs. 21085 records in RAM.
INFO 2026-06-03 19:32:28 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 3s. Last read position: chr2:95,108,279
INFO 2026-06-03 19:32:28 MarkDuplicates Tracking 367134 as yet unmatched pairs. 19460 records in RAM.
INFO 2026-06-03 19:32:31 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 2s. Last read position: chr2:108,675,941
INFO 2026-06-03 19:32:31 MarkDuplicates Tracking 365958 as yet unmatched pairs. 18219 records in RAM.
INFO 2026-06-03 19:32:34 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 3s. Last read position: chr2:119,877,518
INFO 2026-06-03 19:32:34 MarkDuplicates Tracking 364839 as yet unmatched pairs. 17066 records in RAM.
INFO 2026-06-03 19:32:37 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 3s. Last read position: chr2:151,464,051
INFO 2026-06-03 19:32:37 MarkDuplicates Tracking 363393 as yet unmatched pairs. 15538 records in RAM.
INFO 2026-06-03 19:32:39 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 2s. Last read position: chr2:174,720,378
INFO 2026-06-03 19:32:39 MarkDuplicates Tracking 362783 as yet unmatched pairs. 14827 records in RAM.
INFO 2026-06-03 19:32:42 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 2s. Last read position: chr2:188,997,734
INFO 2026-06-03 19:32:42 MarkDuplicates Tracking 361750 as yet unmatched pairs. 13746 records in RAM.
INFO 2026-06-03 19:32:45 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 2s. Last read position: chr2:197,494,716
INFO 2026-06-03 19:32:45 MarkDuplicates Tracking 359996 as yet unmatched pairs. 11942 records in RAM.
INFO 2026-06-03 19:32:48 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 3s. Last read position: chr2:215,361,997
INFO 2026-06-03 19:32:48 MarkDuplicates Tracking 367441 as yet unmatched pairs. 19317 records in RAM.
INFO 2026-06-03 19:32:52 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 3s. Last read position: chr2:215,375,629
INFO 2026-06-03 19:32:52 MarkDuplicates Tracking 365581 as yet unmatched pairs. 17429 records in RAM.
INFO 2026-06-03 19:32:54 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 2s. Last read position: chr2:215,386,931
INFO 2026-06-03 19:32:54 MarkDuplicates Tracking 369588 as yet unmatched pairs. 21417 records in RAM.
INFO 2026-06-03 19:32:57 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 2s. Last read position: chr2:215,408,187
INFO 2026-06-03 19:32:57 MarkDuplicates Tracking 363343 as yet unmatched pairs. 15146 records in RAM.
INFO 2026-06-03 19:32:59 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 2s. Last read position: chr2:215,431,840
INFO 2026-06-03 19:32:59 MarkDuplicates Tracking 357454 as yet unmatched pairs. 9236 records in RAM.
INFO 2026-06-03 19:33:02 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 2s. Last read position: chr2:222,634,490
INFO 2026-06-03 19:33:02 MarkDuplicates Tracking 351019 as yet unmatched pairs. 2732 records in RAM.
INFO 2026-06-03 19:33:05 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 2s. Last read position: chr2:237,346,556
INFO 2026-06-03 19:33:05 MarkDuplicates Tracking 349735 as yet unmatched pairs. 1386 records in RAM.
INFO 2026-06-03 19:33:07 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 2s. Last read position: chr3:9,840,720
INFO 2026-06-03 19:33:07 MarkDuplicates Tracking 348082 as yet unmatched pairs. 19216 records in RAM.
INFO 2026-06-03 19:33:11 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 3s. Last read position: chr3:31,626,100
INFO 2026-06-03 19:33:11 MarkDuplicates Tracking 346793 as yet unmatched pairs. 17852 records in RAM.
INFO 2026-06-03 19:33:13 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 2s. Last read position: chr3:45,225,259
INFO 2026-06-03 19:33:13 MarkDuplicates Tracking 345203 as yet unmatched pairs. 16204 records in RAM.
INFO 2026-06-03 19:33:15 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 2s. Last read position: chr3:49,101,384
INFO 2026-06-03 19:33:15 MarkDuplicates Tracking 343751 as yet unmatched pairs. 14697 records in RAM.
INFO 2026-06-03 19:33:17 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 2s. Last read position: chr3:52,510,360
INFO 2026-06-03 19:33:17 MarkDuplicates Tracking 342299 as yet unmatched pairs. 13204 records in RAM.
INFO 2026-06-03 19:33:20 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 2s. Last read position: chr3:88,150,088
INFO 2026-06-03 19:33:20 MarkDuplicates Tracking 340540 as yet unmatched pairs. 11361 records in RAM.
INFO 2026-06-03 19:33:24 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 4s. Last read position: chr3:113,659,751
INFO 2026-06-03 19:33:24 MarkDuplicates Tracking 339238 as yet unmatched pairs. 9992 records in RAM.
INFO 2026-06-03 19:33:27 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 2s. Last read position: chr3:125,560,485
INFO 2026-06-03 19:33:27 MarkDuplicates Tracking 337759 as yet unmatched pairs. 8442 records in RAM.
INFO 2026-06-03 19:33:30 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 2s. Last read position: chr3:130,964,066
INFO 2026-06-03 19:33:30 MarkDuplicates Tracking 336668 as yet unmatched pairs. 7320 records in RAM.
INFO 2026-06-03 19:33:33 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 2s. Last read position: chr3:146,102,763
INFO 2026-06-03 19:33:33 MarkDuplicates Tracking 335084 as yet unmatched pairs. 5657 records in RAM.
INFO 2026-06-03 19:33:35 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 2s. Last read position: chr3:169,116,386
INFO 2026-06-03 19:33:35 MarkDuplicates Tracking 333443 as yet unmatched pairs. 3925 records in RAM.
INFO 2026-06-03 19:33:38 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 3s. Last read position: chr3:184,304,315
INFO 2026-06-03 19:33:38 MarkDuplicates Tracking 332290 as yet unmatched pairs. 2704 records in RAM.
INFO 2026-06-03 19:33:42 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 3s. Last read position: chr3:195,725,602
INFO 2026-06-03 19:33:42 MarkDuplicates Tracking 330557 as yet unmatched pairs. 899 records in RAM.
INFO 2026-06-03 19:33:45 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 3s. Last read position: chr4:1,930,664
INFO 2026-06-03 19:33:45 MarkDuplicates Tracking 329162 as yet unmatched pairs. 9401 records in RAM.
INFO 2026-06-03 19:33:49 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 3s. Last read position: chr4:25,383,318
INFO 2026-06-03 19:33:49 MarkDuplicates Tracking 327428 as yet unmatched pairs. 7604 records in RAM.
INFO 2026-06-03 19:33:52 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 3s. Last read position: chr4:56,931,056
INFO 2026-06-03 19:33:52 MarkDuplicates Tracking 326157 as yet unmatched pairs. 6271 records in RAM.
INFO 2026-06-03 19:33:56 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 3s. Last read position: chr4:83,273,587
INFO 2026-06-03 19:33:56 MarkDuplicates Tracking 324595 as yet unmatched pairs. 4657 records in RAM.
INFO 2026-06-03 19:33:59 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 3s. Last read position: chr4:105,190,349
INFO 2026-06-03 19:33:59 MarkDuplicates Tracking 323211 as yet unmatched pairs. 3232 records in RAM.
INFO 2026-06-03 19:34:02 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 3s. Last read position: chr4:145,064,623
INFO 2026-06-03 19:34:02 MarkDuplicates Tracking 321940 as yet unmatched pairs. 1890 records in RAM.
INFO 2026-06-03 19:34:05 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 2s. Last read position: chr4:184,728,944
INFO 2026-06-03 19:34:05 MarkDuplicates Tracking 320462 as yet unmatched pairs. 355 records in RAM.
INFO 2026-06-03 19:34:07 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 2s. Last read position: chr5:14,336,636
INFO 2026-06-03 19:34:07 MarkDuplicates Tracking 319780 as yet unmatched pairs. 17126 records in RAM.
INFO 2026-06-03 19:34:10 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 2s. Last read position: chr5:37,153,781
INFO 2026-06-03 19:34:10 MarkDuplicates Tracking 317390 as yet unmatched pairs. 14672 records in RAM.
INFO 2026-06-03 19:34:12 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 2s. Last read position: chr5:55,267,686
INFO 2026-06-03 19:34:12 MarkDuplicates Tracking 316050 as yet unmatched pairs. 13262 records in RAM.
INFO 2026-06-03 19:34:14 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 2s. Last read position: chr5:73,498,635
INFO 2026-06-03 19:34:14 MarkDuplicates Tracking 315549 as yet unmatched pairs. 12666 records in RAM.
INFO 2026-06-03 19:34:17 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 2s. Last read position: chr5:94,470,074
INFO 2026-06-03 19:34:17 MarkDuplicates Tracking 313607 as yet unmatched pairs. 10666 records in RAM.
INFO 2026-06-03 19:34:19 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 2s. Last read position: chr5:130,184,296
INFO 2026-06-03 19:34:19 MarkDuplicates Tracking 312297 as yet unmatched pairs. 9272 records in RAM.
INFO 2026-06-03 19:34:22 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 2s. Last read position: chr5:139,836,811
INFO 2026-06-03 19:34:22 MarkDuplicates Tracking 310891 as yet unmatched pairs. 7802 records in RAM.
INFO 2026-06-03 19:34:25 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 2s. Last read position: chr5:150,119,478
INFO 2026-06-03 19:34:25 MarkDuplicates Tracking 310203 as yet unmatched pairs. 7059 records in RAM.
INFO 2026-06-03 19:34:28 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 3s. Last read position: chr5:150,407,171
INFO 2026-06-03 19:34:28 MarkDuplicates Tracking 313493 as yet unmatched pairs. 10314 records in RAM.
INFO 2026-06-03 19:34:31 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 3s. Last read position: chr5:169,588,563
INFO 2026-06-03 19:34:31 MarkDuplicates Tracking 306313 as yet unmatched pairs. 3093 records in RAM.
INFO 2026-06-03 19:34:34 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 2s. Last read position: chr5:177,459,109
INFO 2026-06-03 19:34:34 MarkDuplicates Tracking 305243 as yet unmatched pairs. 1982 records in RAM.
INFO 2026-06-03 19:34:37 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 3s. Last read position: chr5:181,257,127
INFO 2026-06-03 19:34:37 MarkDuplicates Tracking 303374 as yet unmatched pairs. 67 records in RAM.
INFO 2026-06-03 19:34:40 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 3s. Last read position: chr6:15,522,694
INFO 2026-06-03 19:34:40 MarkDuplicates Tracking 301739 as yet unmatched pairs. 25053 records in RAM.
INFO 2026-06-03 19:34:43 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 2s. Last read position: chr6:26,045,584
INFO 2026-06-03 19:34:43 MarkDuplicates Tracking 304246 as yet unmatched pairs. 27471 records in RAM.
INFO 2026-06-03 19:34:46 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 3s. Last read position: chr6:26,285,360
INFO 2026-06-03 19:34:46 MarkDuplicates Tracking 298983 as yet unmatched pairs. 22174 records in RAM.
INFO 2026-06-03 19:34:49 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 2s. Last read position: chr6:27,837,970
INFO 2026-06-03 19:34:49 MarkDuplicates Tracking 297691 as yet unmatched pairs. 20850 records in RAM.
INFO 2026-06-03 19:34:51 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 2s. Last read position: chr6:30,628,117
INFO 2026-06-03 19:34:51 MarkDuplicates Tracking 295932 as yet unmatched pairs. 19050 records in RAM.
INFO 2026-06-03 19:34:53 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 2s. Last read position: chr6:31,637,065
INFO 2026-06-03 19:34:53 MarkDuplicates Tracking 295181 as yet unmatched pairs. 18263 records in RAM.
INFO 2026-06-03 19:34:55 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 2s. Last read position: chr6:32,119,066
INFO 2026-06-03 19:34:55 MarkDuplicates Tracking 293115 as yet unmatched pairs. 16175 records in RAM.
INFO 2026-06-03 19:34:57 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 2s. Last read position: chr6:33,293,493
INFO 2026-06-03 19:34:57 MarkDuplicates Tracking 291642 as yet unmatched pairs. 14665 records in RAM.
INFO 2026-06-03 19:35:00 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 2s. Last read position: chr6:36,596,760
INFO 2026-06-03 19:35:00 MarkDuplicates Tracking 290682 as yet unmatched pairs. 13671 records in RAM.
INFO 2026-06-03 19:35:02 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 2s. Last read position: chr6:43,502,230
INFO 2026-06-03 19:35:02 MarkDuplicates Tracking 288295 as yet unmatched pairs. 11238 records in RAM.
INFO 2026-06-03 19:35:05 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 2s. Last read position: chr6:53,013,662
INFO 2026-06-03 19:35:05 MarkDuplicates Tracking 286764 as yet unmatched pairs. 9657 records in RAM.
INFO 2026-06-03 19:35:07 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 2s. Last read position: chr6:80,022,322
INFO 2026-06-03 19:35:07 MarkDuplicates Tracking 285492 as yet unmatched pairs. 8321 records in RAM.
INFO 2026-06-03 19:35:10 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 2s. Last read position: chr6:100,540,331
INFO 2026-06-03 19:35:10 MarkDuplicates Tracking 284110 as yet unmatched pairs. 6881 records in RAM.
INFO 2026-06-03 19:35:12 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 2s. Last read position: chr6:116,279,578
INFO 2026-06-03 19:35:12 MarkDuplicates Tracking 282775 as yet unmatched pairs. 5490 records in RAM.
INFO 2026-06-03 19:35:14 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 2s. Last read position: chr6:138,334,941
INFO 2026-06-03 19:35:14 MarkDuplicates Tracking 281097 as yet unmatched pairs. 3754 records in RAM.
INFO 2026-06-03 19:35:17 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 2s. Last read position: chr6:153,282,609
INFO 2026-06-03 19:35:17 MarkDuplicates Tracking 279647 as yet unmatched pairs. 2256 records in RAM.
INFO 2026-06-03 19:35:19 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 2s. Last read position: chr6:163,563,665
INFO 2026-06-03 19:35:19 MarkDuplicates Tracking 279359 as yet unmatched pairs. 1909 records in RAM.
INFO 2026-06-03 19:35:21 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 2s. Last read position: chr7:5,378,013
INFO 2026-06-03 19:35:21 MarkDuplicates Tracking 276467 as yet unmatched pairs. 14489 records in RAM.
INFO 2026-06-03 19:35:23 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 2s. Last read position: chr7:22,727,470
INFO 2026-06-03 19:35:23 MarkDuplicates Tracking 274796 as yet unmatched pairs. 12751 records in RAM.
INFO 2026-06-03 19:35:26 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 2s. Last read position: chr7:39,987,609
INFO 2026-06-03 19:35:26 MarkDuplicates Tracking 273367 as yet unmatched pairs. 11267 records in RAM.
INFO 2026-06-03 19:35:28 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 2s. Last read position: chr7:67,067,290
INFO 2026-06-03 19:35:28 MarkDuplicates Tracking 271747 as yet unmatched pairs. 9589 records in RAM.
INFO 2026-06-03 19:35:30 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 2s. Last read position: chr7:76,978,744
INFO 2026-06-03 19:35:30 MarkDuplicates Tracking 270652 as yet unmatched pairs. 8454 records in RAM.
INFO 2026-06-03 19:35:32 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 2s. Last read position: chr7:94,427,203
INFO 2026-06-03 19:35:32 MarkDuplicates Tracking 270389 as yet unmatched pairs. 8155 records in RAM.
INFO 2026-06-03 19:35:34 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 2s. Last read position: chr7:100,881,318
INFO 2026-06-03 19:35:34 MarkDuplicates Tracking 267727 as yet unmatched pairs. 5460 records in RAM.
INFO 2026-06-03 19:35:37 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 2s. Last read position: chr7:116,210,563
INFO 2026-06-03 19:35:37 MarkDuplicates Tracking 266343 as yet unmatched pairs. 4031 records in RAM.
INFO 2026-06-03 19:35:39 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 2s. Last read position: chr7:137,928,278
INFO 2026-06-03 19:35:39 MarkDuplicates Tracking 265220 as yet unmatched pairs. 2870 records in RAM.
INFO 2026-06-03 19:35:41 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 2s. Last read position: chr7:150,793,138
INFO 2026-06-03 19:35:41 MarkDuplicates Tracking 263499 as yet unmatched pairs. 1118 records in RAM.
INFO 2026-06-03 19:35:43 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 2s. Last read position: chr8:11,845,671
INFO 2026-06-03 19:35:43 MarkDuplicates Tracking 267593 as yet unmatched pairs. 23256 records in RAM.
INFO 2026-06-03 19:35:46 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 2s. Last read position: chr8:22,615,519
INFO 2026-06-03 19:35:46 MarkDuplicates Tracking 261173 as yet unmatched pairs. 16802 records in RAM.
INFO 2026-06-03 19:35:48 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 2s. Last read position: chr8:37,840,817
INFO 2026-06-03 19:35:48 MarkDuplicates Tracking 258704 as yet unmatched pairs. 14286 records in RAM.
INFO 2026-06-03 19:35:50 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 2s. Last read position: chr8:43,103,811
INFO 2026-06-03 19:35:50 MarkDuplicates Tracking 257609 as yet unmatched pairs. 13163 records in RAM.
INFO 2026-06-03 19:35:53 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 2s. Last read position: chr8:56,073,195
INFO 2026-06-03 19:35:53 MarkDuplicates Tracking 262245 as yet unmatched pairs. 17751 records in RAM.
INFO 2026-06-03 19:35:55 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 2s. Last read position: chr8:73,292,394
INFO 2026-06-03 19:35:55 MarkDuplicates Tracking 254546 as yet unmatched pairs. 9996 records in RAM.
INFO 2026-06-03 19:35:58 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 3s. Last read position: chr8:98,150,510
INFO 2026-06-03 19:35:58 MarkDuplicates Tracking 253170 as yet unmatched pairs. 8558 records in RAM.
INFO 2026-06-03 19:36:01 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 2s. Last read position: chr8:108,203,086
INFO 2026-06-03 19:36:01 MarkDuplicates Tracking 255008 as yet unmatched pairs. 10334 records in RAM.
INFO 2026-06-03 19:36:03 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 2s. Last read position: chr8:127,736,517
INFO 2026-06-03 19:36:03 MarkDuplicates Tracking 253059 as yet unmatched pairs. 8316 records in RAM.
INFO 2026-06-03 19:36:06 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 2s. Last read position: chr8:143,691,130
INFO 2026-06-03 19:36:06 MarkDuplicates Tracking 248731 as yet unmatched pairs. 3935 records in RAM.
INFO 2026-06-03 19:36:07 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 1s. Last read position: chr8:143,862,996
INFO 2026-06-03 19:36:07 MarkDuplicates Tracking 249307 as yet unmatched pairs. 4500 records in RAM.
INFO 2026-06-03 19:36:09 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 1s. Last read position: chr8:143,992,064
INFO 2026-06-03 19:36:09 MarkDuplicates Tracking 246736 as yet unmatched pairs. 1919 records in RAM.
INFO 2026-06-03 19:36:11 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 2s. Last read position: chr9:2,039,843
INFO 2026-06-03 19:36:11 MarkDuplicates Tracking 244733 as yet unmatched pairs. 20087 records in RAM.
INFO 2026-06-03 19:36:14 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 2s. Last read position: chr9:21,815,445
INFO 2026-06-03 19:36:14 MarkDuplicates Tracking 243483 as yet unmatched pairs. 18783 records in RAM.
INFO 2026-06-03 19:36:16 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 2s. Last read position: chr9:35,699,416
INFO 2026-06-03 19:36:16 MarkDuplicates Tracking 241707 as yet unmatched pairs. 16959 records in RAM.
INFO 2026-06-03 19:36:18 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 1s. Last read position: chr9:73,158,573
INFO 2026-06-03 19:36:18 MarkDuplicates Tracking 242079 as yet unmatched pairs. 17272 records in RAM.
INFO 2026-06-03 19:36:20 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 2s. Last read position: chr9:90,843,950
INFO 2026-06-03 19:36:20 MarkDuplicates Tracking 238639 as yet unmatched pairs. 13798 records in RAM.
INFO 2026-06-03 19:36:23 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 2s. Last read position: chr9:99,132,536
INFO 2026-06-03 19:36:23 MarkDuplicates Tracking 237076 as yet unmatched pairs. 12189 records in RAM.
INFO 2026-06-03 19:36:25 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 2s. Last read position: chr9:113,267,329
INFO 2026-06-03 19:36:25 MarkDuplicates Tracking 235830 as yet unmatched pairs. 10891 records in RAM.
INFO 2026-06-03 19:36:28 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 2s. Last read position: chr9:121,301,980
INFO 2026-06-03 19:36:28 MarkDuplicates Tracking 239764 as yet unmatched pairs. 14780 records in RAM.
INFO 2026-06-03 19:36:30 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 2s. Last read position: chr9:127,093,803
INFO 2026-06-03 19:36:30 MarkDuplicates Tracking 232579 as yet unmatched pairs. 7552 records in RAM.
INFO 2026-06-03 19:36:32 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 2s. Last read position: chr9:128,983,346
INFO 2026-06-03 19:36:32 MarkDuplicates Tracking 230978 as yet unmatched pairs. 5912 records in RAM.
INFO 2026-06-03 19:36:34 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 2s. Last read position: chr9:132,912,289
INFO 2026-06-03 19:36:34 MarkDuplicates Tracking 229044 as yet unmatched pairs. 3954 records in RAM.
INFO 2026-06-03 19:36:36 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 2s. Last read position: chr9:136,476,046
INFO 2026-06-03 19:36:36 MarkDuplicates Tracking 227662 as yet unmatched pairs. 2551 records in RAM.
INFO 2026-06-03 19:36:38 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 2s. Last read position: chr9:137,811,490
INFO 2026-06-03 19:36:38 MarkDuplicates Tracking 225419 as yet unmatched pairs. 275 records in RAM.
INFO 2026-06-03 19:36:41 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 2s. Last read position: chr10:24,524,566
INFO 2026-06-03 19:36:41 MarkDuplicates Tracking 223744 as yet unmatched pairs. 9802 records in RAM.
INFO 2026-06-03 19:36:43 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 2s. Last read position: chr10:45,374,269
INFO 2026-06-03 19:36:43 MarkDuplicates Tracking 222374 as yet unmatched pairs. 8397 records in RAM.
INFO 2026-06-03 19:36:45 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:06:09s. Time for last 1,000,000: 1s. Last read position: chr10:68,742,484
INFO 2026-06-03 19:36:45 MarkDuplicates Tracking 221449 as yet unmatched pairs. 7433 records in RAM.
INFO 2026-06-03 19:36:47 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 2s. Last read position: chr10:78,035,666
INFO 2026-06-03 19:36:47 MarkDuplicates Tracking 222905 as yet unmatched pairs. 8838 records in RAM.
INFO 2026-06-03 19:36:50 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 2s. Last read position: chr10:93,663,066
INFO 2026-06-03 19:36:50 MarkDuplicates Tracking 218180 as yet unmatched pairs. 4069 records in RAM.
INFO 2026-06-03 19:36:52 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 2s. Last read position: chr10:102,473,604
INFO 2026-06-03 19:36:52 MarkDuplicates Tracking 216578 as yet unmatched pairs. 2429 records in RAM.
INFO 2026-06-03 19:36:55 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 2s. Last read position: chr10:123,160,443
INFO 2026-06-03 19:36:55 MarkDuplicates Tracking 215450 as yet unmatched pairs. 1272 records in RAM.
INFO 2026-06-03 19:36:58 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 3s. Last read position: chr11:497,969
INFO 2026-06-03 19:36:58 MarkDuplicates Tracking 213662 as yet unmatched pairs. 28588 records in RAM.
INFO 2026-06-03 19:37:00 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 2s. Last read position: chr11:2,377,495
INFO 2026-06-03 19:37:00 MarkDuplicates Tracking 211899 as yet unmatched pairs. 26793 records in RAM.
INFO 2026-06-03 19:37:03 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 2s. Last read position: chr11:7,992,089
INFO 2026-06-03 19:37:03 MarkDuplicates Tracking 210186 as yet unmatched pairs. 25047 records in RAM.
INFO 2026-06-03 19:37:06 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:06:30s. Time for last 1,000,000: 2s. Last read position: chr11:14,494,418
INFO 2026-06-03 19:37:06 MarkDuplicates Tracking 208280 as yet unmatched pairs. 23110 records in RAM.
INFO 2026-06-03 19:37:09 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:06:33s. Time for last 1,000,000: 3s. Last read position: chr11:34,071,746
INFO 2026-06-03 19:37:09 MarkDuplicates Tracking 207149 as yet unmatched pairs. 21946 records in RAM.
INFO 2026-06-03 19:37:12 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 3s. Last read position: chr11:46,776,344
INFO 2026-06-03 19:37:12 MarkDuplicates Tracking 205377 as yet unmatched pairs. 20145 records in RAM.
INFO 2026-06-03 19:37:15 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 2s. Last read position: chr11:57,802,048
INFO 2026-06-03 19:37:15 MarkDuplicates Tracking 203728 as yet unmatched pairs. 18474 records in RAM.
INFO 2026-06-03 19:37:17 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 2s. Last read position: chr11:62,146,788
INFO 2026-06-03 19:37:17 MarkDuplicates Tracking 202076 as yet unmatched pairs. 16794 records in RAM.
INFO 2026-06-03 19:37:19 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 2s. Last read position: chr11:63,631,082
INFO 2026-06-03 19:37:19 MarkDuplicates Tracking 200667 as yet unmatched pairs. 15374 records in RAM.
INFO 2026-06-03 19:37:21 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 2s. Last read position: chr11:65,133,539
INFO 2026-06-03 19:37:21 MarkDuplicates Tracking 198610 as yet unmatched pairs. 13291 records in RAM.
INFO 2026-06-03 19:37:23 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:06:47s. Time for last 1,000,000: 2s. Last read position: chr11:66,332,226
INFO 2026-06-03 19:37:23 MarkDuplicates Tracking 196796 as yet unmatched pairs. 11401 records in RAM.
INFO 2026-06-03 19:37:26 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 2s. Last read position: chr11:68,413,906
INFO 2026-06-03 19:37:26 MarkDuplicates Tracking 195056 as yet unmatched pairs. 9638 records in RAM.
INFO 2026-06-03 19:37:28 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 2s. Last read position: chr11:73,976,680
INFO 2026-06-03 19:37:28 MarkDuplicates Tracking 194710 as yet unmatched pairs. 9261 records in RAM.
INFO 2026-06-03 19:37:30 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 2s. Last read position: chr11:83,273,816
INFO 2026-06-03 19:37:30 MarkDuplicates Tracking 192088 as yet unmatched pairs. 6611 records in RAM.
INFO 2026-06-03 19:37:33 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 2s. Last read position: chr11:108,189,252
INFO 2026-06-03 19:37:33 MarkDuplicates Tracking 190595 as yet unmatched pairs. 5092 records in RAM.
INFO 2026-06-03 19:37:35 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 2s. Last read position: chr11:118,409,023
INFO 2026-06-03 19:37:35 MarkDuplicates Tracking 189043 as yet unmatched pairs. 3495 records in RAM.
INFO 2026-06-03 19:37:37 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 2s. Last read position: chr11:120,481,395
INFO 2026-06-03 19:37:37 MarkDuplicates Tracking 187506 as yet unmatched pairs. 1930 records in RAM.
INFO 2026-06-03 19:37:40 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:07:03s. Time for last 1,000,000: 2s. Last read position: chr11:130,915,013
INFO 2026-06-03 19:37:40 MarkDuplicates Tracking 186007 as yet unmatched pairs. 409 records in RAM.
INFO 2026-06-03 19:37:42 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 2s. Last read position: chr12:6,557,510
INFO 2026-06-03 19:37:42 MarkDuplicates Tracking 184357 as yet unmatched pairs. 23379 records in RAM.
INFO 2026-06-03 19:37:44 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 2s. Last read position: chr12:7,921,500
INFO 2026-06-03 19:37:44 MarkDuplicates Tracking 182736 as yet unmatched pairs. 21735 records in RAM.
INFO 2026-06-03 19:37:47 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 2s. Last read position: chr12:19,269,780
INFO 2026-06-03 19:37:47 MarkDuplicates Tracking 181651 as yet unmatched pairs. 20624 records in RAM.
INFO 2026-06-03 19:37:49 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 2s. Last read position: chr12:42,398,932
INFO 2026-06-03 19:37:49 MarkDuplicates Tracking 180313 as yet unmatched pairs. 19243 records in RAM.
INFO 2026-06-03 19:37:51 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:07:15s. Time for last 1,000,000: 2s. Last read position: chr12:49,103,782
INFO 2026-06-03 19:37:51 MarkDuplicates Tracking 178363 as yet unmatched pairs. 17271 records in RAM.
INFO 2026-06-03 19:37:54 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:07:18s. Time for last 1,000,000: 2s. Last read position: chr12:50,991,649
INFO 2026-06-03 19:37:54 MarkDuplicates Tracking 177270 as yet unmatched pairs. 16152 records in RAM.
INFO 2026-06-03 19:37:57 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:07:21s. Time for last 1,000,000: 2s. Last read position: chr12:54,054,969
INFO 2026-06-03 19:37:57 MarkDuplicates Tracking 175556 as yet unmatched pairs. 14425 records in RAM.
INFO 2026-06-03 19:37:59 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:07:23s. Time for last 1,000,000: 2s. Last read position: chr12:56,181,524
INFO 2026-06-03 19:37:59 MarkDuplicates Tracking 174413 as yet unmatched pairs. 13261 records in RAM.
INFO 2026-06-03 19:38:01 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:07:25s. Time for last 1,000,000: 2s. Last read position: chr12:57,179,414
INFO 2026-06-03 19:38:01 MarkDuplicates Tracking 172795 as yet unmatched pairs. 11632 records in RAM.
INFO 2026-06-03 19:38:04 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:07:28s. Time for last 1,000,000: 2s. Last read position: chr12:67,305,647
INFO 2026-06-03 19:38:04 MarkDuplicates Tracking 171404 as yet unmatched pairs. 10217 records in RAM.
INFO 2026-06-03 19:38:06 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:07:30s. Time for last 1,000,000: 2s. Last read position: chr12:89,642,188
INFO 2026-06-03 19:38:06 MarkDuplicates Tracking 169767 as yet unmatched pairs. 8556 records in RAM.
INFO 2026-06-03 19:38:09 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:07:32s. Time for last 1,000,000: 2s. Last read position: chr12:103,946,685
INFO 2026-06-03 19:38:09 MarkDuplicates Tracking 169164 as yet unmatched pairs. 7917 records in RAM.
INFO 2026-06-03 19:38:11 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:07:35s. Time for last 1,000,000: 2s. Last read position: chr12:112,022,355
INFO 2026-06-03 19:38:11 MarkDuplicates Tracking 166944 as yet unmatched pairs. 5666 records in RAM.
INFO 2026-06-03 19:38:14 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:07:38s. Time for last 1,000,000: 3s. Last read position: chr12:120,184,230
INFO 2026-06-03 19:38:14 MarkDuplicates Tracking 165146 as yet unmatched pairs. 3837 records in RAM.
INFO 2026-06-03 19:38:16 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:07:40s. Time for last 1,000,000: 2s. Last read position: chr12:123,327,749
INFO 2026-06-03 19:38:16 MarkDuplicates Tracking 163699 as yet unmatched pairs. 2370 records in RAM.
INFO 2026-06-03 19:38:19 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:07:43s. Time for last 1,000,000: 2s. Last read position: chr12:132,743,190
INFO 2026-06-03 19:38:19 MarkDuplicates Tracking 161783 as yet unmatched pairs. 429 records in RAM.
INFO 2026-06-03 19:38:21 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:07:45s. Time for last 1,000,000: 2s. Last read position: chr13:27,254,225
INFO 2026-06-03 19:38:21 MarkDuplicates Tracking 161858 as yet unmatched pairs. 8505 records in RAM.
INFO 2026-06-03 19:38:24 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:07:47s. Time for last 1,000,000: 2s. Last read position: chr13:37,584,060
INFO 2026-06-03 19:38:24 MarkDuplicates Tracking 160511 as yet unmatched pairs. 7142 records in RAM.
INFO 2026-06-03 19:38:26 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:07:50s. Time for last 1,000,000: 2s. Last read position: chr13:49,467,795
INFO 2026-06-03 19:38:26 MarkDuplicates Tracking 157482 as yet unmatched pairs. 4093 records in RAM.
INFO 2026-06-03 19:38:28 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:07:52s. Time for last 1,000,000: 2s. Last read position: chr13:98,409,495
INFO 2026-06-03 19:38:28 MarkDuplicates Tracking 156115 as yet unmatched pairs. 2681 records in RAM.
INFO 2026-06-03 19:38:31 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:07:55s. Time for last 1,000,000: 2s. Last read position: chr13:110,503,133
INFO 2026-06-03 19:38:31 MarkDuplicates Tracking 154746 as yet unmatched pairs. 1287 records in RAM.
INFO 2026-06-03 19:38:33 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:07:57s. Time for last 1,000,000: 2s. Last read position: chr14:21,468,644
INFO 2026-06-03 19:38:33 MarkDuplicates Tracking 152760 as yet unmatched pairs. 11619 records in RAM.
INFO 2026-06-03 19:38:36 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:07:59s. Time for last 1,000,000: 2s. Last read position: chr14:25,267,114
INFO 2026-06-03 19:38:36 MarkDuplicates Tracking 150987 as yet unmatched pairs. 9833 records in RAM.
INFO 2026-06-03 19:38:38 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:08:02s. Time for last 1,000,000: 2s. Last read position: chr14:50,174,374
INFO 2026-06-03 19:38:38 MarkDuplicates Tracking 149864 as yet unmatched pairs. 8648 records in RAM.
INFO 2026-06-03 19:38:41 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 2s. Last read position: chr14:63,941,777
INFO 2026-06-03 19:38:41 MarkDuplicates Tracking 148340 as yet unmatched pairs. 7097 records in RAM.
INFO 2026-06-03 19:38:44 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:08:08s. Time for last 1,000,000: 2s. Last read position: chr14:69,399,273
INFO 2026-06-03 19:38:44 MarkDuplicates Tracking 146742 as yet unmatched pairs. 5481 records in RAM.
INFO 2026-06-03 19:38:46 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:08:10s. Time for last 1,000,000: 2s. Last read position: chr14:77,521,550
INFO 2026-06-03 19:38:46 MarkDuplicates Tracking 145376 as yet unmatched pairs. 4104 records in RAM.
INFO 2026-06-03 19:38:48 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:08:12s. Time for last 1,000,000: 2s. Last read position: chr14:99,175,929
INFO 2026-06-03 19:38:48 MarkDuplicates Tracking 143709 as yet unmatched pairs. 2408 records in RAM.
INFO 2026-06-03 19:38:51 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:08:15s. Time for last 1,000,000: 2s. Last read position: chr14:103,738,687
INFO 2026-06-03 19:38:51 MarkDuplicates Tracking 142066 as yet unmatched pairs. 728 records in RAM.
INFO 2026-06-03 19:38:53 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:08:17s. Time for last 1,000,000: 2s. Last read position: chr15:34,003,157
INFO 2026-06-03 19:38:53 MarkDuplicates Tracking 140594 as yet unmatched pairs. 9660 records in RAM.
INFO 2026-06-03 19:38:55 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 2s. Last read position: chr15:42,339,805
INFO 2026-06-03 19:38:55 MarkDuplicates Tracking 139077 as yet unmatched pairs. 8130 records in RAM.
INFO 2026-06-03 19:38:58 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 2s. Last read position: chr15:51,491,726
INFO 2026-06-03 19:38:58 MarkDuplicates Tracking 137682 as yet unmatched pairs. 6712 records in RAM.
INFO 2026-06-03 19:39:00 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:08:24s. Time for last 1,000,000: 2s. Last read position: chr15:63,756,618
INFO 2026-06-03 19:39:00 MarkDuplicates Tracking 136339 as yet unmatched pairs. 5348 records in RAM.
INFO 2026-06-03 19:39:02 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:08:26s. Time for last 1,000,000: 2s. Last read position: chr15:72,783,270
INFO 2026-06-03 19:39:02 MarkDuplicates Tracking 134737 as yet unmatched pairs. 3736 records in RAM.
INFO 2026-06-03 19:39:05 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 2s. Last read position: chr15:82,434,326
INFO 2026-06-03 19:39:05 MarkDuplicates Tracking 132945 as yet unmatched pairs. 1924 records in RAM.
INFO 2026-06-03 19:39:08 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 3s. Last read position: chr15:92,985,546
INFO 2026-06-03 19:39:08 MarkDuplicates Tracking 131514 as yet unmatched pairs. 471 records in RAM.
INFO 2026-06-03 19:39:11 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 2s. Last read position: chr16:1,792,328
INFO 2026-06-03 19:39:11 MarkDuplicates Tracking 129448 as yet unmatched pairs. 19933 records in RAM.
INFO 2026-06-03 19:39:13 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 2s. Last read position: chr16:2,777,000
INFO 2026-06-03 19:39:13 MarkDuplicates Tracking 127902 as yet unmatched pairs. 18366 records in RAM.
INFO 2026-06-03 19:39:16 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:08:39s. Time for last 1,000,000: 2s. Last read position: chr16:11,887,662
INFO 2026-06-03 19:39:16 MarkDuplicates Tracking 126039 as yet unmatched pairs. 16483 records in RAM.
INFO 2026-06-03 19:39:17 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:08:41s. Time for last 1,000,000: 1s. Last read position: chr16:16,318,533
INFO 2026-06-03 19:39:17 MarkDuplicates Tracking 125128 as yet unmatched pairs. 15555 records in RAM.
INFO 2026-06-03 19:39:19 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:08:43s. Time for last 1,000,000: 1s. Last read position: chr16:18,809,528
INFO 2026-06-03 19:39:19 MarkDuplicates Tracking 124543 as yet unmatched pairs. 14965 records in RAM.
INFO 2026-06-03 19:39:22 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:08:45s. Time for last 1,000,000: 2s. Last read position: chr16:21,895,663
INFO 2026-06-03 19:39:22 MarkDuplicates Tracking 123290 as yet unmatched pairs. 13705 records in RAM.
INFO 2026-06-03 19:39:24 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 2s. Last read position: chr16:28,106,110
INFO 2026-06-03 19:39:24 MarkDuplicates Tracking 122542 as yet unmatched pairs. 12940 records in RAM.
INFO 2026-06-03 19:39:26 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:08:50s. Time for last 1,000,000: 2s. Last read position: chr16:29,663,891
INFO 2026-06-03 19:39:26 MarkDuplicates Tracking 121618 as yet unmatched pairs. 12012 records in RAM.
INFO 2026-06-03 19:39:28 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:08:52s. Time for last 1,000,000: 2s. Last read position: chr16:30,707,610
INFO 2026-06-03 19:39:28 MarkDuplicates Tracking 119879 as yet unmatched pairs. 10262 records in RAM.
INFO 2026-06-03 19:39:31 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:08:55s. Time for last 1,000,000: 2s. Last read position: chr16:46,682,161
INFO 2026-06-03 19:39:31 MarkDuplicates Tracking 118154 as yet unmatched pairs. 8524 records in RAM.
INFO 2026-06-03 19:39:33 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:08:57s. Time for last 1,000,000: 2s. Last read position: chr16:58,014,316
INFO 2026-06-03 19:39:33 MarkDuplicates Tracking 116530 as yet unmatched pairs. 6890 records in RAM.
INFO 2026-06-03 19:39:36 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:09:00s. Time for last 1,000,000: 2s. Last read position: chr16:68,563,976
INFO 2026-06-03 19:39:36 MarkDuplicates Tracking 114736 as yet unmatched pairs. 5081 records in RAM.
INFO 2026-06-03 19:39:38 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:09:02s. Time for last 1,000,000: 2s. Last read position: chr16:74,917,950
INFO 2026-06-03 19:39:38 MarkDuplicates Tracking 113266 as yet unmatched pairs. 3594 records in RAM.
INFO 2026-06-03 19:39:41 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:09:04s. Time for last 1,000,000: 2s. Last read position: chr16:88,432,344
INFO 2026-06-03 19:39:41 MarkDuplicates Tracking 111404 as yet unmatched pairs. 1710 records in RAM.
INFO 2026-06-03 19:39:43 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:09:07s. Time for last 1,000,000: 2s. Last read position: chr17:1,345,467
INFO 2026-06-03 19:39:43 MarkDuplicates Tracking 113064 as yet unmatched pairs. 34056 records in RAM.
INFO 2026-06-03 19:39:46 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:09:09s. Time for last 1,000,000: 2s. Last read position: chr17:4,798,331
INFO 2026-06-03 19:39:46 MarkDuplicates Tracking 107974 as yet unmatched pairs. 28951 records in RAM.
INFO 2026-06-03 19:39:49 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:09:13s. Time for last 1,000,000: 3s. Last read position: chr17:7,580,217
INFO 2026-06-03 19:39:49 MarkDuplicates Tracking 106974 as yet unmatched pairs. 27940 records in RAM.
INFO 2026-06-03 19:39:52 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 2s. Last read position: chr17:16,382,432
INFO 2026-06-03 19:39:52 MarkDuplicates Tracking 106203 as yet unmatched pairs. 27148 records in RAM.
INFO 2026-06-03 19:39:54 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:09:18s. Time for last 1,000,000: 2s. Last read position: chr17:27,640,546
INFO 2026-06-03 19:39:54 MarkDuplicates Tracking 103592 as yet unmatched pairs. 24531 records in RAM.
INFO 2026-06-03 19:39:56 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 2s. Last read position: chr17:31,327,781
INFO 2026-06-03 19:39:56 MarkDuplicates Tracking 102088 as yet unmatched pairs. 23012 records in RAM.
INFO 2026-06-03 19:39:59 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:09:23s. Time for last 1,000,000: 2s. Last read position: chr17:37,125,714
INFO 2026-06-03 19:39:59 MarkDuplicates Tracking 100442 as yet unmatched pairs. 21355 records in RAM.
INFO 2026-06-03 19:40:01 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 2s. Last read position: chr17:40,264,966
INFO 2026-06-03 19:40:01 MarkDuplicates Tracking 98959 as yet unmatched pairs. 19867 records in RAM.
INFO 2026-06-03 19:40:04 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:09:28s. Time for last 1,000,000: 3s. Last read position: chr17:43,000,042
INFO 2026-06-03 19:40:04 MarkDuplicates Tracking 98169 as yet unmatched pairs. 19068 records in RAM.
INFO 2026-06-03 19:40:08 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:09:32s. Time for last 1,000,000: 3s. Last read position: chr17:46,172,067
INFO 2026-06-03 19:40:08 MarkDuplicates Tracking 95900 as yet unmatched pairs. 16793 records in RAM.
INFO 2026-06-03 19:40:11 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 3s. Last read position: chr17:50,186,835
INFO 2026-06-03 19:40:11 MarkDuplicates Tracking 97094 as yet unmatched pairs. 17982 records in RAM.
INFO 2026-06-03 19:40:15 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:09:38s. Time for last 1,000,000: 3s. Last read position: chr17:50,190,893
INFO 2026-06-03 19:40:15 MarkDuplicates Tracking 102653 as yet unmatched pairs. 23521 records in RAM.
INFO 2026-06-03 19:40:18 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:09:41s. Time for last 1,000,000: 2s. Last read position: chr17:50,195,924
INFO 2026-06-03 19:40:18 MarkDuplicates Tracking 99818 as yet unmatched pairs. 20675 records in RAM.
INFO 2026-06-03 19:40:20 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 2s. Last read position: chr17:51,166,444
INFO 2026-06-03 19:40:20 MarkDuplicates Tracking 89321 as yet unmatched pairs. 10159 records in RAM.
INFO 2026-06-03 19:40:23 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:09:46s. Time for last 1,000,000: 2s. Last read position: chr17:59,738,842
INFO 2026-06-03 19:40:23 MarkDuplicates Tracking 87368 as yet unmatched pairs. 8202 records in RAM.
INFO 2026-06-03 19:40:25 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:09:49s. Time for last 1,000,000: 2s. Last read position: chr17:67,166,564
INFO 2026-06-03 19:40:25 MarkDuplicates Tracking 85899 as yet unmatched pairs. 6724 records in RAM.
INFO 2026-06-03 19:40:28 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:09:51s. Time for last 1,000,000: 2s. Last read position: chr17:75,522,151
INFO 2026-06-03 19:40:28 MarkDuplicates Tracking 84405 as yet unmatched pairs. 5221 records in RAM.
INFO 2026-06-03 19:40:30 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:09:54s. Time for last 1,000,000: 2s. Last read position: chr17:79,834,510
INFO 2026-06-03 19:40:30 MarkDuplicates Tracking 82472 as yet unmatched pairs. 3275 records in RAM.
INFO 2026-06-03 19:40:32 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:09:56s. Time for last 1,000,000: 2s. Last read position: chr17:81,890,803
INFO 2026-06-03 19:40:32 MarkDuplicates Tracking 80623 as yet unmatched pairs. 1406 records in RAM.
INFO 2026-06-03 19:40:36 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 3s. Last read position: chr18:8,085,677
INFO 2026-06-03 19:40:36 MarkDuplicates Tracking 78727 as yet unmatched pairs. 3948 records in RAM.
INFO 2026-06-03 19:40:39 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:10:03s. Time for last 1,000,000: 3s. Last read position: chr18:36,174,508
INFO 2026-06-03 19:40:39 MarkDuplicates Tracking 77329 as yet unmatched pairs. 2536 records in RAM.
INFO 2026-06-03 19:40:42 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:10:05s. Time for last 1,000,000: 2s. Last read position: chr18:62,575,484
INFO 2026-06-03 19:40:42 MarkDuplicates Tracking 75786 as yet unmatched pairs. 982 records in RAM.
INFO 2026-06-03 19:40:45 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:10:08s. Time for last 1,000,000: 2s. Last read position: chr19:1,094,031
INFO 2026-06-03 19:40:45 MarkDuplicates Tracking 73658 as yet unmatched pairs. 31361 records in RAM.
INFO 2026-06-03 19:40:47 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:10:10s. Time for last 1,000,000: 2s. Last read position: chr19:2,291,447
INFO 2026-06-03 19:40:47 MarkDuplicates Tracking 71612 as yet unmatched pairs. 29312 records in RAM.
INFO 2026-06-03 19:40:49 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:10:13s. Time for last 1,000,000: 2s. Last read position: chr19:5,611,417
INFO 2026-06-03 19:40:49 MarkDuplicates Tracking 69652 as yet unmatched pairs. 27347 records in RAM.
INFO 2026-06-03 19:40:52 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:10:16s. Time for last 1,000,000: 3s. Last read position: chr19:8,465,432
INFO 2026-06-03 19:40:52 MarkDuplicates Tracking 68481 as yet unmatched pairs. 26172 records in RAM.
INFO 2026-06-03 19:40:55 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:10:19s. Time for last 1,000,000: 2s. Last read position: chr19:10,712,218
INFO 2026-06-03 19:40:55 MarkDuplicates Tracking 66084 as yet unmatched pairs. 23768 records in RAM.
INFO 2026-06-03 19:40:58 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:10:21s. Time for last 1,000,000: 2s. Last read position: chr19:12,940,348
INFO 2026-06-03 19:40:58 MarkDuplicates Tracking 64893 as yet unmatched pairs. 22575 records in RAM.
INFO 2026-06-03 19:41:00 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:10:24s. Time for last 1,000,000: 2s. Last read position: chr19:15,244,443
INFO 2026-06-03 19:41:00 MarkDuplicates Tracking 62815 as yet unmatched pairs. 20495 records in RAM.
INFO 2026-06-03 19:41:02 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 2s. Last read position: chr19:17,862,932
INFO 2026-06-03 19:41:02 MarkDuplicates Tracking 63268 as yet unmatched pairs. 20941 records in RAM.
INFO 2026-06-03 19:41:05 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:10:29s. Time for last 1,000,000: 2s. Last read position: chr19:20,646,379
INFO 2026-06-03 19:41:05 MarkDuplicates Tracking 58807 as yet unmatched pairs. 16477 records in RAM.
INFO 2026-06-03 19:41:08 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:10:32s. Time for last 1,000,000: 2s. Last read position: chr19:36,125,664
INFO 2026-06-03 19:41:08 MarkDuplicates Tracking 56985 as yet unmatched pairs. 14649 records in RAM.
INFO 2026-06-03 19:41:11 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:10:34s. Time for last 1,000,000: 2s. Last read position: chr19:39,915,193
INFO 2026-06-03 19:41:11 MarkDuplicates Tracking 55309 as yet unmatched pairs. 12961 records in RAM.
INFO 2026-06-03 19:41:13 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:10:37s. Time for last 1,000,000: 2s. Last read position: chr19:42,272,881
INFO 2026-06-03 19:41:13 MarkDuplicates Tracking 53867 as yet unmatched pairs. 11516 records in RAM.
INFO 2026-06-03 19:41:16 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:10:40s. Time for last 1,000,000: 2s. Last read position: chr19:45,064,464
INFO 2026-06-03 19:41:16 MarkDuplicates Tracking 51572 as yet unmatched pairs. 9211 records in RAM.
INFO 2026-06-03 19:41:19 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:10:43s. Time for last 1,000,000: 2s. Last read position: chr19:48,390,444
INFO 2026-06-03 19:41:19 MarkDuplicates Tracking 49638 as yet unmatched pairs. 7274 records in RAM.
INFO 2026-06-03 19:41:22 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 3s. Last read position: chr19:49,686,699
INFO 2026-06-03 19:41:22 MarkDuplicates Tracking 48141 as yet unmatched pairs. 5774 records in RAM.
INFO 2026-06-03 19:43:03 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:12:26s. Time for last 1,000,000: 100s. Last read position: chr19:54,144,116
INFO 2026-06-03 19:43:03 MarkDuplicates Tracking 46012 as yet unmatched pairs. 3642 records in RAM.
INFO 2026-06-03 19:43:06 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:12:29s. Time for last 1,000,000: 3s. Last read position: chr19:55,669,130
INFO 2026-06-03 19:43:06 MarkDuplicates Tracking 44610 as yet unmatched pairs. 2237 records in RAM.
INFO 2026-06-03 19:43:09 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:12:33s. Time for last 1,000,000: 3s. Last read position: chr20:422,219
INFO 2026-06-03 19:43:09 MarkDuplicates Tracking 42357 as yet unmatched pairs. 11885 records in RAM.
INFO 2026-06-03 19:43:13 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:12:36s. Time for last 1,000,000: 3s. Last read position: chr20:5,185,764
INFO 2026-06-03 19:43:13 MarkDuplicates Tracking 40593 as yet unmatched pairs. 10120 records in RAM.
INFO 2026-06-03 19:43:16 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:12:40s. Time for last 1,000,000: 3s. Last read position: chr20:31,722,060
INFO 2026-06-03 19:43:16 MarkDuplicates Tracking 38945 as yet unmatched pairs. 8463 records in RAM.
INFO 2026-06-03 19:43:19 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:12:43s. Time for last 1,000,000: 3s. Last read position: chr20:35,707,171
INFO 2026-06-03 19:43:19 MarkDuplicates Tracking 38213 as yet unmatched pairs. 7726 records in RAM.
INFO 2026-06-03 19:43:22 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:12:46s. Time for last 1,000,000: 2s. Last read position: chr20:43,702,868
INFO 2026-06-03 19:43:22 MarkDuplicates Tracking 35949 as yet unmatched pairs. 5457 records in RAM.
INFO 2026-06-03 19:43:25 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:12:49s. Time for last 1,000,000: 2s. Last read position: chr20:49,225,150
INFO 2026-06-03 19:43:25 MarkDuplicates Tracking 34012 as yet unmatched pairs. 3514 records in RAM.
INFO 2026-06-03 19:43:28 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:12:51s. Time for last 1,000,000: 2s. Last read position: chr20:59,037,236
INFO 2026-06-03 19:43:28 MarkDuplicates Tracking 32474 as yet unmatched pairs. 1957 records in RAM.
INFO 2026-06-03 19:43:31 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:12:54s. Time for last 1,000,000: 2s. Last read position: chr21:6,484,637
INFO 2026-06-03 19:43:31 MarkDuplicates Tracking 30529 as yet unmatched pairs. 5497 records in RAM.
INFO 2026-06-03 19:43:33 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:12:57s. Time for last 1,000,000: 2s. Last read position: chr21:31,663,830
INFO 2026-06-03 19:43:33 MarkDuplicates Tracking 29921 as yet unmatched pairs. 4880 records in RAM.
INFO 2026-06-03 19:43:36 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:12:59s. Time for last 1,000,000: 2s. Last read position: chr21:39,898,514
INFO 2026-06-03 19:43:36 MarkDuplicates Tracking 28211 as yet unmatched pairs. 3166 records in RAM.
INFO 2026-06-03 19:43:38 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:13:02s. Time for last 1,000,000: 2s. Last read position: chr21:46,002,587
INFO 2026-06-03 19:43:38 MarkDuplicates Tracking 26406 as yet unmatched pairs. 1354 records in RAM.
INFO 2026-06-03 19:43:41 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:13:05s. Time for last 1,000,000: 3s. Last read position: chr22:21,799,038
INFO 2026-06-03 19:43:41 MarkDuplicates Tracking 24166 as yet unmatched pairs. 8356 records in RAM.
INFO 2026-06-03 19:43:44 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:13:08s. Time for last 1,000,000: 2s. Last read position: chr22:29,528,084
INFO 2026-06-03 19:43:44 MarkDuplicates Tracking 22312 as yet unmatched pairs. 6501 records in RAM.
INFO 2026-06-03 19:43:47 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:13:11s. Time for last 1,000,000: 2s. Last read position: chr22:36,490,031
INFO 2026-06-03 19:43:47 MarkDuplicates Tracking 20613 as yet unmatched pairs. 4801 records in RAM.
INFO 2026-06-03 19:43:49 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:13:13s. Time for last 1,000,000: 2s. Last read position: chr22:40,856,451
INFO 2026-06-03 19:43:49 MarkDuplicates Tracking 18884 as yet unmatched pairs. 3072 records in RAM.
INFO 2026-06-03 19:43:52 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:13:15s. Time for last 1,000,000: 2s. Last read position: chr22:50,210,779
INFO 2026-06-03 19:43:52 MarkDuplicates Tracking 17005 as yet unmatched pairs. 1190 records in RAM.
INFO 2026-06-03 19:43:56 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:13:19s. Time for last 1,000,000: 3s. Last read position: chrX:11,759,855
INFO 2026-06-03 19:43:56 MarkDuplicates Tracking 15047 as yet unmatched pairs. 12877 records in RAM.
INFO 2026-06-03 19:43:58 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:13:22s. Time for last 1,000,000: 2s. Last read position: chrX:37,840,521
INFO 2026-06-03 19:43:58 MarkDuplicates Tracking 13460 as yet unmatched pairs. 11286 records in RAM.
INFO 2026-06-03 19:44:01 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:13:25s. Time for last 1,000,000: 2s. Last read position: chrX:47,584,956
INFO 2026-06-03 19:44:01 MarkDuplicates Tracking 12875 as yet unmatched pairs. 10701 records in RAM.
INFO 2026-06-03 19:44:04 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:13:28s. Time for last 1,000,000: 3s. Last read position: chrX:53,568,730
INFO 2026-06-03 19:44:04 MarkDuplicates Tracking 10583 as yet unmatched pairs. 8408 records in RAM.
INFO 2026-06-03 19:44:08 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:13:31s. Time for last 1,000,000: 3s. Last read position: chrX:71,298,743
INFO 2026-06-03 19:44:08 MarkDuplicates Tracking 10532 as yet unmatched pairs. 8357 records in RAM.
INFO 2026-06-03 19:44:11 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:13:35s. Time for last 1,000,000: 3s. Last read position: chrX:97,141,741
INFO 2026-06-03 19:44:11 MarkDuplicates Tracking 7427 as yet unmatched pairs. 5249 records in RAM.
INFO 2026-06-03 19:44:14 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:13:38s. Time for last 1,000,000: 3s. Last read position: chrX:120,604,232
INFO 2026-06-03 19:44:14 MarkDuplicates Tracking 6140 as yet unmatched pairs. 3960 records in RAM.
INFO 2026-06-03 19:44:18 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:13:42s. Time for last 1,000,000: 3s. Last read position: chrX:153,505,267
INFO 2026-06-03 19:44:18 MarkDuplicates Tracking 5023 as yet unmatched pairs. 2843 records in RAM.
INFO 2026-06-03 19:44:21 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:13:45s. Time for last 1,000,000: 2s. Last read position: chrX:154,466,731
INFO 2026-06-03 19:44:21 MarkDuplicates Tracking 2724 as yet unmatched pairs. 544 records in RAM.
INFO 2026-06-03 19:44:24 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:13:48s. Time for last 1,000,000: 2s. Last read position: KI270711.1:6,094
INFO 2026-06-03 19:44:24 MarkDuplicates Tracking 1929 as yet unmatched pairs. 923 records in RAM.
INFO 2026-06-03 19:44:25 MarkDuplicates Read 276561237 records. 0 pairs never matched.
INFO 2026-06-03 19:44:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 26028812272; totalMemory: 37144756224; maxMemory: 63585648640
INFO 2026-06-03 19:44:39 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-03 19:44:44 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-03 19:45:19 MarkDuplicates Traversing fragment information and detecting duplicates.
WARNING 2026-06-03 19:45:19 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
INFO 2026-06-03 19:46:20 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-03 19:46:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 34381523768; totalMemory: 50331648000; maxMemory: 63585648640
INFO 2026-06-03 19:46:25 MarkDuplicates Marking 82032372 records as duplicates.
INFO 2026-06-03 19:46:25 MarkDuplicates Found 9152445 optical duplicate clusters.
INFO 2026-06-03 19:46:25 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-03 19:46:53 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:27s. Time for last 10,000,000: 27s. Last read position: chr1:47,272,097
INFO 2026-06-03 19:47:19 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:54s. Time for last 10,000,000: 26s. Last read position: chr1:149,811,991
INFO 2026-06-03 19:47:46 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:20s. Time for last 10,000,000: 26s. Last read position: chr1:226,159,276
INFO 2026-06-03 19:48:09 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:43s. Time for last 10,000,000: 23s. Last read position: chr2:108,675,941
INFO 2026-06-03 19:48:28 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:02:03s. Time for last 10,000,000: 19s. Last read position: chr2:215,431,840
INFO 2026-06-03 19:48:50 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:25s. Time for last 10,000,000: 21s. Last read position: chr3:125,560,485
INFO 2026-06-03 19:49:17 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:52s. Time for last 10,000,000: 27s. Last read position: chr4:105,190,349
INFO 2026-06-03 19:49:41 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:03:16s. Time for last 10,000,000: 24s. Last read position: chr5:150,119,478
INFO 2026-06-03 19:50:08 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:03:43s. Time for last 10,000,000: 27s. Last read position: chr6:31,637,065
INFO 2026-06-03 19:50:39 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:04:13s. Time for last 10,000,000: 30s. Last read position: chr6:153,282,609
INFO 2026-06-03 19:51:10 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:04:44s. Time for last 10,000,000: 31s. Last read position: chr7:137,928,278
INFO 2026-06-03 19:51:34 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:05:08s. Time for last 10,000,000: 23s. Last read position: chr8:127,736,517
INFO 2026-06-03 19:52:05 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:05:39s. Time for last 10,000,000: 31s. Last read position: chr9:113,267,329
INFO 2026-06-03 19:52:35 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:06:10s. Time for last 10,000,000: 30s. Last read position: chr10:78,035,666
INFO 2026-06-03 19:53:06 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:06:40s. Time for last 10,000,000: 30s. Last read position: chr11:57,802,048
INFO 2026-06-03 19:53:37 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:07:11s. Time for last 10,000,000: 30s. Last read position: chr11:120,481,395
INFO 2026-06-03 19:54:08 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:07:42s. Time for last 10,000,000: 31s. Last read position: chr12:57,179,414
INFO 2026-06-03 19:54:38 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:08:13s. Time for last 10,000,000: 30s. Last read position: chr13:49,467,795
INFO 2026-06-03 19:55:10 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:08:44s. Time for last 10,000,000: 31s. Last read position: chr14:103,738,687
INFO 2026-06-03 19:55:40 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:09:14s. Time for last 10,000,000: 29s. Last read position: chr16:11,887,662
INFO 2026-06-03 19:56:10 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:09:44s. Time for last 10,000,000: 30s. Last read position: chr16:74,917,950
INFO 2026-06-03 19:56:38 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:10:13s. Time for last 10,000,000: 28s. Last read position: chr17:43,000,042
INFO 2026-06-03 19:57:08 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:10:42s. Time for last 10,000,000: 29s. Last read position: chr17:81,890,803
INFO 2026-06-03 19:57:35 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:11:09s. Time for last 10,000,000: 26s. Last read position: chr19:15,244,443
INFO 2026-06-03 19:58:04 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:11:38s. Time for last 10,000,000: 28s. Last read position: chr19:55,669,130
INFO 2026-06-03 19:58:33 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:12:08s. Time for last 10,000,000: 29s. Last read position: chr21:39,898,514
INFO 2026-06-03 19:59:04 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:12:38s. Time for last 10,000,000: 30s. Last read position: chrX:53,568,730
INFO 2026-06-03 19:59:30 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-03 19:59:30 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-03 19:59:30 MarkDuplicates Getting Memory Stats.
INFO 2026-06-03 19:59:30 MarkDuplicates Before output close freeMemory: 203913704; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-03 19:59:30 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-03 19:59:30 MarkDuplicates After output close freeMemory: 104231112; totalMemory: 134217728; maxMemory: 63585648640
[Wed Jun 03 19:59:30 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 28.93 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory