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/75/b1cdf20894e4f6760af3acd827c856/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/8eadecd22fbd1e2e1a2f97efa0369e/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/b1cdf20894e4f6760af3acd827c856/.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 BT-20_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bam --METRICS_FILE BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:44:30.053 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 07:44:30 GMT 2026] MarkDuplicates --INPUT BT-20_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT BT-20_FFPE_RNA_0001_B23LG7FLT4_1.md.bam --METRICS_FILE BT-20_FFPE_RNA_0001_B23LG7FLT4_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 07:44:30 GMT 2026] Executing as ?@nf-75b1cdf20894e4f6760af3acd827c856-d67ba-dkw8l 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 07:44:30 MarkDuplicates Start of doWork freeMemory: 105828712; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:44:30 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:44:30 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:44:35 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:8,016,337
INFO 2026-06-08 07:44:35 MarkDuplicates Tracking 1816 as yet unmatched pairs. 4 records in RAM.
INFO 2026-06-08 07:44:39 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 3s. Last read position: chr1:12,607,362
INFO 2026-06-08 07:44:39 MarkDuplicates Tracking 3722 as yet unmatched pairs. 5 records in RAM.
INFO 2026-06-08 07:44:42 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 3s. Last read position: chr1:21,349,813
INFO 2026-06-08 07:44:42 MarkDuplicates Tracking 5406 as yet unmatched pairs. 3 records in RAM.
INFO 2026-06-08 07:44:45 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 2s. Last read position: chr1:26,958,185
INFO 2026-06-08 07:44:45 MarkDuplicates Tracking 7275 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 07:44:47 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 2s. Last read position: chr1:35,184,500
INFO 2026-06-08 07:44:47 MarkDuplicates Tracking 9169 as yet unmatched pairs. 25 records in RAM.
INFO 2026-06-08 07:44:51 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 3s. Last read position: chr1:43,303,327
INFO 2026-06-08 07:44:51 MarkDuplicates Tracking 10959 as yet unmatched pairs. 5 records in RAM.
INFO 2026-06-08 07:44:55 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 3s. Last read position: chr1:56,444,867
INFO 2026-06-08 07:44:55 MarkDuplicates Tracking 12699 as yet unmatched pairs. 7 records in RAM.
INFO 2026-06-08 07:44:58 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 3s. Last read position: chr1:93,562,352
INFO 2026-06-08 07:44:58 MarkDuplicates Tracking 14448 as yet unmatched pairs. 6 records in RAM.
INFO 2026-06-08 07:45:02 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 3s. Last read position: chr1:119,618,834
INFO 2026-06-08 07:45:02 MarkDuplicates Tracking 16161 as yet unmatched pairs. 6 records in RAM.
INFO 2026-06-08 07:45:05 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 2s. Last read position: chr1:148,590,894
INFO 2026-06-08 07:45:05 MarkDuplicates Tracking 17276 as yet unmatched pairs. 6 records in RAM.
INFO 2026-06-08 07:45:08 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 3s. Last read position: chr1:153,689,805
INFO 2026-06-08 07:45:08 MarkDuplicates Tracking 18815 as yet unmatched pairs. 7 records in RAM.
INFO 2026-06-08 07:45:11 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 3s. Last read position: chr1:156,225,067
INFO 2026-06-08 07:45:11 MarkDuplicates Tracking 20611 as yet unmatched pairs. 11 records in RAM.
INFO 2026-06-08 07:45:14 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chr1:171,557,318
INFO 2026-06-08 07:45:14 MarkDuplicates Tracking 22418 as yet unmatched pairs. 36 records in RAM.
INFO 2026-06-08 07:45:17 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 3s. Last read position: chr1:201,209,927
INFO 2026-06-08 07:45:17 MarkDuplicates Tracking 24266 as yet unmatched pairs. 63 records in RAM.
INFO 2026-06-08 07:45:21 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 3s. Last read position: chr1:206,447,141
INFO 2026-06-08 07:45:21 MarkDuplicates Tracking 25888 as yet unmatched pairs. 5 records in RAM.
INFO 2026-06-08 07:45:23 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 2s. Last read position: chr1:228,367,106
INFO 2026-06-08 07:45:23 MarkDuplicates Tracking 27730 as yet unmatched pairs. 4 records in RAM.
INFO 2026-06-08 07:45:27 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 3s. Last read position: chr2:3,580,157
INFO 2026-06-08 07:45:27 MarkDuplicates Tracking 29555 as yet unmatched pairs. 29100 records in RAM.
INFO 2026-06-08 07:45:30 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 3s. Last read position: chr2:25,282,462
INFO 2026-06-08 07:45:30 MarkDuplicates Tracking 31129 as yet unmatched pairs. 30651 records in RAM.
INFO 2026-06-08 07:45:34 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 3s. Last read position: chr2:32,916,264
INFO 2026-06-08 07:45:34 MarkDuplicates Tracking 150249 as yet unmatched pairs. 26426 records in RAM.
INFO 2026-06-08 07:45:37 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 2s. Last read position: chr2:37,007,082
INFO 2026-06-08 07:45:37 MarkDuplicates Tracking 320874 as yet unmatched pairs. 18507 records in RAM.
INFO 2026-06-08 07:45:39 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 2s. Last read position: chr2:55,322,600
INFO 2026-06-08 07:45:39 MarkDuplicates Tracking 319107 as yet unmatched pairs. 16711 records in RAM.
INFO 2026-06-08 07:45:43 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 3s. Last read position: chr2:74,346,287
INFO 2026-06-08 07:45:43 MarkDuplicates Tracking 317393 as yet unmatched pairs. 14964 records in RAM.
INFO 2026-06-08 07:45:46 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 3s. Last read position: chr2:97,647,346
INFO 2026-06-08 07:45:46 MarkDuplicates Tracking 315772 as yet unmatched pairs. 13320 records in RAM.
INFO 2026-06-08 07:45:50 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 3s. Last read position: chr2:110,535,051
INFO 2026-06-08 07:45:50 MarkDuplicates Tracking 314524 as yet unmatched pairs. 12050 records in RAM.
INFO 2026-06-08 07:45:52 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 2s. Last read position: chr2:135,778,965
INFO 2026-06-08 07:45:52 MarkDuplicates Tracking 313018 as yet unmatched pairs. 10504 records in RAM.
INFO 2026-06-08 07:45:55 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 2s. Last read position: chr2:176,123,093
INFO 2026-06-08 07:45:55 MarkDuplicates Tracking 311536 as yet unmatched pairs. 8983 records in RAM.
INFO 2026-06-08 07:45:58 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 3s. Last read position: chr2:189,010,818
INFO 2026-06-08 07:45:58 MarkDuplicates Tracking 309562 as yet unmatched pairs. 6993 records in RAM.
INFO 2026-06-08 07:46:01 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 2s. Last read position: chr2:215,430,734
INFO 2026-06-08 07:46:01 MarkDuplicates Tracking 307821 as yet unmatched pairs. 5226 records in RAM.
INFO 2026-06-08 07:46:04 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 2s. Last read position: chr2:219,556,084
INFO 2026-06-08 07:46:04 MarkDuplicates Tracking 306002 as yet unmatched pairs. 3400 records in RAM.
INFO 2026-06-08 07:46:07 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 3s. Last read position: chr2:237,376,947
INFO 2026-06-08 07:46:07 MarkDuplicates Tracking 304234 as yet unmatched pairs. 1513 records in RAM.
INFO 2026-06-08 07:46:10 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 2s. Last read position: chr3:9,757,110
INFO 2026-06-08 07:46:10 MarkDuplicates Tracking 302357 as yet unmatched pairs. 16343 records in RAM.
INFO 2026-06-08 07:46:12 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 2s. Last read position: chr3:32,336,136
INFO 2026-06-08 07:46:12 MarkDuplicates Tracking 300642 as yet unmatched pairs. 14598 records in RAM.
INFO 2026-06-08 07:46:15 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 2s. Last read position: chr3:47,123,962
INFO 2026-06-08 07:46:15 MarkDuplicates Tracking 298852 as yet unmatched pairs. 12790 records in RAM.
INFO 2026-06-08 07:46:18 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 2s. Last read position: chr3:49,533,053
INFO 2026-06-08 07:46:18 MarkDuplicates Tracking 296973 as yet unmatched pairs. 10908 records in RAM.
INFO 2026-06-08 07:46:21 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 3s. Last read position: chr3:58,081,638
INFO 2026-06-08 07:46:21 MarkDuplicates Tracking 295151 as yet unmatched pairs. 9074 records in RAM.
INFO 2026-06-08 07:46:24 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 3s. Last read position: chr3:96,814,720
INFO 2026-06-08 07:46:24 MarkDuplicates Tracking 293674 as yet unmatched pairs. 7577 records in RAM.
INFO 2026-06-08 07:46:27 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 3s. Last read position: chr3:123,647,321
INFO 2026-06-08 07:46:27 MarkDuplicates Tracking 291966 as yet unmatched pairs. 5851 records in RAM.
INFO 2026-06-08 07:46:31 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 3s. Last read position: chr3:136,601,316
INFO 2026-06-08 07:46:31 MarkDuplicates Tracking 290124 as yet unmatched pairs. 3982 records in RAM.
INFO 2026-06-08 07:46:33 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 2s. Last read position: chr3:170,178,818
INFO 2026-06-08 07:46:33 MarkDuplicates Tracking 288472 as yet unmatched pairs. 2309 records in RAM.
INFO 2026-06-08 07:46:36 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 3s. Last read position: chr3:194,406,045
INFO 2026-06-08 07:46:36 MarkDuplicates Tracking 286777 as yet unmatched pairs. 587 records in RAM.
INFO 2026-06-08 07:46:40 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 3s. Last read position: chr4:2,950,016
INFO 2026-06-08 07:46:40 MarkDuplicates Tracking 284991 as yet unmatched pairs. 10125 records in RAM.
INFO 2026-06-08 07:46:43 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 2s. Last read position: chr4:21,245,162
INFO 2026-06-08 07:46:43 MarkDuplicates Tracking 283046 as yet unmatched pairs. 8159 records in RAM.
INFO 2026-06-08 07:46:45 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 2s. Last read position: chr4:54,281,570
INFO 2026-06-08 07:46:45 MarkDuplicates Tracking 281563 as yet unmatched pairs. 6641 records in RAM.
INFO 2026-06-08 07:46:48 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 3s. Last read position: chr4:87,114,921
INFO 2026-06-08 07:46:48 MarkDuplicates Tracking 279940 as yet unmatched pairs. 4987 records in RAM.
INFO 2026-06-08 07:46:51 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 3s. Last read position: chr4:119,271,522
INFO 2026-06-08 07:46:51 MarkDuplicates Tracking 278368 as yet unmatched pairs. 3389 records in RAM.
INFO 2026-06-08 07:46:54 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 2s. Last read position: chr4:155,690,080
INFO 2026-06-08 07:46:54 MarkDuplicates Tracking 276703 as yet unmatched pairs. 1686 records in RAM.
INFO 2026-06-08 07:46:57 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 3s. Last read position: chr5:1,625,712
INFO 2026-06-08 07:46:57 MarkDuplicates Tracking 274686 as yet unmatched pairs. 13326 records in RAM.
INFO 2026-06-08 07:46:59 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 2s. Last read position: chr5:39,377,237
INFO 2026-06-08 07:46:59 MarkDuplicates Tracking 273037 as yet unmatched pairs. 11649 records in RAM.
INFO 2026-06-08 07:47:01 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 1s. Last read position: chr5:71,509,711
INFO 2026-06-08 07:47:01 MarkDuplicates Tracking 271807 as yet unmatched pairs. 10394 records in RAM.
INFO 2026-06-08 07:47:03 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 1s. Last read position: chr5:110,740,874
INFO 2026-06-08 07:47:03 MarkDuplicates Tracking 270276 as yet unmatched pairs. 8828 records in RAM.
INFO 2026-06-08 07:47:05 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 2s. Last read position: chr5:138,467,088
INFO 2026-06-08 07:47:05 MarkDuplicates Tracking 268588 as yet unmatched pairs. 7125 records in RAM.
INFO 2026-06-08 07:47:07 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 2s. Last read position: chr5:141,494,813
INFO 2026-06-08 07:47:07 MarkDuplicates Tracking 266977 as yet unmatched pairs. 5326 records in RAM.
INFO 2026-06-08 07:47:11 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 3s. Last read position: chr5:150,649,849
INFO 2026-06-08 07:47:11 MarkDuplicates Tracking 265215 as yet unmatched pairs. 3552 records in RAM.
INFO 2026-06-08 07:47:14 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 3s. Last read position: chr5:176,433,313
INFO 2026-06-08 07:47:14 MarkDuplicates Tracking 263508 as yet unmatched pairs. 1827 records in RAM.
INFO 2026-06-08 07:47:17 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 3s. Last read position: chr6:2,348,869
INFO 2026-06-08 07:47:17 MarkDuplicates Tracking 261658 as yet unmatched pairs. 16083 records in RAM.
INFO 2026-06-08 07:47:20 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 2s. Last read position: chr6:26,124,406
INFO 2026-06-08 07:47:20 MarkDuplicates Tracking 260038 as yet unmatched pairs. 14427 records in RAM.
INFO 2026-06-08 07:47:23 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 2s. Last read position: chr6:31,828,010
INFO 2026-06-08 07:47:23 MarkDuplicates Tracking 258307 as yet unmatched pairs. 12687 records in RAM.
INFO 2026-06-08 07:47:25 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 1s. Last read position: chr6:33,320,080
INFO 2026-06-08 07:47:25 MarkDuplicates Tracking 256576 as yet unmatched pairs. 10954 records in RAM.
INFO 2026-06-08 07:47:27 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 2s. Last read position: chr6:43,338,636
INFO 2026-06-08 07:47:27 MarkDuplicates Tracking 254636 as yet unmatched pairs. 8995 records in RAM.
INFO 2026-06-08 07:47:29 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 1s. Last read position: chr6:75,156,387
INFO 2026-06-08 07:47:29 MarkDuplicates Tracking 253158 as yet unmatched pairs. 7502 records in RAM.
INFO 2026-06-08 07:47:32 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 2s. Last read position: chr6:111,314,055
INFO 2026-06-08 07:47:32 MarkDuplicates Tracking 251540 as yet unmatched pairs. 5858 records in RAM.
INFO 2026-06-08 07:47:35 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 3s. Last read position: chr6:142,753,452
INFO 2026-06-08 07:47:35 MarkDuplicates Tracking 249780 as yet unmatched pairs. 4080 records in RAM.
INFO 2026-06-08 07:47:38 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 3s. Last read position: chr6:151,961,198
INFO 2026-06-08 07:47:38 MarkDuplicates Tracking 247860 as yet unmatched pairs. 2155 records in RAM.
INFO 2026-06-08 07:47:42 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 3s. Last read position: chr6:167,965,942
INFO 2026-06-08 07:47:42 MarkDuplicates Tracking 246052 as yet unmatched pairs. 339 records in RAM.
INFO 2026-06-08 07:47:45 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 3s. Last read position: chr7:5,527,722
INFO 2026-06-08 07:47:45 MarkDuplicates Tracking 244048 as yet unmatched pairs. 16744 records in RAM.
INFO 2026-06-08 07:47:48 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 2s. Last read position: chr7:31,302,196
INFO 2026-06-08 07:47:48 MarkDuplicates Tracking 242123 as yet unmatched pairs. 14795 records in RAM.
INFO 2026-06-08 07:47:50 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 2s. Last read position: chr7:45,083,440
INFO 2026-06-08 07:47:50 MarkDuplicates Tracking 240397 as yet unmatched pairs. 13054 records in RAM.
INFO 2026-06-08 07:47:52 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 1s. Last read position: chr7:72,925,619
INFO 2026-06-08 07:47:52 MarkDuplicates Tracking 238833 as yet unmatched pairs. 11457 records in RAM.
INFO 2026-06-08 07:47:54 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 1s. Last read position: chr7:75,987,365
INFO 2026-06-08 07:47:54 MarkDuplicates Tracking 237846 as yet unmatched pairs. 10463 records in RAM.
INFO 2026-06-08 07:47:55 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 1s. Last read position: chr7:97,966,851
INFO 2026-06-08 07:47:55 MarkDuplicates Tracking 236245 as yet unmatched pairs. 8840 records in RAM.
INFO 2026-06-08 07:47:58 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 2s. Last read position: chr7:102,197,288
INFO 2026-06-08 07:47:58 MarkDuplicates Tracking 234341 as yet unmatched pairs. 6922 records in RAM.
INFO 2026-06-08 07:48:01 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 2s. Last read position: chr7:111,794,689
INFO 2026-06-08 07:48:01 MarkDuplicates Tracking 233122 as yet unmatched pairs. 5686 records in RAM.
INFO 2026-06-08 07:48:04 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 2s. Last read position: chr7:134,933,724
INFO 2026-06-08 07:48:04 MarkDuplicates Tracking 231764 as yet unmatched pairs. 4303 records in RAM.
INFO 2026-06-08 07:48:06 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 2s. Last read position: chr7:143,604,605
INFO 2026-06-08 07:48:06 MarkDuplicates Tracking 229710 as yet unmatched pairs. 2236 records in RAM.
INFO 2026-06-08 07:48:09 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 2s. Last read position: chr7:153,750,920
INFO 2026-06-08 07:48:09 MarkDuplicates Tracking 228103 as yet unmatched pairs. 617 records in RAM.
INFO 2026-06-08 07:48:13 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 3s. Last read position: chr8:22,148,611
INFO 2026-06-08 07:48:13 MarkDuplicates Tracking 226523 as yet unmatched pairs. 8789 records in RAM.
INFO 2026-06-08 07:48:15 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 2s. Last read position: chr8:38,278,281
INFO 2026-06-08 07:48:15 MarkDuplicates Tracking 224806 as yet unmatched pairs. 7058 records in RAM.
INFO 2026-06-08 07:48:18 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 3s. Last read position: chr8:67,064,487
INFO 2026-06-08 07:48:18 MarkDuplicates Tracking 223187 as yet unmatched pairs. 5419 records in RAM.
INFO 2026-06-08 07:48:20 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 2s. Last read position: chr8:100,721,366
INFO 2026-06-08 07:48:20 MarkDuplicates Tracking 221561 as yet unmatched pairs. 3771 records in RAM.
INFO 2026-06-08 07:48:23 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 2s. Last read position: chr8:142,664,630
INFO 2026-06-08 07:48:23 MarkDuplicates Tracking 219882 as yet unmatched pairs. 2065 records in RAM.
INFO 2026-06-08 07:48:24 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 1s. Last read position: chr8:144,792,016
INFO 2026-06-08 07:48:24 MarkDuplicates Tracking 217955 as yet unmatched pairs. 100 records in RAM.
INFO 2026-06-08 07:48:26 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 2s. Last read position: chr9:26,722,953
INFO 2026-06-08 07:48:26 MarkDuplicates Tracking 216408 as yet unmatched pairs. 14323 records in RAM.
INFO 2026-06-08 07:48:29 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 2s. Last read position: chr9:41,448,914
INFO 2026-06-08 07:48:29 MarkDuplicates Tracking 214609 as yet unmatched pairs. 12452 records in RAM.
INFO 2026-06-08 07:48:31 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 2s. Last read position: chr9:92,514,771
INFO 2026-06-08 07:48:31 MarkDuplicates Tracking 213148 as yet unmatched pairs. 10977 records in RAM.
INFO 2026-06-08 07:48:35 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 3s. Last read position: chr9:99,221,812
INFO 2026-06-08 07:48:35 MarkDuplicates Tracking 211276 as yet unmatched pairs. 9096 records in RAM.
INFO 2026-06-08 07:48:37 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 2s. Last read position: chr9:114,288,464
INFO 2026-06-08 07:48:37 MarkDuplicates Tracking 209660 as yet unmatched pairs. 7471 records in RAM.
INFO 2026-06-08 07:48:40 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 2s. Last read position: chr9:127,447,878
INFO 2026-06-08 07:48:40 MarkDuplicates Tracking 207806 as yet unmatched pairs. 5605 records in RAM.
INFO 2026-06-08 07:48:44 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 3s. Last read position: chr9:131,192,265
INFO 2026-06-08 07:48:44 MarkDuplicates Tracking 205730 as yet unmatched pairs. 3520 records in RAM.
INFO 2026-06-08 07:48:47 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 2s. Last read position: chr9:136,377,984
INFO 2026-06-08 07:48:47 MarkDuplicates Tracking 203800 as yet unmatched pairs. 1575 records in RAM.
INFO 2026-06-08 07:48:49 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 2s. Last read position: chr10:5,906,445
INFO 2026-06-08 07:48:49 MarkDuplicates Tracking 201811 as yet unmatched pairs. 11290 records in RAM.
INFO 2026-06-08 07:48:51 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 2s. Last read position: chr10:31,520,234
INFO 2026-06-08 07:48:51 MarkDuplicates Tracking 200179 as yet unmatched pairs. 9636 records in RAM.
INFO 2026-06-08 07:48:54 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 2s. Last read position: chr10:58,787,057
INFO 2026-06-08 07:48:54 MarkDuplicates Tracking 198812 as yet unmatched pairs. 8249 records in RAM.
INFO 2026-06-08 07:48:56 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 2s. Last read position: chr10:75,021,267
INFO 2026-06-08 07:48:56 MarkDuplicates Tracking 197004 as yet unmatched pairs. 6421 records in RAM.
INFO 2026-06-08 07:48:58 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr10:87,864,387
INFO 2026-06-08 07:48:58 MarkDuplicates Tracking 195560 as yet unmatched pairs. 4963 records in RAM.
INFO 2026-06-08 07:49:00 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr10:101,356,798
INFO 2026-06-08 07:49:00 MarkDuplicates Tracking 193831 as yet unmatched pairs. 3220 records in RAM.
INFO 2026-06-08 07:49:03 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 2s. Last read position: chr10:117,543,483
INFO 2026-06-08 07:49:03 MarkDuplicates Tracking 192222 as yet unmatched pairs. 1564 records in RAM.
INFO 2026-06-08 07:49:06 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 3s. Last read position: chr11:309,134
INFO 2026-06-08 07:49:06 MarkDuplicates Tracking 190581 as yet unmatched pairs. 20969 records in RAM.
INFO 2026-06-08 07:49:09 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 2s. Last read position: chr11:3,369,724
INFO 2026-06-08 07:49:09 MarkDuplicates Tracking 188366 as yet unmatched pairs. 18745 records in RAM.
INFO 2026-06-08 07:49:12 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 3s. Last read position: chr11:12,870,869
INFO 2026-06-08 07:49:12 MarkDuplicates Tracking 186567 as yet unmatched pairs. 16934 records in RAM.
INFO 2026-06-08 07:49:15 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 3s. Last read position: chr11:46,320,716
INFO 2026-06-08 07:49:15 MarkDuplicates Tracking 184933 as yet unmatched pairs. 15281 records in RAM.
INFO 2026-06-08 07:49:18 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 2s. Last read position: chr11:62,520,593
INFO 2026-06-08 07:49:18 MarkDuplicates Tracking 183140 as yet unmatched pairs. 13428 records in RAM.
INFO 2026-06-08 07:49:20 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 2s. Last read position: chr11:64,911,263
INFO 2026-06-08 07:49:20 MarkDuplicates Tracking 181021 as yet unmatched pairs. 11305 records in RAM.
INFO 2026-06-08 07:49:23 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 2s. Last read position: chr11:65,865,943
INFO 2026-06-08 07:49:23 MarkDuplicates Tracking 179172 as yet unmatched pairs. 9451 records in RAM.
INFO 2026-06-08 07:49:26 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 2s. Last read position: chr11:68,892,436
INFO 2026-06-08 07:49:26 MarkDuplicates Tracking 177604 as yet unmatched pairs. 7878 records in RAM.
INFO 2026-06-08 07:49:29 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 2s. Last read position: chr11:75,400,783
INFO 2026-06-08 07:49:29 MarkDuplicates Tracking 175744 as yet unmatched pairs. 6007 records in RAM.
INFO 2026-06-08 07:49:31 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 2s. Last read position: chr11:101,127,977
INFO 2026-06-08 07:49:31 MarkDuplicates Tracking 173899 as yet unmatched pairs. 4134 records in RAM.
INFO 2026-06-08 07:49:34 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 2s. Last read position: chr11:117,345,873
INFO 2026-06-08 07:49:34 MarkDuplicates Tracking 171762 as yet unmatched pairs. 1985 records in RAM.
INFO 2026-06-08 07:49:37 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 3s. Last read position: chr11:128,810,808
INFO 2026-06-08 07:49:37 MarkDuplicates Tracking 170088 as yet unmatched pairs. 299 records in RAM.
INFO 2026-06-08 07:49:40 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 3s. Last read position: chr12:6,935,552
INFO 2026-06-08 07:49:40 MarkDuplicates Tracking 168208 as yet unmatched pairs. 16465 records in RAM.
INFO 2026-06-08 07:49:43 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 2s. Last read position: chr12:23,950,912
INFO 2026-06-08 07:49:43 MarkDuplicates Tracking 166505 as yet unmatched pairs. 14756 records in RAM.
INFO 2026-06-08 07:49:45 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 2s. Last read position: chr12:49,041,050
INFO 2026-06-08 07:49:45 MarkDuplicates Tracking 164887 as yet unmatched pairs. 13127 records in RAM.
INFO 2026-06-08 07:49:48 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 2s. Last read position: chr12:53,463,849
INFO 2026-06-08 07:49:48 MarkDuplicates Tracking 162972 as yet unmatched pairs. 11210 records in RAM.
INFO 2026-06-08 07:49:51 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 2s. Last read position: chr12:57,093,454
INFO 2026-06-08 07:49:51 MarkDuplicates Tracking 161274 as yet unmatched pairs. 9511 records in RAM.
INFO 2026-06-08 07:49:54 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 3s. Last read position: chr12:62,690,276
INFO 2026-06-08 07:49:54 MarkDuplicates Tracking 159259 as yet unmatched pairs. 7494 records in RAM.
INFO 2026-06-08 07:49:56 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 1s. Last read position: chr12:100,072,692
INFO 2026-06-08 07:49:56 MarkDuplicates Tracking 157746 as yet unmatched pairs. 5957 records in RAM.
INFO 2026-06-08 07:49:58 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 1s. Last read position: chr12:112,405,979
INFO 2026-06-08 07:49:58 MarkDuplicates Tracking 156056 as yet unmatched pairs. 4256 records in RAM.
INFO 2026-06-08 07:50:00 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 1s. Last read position: chr12:122,354,492
INFO 2026-06-08 07:50:00 MarkDuplicates Tracking 154110 as yet unmatched pairs. 2296 records in RAM.
INFO 2026-06-08 07:50:02 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 1s. Last read position: chr12:132,563,150
INFO 2026-06-08 07:50:02 MarkDuplicates Tracking 152228 as yet unmatched pairs. 409 records in RAM.
INFO 2026-06-08 07:50:05 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 3s. Last read position: chr13:35,236,386
INFO 2026-06-08 07:50:05 MarkDuplicates Tracking 150523 as yet unmatched pairs. 3491 records in RAM.
INFO 2026-06-08 07:50:08 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 3s. Last read position: chr13:75,621,794
INFO 2026-06-08 07:50:08 MarkDuplicates Tracking 148927 as yet unmatched pairs. 1876 records in RAM.
INFO 2026-06-08 07:50:10 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 2s. Last read position: chr13:113,811,799
INFO 2026-06-08 07:50:10 MarkDuplicates Tracking 147263 as yet unmatched pairs. 189 records in RAM.
INFO 2026-06-08 07:50:12 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 1s. Last read position: chr14:24,376,034
INFO 2026-06-08 07:50:12 MarkDuplicates Tracking 145488 as yet unmatched pairs. 7643 records in RAM.
INFO 2026-06-08 07:50:14 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 1s. Last read position: chr14:49,586,764
INFO 2026-06-08 07:50:14 MarkDuplicates Tracking 144191 as yet unmatched pairs. 6330 records in RAM.
INFO 2026-06-08 07:50:16 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 2s. Last read position: chr14:65,095,747
INFO 2026-06-08 07:50:16 MarkDuplicates Tracking 142719 as yet unmatched pairs. 4847 records in RAM.
INFO 2026-06-08 07:50:19 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 2s. Last read position: chr14:75,281,278
INFO 2026-06-08 07:50:19 MarkDuplicates Tracking 140987 as yet unmatched pairs. 3106 records in RAM.
INFO 2026-06-08 07:50:22 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 2s. Last read position: chr14:101,925,122
INFO 2026-06-08 07:50:22 MarkDuplicates Tracking 139281 as yet unmatched pairs. 1330 records in RAM.
INFO 2026-06-08 07:50:25 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 3s. Last read position: chr15:28,229,497
INFO 2026-06-08 07:50:25 MarkDuplicates Tracking 137623 as yet unmatched pairs. 10150 records in RAM.
INFO 2026-06-08 07:50:27 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 2s. Last read position: chr15:41,770,864
INFO 2026-06-08 07:50:27 MarkDuplicates Tracking 136060 as yet unmatched pairs. 8577 records in RAM.
INFO 2026-06-08 07:50:29 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 2s. Last read position: chr15:57,232,757
INFO 2026-06-08 07:50:29 MarkDuplicates Tracking 134235 as yet unmatched pairs. 6745 records in RAM.
INFO 2026-06-08 07:50:31 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 1s. Last read position: chr15:66,499,431
INFO 2026-06-08 07:50:31 MarkDuplicates Tracking 132415 as yet unmatched pairs. 4919 records in RAM.
INFO 2026-06-08 07:50:34 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 2s. Last read position: chr15:75,609,936
INFO 2026-06-08 07:50:34 MarkDuplicates Tracking 130489 as yet unmatched pairs. 2981 records in RAM.
INFO 2026-06-08 07:50:36 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 1s. Last read position: chr15:87,977,773
INFO 2026-06-08 07:50:36 MarkDuplicates Tracking 129211 as yet unmatched pairs. 1688 records in RAM.
INFO 2026-06-08 07:50:38 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 2s. Last read position: chr16:488,940
INFO 2026-06-08 07:50:38 MarkDuplicates Tracking 127251 as yet unmatched pairs. 18210 records in RAM.
INFO 2026-06-08 07:50:40 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 1s. Last read position: chr16:2,253,921
INFO 2026-06-08 07:50:40 MarkDuplicates Tracking 125154 as yet unmatched pairs. 16107 records in RAM.
INFO 2026-06-08 07:50:42 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 2s. Last read position: chr16:4,336,986
INFO 2026-06-08 07:50:42 MarkDuplicates Tracking 123191 as yet unmatched pairs. 14142 records in RAM.
INFO 2026-06-08 07:50:45 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 2s. Last read position: chr16:15,070,150
INFO 2026-06-08 07:50:45 MarkDuplicates Tracking 121802 as yet unmatched pairs. 12745 records in RAM.
INFO 2026-06-08 07:50:48 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 2s. Last read position: chr16:16,321,237
INFO 2026-06-08 07:50:48 MarkDuplicates Tracking 120347 as yet unmatched pairs. 11290 records in RAM.
INFO 2026-06-08 07:50:50 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 2s. Last read position: chr16:20,741,613
INFO 2026-06-08 07:50:50 MarkDuplicates Tracking 119721 as yet unmatched pairs. 10663 records in RAM.
INFO 2026-06-08 07:50:52 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 2s. Last read position: chr16:21,904,516
INFO 2026-06-08 07:50:52 MarkDuplicates Tracking 119175 as yet unmatched pairs. 10115 records in RAM.
INFO 2026-06-08 07:50:55 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 2s. Last read position: chr16:28,380,509
INFO 2026-06-08 07:50:55 MarkDuplicates Tracking 118239 as yet unmatched pairs. 9169 records in RAM.
INFO 2026-06-08 07:50:58 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 2s. Last read position: chr16:29,807,527
INFO 2026-06-08 07:50:58 MarkDuplicates Tracking 117448 as yet unmatched pairs. 8373 records in RAM.
INFO 2026-06-08 07:51:00 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 2s. Last read position: chr16:30,905,052
INFO 2026-06-08 07:51:00 MarkDuplicates Tracking 116172 as yet unmatched pairs. 7093 records in RAM.
INFO 2026-06-08 07:51:03 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:06:31s. Time for last 1,000,000: 2s. Last read position: chr16:57,521,110
INFO 2026-06-08 07:51:03 MarkDuplicates Tracking 114325 as yet unmatched pairs. 5231 records in RAM.
INFO 2026-06-08 07:51:06 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 2s. Last read position: chr16:70,463,739
INFO 2026-06-08 07:51:06 MarkDuplicates Tracking 112524 as yet unmatched pairs. 3421 records in RAM.
INFO 2026-06-08 07:51:09 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 2s. Last read position: chr16:85,292,995
INFO 2026-06-08 07:51:09 MarkDuplicates Tracking 110590 as yet unmatched pairs. 1475 records in RAM.
INFO 2026-06-08 07:51:12 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 3s. Last read position: chr17:1,423,573
INFO 2026-06-08 07:51:12 MarkDuplicates Tracking 108746 as yet unmatched pairs. 27350 records in RAM.
INFO 2026-06-08 07:51:15 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 2s. Last read position: chr17:7,220,477
INFO 2026-06-08 07:51:15 MarkDuplicates Tracking 106810 as yet unmatched pairs. 25413 records in RAM.
INFO 2026-06-08 07:51:18 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:06:46s. Time for last 1,000,000: 3s. Last read position: chr17:7,884,911
INFO 2026-06-08 07:51:18 MarkDuplicates Tracking 105045 as yet unmatched pairs. 23648 records in RAM.
INFO 2026-06-08 07:51:21 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 2s. Last read position: chr17:17,814,660
INFO 2026-06-08 07:51:21 MarkDuplicates Tracking 103262 as yet unmatched pairs. 21860 records in RAM.
INFO 2026-06-08 07:51:24 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:06:51s. Time for last 1,000,000: 2s. Last read position: chr17:30,776,883
INFO 2026-06-08 07:51:24 MarkDuplicates Tracking 101603 as yet unmatched pairs. 20189 records in RAM.
INFO 2026-06-08 07:51:26 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 2s. Last read position: chr17:38,914,466
INFO 2026-06-08 07:51:26 MarkDuplicates Tracking 100032 as yet unmatched pairs. 18614 records in RAM.
INFO 2026-06-08 07:51:29 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:06:57s. Time for last 1,000,000: 2s. Last read position: chr17:43,201,725
INFO 2026-06-08 07:51:29 MarkDuplicates Tracking 97949 as yet unmatched pairs. 16526 records in RAM.
INFO 2026-06-08 07:51:32 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:07:00s. Time for last 1,000,000: 2s. Last read position: chr17:47,916,617
INFO 2026-06-08 07:51:32 MarkDuplicates Tracking 96532 as yet unmatched pairs. 15103 records in RAM.
INFO 2026-06-08 07:51:35 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:07:03s. Time for last 1,000,000: 3s. Last read position: chr17:50,186,850
INFO 2026-06-08 07:51:35 MarkDuplicates Tracking 95684 as yet unmatched pairs. 14254 records in RAM.
INFO 2026-06-08 07:51:39 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 3s. Last read position: chr17:50,189,858
INFO 2026-06-08 07:51:39 MarkDuplicates Tracking 92805 as yet unmatched pairs. 11375 records in RAM.
INFO 2026-06-08 07:51:41 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:07:09s. Time for last 1,000,000: 2s. Last read position: chr17:50,195,467
INFO 2026-06-08 07:51:41 MarkDuplicates Tracking 90268 as yet unmatched pairs. 8837 records in RAM.
INFO 2026-06-08 07:51:43 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:07:11s. Time for last 1,000,000: 2s. Last read position: chr17:50,383,035
INFO 2026-06-08 07:51:43 MarkDuplicates Tracking 88100 as yet unmatched pairs. 6669 records in RAM.
INFO 2026-06-08 07:51:46 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 2s. Last read position: chr17:64,504,047
INFO 2026-06-08 07:51:46 MarkDuplicates Tracking 86254 as yet unmatched pairs. 4817 records in RAM.
INFO 2026-06-08 07:51:48 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:07:16s. Time for last 1,000,000: 2s. Last read position: chr17:75,590,878
INFO 2026-06-08 07:51:48 MarkDuplicates Tracking 84486 as yet unmatched pairs. 3033 records in RAM.
INFO 2026-06-08 07:51:51 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:07:19s. Time for last 1,000,000: 2s. Last read position: chr17:80,995,721
INFO 2026-06-08 07:51:51 MarkDuplicates Tracking 82582 as yet unmatched pairs. 1119 records in RAM.
INFO 2026-06-08 07:51:54 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:07:22s. Time for last 1,000,000: 2s. Last read position: chr18:10,471,651
INFO 2026-06-08 07:51:54 MarkDuplicates Tracking 80696 as yet unmatched pairs. 3583 records in RAM.
INFO 2026-06-08 07:51:57 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:07:25s. Time for last 1,000,000: 3s. Last read position: chr18:51,196,942
INFO 2026-06-08 07:51:57 MarkDuplicates Tracking 78960 as yet unmatched pairs. 1837 records in RAM.
INFO 2026-06-08 07:52:00 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:07:28s. Time for last 1,000,000: 3s. Last read position: chr18:79,923,286
INFO 2026-06-08 07:52:00 MarkDuplicates Tracking 77167 as yet unmatched pairs. 37 records in RAM.
INFO 2026-06-08 07:52:04 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:07:32s. Time for last 1,000,000: 4s. Last read position: chr19:2,512,151
INFO 2026-06-08 07:52:04 MarkDuplicates Tracking 74843 as yet unmatched pairs. 24768 records in RAM.
INFO 2026-06-08 07:52:07 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:07:35s. Time for last 1,000,000: 2s. Last read position: chr19:6,413,916
INFO 2026-06-08 07:52:07 MarkDuplicates Tracking 72951 as yet unmatched pairs. 22874 records in RAM.
INFO 2026-06-08 07:52:11 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:07:39s. Time for last 1,000,000: 3s. Last read position: chr19:9,974,342
INFO 2026-06-08 07:52:11 MarkDuplicates Tracking 70975 as yet unmatched pairs. 20894 records in RAM.
INFO 2026-06-08 07:52:14 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:07:41s. Time for last 1,000,000: 2s. Last read position: chr19:12,949,289
INFO 2026-06-08 07:52:14 MarkDuplicates Tracking 68918 as yet unmatched pairs. 18836 records in RAM.
INFO 2026-06-08 07:52:17 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:07:45s. Time for last 1,000,000: 3s. Last read position: chr19:15,403,498
INFO 2026-06-08 07:52:17 MarkDuplicates Tracking 66993 as yet unmatched pairs. 16910 records in RAM.
INFO 2026-06-08 07:52:21 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:07:48s. Time for last 1,000,000: 3s. Last read position: chr19:18,891,271
INFO 2026-06-08 07:52:21 MarkDuplicates Tracking 64879 as yet unmatched pairs. 14788 records in RAM.
INFO 2026-06-08 07:52:23 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:07:51s. Time for last 1,000,000: 2s. Last read position: chr19:35,786,797
INFO 2026-06-08 07:52:23 MarkDuplicates Tracking 62837 as yet unmatched pairs. 12740 records in RAM.
INFO 2026-06-08 07:52:26 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:07:54s. Time for last 1,000,000: 2s. Last read position: chr19:40,242,671
INFO 2026-06-08 07:52:26 MarkDuplicates Tracking 60994 as yet unmatched pairs. 10893 records in RAM.
INFO 2026-06-08 07:52:29 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:07:56s. Time for last 1,000,000: 2s. Last read position: chr19:42,291,340
INFO 2026-06-08 07:52:29 MarkDuplicates Tracking 59103 as yet unmatched pairs. 9000 records in RAM.
INFO 2026-06-08 07:52:31 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:07:59s. Time for last 1,000,000: 2s. Last read position: chr19:46,387,360
INFO 2026-06-08 07:52:31 MarkDuplicates Tracking 56882 as yet unmatched pairs. 6749 records in RAM.
INFO 2026-06-08 07:52:35 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:08:03s. Time for last 1,000,000: 3s. Last read position: chr19:49,497,560
INFO 2026-06-08 07:52:35 MarkDuplicates Tracking 54940 as yet unmatched pairs. 4802 records in RAM.
INFO 2026-06-08 07:52:38 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:08:06s. Time for last 1,000,000: 3s. Last read position: chr19:54,121,900
INFO 2026-06-08 07:52:38 MarkDuplicates Tracking 52847 as yet unmatched pairs. 2705 records in RAM.
INFO 2026-06-08 07:52:41 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:08:08s. Time for last 1,000,000: 2s. Last read position: chr19:57,336,815
INFO 2026-06-08 07:52:41 MarkDuplicates Tracking 50871 as yet unmatched pairs. 726 records in RAM.
INFO 2026-06-08 07:52:44 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:08:12s. Time for last 1,000,000: 3s. Last read position: chr20:6,778,770
INFO 2026-06-08 07:52:44 MarkDuplicates Tracking 48936 as yet unmatched pairs. 7098 records in RAM.
INFO 2026-06-08 07:52:47 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:08:15s. Time for last 1,000,000: 3s. Last read position: chr20:33,644,488
INFO 2026-06-08 07:52:47 MarkDuplicates Tracking 47280 as yet unmatched pairs. 5427 records in RAM.
INFO 2026-06-08 07:52:50 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:08:18s. Time for last 1,000,000: 2s. Last read position: chr20:43,460,756
INFO 2026-06-08 07:52:50 MarkDuplicates Tracking 45487 as yet unmatched pairs. 3631 records in RAM.
INFO 2026-06-08 07:52:53 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:08:20s. Time for last 1,000,000: 2s. Last read position: chr20:57,709,552
INFO 2026-06-08 07:52:53 MarkDuplicates Tracking 43634 as yet unmatched pairs. 1768 records in RAM.
INFO 2026-06-08 07:52:56 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 3s. Last read position: chr21:8,210,326
INFO 2026-06-08 07:52:56 MarkDuplicates Tracking 41723 as yet unmatched pairs. 12148 records in RAM.
INFO 2026-06-08 07:52:57 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 1s. Last read position: chr21:8,216,085
INFO 2026-06-08 07:52:57 MarkDuplicates Tracking 40733 as yet unmatched pairs. 11134 records in RAM.
INFO 2026-06-08 07:52:59 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:08:27s. Time for last 1,000,000: 2s. Last read position: chr21:8,217,310
INFO 2026-06-08 07:52:59 MarkDuplicates Tracking 39203 as yet unmatched pairs. 9591 records in RAM.
INFO 2026-06-08 07:53:01 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 2s. Last read position: chr21:8,258,945
INFO 2026-06-08 07:53:01 MarkDuplicates Tracking 38741 as yet unmatched pairs. 9126 records in RAM.
INFO 2026-06-08 07:53:04 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:08:31s. Time for last 1,000,000: 2s. Last read position: chr21:8,395,870
INFO 2026-06-08 07:53:04 MarkDuplicates Tracking 38388 as yet unmatched pairs. 8769 records in RAM.
INFO 2026-06-08 07:53:06 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 2s. Last read position: chr21:8,399,875
INFO 2026-06-08 07:53:06 MarkDuplicates Tracking 37145 as yet unmatched pairs. 7513 records in RAM.
INFO 2026-06-08 07:53:08 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:08:36s. Time for last 1,000,000: 2s. Last read position: chr21:8,401,708
INFO 2026-06-08 07:53:08 MarkDuplicates Tracking 35220 as yet unmatched pairs. 5574 records in RAM.
INFO 2026-06-08 07:53:10 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:08:38s. Time for last 1,000,000: 1s. Last read position: chr21:8,441,999
INFO 2026-06-08 07:53:10 MarkDuplicates Tracking 34643 as yet unmatched pairs. 4997 records in RAM.
INFO 2026-06-08 07:53:12 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:08:39s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,138
INFO 2026-06-08 07:53:12 MarkDuplicates Tracking 34005 as yet unmatched pairs. 4356 records in RAM.
INFO 2026-06-08 07:53:14 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:08:41s. Time for last 1,000,000: 1s. Last read position: chr21:25,975,109
INFO 2026-06-08 07:53:14 MarkDuplicates Tracking 33388 as yet unmatched pairs. 3738 records in RAM.
INFO 2026-06-08 07:53:16 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:08:44s. Time for last 1,000,000: 2s. Last read position: chr21:44,984,084
INFO 2026-06-08 07:53:16 MarkDuplicates Tracking 31672 as yet unmatched pairs. 2017 records in RAM.
INFO 2026-06-08 07:53:20 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 3s. Last read position: chr22:17,548,855
INFO 2026-06-08 07:53:20 MarkDuplicates Tracking 29579 as yet unmatched pairs. 9538 records in RAM.
INFO 2026-06-08 07:53:23 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 3s. Last read position: chr22:24,042,950
INFO 2026-06-08 07:53:23 MarkDuplicates Tracking 27426 as yet unmatched pairs. 7383 records in RAM.
INFO 2026-06-08 07:53:26 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 2s. Last read position: chr22:31,715,975
INFO 2026-06-08 07:53:26 MarkDuplicates Tracking 25460 as yet unmatched pairs. 5417 records in RAM.
INFO 2026-06-08 07:53:28 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:08:56s. Time for last 1,000,000: 2s. Last read position: chr22:38,866,964
INFO 2026-06-08 07:53:28 MarkDuplicates Tracking 23586 as yet unmatched pairs. 3538 records in RAM.
INFO 2026-06-08 07:53:31 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:08:59s. Time for last 1,000,000: 2s. Last read position: chr22:45,533,144
INFO 2026-06-08 07:53:31 MarkDuplicates Tracking 21668 as yet unmatched pairs. 1618 records in RAM.
INFO 2026-06-08 07:53:34 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:09:02s. Time for last 1,000,000: 2s. Last read position: chrX:3,818,015
INFO 2026-06-08 07:53:34 MarkDuplicates Tracking 19674 as yet unmatched pairs. 9229 records in RAM.
INFO 2026-06-08 07:53:37 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 3s. Last read position: chrX:41,727,347
INFO 2026-06-08 07:53:37 MarkDuplicates Tracking 18081 as yet unmatched pairs. 7555 records in RAM.
INFO 2026-06-08 07:53:40 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 2s. Last read position: chrX:54,549,855
INFO 2026-06-08 07:53:40 MarkDuplicates Tracking 16434 as yet unmatched pairs. 5901 records in RAM.
INFO 2026-06-08 07:53:43 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:09:11s. Time for last 1,000,000: 2s. Last read position: chrX:85,984,239
INFO 2026-06-08 07:53:43 MarkDuplicates Tracking 14806 as yet unmatched pairs. 4270 records in RAM.
INFO 2026-06-08 07:53:46 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:09:13s. Time for last 1,000,000: 2s. Last read position: chrX:130,013,658
INFO 2026-06-08 07:53:46 MarkDuplicates Tracking 13348 as yet unmatched pairs. 2811 records in RAM.
INFO 2026-06-08 07:53:48 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 2s. Last read position: chrX:154,360,356
INFO 2026-06-08 07:53:48 MarkDuplicates Tracking 11381 as yet unmatched pairs. 834 records in RAM.
INFO 2026-06-08 07:53:50 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:09:18s. Time for last 1,000,000: 2s. Last read position: GL000220.1:109,774
INFO 2026-06-08 07:53:50 MarkDuplicates Tracking 10023 as yet unmatched pairs. 1908 records in RAM.
INFO 2026-06-08 07:53:52 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 1s. Last read position: GL000220.1:114,510
INFO 2026-06-08 07:53:52 MarkDuplicates Tracking 9792 as yet unmatched pairs. 1677 records in RAM.
INFO 2026-06-08 07:53:54 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 1s. Last read position: GL000220.1:116,465
INFO 2026-06-08 07:53:54 MarkDuplicates Tracking 8271 as yet unmatched pairs. 154 records in RAM.
INFO 2026-06-08 07:53:56 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:09:24s. Time for last 1,000,000: 2s. Last read position: GL000220.1:157,857
INFO 2026-06-08 07:53:56 MarkDuplicates Tracking 8267 as yet unmatched pairs. 150 records in RAM.
INFO 2026-06-08 07:53:59 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:09:27s. Time for last 1,000,000: 2s. Last read position: GL000220.1:159,541
INFO 2026-06-08 07:53:59 MarkDuplicates Tracking 8134 as yet unmatched pairs. 17 records in RAM.
INFO 2026-06-08 07:54:00 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:09:28s. Time for last 1,000,000: 1s. Last read position: GL000220.1:160,766
INFO 2026-06-08 07:54:00 MarkDuplicates Tracking 8118 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 07:54:03 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:09:31s. Time for last 1,000,000: 2s. Last read position: KI270733.1:131,015
INFO 2026-06-08 07:54:03 MarkDuplicates Tracking 6302 as yet unmatched pairs. 6275 records in RAM.
INFO 2026-06-08 07:54:05 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:09:33s. Time for last 1,000,000: 2s. Last read position: KI270733.1:133,168
INFO 2026-06-08 07:54:05 MarkDuplicates Tracking 2196 as yet unmatched pairs. 2169 records in RAM.
INFO 2026-06-08 07:54:08 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 2s. Last read position: KI270733.1:134,977
INFO 2026-06-08 07:54:08 MarkDuplicates Tracking 717 as yet unmatched pairs. 690 records in RAM.
INFO 2026-06-08 07:54:10 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:09:38s. Time for last 1,000,000: 2s. Last read position: KI270733.1:176,129
INFO 2026-06-08 07:54:10 MarkDuplicates Tracking 186 as yet unmatched pairs. 159 records in RAM.
INFO 2026-06-08 07:54:12 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:09:39s. Time for last 1,000,000: 1s. Last read position: KI270733.1:178,267
INFO 2026-06-08 07:54:12 MarkDuplicates Tracking 76 as yet unmatched pairs. 49 records in RAM.
INFO 2026-06-08 07:54:13 MarkDuplicates Read 213773063 records. 0 pairs never matched.
INFO 2026-06-08 07:54:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 38068793160; totalMemory: 60028878848; maxMemory: 63585648640
INFO 2026-06-08 07:54:26 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 07:54:34 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 07:54:49 OpticalDuplicateFinder Large duplicate set. size = 1073
INFO 2026-06-08 07:54:49 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,398
INFO 2026-06-08 07:54:49 OpticalDuplicateFinder Large duplicate set. size = 1874
INFO 2026-06-08 07:54:49 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,935
INFO 2026-06-08 07:54:49 OpticalDuplicateFinder Large duplicate set. size = 3714
INFO 2026-06-08 07:54:49 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,243
INFO 2026-06-08 07:54:49 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,341
INFO 2026-06-08 07:54:49 OpticalDuplicateFinder compared 3,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,167
INFO 2026-06-08 07:54:49 OpticalDuplicateFinder Large duplicate set. size = 3343
INFO 2026-06-08 07:54:49 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,428
INFO 2026-06-08 07:54:49 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:15,441
INFO 2026-06-08 07:54:49 OpticalDuplicateFinder compared 3,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,551
INFO 2026-06-08 07:54:49 OpticalDuplicateFinder Large duplicate set. size = 2422
INFO 2026-06-08 07:54:49 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,711
INFO 2026-06-08 07:54:49 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,822
INFO 2026-06-08 07:55:11 OpticalDuplicateFinder Large duplicate set. size = 1426
INFO 2026-06-08 07:55:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,963
INFO 2026-06-08 07:55:11 OpticalDuplicateFinder Large duplicate set. size = 1021
INFO 2026-06-08 07:55:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,630
INFO 2026-06-08 07:55:11 OpticalDuplicateFinder Large duplicate set. size = 1043
INFO 2026-06-08 07:55:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,113
INFO 2026-06-08 07:55:11 OpticalDuplicateFinder Large duplicate set. size = 1017
INFO 2026-06-08 07:55:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:7,448
INFO 2026-06-08 07:55:11 OpticalDuplicateFinder Large duplicate set. size = 1434
INFO 2026-06-08 07:55:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,214
INFO 2026-06-08 07:55:14 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 07:55:36 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 07:55:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300815352; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-08 07:55:42 MarkDuplicates Marking 105020394 records as duplicates.
INFO 2026-06-08 07:55:42 MarkDuplicates Found 1852544 optical duplicate clusters.
INFO 2026-06-08 07:55:42 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 07:56:11 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:28s. Time for last 10,000,000: 28s. Last read position: chr1:148,590,894
INFO 2026-06-08 07:56:40 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:57s. Time for last 10,000,000: 29s. Last read position: chr2:37,007,082
INFO 2026-06-08 07:57:09 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:26s. Time for last 10,000,000: 28s. Last read position: chr2:237,376,947
INFO 2026-06-08 07:57:38 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:55s. Time for last 10,000,000: 28s. Last read position: chr3:194,406,045
INFO 2026-06-08 07:58:07 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:02:24s. Time for last 10,000,000: 29s. Last read position: chr5:110,740,874
INFO 2026-06-08 07:58:35 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:52s. Time for last 10,000,000: 27s. Last read position: chr6:75,156,387
INFO 2026-06-08 07:59:02 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:03:20s. Time for last 10,000,000: 27s. Last read position: chr7:97,966,851
INFO 2026-06-08 07:59:32 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:03:50s. Time for last 10,000,000: 29s. Last read position: chr8:142,664,630
INFO 2026-06-08 08:00:01 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:04:18s. Time for last 10,000,000: 28s. Last read position: chr10:5,906,445
INFO 2026-06-08 08:00:29 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:04:46s. Time for last 10,000,000: 28s. Last read position: chr11:46,320,716
INFO 2026-06-08 08:00:57 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:05:15s. Time for last 10,000,000: 28s. Last read position: chr12:23,950,912
INFO 2026-06-08 08:01:27 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:05:44s. Time for last 10,000,000: 29s. Last read position: chr13:75,621,794
INFO 2026-06-08 08:01:57 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:06:15s. Time for last 10,000,000: 30s. Last read position: chr15:66,499,431
INFO 2026-06-08 08:02:27 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:06:45s. Time for last 10,000,000: 30s. Last read position: chr16:28,380,509
INFO 2026-06-08 08:02:55 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:07:13s. Time for last 10,000,000: 27s. Last read position: chr17:30,776,883
INFO 2026-06-08 08:03:23 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:07:40s. Time for last 10,000,000: 27s. Last read position: chr17:80,995,721
INFO 2026-06-08 08:03:50 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:08:08s. Time for last 10,000,000: 27s. Last read position: chr19:35,786,797
INFO 2026-06-08 08:04:18 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:08:35s. Time for last 10,000,000: 27s. Last read position: chr20:57,709,552
INFO 2026-06-08 08:04:43 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:09:01s. Time for last 10,000,000: 25s. Last read position: chr21:25,975,109
INFO 2026-06-08 08:05:10 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:09:27s. Time for last 10,000,000: 26s. Last read position: chrX:85,984,239
INFO 2026-06-08 08:05:36 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:09:53s. Time for last 10,000,000: 25s. Last read position: KI270733.1:133,168
INFO 2026-06-08 08:05:55 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:05:55 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:05:55 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:05:56 MarkDuplicates Before output close freeMemory: 201705096; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:05:56 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:05:56 MarkDuplicates After output close freeMemory: 104295928; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 08:05:56 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 21.44 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory