Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/ddfcbb0693bc896de23657a14f3eb3/tih_rna_sample_00586_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam
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/1a/024336e116bc083ef08a44cd1b0a70/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/024336e116bc083ef08a44cd1b0a70/.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 tih_rna_sample_00586_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00586_B23MVV7LT4_1.md.bam --METRICS_FILE tih_rna_sample_00586_B23MVV7LT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
08:45:19.144 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Jun 08 08:45:19 GMT 2026] MarkDuplicates --INPUT tih_rna_sample_00586_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00586_B23MVV7LT4_1.md.bam --METRICS_FILE tih_rna_sample_00586_B23MVV7LT4_1.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 08:45:19 GMT 2026] Executing as ?@nf-1a024336e116bc083ef08a44cd1b0a70-974b8-v245l on Linux 6.12.88 amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0
INFO 2026-06-08 08:45:19 MarkDuplicates Start of doWork freeMemory: 105828552; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 08:45:19 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 08:45:19 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 08:45:23 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:1,642,664
INFO 2026-06-08 08:45:23 MarkDuplicates Tracking 3674 as yet unmatched pairs. 435 records in RAM.
INFO 2026-06-08 08:45:26 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 3s. Last read position: chr1:8,358,457
INFO 2026-06-08 08:45:26 MarkDuplicates Tracking 7013 as yet unmatched pairs. 676 records in RAM.
INFO 2026-06-08 08:45:28 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: chr1:11,925,543
INFO 2026-06-08 08:45:28 MarkDuplicates Tracking 9415 as yet unmatched pairs. 237 records in RAM.
INFO 2026-06-08 08:45:30 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: chr1:16,972,462
INFO 2026-06-08 08:45:30 MarkDuplicates Tracking 12188 as yet unmatched pairs. 47 records in RAM.
INFO 2026-06-08 08:45:33 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 2s. Last read position: chr1:20,747,637
INFO 2026-06-08 08:45:33 MarkDuplicates Tracking 15593 as yet unmatched pairs. 680 records in RAM.
INFO 2026-06-08 08:45:36 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 2s. Last read position: chr1:22,639,218
INFO 2026-06-08 08:45:36 MarkDuplicates Tracking 22255 as yet unmatched pairs. 4285 records in RAM.
INFO 2026-06-08 08:45:38 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 2s. Last read position: chr1:25,246,924
INFO 2026-06-08 08:45:38 MarkDuplicates Tracking 21923 as yet unmatched pairs. 1140 records in RAM.
INFO 2026-06-08 08:45:40 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: chr1:27,989,783
INFO 2026-06-08 08:45:40 MarkDuplicates Tracking 23735 as yet unmatched pairs. 162 records in RAM.
INFO 2026-06-08 08:45:42 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 2s. Last read position: chr1:32,334,710
INFO 2026-06-08 08:45:42 MarkDuplicates Tracking 27269 as yet unmatched pairs. 851 records in RAM.
INFO 2026-06-08 08:45:44 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 1s. Last read position: chr1:36,178,549
INFO 2026-06-08 08:45:44 MarkDuplicates Tracking 30018 as yet unmatched pairs. 559 records in RAM.
INFO 2026-06-08 08:45:45 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 1s. Last read position: chr1:40,064,238
INFO 2026-06-08 08:45:45 MarkDuplicates Tracking 33742 as yet unmatched pairs. 1506 records in RAM.
INFO 2026-06-08 08:45:48 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 2s. Last read position: chr1:43,667,925
INFO 2026-06-08 08:45:48 MarkDuplicates Tracking 35357 as yet unmatched pairs. 282 records in RAM.
INFO 2026-06-08 08:45:50 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 1s. Last read position: chr1:47,183,597
INFO 2026-06-08 08:45:50 MarkDuplicates Tracking 38198 as yet unmatched pairs. 319 records in RAM.
INFO 2026-06-08 08:45:51 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 1s. Last read position: chr1:59,832,193
INFO 2026-06-08 08:45:51 MarkDuplicates Tracking 40874 as yet unmatched pairs. 172 records in RAM.
INFO 2026-06-08 08:45:54 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 2s. Last read position: chr1:86,473,488
INFO 2026-06-08 08:45:54 MarkDuplicates Tracking 46811 as yet unmatched pairs. 3678 records in RAM.
INFO 2026-06-08 08:45:56 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 2s. Last read position: chr1:92,834,806
INFO 2026-06-08 08:45:56 MarkDuplicates Tracking 45981 as yet unmatched pairs. 516 records in RAM.
INFO 2026-06-08 08:45:57 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 1s. Last read position: chr1:109,910,744
INFO 2026-06-08 08:45:57 MarkDuplicates Tracking 48025 as yet unmatched pairs. 55 records in RAM.
INFO 2026-06-08 08:45:59 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 1s. Last read position: chr1:114,510,674
INFO 2026-06-08 08:45:59 MarkDuplicates Tracking 52034 as yet unmatched pairs. 1329 records in RAM.
INFO 2026-06-08 08:46:01 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 1s. Last read position: chr1:119,997,157
INFO 2026-06-08 08:46:01 MarkDuplicates Tracking 54564 as yet unmatched pairs. 1264 records in RAM.
INFO 2026-06-08 08:46:03 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chr1:148,558,355
INFO 2026-06-08 08:46:03 MarkDuplicates Tracking 54919 as yet unmatched pairs. 169 records in RAM.
INFO 2026-06-08 08:46:05 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 1s. Last read position: chr1:149,886,335
INFO 2026-06-08 08:46:05 MarkDuplicates Tracking 57549 as yet unmatched pairs. 1361 records in RAM.
INFO 2026-06-08 08:46:06 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 1s. Last read position: chr1:151,316,219
INFO 2026-06-08 08:46:06 MarkDuplicates Tracking 59534 as yet unmatched pairs. 656 records in RAM.
INFO 2026-06-08 08:46:08 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 1s. Last read position: chr1:154,173,096
INFO 2026-06-08 08:46:08 MarkDuplicates Tracking 67241 as yet unmatched pairs. 5708 records in RAM.
INFO 2026-06-08 08:46:10 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 1s. Last read position: chr1:155,186,651
INFO 2026-06-08 08:46:10 MarkDuplicates Tracking 66531 as yet unmatched pairs. 2166 records in RAM.
INFO 2026-06-08 08:46:12 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 2s. Last read position: chr1:156,058,050
INFO 2026-06-08 08:46:12 MarkDuplicates Tracking 66949 as yet unmatched pairs. 286 records in RAM.
INFO 2026-06-08 08:46:14 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 1s. Last read position: chr1:160,205,454
INFO 2026-06-08 08:46:14 MarkDuplicates Tracking 69886 as yet unmatched pairs. 314 records in RAM.
INFO 2026-06-08 08:46:15 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 1s. Last read position: chr1:162,581,369
INFO 2026-06-08 08:46:15 MarkDuplicates Tracking 72658 as yet unmatched pairs. 513 records in RAM.
INFO 2026-06-08 08:46:17 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 1s. Last read position: chr1:171,589,576
INFO 2026-06-08 08:46:17 MarkDuplicates Tracking 75292 as yet unmatched pairs. 522 records in RAM.
INFO 2026-06-08 08:46:19 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 2s. Last read position: chr1:183,550,754
INFO 2026-06-08 08:46:19 MarkDuplicates Tracking 77822 as yet unmatched pairs. 192 records in RAM.
INFO 2026-06-08 08:46:22 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 2s. Last read position: chr1:201,649,267
INFO 2026-06-08 08:46:22 MarkDuplicates Tracking 80507 as yet unmatched pairs. 278 records in RAM.
INFO 2026-06-08 08:46:23 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 1s. Last read position: chr1:205,306,277
INFO 2026-06-08 08:46:23 MarkDuplicates Tracking 83041 as yet unmatched pairs. 57 records in RAM.
INFO 2026-06-08 08:46:25 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 2s. Last read position: chr1:206,932,505
INFO 2026-06-08 08:46:25 MarkDuplicates Tracking 126688 as yet unmatched pairs. 41049 records in RAM.
INFO 2026-06-08 08:46:28 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 2s. Last read position: chr1:206,935,533
INFO 2026-06-08 08:46:28 MarkDuplicates Tracking 144917 as yet unmatched pairs. 55928 records in RAM.
INFO 2026-06-08 08:46:30 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 1s. Last read position: chr1:206,937,582
INFO 2026-06-08 08:46:30 MarkDuplicates Tracking 99653 as yet unmatched pairs. 7938 records in RAM.
INFO 2026-06-08 08:46:32 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 1s. Last read position: chr1:208,045,844
INFO 2026-06-08 08:46:32 MarkDuplicates Tracking 94277 as yet unmatched pairs. 11 records in RAM.
INFO 2026-06-08 08:46:34 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 2s. Last read position: chr1:225,038,694
INFO 2026-06-08 08:46:34 MarkDuplicates Tracking 96887 as yet unmatched pairs. 32 records in RAM.
INFO 2026-06-08 08:46:35 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 1s. Last read position: chr1:230,067,397
INFO 2026-06-08 08:46:35 MarkDuplicates Tracking 100160 as yet unmatched pairs. 61 records in RAM.
INFO 2026-06-08 08:46:37 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 1s. Last read position: chr1:244,863,690
INFO 2026-06-08 08:46:37 MarkDuplicates Tracking 105196 as yet unmatched pairs. 2243 records in RAM.
INFO 2026-06-08 08:46:39 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 2s. Last read position: chr2:11,787,108
INFO 2026-06-08 08:46:39 MarkDuplicates Tracking 106080 as yet unmatched pairs. 105359 records in RAM.
INFO 2026-06-08 08:46:41 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 1s. Last read position: chr2:27,040,070
INFO 2026-06-08 08:46:41 MarkDuplicates Tracking 109532 as yet unmatched pairs. 108793 records in RAM.
INFO 2026-06-08 08:46:44 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 2s. Last read position: chr2:31,386,419
INFO 2026-06-08 08:46:44 MarkDuplicates Tracking 113161 as yet unmatched pairs. 112404 records in RAM.
INFO 2026-06-08 08:46:46 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,264
INFO 2026-06-08 08:46:46 MarkDuplicates Tracking 302466 as yet unmatched pairs. 97492 records in RAM.
INFO 2026-06-08 08:46:48 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,399
INFO 2026-06-08 08:46:48 MarkDuplicates Tracking 869638 as yet unmatched pairs. 55344 records in RAM.
INFO 2026-06-08 08:46:50 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,406
INFO 2026-06-08 08:46:50 MarkDuplicates Tracking 889547 as yet unmatched pairs. 53759 records in RAM.
INFO 2026-06-08 08:46:51 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 1s. Last read position: chr2:42,764,008
INFO 2026-06-08 08:46:51 MarkDuplicates Tracking 946629 as yet unmatched pairs. 47718 records in RAM.
INFO 2026-06-08 08:46:53 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 1s. Last read position: chr2:54,616,256
INFO 2026-06-08 08:46:53 MarkDuplicates Tracking 944207 as yet unmatched pairs. 45270 records in RAM.
INFO 2026-06-08 08:46:55 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 1s. Last read position: chr2:65,016,441
INFO 2026-06-08 08:46:55 MarkDuplicates Tracking 941397 as yet unmatched pairs. 42437 records in RAM.
INFO 2026-06-08 08:46:57 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 1s. Last read position: chr2:74,047,073
INFO 2026-06-08 08:46:57 MarkDuplicates Tracking 939035 as yet unmatched pairs. 40056 records in RAM.
INFO 2026-06-08 08:46:58 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 1s. Last read position: chr2:84,905,698
INFO 2026-06-08 08:46:58 MarkDuplicates Tracking 937075 as yet unmatched pairs. 38090 records in RAM.
INFO 2026-06-08 08:47:00 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 1s. Last read position: chr2:95,906,649
INFO 2026-06-08 08:47:00 MarkDuplicates Tracking 933596 as yet unmatched pairs. 34591 records in RAM.
INFO 2026-06-08 08:47:01 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 1s. Last read position: chr2:101,569,225
INFO 2026-06-08 08:47:01 MarkDuplicates Tracking 930550 as yet unmatched pairs. 31512 records in RAM.
INFO 2026-06-08 08:47:03 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 1s. Last read position: chr2:111,856,654
INFO 2026-06-08 08:47:03 MarkDuplicates Tracking 928706 as yet unmatched pairs. 29644 records in RAM.
INFO 2026-06-08 08:47:05 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 1s. Last read position: chr2:127,709,698
INFO 2026-06-08 08:47:05 MarkDuplicates Tracking 926494 as yet unmatched pairs. 27410 records in RAM.
INFO 2026-06-08 08:47:07 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 1s. Last read position: chr2:157,430,375
INFO 2026-06-08 08:47:07 MarkDuplicates Tracking 923857 as yet unmatched pairs. 24749 records in RAM.
INFO 2026-06-08 08:47:09 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 2s. Last read position: chr2:174,567,152
INFO 2026-06-08 08:47:09 MarkDuplicates Tracking 922587 as yet unmatched pairs. 23451 records in RAM.
INFO 2026-06-08 08:47:12 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 2s. Last read position: chr2:188,999,851
INFO 2026-06-08 08:47:12 MarkDuplicates Tracking 920321 as yet unmatched pairs. 21177 records in RAM.
INFO 2026-06-08 08:47:14 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 1s. Last read position: chr2:197,494,687
INFO 2026-06-08 08:47:14 MarkDuplicates Tracking 917205 as yet unmatched pairs. 18041 records in RAM.
INFO 2026-06-08 08:47:15 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 1s. Last read position: chr2:208,243,172
INFO 2026-06-08 08:47:15 MarkDuplicates Tracking 913585 as yet unmatched pairs. 14402 records in RAM.
INFO 2026-06-08 08:47:17 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 1s. Last read position: chr2:216,415,083
INFO 2026-06-08 08:47:17 MarkDuplicates Tracking 911134 as yet unmatched pairs. 11944 records in RAM.
INFO 2026-06-08 08:47:19 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 1s. Last read position: chr2:219,539,789
INFO 2026-06-08 08:47:19 MarkDuplicates Tracking 908660 as yet unmatched pairs. 9462 records in RAM.
INFO 2026-06-08 08:47:21 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 1s. Last read position: chr2:231,075,530
INFO 2026-06-08 08:47:21 MarkDuplicates Tracking 905534 as yet unmatched pairs. 6322 records in RAM.
INFO 2026-06-08 08:47:22 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 1s. Last read position: chr2:237,376,803
INFO 2026-06-08 08:47:22 MarkDuplicates Tracking 903264 as yet unmatched pairs. 4024 records in RAM.
INFO 2026-06-08 08:47:24 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 1s. Last read position: chr2:241,633,817
INFO 2026-06-08 08:47:24 MarkDuplicates Tracking 899886 as yet unmatched pairs. 632 records in RAM.
INFO 2026-06-08 08:47:26 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 1s. Last read position: chr3:12,584,577
INFO 2026-06-08 08:47:26 MarkDuplicates Tracking 897655 as yet unmatched pairs. 54746 records in RAM.
INFO 2026-06-08 08:47:28 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 1s. Last read position: chr3:31,533,298
INFO 2026-06-08 08:47:28 MarkDuplicates Tracking 894904 as yet unmatched pairs. 51972 records in RAM.
INFO 2026-06-08 08:47:30 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 1s. Last read position: chr3:40,462,127
INFO 2026-06-08 08:47:30 MarkDuplicates Tracking 891397 as yet unmatched pairs. 48450 records in RAM.
INFO 2026-06-08 08:47:31 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 1s. Last read position: chr3:47,002,446
INFO 2026-06-08 08:47:31 MarkDuplicates Tracking 888862 as yet unmatched pairs. 45877 records in RAM.
INFO 2026-06-08 08:47:33 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 2s. Last read position: chr3:48,685,728
INFO 2026-06-08 08:47:33 MarkDuplicates Tracking 885427 as yet unmatched pairs. 42428 records in RAM.
INFO 2026-06-08 08:47:35 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 1s. Last read position: chr3:49,732,897
INFO 2026-06-08 08:47:35 MarkDuplicates Tracking 882516 as yet unmatched pairs. 39508 records in RAM.
INFO 2026-06-08 08:47:36 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 1s. Last read position: chr3:52,292,291
INFO 2026-06-08 08:47:36 MarkDuplicates Tracking 879857 as yet unmatched pairs. 36819 records in RAM.
INFO 2026-06-08 08:47:38 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 1s. Last read position: chr3:57,757,603
INFO 2026-06-08 08:47:38 MarkDuplicates Tracking 876741 as yet unmatched pairs. 33689 records in RAM.
INFO 2026-06-08 08:47:40 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 2s. Last read position: chr3:88,055,377
INFO 2026-06-08 08:47:40 MarkDuplicates Tracking 873903 as yet unmatched pairs. 30842 records in RAM.
INFO 2026-06-08 08:47:42 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 1s. Last read position: chr3:119,216,243
INFO 2026-06-08 08:47:42 MarkDuplicates Tracking 871521 as yet unmatched pairs. 28438 records in RAM.
INFO 2026-06-08 08:47:43 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr3:124,910,430
INFO 2026-06-08 08:47:43 MarkDuplicates Tracking 879216 as yet unmatched pairs. 36123 records in RAM.
INFO 2026-06-08 08:47:45 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 2s. Last read position: chr3:129,315,457
INFO 2026-06-08 08:47:45 MarkDuplicates Tracking 866210 as yet unmatched pairs. 23103 records in RAM.
INFO 2026-06-08 08:47:47 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 1s. Last read position: chr3:142,694,416
INFO 2026-06-08 08:47:47 MarkDuplicates Tracking 864173 as yet unmatched pairs. 21051 records in RAM.
INFO 2026-06-08 08:47:48 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 1s. Last read position: chr3:169,966,825
INFO 2026-06-08 08:47:48 MarkDuplicates Tracking 860750 as yet unmatched pairs. 17611 records in RAM.
INFO 2026-06-08 08:47:50 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 1s. Last read position: chr3:184,317,330
INFO 2026-06-08 08:47:50 MarkDuplicates Tracking 859759 as yet unmatched pairs. 16607 records in RAM.
INFO 2026-06-08 08:47:52 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 1s. Last read position: chr3:194,672,064
INFO 2026-06-08 08:47:52 MarkDuplicates Tracking 855558 as yet unmatched pairs. 12387 records in RAM.
INFO 2026-06-08 08:47:53 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 1s. Last read position: chr3:195,778,936
INFO 2026-06-08 08:47:53 MarkDuplicates Tracking 862502 as yet unmatched pairs. 19317 records in RAM.
INFO 2026-06-08 08:47:55 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 1s. Last read position: chr3:195,780,555
INFO 2026-06-08 08:47:55 MarkDuplicates Tracking 881541 as yet unmatched pairs. 38352 records in RAM.
INFO 2026-06-08 08:47:56 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 1s. Last read position: chr3:195,781,765
INFO 2026-06-08 08:47:56 MarkDuplicates Tracking 886199 as yet unmatched pairs. 43006 records in RAM.
INFO 2026-06-08 08:47:58 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 2s. Last read position: chr3:195,783,183
INFO 2026-06-08 08:47:58 MarkDuplicates Tracking 883070 as yet unmatched pairs. 39869 records in RAM.
INFO 2026-06-08 08:47:59 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 1s. Last read position: chr3:195,784,770
INFO 2026-06-08 08:47:59 MarkDuplicates Tracking 884842 as yet unmatched pairs. 41641 records in RAM.
INFO 2026-06-08 08:48:01 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 1s. Last read position: chr3:195,786,129
INFO 2026-06-08 08:48:01 MarkDuplicates Tracking 870272 as yet unmatched pairs. 27057 records in RAM.
INFO 2026-06-08 08:48:03 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 1s. Last read position: chr3:195,788,790
INFO 2026-06-08 08:48:03 MarkDuplicates Tracking 851466 as yet unmatched pairs. 8242 records in RAM.
INFO 2026-06-08 08:48:05 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 2s. Last read position: chr3:197,855,507
INFO 2026-06-08 08:48:05 MarkDuplicates Tracking 843503 as yet unmatched pairs. 258 records in RAM.
INFO 2026-06-08 08:48:07 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 2s. Last read position: chr4:2,261,737
INFO 2026-06-08 08:48:07 MarkDuplicates Tracking 840844 as yet unmatched pairs. 23983 records in RAM.
INFO 2026-06-08 08:48:09 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 1s. Last read position: chr4:10,097,749
INFO 2026-06-08 08:48:09 MarkDuplicates Tracking 837933 as yet unmatched pairs. 21043 records in RAM.
INFO 2026-06-08 08:48:11 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 1s. Last read position: chr4:39,458,210
INFO 2026-06-08 08:48:11 MarkDuplicates Tracking 834874 as yet unmatched pairs. 17960 records in RAM.
INFO 2026-06-08 08:48:12 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 1s. Last read position: chr4:56,931,172
INFO 2026-06-08 08:48:12 MarkDuplicates Tracking 832380 as yet unmatched pairs. 15446 records in RAM.
INFO 2026-06-08 08:48:14 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 1s. Last read position: chr4:75,657,568
INFO 2026-06-08 08:48:14 MarkDuplicates Tracking 829666 as yet unmatched pairs. 12719 records in RAM.
INFO 2026-06-08 08:48:16 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 1s. Last read position: chr4:87,115,081
INFO 2026-06-08 08:48:16 MarkDuplicates Tracking 827210 as yet unmatched pairs. 10246 records in RAM.
INFO 2026-06-08 08:48:17 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 1s. Last read position: chr4:112,587,828
INFO 2026-06-08 08:48:17 MarkDuplicates Tracking 824096 as yet unmatched pairs. 7116 records in RAM.
INFO 2026-06-08 08:48:19 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 1s. Last read position: chr4:145,119,972
INFO 2026-06-08 08:48:19 MarkDuplicates Tracking 821817 as yet unmatched pairs. 4826 records in RAM.
INFO 2026-06-08 08:48:21 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 1s. Last read position: chr4:168,894,667
INFO 2026-06-08 08:48:21 MarkDuplicates Tracking 819394 as yet unmatched pairs. 2385 records in RAM.
INFO 2026-06-08 08:48:23 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 2s. Last read position: chr5:1,002,167
INFO 2026-06-08 08:48:23 MarkDuplicates Tracking 816102 as yet unmatched pairs. 41285 records in RAM.
INFO 2026-06-08 08:48:24 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 1s. Last read position: chr5:14,487,548
INFO 2026-06-08 08:48:24 MarkDuplicates Tracking 814056 as yet unmatched pairs. 39226 records in RAM.
INFO 2026-06-08 08:48:26 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 1s. Last read position: chr5:42,728,286
INFO 2026-06-08 08:48:26 MarkDuplicates Tracking 810623 as yet unmatched pairs. 35767 records in RAM.
INFO 2026-06-08 08:48:28 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 1s. Last read position: chr5:69,894,594
INFO 2026-06-08 08:48:28 MarkDuplicates Tracking 808224 as yet unmatched pairs. 33340 records in RAM.
INFO 2026-06-08 08:48:29 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 1s. Last read position: chr5:82,276,489
INFO 2026-06-08 08:48:29 MarkDuplicates Tracking 812452 as yet unmatched pairs. 37522 records in RAM.
INFO 2026-06-08 08:48:31 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 1s. Last read position: chr5:113,001,402
INFO 2026-06-08 08:48:31 MarkDuplicates Tracking 803832 as yet unmatched pairs. 28887 records in RAM.
INFO 2026-06-08 08:48:32 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 1s. Last read position: chr5:132,618,241
INFO 2026-06-08 08:48:32 MarkDuplicates Tracking 800940 as yet unmatched pairs. 25982 records in RAM.
INFO 2026-06-08 08:48:35 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 2s. Last read position: chr5:138,557,876
INFO 2026-06-08 08:48:35 MarkDuplicates Tracking 798765 as yet unmatched pairs. 23798 records in RAM.
INFO 2026-06-08 08:48:37 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 1s. Last read position: chr5:141,580,872
INFO 2026-06-08 08:48:37 MarkDuplicates Tracking 795744 as yet unmatched pairs. 20755 records in RAM.
INFO 2026-06-08 08:48:38 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 1s. Last read position: chr5:150,132,863
INFO 2026-06-08 08:48:38 MarkDuplicates Tracking 793187 as yet unmatched pairs. 18175 records in RAM.
INFO 2026-06-08 08:48:40 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 2s. Last read position: chr5:150,405,113
INFO 2026-06-08 08:48:40 MarkDuplicates Tracking 833377 as yet unmatched pairs. 58360 records in RAM.
INFO 2026-06-08 08:48:43 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 2s. Last read position: chr5:151,032,326
INFO 2026-06-08 08:48:43 MarkDuplicates Tracking 787568 as yet unmatched pairs. 12537 records in RAM.
INFO 2026-06-08 08:48:45 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 2s. Last read position: chr5:160,612,779
INFO 2026-06-08 08:48:45 MarkDuplicates Tracking 785858 as yet unmatched pairs. 10805 records in RAM.
INFO 2026-06-08 08:48:47 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 1s. Last read position: chr5:176,238,477
INFO 2026-06-08 08:48:47 MarkDuplicates Tracking 781853 as yet unmatched pairs. 6783 records in RAM.
INFO 2026-06-08 08:48:49 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 1s. Last read position: chr5:178,222,851
INFO 2026-06-08 08:48:49 MarkDuplicates Tracking 779363 as yet unmatched pairs. 4281 records in RAM.
INFO 2026-06-08 08:48:51 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 1s. Last read position: chr5:180,791,902
INFO 2026-06-08 08:48:51 MarkDuplicates Tracking 776826 as yet unmatched pairs. 1723 records in RAM.
INFO 2026-06-08 08:48:53 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 2s. Last read position: chr6:7,230,656
INFO 2026-06-08 08:48:53 MarkDuplicates Tracking 774876 as yet unmatched pairs. 52485 records in RAM.
INFO 2026-06-08 08:48:54 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 1s. Last read position: chr6:18,132,142
INFO 2026-06-08 08:48:54 MarkDuplicates Tracking 770749 as yet unmatched pairs. 48350 records in RAM.
INFO 2026-06-08 08:48:56 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 1s. Last read position: chr6:26,217,255
INFO 2026-06-08 08:48:56 MarkDuplicates Tracking 768085 as yet unmatched pairs. 45673 records in RAM.
INFO 2026-06-08 08:48:58 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 1s. Last read position: chr6:27,831,207
INFO 2026-06-08 08:48:58 MarkDuplicates Tracking 768077 as yet unmatched pairs. 45651 records in RAM.
INFO 2026-06-08 08:49:00 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 1s. Last read position: chr6:29,944,554
INFO 2026-06-08 08:49:00 MarkDuplicates Tracking 779047 as yet unmatched pairs. 56616 records in RAM.
INFO 2026-06-08 08:49:01 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 1s. Last read position: chr6:31,156,787
INFO 2026-06-08 08:49:01 MarkDuplicates Tracking 760579 as yet unmatched pairs. 38137 records in RAM.
INFO 2026-06-08 08:49:03 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 1s. Last read position: chr6:31,632,354
INFO 2026-06-08 08:49:03 MarkDuplicates Tracking 758066 as yet unmatched pairs. 35608 records in RAM.
INFO 2026-06-08 08:49:04 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 1s. Last read position: chr6:31,874,956
INFO 2026-06-08 08:49:04 MarkDuplicates Tracking 757913 as yet unmatched pairs. 35450 records in RAM.
INFO 2026-06-08 08:49:06 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 1s. Last read position: chr6:32,521,974
INFO 2026-06-08 08:49:06 MarkDuplicates Tracking 755888 as yet unmatched pairs. 33413 records in RAM.
INFO 2026-06-08 08:49:08 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 1s. Last read position: chr6:33,069,221
INFO 2026-06-08 08:49:08 MarkDuplicates Tracking 751832 as yet unmatched pairs. 29348 records in RAM.
INFO 2026-06-08 08:49:09 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 1s. Last read position: chr6:33,678,773
INFO 2026-06-08 08:49:09 MarkDuplicates Tracking 747608 as yet unmatched pairs. 25117 records in RAM.
INFO 2026-06-08 08:49:11 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 1s. Last read position: chr6:37,819,980
INFO 2026-06-08 08:49:11 MarkDuplicates Tracking 745093 as yet unmatched pairs. 22588 records in RAM.
INFO 2026-06-08 08:49:13 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 1s. Last read position: chr6:43,770,967
INFO 2026-06-08 08:49:13 MarkDuplicates Tracking 742399 as yet unmatched pairs. 19864 records in RAM.
INFO 2026-06-08 08:49:14 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 1s. Last read position: chr6:63,211,763
INFO 2026-06-08 08:49:14 MarkDuplicates Tracking 739055 as yet unmatched pairs. 16482 records in RAM.
INFO 2026-06-08 08:49:16 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 1s. Last read position: chr6:89,265,690
INFO 2026-06-08 08:49:16 MarkDuplicates Tracking 736245 as yet unmatched pairs. 13644 records in RAM.
INFO 2026-06-08 08:49:18 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 1s. Last read position: chr6:109,452,596
INFO 2026-06-08 08:49:18 MarkDuplicates Tracking 734175 as yet unmatched pairs. 11550 records in RAM.
INFO 2026-06-08 08:49:20 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 1s. Last read position: chr6:130,956,395
INFO 2026-06-08 08:49:20 MarkDuplicates Tracking 731248 as yet unmatched pairs. 8608 records in RAM.
INFO 2026-06-08 08:49:21 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 1s. Last read position: chr6:144,447,670
INFO 2026-06-08 08:49:21 MarkDuplicates Tracking 728863 as yet unmatched pairs. 6199 records in RAM.
INFO 2026-06-08 08:49:23 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 1s. Last read position: chr6:158,767,115
INFO 2026-06-08 08:49:23 MarkDuplicates Tracking 727237 as yet unmatched pairs. 4554 records in RAM.
INFO 2026-06-08 08:49:24 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 1s. Last read position: chr6:170,282,717
INFO 2026-06-08 08:49:24 MarkDuplicates Tracking 723096 as yet unmatched pairs. 403 records in RAM.
INFO 2026-06-08 08:49:27 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 2s. Last read position: chr7:5,009,080
INFO 2026-06-08 08:49:27 MarkDuplicates Tracking 719462 as yet unmatched pairs. 49228 records in RAM.
INFO 2026-06-08 08:49:28 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 1s. Last read position: chr7:5,529,296
INFO 2026-06-08 08:49:28 MarkDuplicates Tracking 732220 as yet unmatched pairs. 61977 records in RAM.
INFO 2026-06-08 08:49:30 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 1s. Last read position: chr7:26,184,763
INFO 2026-06-08 08:49:30 MarkDuplicates Tracking 714080 as yet unmatched pairs. 43804 records in RAM.
INFO 2026-06-08 08:49:31 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 1s. Last read position: chr7:44,051,835
INFO 2026-06-08 08:49:31 MarkDuplicates Tracking 711935 as yet unmatched pairs. 41621 records in RAM.
INFO 2026-06-08 08:49:33 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 1s. Last read position: chr7:55,202,578
INFO 2026-06-08 08:49:33 MarkDuplicates Tracking 708857 as yet unmatched pairs. 38528 records in RAM.
INFO 2026-06-08 08:49:35 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 1s. Last read position: chr7:73,769,402
INFO 2026-06-08 08:49:35 MarkDuplicates Tracking 709508 as yet unmatched pairs. 39168 records in RAM.
INFO 2026-06-08 08:49:36 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 1s. Last read position: chr7:76,330,170
INFO 2026-06-08 08:49:36 MarkDuplicates Tracking 705019 as yet unmatched pairs. 34649 records in RAM.
INFO 2026-06-08 08:49:38 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 1s. Last read position: chr7:93,994,342
INFO 2026-06-08 08:49:38 MarkDuplicates Tracking 701736 as yet unmatched pairs. 31345 records in RAM.
INFO 2026-06-08 08:49:40 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 1s. Last read position: chr7:99,621,381
INFO 2026-06-08 08:49:40 MarkDuplicates Tracking 698982 as yet unmatched pairs. 28565 records in RAM.
INFO 2026-06-08 08:49:41 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 1s. Last read position: chr7:100,884,477
INFO 2026-06-08 08:49:41 MarkDuplicates Tracking 695799 as yet unmatched pairs. 25379 records in RAM.
INFO 2026-06-08 08:49:43 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 1s. Last read position: chr7:100,993,594
INFO 2026-06-08 08:49:43 MarkDuplicates Tracking 697234 as yet unmatched pairs. 26811 records in RAM.
INFO 2026-06-08 08:49:44 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 1s. Last read position: chr7:100,995,085
INFO 2026-06-08 08:49:44 MarkDuplicates Tracking 696066 as yet unmatched pairs. 25635 records in RAM.
INFO 2026-06-08 08:49:46 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 1s. Last read position: chr7:100,996,397
INFO 2026-06-08 08:49:46 MarkDuplicates Tracking 715474 as yet unmatched pairs. 45043 records in RAM.
INFO 2026-06-08 08:49:47 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr7:100,997,150
INFO 2026-06-08 08:49:47 MarkDuplicates Tracking 706330 as yet unmatched pairs. 35892 records in RAM.
INFO 2026-06-08 08:49:49 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr7:100,998,301
INFO 2026-06-08 08:49:49 MarkDuplicates Tracking 695884 as yet unmatched pairs. 25445 records in RAM.
INFO 2026-06-08 08:49:50 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 1s. Last read position: chr7:100,999,070
INFO 2026-06-08 08:49:50 MarkDuplicates Tracking 700009 as yet unmatched pairs. 29567 records in RAM.
INFO 2026-06-08 08:49:52 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 1s. Last read position: chr7:101,000,176
INFO 2026-06-08 08:49:52 MarkDuplicates Tracking 707157 as yet unmatched pairs. 36711 records in RAM.
INFO 2026-06-08 08:49:54 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 1s. Last read position: chr7:101,001,187
INFO 2026-06-08 08:49:54 MarkDuplicates Tracking 701039 as yet unmatched pairs. 30593 records in RAM.
INFO 2026-06-08 08:49:55 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 1s. Last read position: chr7:101,002,176
INFO 2026-06-08 08:49:55 MarkDuplicates Tracking 691931 as yet unmatched pairs. 21485 records in RAM.
INFO 2026-06-08 08:49:56 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 1s. Last read position: chr7:101,004,353
INFO 2026-06-08 08:49:56 MarkDuplicates Tracking 687044 as yet unmatched pairs. 16598 records in RAM.
INFO 2026-06-08 08:49:58 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 1s. Last read position: chr7:105,074,686
INFO 2026-06-08 08:49:58 MarkDuplicates Tracking 685009 as yet unmatched pairs. 14546 records in RAM.
INFO 2026-06-08 08:49:59 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 1s. Last read position: chr7:127,652,380
INFO 2026-06-08 08:49:59 MarkDuplicates Tracking 687725 as yet unmatched pairs. 17241 records in RAM.
INFO 2026-06-08 08:50:01 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 1s. Last read position: chr7:135,168,849
INFO 2026-06-08 08:50:01 MarkDuplicates Tracking 680311 as yet unmatched pairs. 9820 records in RAM.
INFO 2026-06-08 08:50:03 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 1s. Last read position: chr7:143,268,094
INFO 2026-06-08 08:50:03 MarkDuplicates Tracking 677902 as yet unmatched pairs. 7392 records in RAM.
INFO 2026-06-08 08:50:04 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 1s. Last read position: chr7:150,371,445
INFO 2026-06-08 08:50:04 MarkDuplicates Tracking 675896 as yet unmatched pairs. 5382 records in RAM.
INFO 2026-06-08 08:50:06 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 1s. Last read position: chr7:152,265,187
INFO 2026-06-08 08:50:06 MarkDuplicates Tracking 672381 as yet unmatched pairs. 1862 records in RAM.
INFO 2026-06-08 08:50:08 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 1s. Last read position: chr8:11,850,910
INFO 2026-06-08 08:50:08 MarkDuplicates Tracking 670573 as yet unmatched pairs. 33826 records in RAM.
INFO 2026-06-08 08:50:10 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 1s. Last read position: chr8:23,328,429
INFO 2026-06-08 08:50:10 MarkDuplicates Tracking 666365 as yet unmatched pairs. 29609 records in RAM.
INFO 2026-06-08 08:50:11 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 1s. Last read position: chr8:37,698,302
INFO 2026-06-08 08:50:11 MarkDuplicates Tracking 663296 as yet unmatched pairs. 26525 records in RAM.
INFO 2026-06-08 08:50:13 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 1s. Last read position: chr8:43,069,561
INFO 2026-06-08 08:50:13 MarkDuplicates Tracking 660688 as yet unmatched pairs. 23911 records in RAM.
INFO 2026-06-08 08:50:15 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 1s. Last read position: chr8:67,232,889
INFO 2026-06-08 08:50:15 MarkDuplicates Tracking 657844 as yet unmatched pairs. 21046 records in RAM.
INFO 2026-06-08 08:50:16 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 1s. Last read position: chr8:94,876,132
INFO 2026-06-08 08:50:16 MarkDuplicates Tracking 655302 as yet unmatched pairs. 18470 records in RAM.
INFO 2026-06-08 08:50:18 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 1s. Last read position: chr8:108,228,328
INFO 2026-06-08 08:50:18 MarkDuplicates Tracking 653631 as yet unmatched pairs. 16778 records in RAM.
INFO 2026-06-08 08:50:20 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 1s. Last read position: chr8:140,023,956
INFO 2026-06-08 08:50:20 MarkDuplicates Tracking 650178 as yet unmatched pairs. 13301 records in RAM.
INFO 2026-06-08 08:50:22 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 2s. Last read position: chr8:143,858,303
INFO 2026-06-08 08:50:22 MarkDuplicates Tracking 646797 as yet unmatched pairs. 9898 records in RAM.
INFO 2026-06-08 08:50:23 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 1s. Last read position: chr8:143,862,547
INFO 2026-06-08 08:50:23 MarkDuplicates Tracking 646627 as yet unmatched pairs. 9725 records in RAM.
INFO 2026-06-08 08:50:24 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 1s. Last read position: chr8:143,867,758
INFO 2026-06-08 08:50:24 MarkDuplicates Tracking 645051 as yet unmatched pairs. 8144 records in RAM.
INFO 2026-06-08 08:50:26 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 1s. Last read position: chr8:143,984,662
INFO 2026-06-08 08:50:26 MarkDuplicates Tracking 641933 as yet unmatched pairs. 5020 records in RAM.
INFO 2026-06-08 08:50:27 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 1s. Last read position: chr8:144,614,426
INFO 2026-06-08 08:50:27 MarkDuplicates Tracking 637278 as yet unmatched pairs. 338 records in RAM.
INFO 2026-06-08 08:50:29 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 2s. Last read position: chr9:19,276,207
INFO 2026-06-08 08:50:29 MarkDuplicates Tracking 635253 as yet unmatched pairs. 38274 records in RAM.
INFO 2026-06-08 08:50:31 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 1s. Last read position: chr9:35,077,042
INFO 2026-06-08 08:50:31 MarkDuplicates Tracking 632141 as yet unmatched pairs. 35155 records in RAM.
INFO 2026-06-08 08:50:33 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 1s. Last read position: chr9:68,241,982
INFO 2026-06-08 08:50:33 MarkDuplicates Tracking 629329 as yet unmatched pairs. 32292 records in RAM.
INFO 2026-06-08 08:50:35 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 1s. Last read position: chr9:86,308,559
INFO 2026-06-08 08:50:35 MarkDuplicates Tracking 627062 as yet unmatched pairs. 30024 records in RAM.
INFO 2026-06-08 08:50:36 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 1s. Last read position: chr9:94,374,849
INFO 2026-06-08 08:50:36 MarkDuplicates Tracking 624190 as yet unmatched pairs. 27134 records in RAM.
INFO 2026-06-08 08:50:38 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 1s. Last read position: chr9:108,893,042
INFO 2026-06-08 08:50:38 MarkDuplicates Tracking 621109 as yet unmatched pairs. 24028 records in RAM.
INFO 2026-06-08 08:50:40 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 2s. Last read position: chr9:116,219,945
INFO 2026-06-08 08:50:40 MarkDuplicates Tracking 618118 as yet unmatched pairs. 21027 records in RAM.
INFO 2026-06-08 08:50:42 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 1s. Last read position: chr9:125,240,871
INFO 2026-06-08 08:50:42 MarkDuplicates Tracking 619198 as yet unmatched pairs. 22085 records in RAM.
INFO 2026-06-08 08:50:44 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 2s. Last read position: chr9:128,151,929
INFO 2026-06-08 08:50:44 MarkDuplicates Tracking 623752 as yet unmatched pairs. 26611 records in RAM.
INFO 2026-06-08 08:50:46 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 2s. Last read position: chr9:129,008,712
INFO 2026-06-08 08:50:46 MarkDuplicates Tracking 611629 as yet unmatched pairs. 14468 records in RAM.
INFO 2026-06-08 08:50:48 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 1s. Last read position: chr9:131,487,939
INFO 2026-06-08 08:50:48 MarkDuplicates Tracking 607435 as yet unmatched pairs. 10268 records in RAM.
INFO 2026-06-08 08:50:50 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 1s. Last read position: chr9:134,907,430
INFO 2026-06-08 08:50:50 MarkDuplicates Tracking 604018 as yet unmatched pairs. 6828 records in RAM.
INFO 2026-06-08 08:50:51 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 1s. Last read position: chr9:136,908,099
INFO 2026-06-08 08:50:51 MarkDuplicates Tracking 601212 as yet unmatched pairs. 4006 records in RAM.
INFO 2026-06-08 08:50:53 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 1s. Last read position: chr10:286,273
INFO 2026-06-08 08:50:53 MarkDuplicates Tracking 597205 as yet unmatched pairs. 36890 records in RAM.
INFO 2026-06-08 08:50:55 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 1s. Last read position: chr10:14,897,180
INFO 2026-06-08 08:50:55 MarkDuplicates Tracking 594716 as yet unmatched pairs. 34390 records in RAM.
INFO 2026-06-08 08:50:57 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 1s. Last read position: chr10:32,022,922
INFO 2026-06-08 08:50:57 MarkDuplicates Tracking 593320 as yet unmatched pairs. 32984 records in RAM.
INFO 2026-06-08 08:50:58 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 1s. Last read position: chr10:48,010,850
INFO 2026-06-08 08:50:58 MarkDuplicates Tracking 589758 as yet unmatched pairs. 29417 records in RAM.
INFO 2026-06-08 08:51:00 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 1s. Last read position: chr10:70,153,934
INFO 2026-06-08 08:51:00 MarkDuplicates Tracking 587831 as yet unmatched pairs. 27474 records in RAM.
INFO 2026-06-08 08:51:01 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 1s. Last read position: chr10:76,058,733
INFO 2026-06-08 08:51:01 MarkDuplicates Tracking 584398 as yet unmatched pairs. 24030 records in RAM.
INFO 2026-06-08 08:51:03 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 1s. Last read position: chr10:89,414,733
INFO 2026-06-08 08:51:03 MarkDuplicates Tracking 582083 as yet unmatched pairs. 21704 records in RAM.
INFO 2026-06-08 08:51:05 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 1s. Last read position: chr10:97,476,931
INFO 2026-06-08 08:51:05 MarkDuplicates Tracking 579225 as yet unmatched pairs. 18836 records in RAM.
INFO 2026-06-08 08:51:07 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 1s. Last read position: chr10:102,485,604
INFO 2026-06-08 08:51:07 MarkDuplicates Tracking 576166 as yet unmatched pairs. 15765 records in RAM.
INFO 2026-06-08 08:51:08 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 1s. Last read position: chr10:116,968,674
INFO 2026-06-08 08:51:08 MarkDuplicates Tracking 574050 as yet unmatched pairs. 13639 records in RAM.
INFO 2026-06-08 08:51:10 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 2s. Last read position: chr10:122,579,659
INFO 2026-06-08 08:51:10 MarkDuplicates Tracking 581945 as yet unmatched pairs. 21527 records in RAM.
INFO 2026-06-08 08:51:12 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 1s. Last read position: chr10:122,588,989
INFO 2026-06-08 08:51:12 MarkDuplicates Tracking 582434 as yet unmatched pairs. 22016 records in RAM.
INFO 2026-06-08 08:51:14 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 1s. Last read position: chr10:122,598,859
INFO 2026-06-08 08:51:14 MarkDuplicates Tracking 581326 as yet unmatched pairs. 20907 records in RAM.
INFO 2026-06-08 08:51:15 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 1s. Last read position: chr10:122,605,987
INFO 2026-06-08 08:51:15 MarkDuplicates Tracking 578610 as yet unmatched pairs. 18190 records in RAM.
INFO 2026-06-08 08:51:16 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 1s. Last read position: chr10:122,614,188
INFO 2026-06-08 08:51:16 MarkDuplicates Tracking 578852 as yet unmatched pairs. 18432 records in RAM.
INFO 2026-06-08 08:51:18 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 1s. Last read position: chr10:122,640,219
INFO 2026-06-08 08:51:18 MarkDuplicates Tracking 567646 as yet unmatched pairs. 7219 records in RAM.
INFO 2026-06-08 08:51:19 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 1s. Last read position: chr10:133,465,494
INFO 2026-06-08 08:51:19 MarkDuplicates Tracking 560479 as yet unmatched pairs. 33 records in RAM.
INFO 2026-06-08 08:51:22 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 2s. Last read position: chr11:618,812
INFO 2026-06-08 08:51:22 MarkDuplicates Tracking 557914 as yet unmatched pairs. 67138 records in RAM.
INFO 2026-06-08 08:51:23 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 1s. Last read position: chr11:1,082,383
INFO 2026-06-08 08:51:23 MarkDuplicates Tracking 561719 as yet unmatched pairs. 70931 records in RAM.
INFO 2026-06-08 08:51:25 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 1s. Last read position: chr11:1,228,625
INFO 2026-06-08 08:51:25 MarkDuplicates Tracking 553993 as yet unmatched pairs. 63191 records in RAM.
INFO 2026-06-08 08:51:27 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 1s. Last read position: chr11:1,244,538
INFO 2026-06-08 08:51:27 MarkDuplicates Tracking 551277 as yet unmatched pairs. 60471 records in RAM.
INFO 2026-06-08 08:51:28 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 1s. Last read position: chr11:1,248,195
INFO 2026-06-08 08:51:28 MarkDuplicates Tracking 549441 as yet unmatched pairs. 58633 records in RAM.
INFO 2026-06-08 08:51:30 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:06:09s. Time for last 1,000,000: 2s. Last read position: chr11:1,261,490
INFO 2026-06-08 08:51:30 MarkDuplicates Tracking 547305 as yet unmatched pairs. 56493 records in RAM.
INFO 2026-06-08 08:51:32 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 1s. Last read position: chr11:6,223,795
INFO 2026-06-08 08:51:32 MarkDuplicates Tracking 545174 as yet unmatched pairs. 54338 records in RAM.
INFO 2026-06-08 08:51:34 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 1s. Last read position: chr11:11,896,394
INFO 2026-06-08 08:51:34 MarkDuplicates Tracking 540343 as yet unmatched pairs. 49491 records in RAM.
INFO 2026-06-08 08:51:36 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 2s. Last read position: chr11:32,934,941
INFO 2026-06-08 08:51:36 MarkDuplicates Tracking 537800 as yet unmatched pairs. 46938 records in RAM.
INFO 2026-06-08 08:51:38 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 1s. Last read position: chr11:46,316,356
INFO 2026-06-08 08:51:38 MarkDuplicates Tracking 537685 as yet unmatched pairs. 46802 records in RAM.
INFO 2026-06-08 08:51:39 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 1s. Last read position: chr11:57,309,175
INFO 2026-06-08 08:51:39 MarkDuplicates Tracking 533110 as yet unmatched pairs. 42223 records in RAM.
INFO 2026-06-08 08:51:41 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 1s. Last read position: chr11:60,951,114
INFO 2026-06-08 08:51:41 MarkDuplicates Tracking 530037 as yet unmatched pairs. 39135 records in RAM.
INFO 2026-06-08 08:51:43 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 1s. Last read position: chr11:62,572,582
INFO 2026-06-08 08:51:43 MarkDuplicates Tracking 527910 as yet unmatched pairs. 37002 records in RAM.
INFO 2026-06-08 08:51:45 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 1s. Last read position: chr11:64,226,634
INFO 2026-06-08 08:51:45 MarkDuplicates Tracking 524368 as yet unmatched pairs. 33452 records in RAM.
INFO 2026-06-08 08:51:46 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 1s. Last read position: chr11:64,913,274
INFO 2026-06-08 08:51:46 MarkDuplicates Tracking 520680 as yet unmatched pairs. 29761 records in RAM.
INFO 2026-06-08 08:51:48 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 1s. Last read position: chr11:65,641,335
INFO 2026-06-08 08:51:48 MarkDuplicates Tracking 517913 as yet unmatched pairs. 26978 records in RAM.
INFO 2026-06-08 08:51:50 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 1s. Last read position: chr11:66,643,489
INFO 2026-06-08 08:51:50 MarkDuplicates Tracking 514370 as yet unmatched pairs. 23429 records in RAM.
INFO 2026-06-08 08:51:52 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:06:31s. Time for last 1,000,000: 1s. Last read position: chr11:68,036,480
INFO 2026-06-08 08:51:52 MarkDuplicates Tracking 510913 as yet unmatched pairs. 19966 records in RAM.
INFO 2026-06-08 08:51:54 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:06:33s. Time for last 1,000,000: 1s. Last read position: chr11:72,013,724
INFO 2026-06-08 08:51:54 MarkDuplicates Tracking 507802 as yet unmatched pairs. 16850 records in RAM.
INFO 2026-06-08 08:51:55 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 1s. Last read position: chr11:75,404,174
INFO 2026-06-08 08:51:55 MarkDuplicates Tracking 507267 as yet unmatched pairs. 16303 records in RAM.
INFO 2026-06-08 08:51:57 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 1s. Last read position: chr11:94,180,123
INFO 2026-06-08 08:51:57 MarkDuplicates Tracking 501905 as yet unmatched pairs. 10931 records in RAM.
INFO 2026-06-08 08:51:59 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 1s. Last read position: chr11:114,312,327
INFO 2026-06-08 08:51:59 MarkDuplicates Tracking 499440 as yet unmatched pairs. 8461 records in RAM.
INFO 2026-06-08 08:52:00 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 1s. Last read position: chr11:118,901,617
INFO 2026-06-08 08:52:00 MarkDuplicates Tracking 497099 as yet unmatched pairs. 6115 records in RAM.
INFO 2026-06-08 08:52:03 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 2s. Last read position: chr11:124,751,463
INFO 2026-06-08 08:52:03 MarkDuplicates Tracking 495030 as yet unmatched pairs. 4034 records in RAM.
INFO 2026-06-08 08:52:06 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 2s. Last read position: chr11:134,202,832
INFO 2026-06-08 08:52:06 MarkDuplicates Tracking 491345 as yet unmatched pairs. 346 records in RAM.
INFO 2026-06-08 08:52:08 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:06:47s. Time for last 1,000,000: 2s. Last read position: chr12:6,200,468
INFO 2026-06-08 08:52:08 MarkDuplicates Tracking 489757 as yet unmatched pairs. 48760 records in RAM.
INFO 2026-06-08 08:52:09 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 1s. Last read position: chr12:6,940,869
INFO 2026-06-08 08:52:09 MarkDuplicates Tracking 485783 as yet unmatched pairs. 44772 records in RAM.
INFO 2026-06-08 08:52:11 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 1s. Last read position: chr12:11,869,804
INFO 2026-06-08 08:52:11 MarkDuplicates Tracking 484832 as yet unmatched pairs. 43808 records in RAM.
INFO 2026-06-08 08:52:13 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 1s. Last read position: chr12:29,311,047
INFO 2026-06-08 08:52:13 MarkDuplicates Tracking 480587 as yet unmatched pairs. 39559 records in RAM.
INFO 2026-06-08 08:52:15 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 1s. Last read position: chr12:48,836,132
INFO 2026-06-08 08:52:15 MarkDuplicates Tracking 477957 as yet unmatched pairs. 36917 records in RAM.
INFO 2026-06-08 08:52:16 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 1s. Last read position: chr12:49,759,239
INFO 2026-06-08 08:52:16 MarkDuplicates Tracking 477484 as yet unmatched pairs. 36442 records in RAM.
INFO 2026-06-08 08:52:18 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:06:57s. Time for last 1,000,000: 1s. Last read position: chr12:53,295,552
INFO 2026-06-08 08:52:18 MarkDuplicates Tracking 472345 as yet unmatched pairs. 31298 records in RAM.
INFO 2026-06-08 08:52:20 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 1s. Last read position: chr12:55,938,971
INFO 2026-06-08 08:52:20 MarkDuplicates Tracking 469932 as yet unmatched pairs. 28885 records in RAM.
INFO 2026-06-08 08:52:22 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 1s. Last read position: chr12:56,614,051
INFO 2026-06-08 08:52:22 MarkDuplicates Tracking 468028 as yet unmatched pairs. 26966 records in RAM.
INFO 2026-06-08 08:52:23 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 1s. Last read position: chr12:57,196,095
INFO 2026-06-08 08:52:23 MarkDuplicates Tracking 465516 as yet unmatched pairs. 24451 records in RAM.
INFO 2026-06-08 08:52:26 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 3s. Last read position: chr12:64,721,679
INFO 2026-06-08 08:52:26 MarkDuplicates Tracking 462166 as yet unmatched pairs. 21095 records in RAM.
INFO 2026-06-08 08:52:28 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:07:07s. Time for last 1,000,000: 1s. Last read position: chr12:89,522,771
INFO 2026-06-08 08:52:28 MarkDuplicates Tracking 459764 as yet unmatched pairs. 18674 records in RAM.
INFO 2026-06-08 08:52:30 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:07:09s. Time for last 1,000,000: 1s. Last read position: chr12:103,946,686
INFO 2026-06-08 08:52:30 MarkDuplicates Tracking 458959 as yet unmatched pairs. 17868 records in RAM.
INFO 2026-06-08 08:52:31 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:07:11s. Time for last 1,000,000: 1s. Last read position: chr12:110,492,065
INFO 2026-06-08 08:52:31 MarkDuplicates Tracking 454664 as yet unmatched pairs. 13561 records in RAM.
INFO 2026-06-08 08:52:33 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:07:12s. Time for last 1,000,000: 1s. Last read position: chr12:113,387,006
INFO 2026-06-08 08:52:33 MarkDuplicates Tracking 451162 as yet unmatched pairs. 10053 records in RAM.
INFO 2026-06-08 08:52:35 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:07:14s. Time for last 1,000,000: 1s. Last read position: chr12:120,695,106
INFO 2026-06-08 08:52:35 MarkDuplicates Tracking 448731 as yet unmatched pairs. 7614 records in RAM.
INFO 2026-06-08 08:52:36 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:07:16s. Time for last 1,000,000: 1s. Last read position: chr12:123,423,144
INFO 2026-06-08 08:52:36 MarkDuplicates Tracking 445460 as yet unmatched pairs. 4324 records in RAM.
INFO 2026-06-08 08:52:38 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:07:17s. Time for last 1,000,000: 1s. Last read position: chr12:132,571,504
INFO 2026-06-08 08:52:38 MarkDuplicates Tracking 442901 as yet unmatched pairs. 1754 records in RAM.
INFO 2026-06-08 08:52:40 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:07:19s. Time for last 1,000,000: 1s. Last read position: chr13:27,116,487
INFO 2026-06-08 08:52:40 MarkDuplicates Tracking 440119 as yet unmatched pairs. 15040 records in RAM.
INFO 2026-06-08 08:52:42 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:07:21s. Time for last 1,000,000: 1s. Last read position: chr13:44,434,803
INFO 2026-06-08 08:52:42 MarkDuplicates Tracking 437811 as yet unmatched pairs. 12722 records in RAM.
INFO 2026-06-08 08:52:43 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:07:22s. Time for last 1,000,000: 1s. Last read position: chr13:53,028,951
INFO 2026-06-08 08:52:43 MarkDuplicates Tracking 459603 as yet unmatched pairs. 34506 records in RAM.
INFO 2026-06-08 08:52:45 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:07:24s. Time for last 1,000,000: 2s. Last read position: chr13:71,675,342
INFO 2026-06-08 08:52:45 MarkDuplicates Tracking 432178 as yet unmatched pairs. 7079 records in RAM.
INFO 2026-06-08 08:52:47 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:07:26s. Time for last 1,000,000: 1s. Last read position: chr13:100,668,603
INFO 2026-06-08 08:52:47 MarkDuplicates Tracking 429672 as yet unmatched pairs. 4567 records in RAM.
INFO 2026-06-08 08:52:49 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:07:28s. Time for last 1,000,000: 1s. Last read position: chr13:112,881,783
INFO 2026-06-08 08:52:49 MarkDuplicates Tracking 426549 as yet unmatched pairs. 1432 records in RAM.
INFO 2026-06-08 08:52:51 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:07:30s. Time for last 1,000,000: 2s. Last read position: chr14:21,427,997
INFO 2026-06-08 08:52:51 MarkDuplicates Tracking 423443 as yet unmatched pairs. 33743 records in RAM.
INFO 2026-06-08 08:52:53 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:07:32s. Time for last 1,000,000: 1s. Last read position: chr14:24,138,483
INFO 2026-06-08 08:52:53 MarkDuplicates Tracking 422278 as yet unmatched pairs. 32575 records in RAM.
INFO 2026-06-08 08:52:55 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:07:34s. Time for last 1,000,000: 1s. Last read position: chr14:34,435,262
INFO 2026-06-08 08:52:55 MarkDuplicates Tracking 417809 as yet unmatched pairs. 28099 records in RAM.
INFO 2026-06-08 08:52:56 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:07:36s. Time for last 1,000,000: 1s. Last read position: chr14:52,859,575
INFO 2026-06-08 08:52:56 MarkDuplicates Tracking 415031 as yet unmatched pairs. 25290 records in RAM.
INFO 2026-06-08 08:52:59 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:07:38s. Time for last 1,000,000: 2s. Last read position: chr14:64,216,330
INFO 2026-06-08 08:52:59 MarkDuplicates Tracking 412632 as yet unmatched pairs. 22880 records in RAM.
INFO 2026-06-08 08:53:01 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:07:40s. Time for last 1,000,000: 2s. Last read position: chr14:71,108,655
INFO 2026-06-08 08:53:01 MarkDuplicates Tracking 409928 as yet unmatched pairs. 20150 records in RAM.
INFO 2026-06-08 08:54:05 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:08:44s. Time for last 1,000,000: 64s. Last read position: chr14:77,458,120
INFO 2026-06-08 08:54:05 MarkDuplicates Tracking 407048 as yet unmatched pairs. 17268 records in RAM.
INFO 2026-06-08 08:54:08 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:08:47s. Time for last 1,000,000: 2s. Last read position: chr14:94,111,685
INFO 2026-06-08 08:54:08 MarkDuplicates Tracking 407650 as yet unmatched pairs. 17858 records in RAM.
INFO 2026-06-08 08:54:10 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 1s. Last read position: chr14:102,016,781
INFO 2026-06-08 08:54:10 MarkDuplicates Tracking 401762 as yet unmatched pairs. 11956 records in RAM.
INFO 2026-06-08 08:54:12 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 1s. Last read position: chr14:104,883,931
INFO 2026-06-08 08:54:12 MarkDuplicates Tracking 398573 as yet unmatched pairs. 8759 records in RAM.
INFO 2026-06-08 08:54:14 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:08:53s. Time for last 1,000,000: 1s. Last read position: chr14:105,587,812
INFO 2026-06-08 08:54:14 MarkDuplicates Tracking 407840 as yet unmatched pairs. 18019 records in RAM.
INFO 2026-06-08 08:54:16 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:08:55s. Time for last 1,000,000: 2s. Last read position: chr14:105,707,415
INFO 2026-06-08 08:54:16 MarkDuplicates Tracking 405802 as yet unmatched pairs. 15979 records in RAM.
INFO 2026-06-08 08:54:18 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:08:57s. Time for last 1,000,000: 2s. Last read position: chr14:105,855,794
INFO 2026-06-08 08:54:18 MarkDuplicates Tracking 396161 as yet unmatched pairs. 6337 records in RAM.
INFO 2026-06-08 08:54:20 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:08:59s. Time for last 1,000,000: 2s. Last read position: chr15:30,092,077
INFO 2026-06-08 08:54:20 MarkDuplicates Tracking 388480 as yet unmatched pairs. 32846 records in RAM.
INFO 2026-06-08 08:54:22 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:09:01s. Time for last 1,000,000: 1s. Last read position: chr15:40,001,043
INFO 2026-06-08 08:54:22 MarkDuplicates Tracking 386212 as yet unmatched pairs. 30575 records in RAM.
INFO 2026-06-08 08:54:24 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:09:04s. Time for last 1,000,000: 2s. Last read position: chr15:42,694,075
INFO 2026-06-08 08:54:24 MarkDuplicates Tracking 383416 as yet unmatched pairs. 27771 records in RAM.
INFO 2026-06-08 08:54:26 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 1s. Last read position: chr15:44,847,412
INFO 2026-06-08 08:54:26 MarkDuplicates Tracking 380980 as yet unmatched pairs. 25329 records in RAM.
INFO 2026-06-08 08:54:28 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 2s. Last read position: chr15:45,106,279
INFO 2026-06-08 08:54:28 MarkDuplicates Tracking 382643 as yet unmatched pairs. 26990 records in RAM.
INFO 2026-06-08 08:54:31 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:09:10s. Time for last 1,000,000: 2s. Last read position: chr15:45,135,781
INFO 2026-06-08 08:54:31 MarkDuplicates Tracking 377228 as yet unmatched pairs. 21573 records in RAM.
INFO 2026-06-08 08:54:34 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:09:13s. Time for last 1,000,000: 3s. Last read position: chr15:58,888,524
INFO 2026-06-08 08:54:34 MarkDuplicates Tracking 372581 as yet unmatched pairs. 16920 records in RAM.
INFO 2026-06-08 08:54:36 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:09:15s. Time for last 1,000,000: 1s. Last read position: chr15:64,162,114
INFO 2026-06-08 08:54:36 MarkDuplicates Tracking 372702 as yet unmatched pairs. 17037 records in RAM.
INFO 2026-06-08 08:54:38 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:09:17s. Time for last 1,000,000: 1s. Last read position: chr15:72,217,441
INFO 2026-06-08 08:54:38 MarkDuplicates Tracking 368020 as yet unmatched pairs. 12345 records in RAM.
INFO 2026-06-08 08:54:39 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:09:19s. Time for last 1,000,000: 1s. Last read position: chr15:75,211,053
INFO 2026-06-08 08:54:39 MarkDuplicates Tracking 364054 as yet unmatched pairs. 8365 records in RAM.
INFO 2026-06-08 08:54:41 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:09:21s. Time for last 1,000,000: 1s. Last read position: chr15:82,524,301
INFO 2026-06-08 08:54:41 MarkDuplicates Tracking 360980 as yet unmatched pairs. 5283 records in RAM.
INFO 2026-06-08 08:54:43 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 1s. Last read position: chr15:90,230,379
INFO 2026-06-08 08:54:43 MarkDuplicates Tracking 359401 as yet unmatched pairs. 3699 records in RAM.
INFO 2026-06-08 08:54:45 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 2s. Last read position: chr16:36,219
INFO 2026-06-08 08:54:45 MarkDuplicates Tracking 355719 as yet unmatched pairs. 56118 records in RAM.
INFO 2026-06-08 08:54:47 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:09:26s. Time for last 1,000,000: 1s. Last read position: chr16:1,451,789
INFO 2026-06-08 08:54:47 MarkDuplicates Tracking 352453 as yet unmatched pairs. 52844 records in RAM.
INFO 2026-06-08 08:54:49 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:09:28s. Time for last 1,000,000: 1s. Last read position: chr16:2,234,626
INFO 2026-06-08 08:54:49 MarkDuplicates Tracking 348845 as yet unmatched pairs. 49231 records in RAM.
INFO 2026-06-08 08:54:51 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:09:31s. Time for last 1,000,000: 2s. Last read position: chr16:2,972,939
INFO 2026-06-08 08:54:51 MarkDuplicates Tracking 345926 as yet unmatched pairs. 46311 records in RAM.
INFO 2026-06-08 08:54:54 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:09:33s. Time for last 1,000,000: 2s. Last read position: chr16:5,025,594
INFO 2026-06-08 08:54:54 MarkDuplicates Tracking 342832 as yet unmatched pairs. 43215 records in RAM.
INFO 2026-06-08 08:54:56 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 1s. Last read position: chr16:14,857,286
INFO 2026-06-08 08:54:56 MarkDuplicates Tracking 340134 as yet unmatched pairs. 40509 records in RAM.
INFO 2026-06-08 08:54:57 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:09:36s. Time for last 1,000,000: 1s. Last read position: chr16:16,322,743
INFO 2026-06-08 08:54:57 MarkDuplicates Tracking 338316 as yet unmatched pairs. 38689 records in RAM.
INFO 2026-06-08 08:54:59 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:09:38s. Time for last 1,000,000: 1s. Last read position: chr16:18,868,208
INFO 2026-06-08 08:54:59 MarkDuplicates Tracking 336530 as yet unmatched pairs. 36901 records in RAM.
INFO 2026-06-08 08:55:01 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:09:40s. Time for last 1,000,000: 1s. Last read position: chr16:21,834,940
INFO 2026-06-08 08:55:01 MarkDuplicates Tracking 334747 as yet unmatched pairs. 35117 records in RAM.
INFO 2026-06-08 08:55:02 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:09:41s. Time for last 1,000,000: 1s. Last read position: chr16:22,534,903
INFO 2026-06-08 08:55:02 MarkDuplicates Tracking 334504 as yet unmatched pairs. 34872 records in RAM.
INFO 2026-06-08 08:55:04 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:09:43s. Time for last 1,000,000: 1s. Last read position: chr16:28,482,659
INFO 2026-06-08 08:55:04 MarkDuplicates Tracking 332563 as yet unmatched pairs. 32927 records in RAM.
INFO 2026-06-08 08:55:06 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:09:45s. Time for last 1,000,000: 1s. Last read position: chr16:29,449,208
INFO 2026-06-08 08:55:06 MarkDuplicates Tracking 332008 as yet unmatched pairs. 32369 records in RAM.
INFO 2026-06-08 08:55:08 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:09:47s. Time for last 1,000,000: 1s. Last read position: chr16:29,963,566
INFO 2026-06-08 08:55:08 MarkDuplicates Tracking 328059 as yet unmatched pairs. 28412 records in RAM.
INFO 2026-06-08 08:55:10 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:09:49s. Time for last 1,000,000: 2s. Last read position: chr16:30,343,149
INFO 2026-06-08 08:55:10 MarkDuplicates Tracking 325555 as yet unmatched pairs. 25907 records in RAM.
INFO 2026-06-08 08:55:12 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:09:51s. Time for last 1,000,000: 2s. Last read position: chr16:31,078,194
INFO 2026-06-08 08:55:12 MarkDuplicates Tracking 322493 as yet unmatched pairs. 22842 records in RAM.
INFO 2026-06-08 08:55:14 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:09:53s. Time for last 1,000,000: 1s. Last read position: chr16:51,646,497
INFO 2026-06-08 08:55:14 MarkDuplicates Tracking 319570 as yet unmatched pairs. 19912 records in RAM.
INFO 2026-06-08 08:55:16 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:09:55s. Time for last 1,000,000: 2s. Last read position: chr16:57,755,119
INFO 2026-06-08 08:55:16 MarkDuplicates Tracking 316934 as yet unmatched pairs. 17262 records in RAM.
INFO 2026-06-08 08:55:18 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:09:57s. Time for last 1,000,000: 2s. Last read position: chr16:67,675,084
INFO 2026-06-08 08:55:18 MarkDuplicates Tracking 313865 as yet unmatched pairs. 14181 records in RAM.
INFO 2026-06-08 08:55:20 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 2s. Last read position: chr16:70,254,030
INFO 2026-06-08 08:55:20 MarkDuplicates Tracking 311734 as yet unmatched pairs. 12044 records in RAM.
INFO 2026-06-08 08:55:23 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:10:02s. Time for last 1,000,000: 3s. Last read position: chr16:75,648,237
INFO 2026-06-08 08:55:23 MarkDuplicates Tracking 308328 as yet unmatched pairs. 8633 records in RAM.
INFO 2026-06-08 08:55:25 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:10:04s. Time for last 1,000,000: 1s. Last read position: chr16:87,834,335
INFO 2026-06-08 08:55:25 MarkDuplicates Tracking 305320 as yet unmatched pairs. 5613 records in RAM.
INFO 2026-06-08 08:55:27 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 1s. Last read position: chr16:89,300,647
INFO 2026-06-08 08:55:27 MarkDuplicates Tracking 302060 as yet unmatched pairs. 2350 records in RAM.
INFO 2026-06-08 08:55:29 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:10:08s. Time for last 1,000,000: 2s. Last read position: chr17:1,364,904
INFO 2026-06-08 08:55:29 MarkDuplicates Tracking 304034 as yet unmatched pairs. 83434 records in RAM.
INFO 2026-06-08 08:55:31 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:10:10s. Time for last 1,000,000: 1s. Last read position: chr17:3,663,724
INFO 2026-06-08 08:55:31 MarkDuplicates Tracking 296692 as yet unmatched pairs. 76091 records in RAM.
INFO 2026-06-08 08:55:33 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 1s. Last read position: chr17:4,895,801
INFO 2026-06-08 08:55:33 MarkDuplicates Tracking 293096 as yet unmatched pairs. 72488 records in RAM.
INFO 2026-06-08 08:55:35 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:10:14s. Time for last 1,000,000: 1s. Last read position: chr17:7,259,574
INFO 2026-06-08 08:55:35 MarkDuplicates Tracking 289801 as yet unmatched pairs. 69191 records in RAM.
INFO 2026-06-08 08:55:37 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:10:17s. Time for last 1,000,000: 2s. Last read position: chr17:7,851,750
INFO 2026-06-08 08:55:37 MarkDuplicates Tracking 287166 as yet unmatched pairs. 66551 records in RAM.
INFO 2026-06-08 08:55:39 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:10:18s. Time for last 1,000,000: 1s. Last read position: chr17:16,381,152
INFO 2026-06-08 08:55:39 MarkDuplicates Tracking 287271 as yet unmatched pairs. 66655 records in RAM.
INFO 2026-06-08 08:55:41 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:10:20s. Time for last 1,000,000: 1s. Last read position: chr17:19,648,832
INFO 2026-06-08 08:55:41 MarkDuplicates Tracking 281371 as yet unmatched pairs. 60752 records in RAM.
INFO 2026-06-08 08:55:43 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:10:22s. Time for last 1,000,000: 1s. Last read position: chr17:28,357,293
INFO 2026-06-08 08:55:43 MarkDuplicates Tracking 279532 as yet unmatched pairs. 58902 records in RAM.
INFO 2026-06-08 08:55:45 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:10:24s. Time for last 1,000,000: 2s. Last read position: chr17:30,840,677
INFO 2026-06-08 08:55:45 MarkDuplicates Tracking 275671 as yet unmatched pairs. 55039 records in RAM.
INFO 2026-06-08 08:55:47 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 2s. Last read position: chr17:36,527,515
INFO 2026-06-08 08:55:47 MarkDuplicates Tracking 273380 as yet unmatched pairs. 52734 records in RAM.
INFO 2026-06-08 08:55:49 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:10:29s. Time for last 1,000,000: 2s. Last read position: chr17:39,653,627
INFO 2026-06-08 08:55:49 MarkDuplicates Tracking 271106 as yet unmatched pairs. 50458 records in RAM.
INFO 2026-06-08 08:55:51 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:10:31s. Time for last 1,000,000: 1s. Last read position: chr17:40,880,102
INFO 2026-06-08 08:55:51 MarkDuplicates Tracking 268182 as yet unmatched pairs. 47533 records in RAM.
INFO 2026-06-08 08:55:53 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:10:32s. Time for last 1,000,000: 1s. Last read position: chr17:42,838,788
INFO 2026-06-08 08:55:53 MarkDuplicates Tracking 265351 as yet unmatched pairs. 44702 records in RAM.
INFO 2026-06-08 08:55:55 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:10:34s. Time for last 1,000,000: 1s. Last read position: chr17:45,245,098
INFO 2026-06-08 08:55:55 MarkDuplicates Tracking 262599 as yet unmatched pairs. 41950 records in RAM.
INFO 2026-06-08 08:55:57 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:10:36s. Time for last 1,000,000: 1s. Last read position: chr17:47,981,308
INFO 2026-06-08 08:55:57 MarkDuplicates Tracking 260314 as yet unmatched pairs. 39658 records in RAM.
INFO 2026-06-08 08:55:59 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:10:38s. Time for last 1,000,000: 1s. Last read position: chr17:50,188,097
INFO 2026-06-08 08:55:59 MarkDuplicates Tracking 279743 as yet unmatched pairs. 59079 records in RAM.
INFO 2026-06-08 08:56:01 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:10:40s. Time for last 1,000,000: 2s. Last read position: chr17:50,192,674
INFO 2026-06-08 08:56:01 MarkDuplicates Tracking 275399 as yet unmatched pairs. 54734 records in RAM.
INFO 2026-06-08 08:56:03 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:10:42s. Time for last 1,000,000: 2s. Last read position: chr17:50,196,634
INFO 2026-06-08 08:56:03 MarkDuplicates Tracking 269797 as yet unmatched pairs. 49128 records in RAM.
INFO 2026-06-08 08:56:05 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:10:45s. Time for last 1,000,000: 2s. Last read position: chr17:55,403,804
INFO 2026-06-08 08:56:05 MarkDuplicates Tracking 247620 as yet unmatched pairs. 26943 records in RAM.
INFO 2026-06-08 08:56:07 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 1s. Last read position: chr17:60,156,618
INFO 2026-06-08 08:56:07 MarkDuplicates Tracking 245296 as yet unmatched pairs. 24607 records in RAM.
INFO 2026-06-08 08:56:09 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:10:48s. Time for last 1,000,000: 1s. Last read position: chr17:65,014,598
INFO 2026-06-08 08:56:09 MarkDuplicates Tracking 242377 as yet unmatched pairs. 21681 records in RAM.
INFO 2026-06-08 08:56:11 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:10:50s. Time for last 1,000,000: 1s. Last read position: chr17:75,039,251
INFO 2026-06-08 08:56:11 MarkDuplicates Tracking 239807 as yet unmatched pairs. 19111 records in RAM.
INFO 2026-06-08 08:56:13 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:10:52s. Time for last 1,000,000: 1s. Last read position: chr17:75,778,661
INFO 2026-06-08 08:56:13 MarkDuplicates Tracking 240429 as yet unmatched pairs. 19733 records in RAM.
INFO 2026-06-08 08:56:15 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:10:54s. Time for last 1,000,000: 2s. Last read position: chr17:78,120,693
INFO 2026-06-08 08:56:15 MarkDuplicates Tracking 234333 as yet unmatched pairs. 13636 records in RAM.
INFO 2026-06-08 08:56:17 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:10:57s. Time for last 1,000,000: 2s. Last read position: chr17:80,288,723
INFO 2026-06-08 08:56:17 MarkDuplicates Tracking 231146 as yet unmatched pairs. 10447 records in RAM.
INFO 2026-06-08 08:56:19 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:10:59s. Time for last 1,000,000: 2s. Last read position: chr17:81,208,972
INFO 2026-06-08 08:56:19 MarkDuplicates Tracking 227159 as yet unmatched pairs. 6453 records in RAM.
INFO 2026-06-08 08:56:21 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:11:01s. Time for last 1,000,000: 2s. Last read position: chr17:81,905,072
INFO 2026-06-08 08:56:21 MarkDuplicates Tracking 224018 as yet unmatched pairs. 3308 records in RAM.
INFO 2026-06-08 08:56:24 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:11:03s. Time for last 1,000,000: 2s. Last read position: chr18:670,735
INFO 2026-06-08 08:56:24 MarkDuplicates Tracking 221164 as yet unmatched pairs. 10601 records in RAM.
INFO 2026-06-08 08:56:26 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:11:05s. Time for last 1,000,000: 2s. Last read position: chr18:23,898,974
INFO 2026-06-08 08:56:26 MarkDuplicates Tracking 218127 as yet unmatched pairs. 7551 records in RAM.
INFO 2026-06-08 08:56:28 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:11:07s. Time for last 1,000,000: 1s. Last read position: chr18:49,794,307
INFO 2026-06-08 08:56:28 MarkDuplicates Tracking 215855 as yet unmatched pairs. 5275 records in RAM.
INFO 2026-06-08 08:56:30 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:11:09s. Time for last 1,000,000: 1s. Last read position: chr18:62,860,478
INFO 2026-06-08 08:56:30 MarkDuplicates Tracking 212252 as yet unmatched pairs. 1665 records in RAM.
INFO 2026-06-08 08:56:33 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:11:12s. Time for last 1,000,000: 2s. Last read position: chr19:805,154
INFO 2026-06-08 08:56:33 MarkDuplicates Tracking 210219 as yet unmatched pairs. 111759 records in RAM.
INFO 2026-06-08 08:56:35 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:11:15s. Time for last 1,000,000: 2s. Last read position: chr19:1,300,590
INFO 2026-06-08 08:56:35 MarkDuplicates Tracking 206082 as yet unmatched pairs. 107621 records in RAM.
INFO 2026-06-08 08:56:37 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:11:17s. Time for last 1,000,000: 1s. Last read position: chr19:2,246,751
INFO 2026-06-08 08:56:37 MarkDuplicates Tracking 202719 as yet unmatched pairs. 104258 records in RAM.
INFO 2026-06-08 08:56:39 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:11:18s. Time for last 1,000,000: 1s. Last read position: chr19:4,094,488
INFO 2026-06-08 08:56:39 MarkDuplicates Tracking 199743 as yet unmatched pairs. 101282 records in RAM.
INFO 2026-06-08 08:56:41 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:11:20s. Time for last 1,000,000: 1s. Last read position: chr19:5,831,616
INFO 2026-06-08 08:56:41 MarkDuplicates Tracking 196660 as yet unmatched pairs. 98199 records in RAM.
INFO 2026-06-08 08:56:43 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:11:22s. Time for last 1,000,000: 1s. Last read position: chr19:7,555,269
INFO 2026-06-08 08:56:43 MarkDuplicates Tracking 192710 as yet unmatched pairs. 94247 records in RAM.
INFO 2026-06-08 08:56:45 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:11:24s. Time for last 1,000,000: 1s. Last read position: chr19:10,175,606
INFO 2026-06-08 08:56:45 MarkDuplicates Tracking 189773 as yet unmatched pairs. 91308 records in RAM.
INFO 2026-06-08 08:56:47 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:11:26s. Time for last 1,000,000: 2s. Last read position: chr19:11,058,838
INFO 2026-06-08 08:56:47 MarkDuplicates Tracking 186902 as yet unmatched pairs. 88436 records in RAM.
INFO 2026-06-08 08:56:49 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:11:28s. Time for last 1,000,000: 2s. Last read position: chr19:12,940,091
INFO 2026-06-08 08:56:49 MarkDuplicates Tracking 186131 as yet unmatched pairs. 87665 records in RAM.
INFO 2026-06-08 08:56:51 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:11:30s. Time for last 1,000,000: 1s. Last read position: chr19:14,516,690
INFO 2026-06-08 08:56:51 MarkDuplicates Tracking 183468 as yet unmatched pairs. 84996 records in RAM.
INFO 2026-06-08 08:56:52 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:11:32s. Time for last 1,000,000: 1s. Last read position: chr19:16,519,230
INFO 2026-06-08 08:56:52 MarkDuplicates Tracking 177585 as yet unmatched pairs. 79113 records in RAM.
INFO 2026-06-08 08:56:54 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:11:34s. Time for last 1,000,000: 1s. Last read position: chr19:18,083,464
INFO 2026-06-08 08:56:54 MarkDuplicates Tracking 174458 as yet unmatched pairs. 75985 records in RAM.
INFO 2026-06-08 08:56:56 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:11:35s. Time for last 1,000,000: 1s. Last read position: chr19:19,527,309
INFO 2026-06-08 08:56:56 MarkDuplicates Tracking 172022 as yet unmatched pairs. 73549 records in RAM.
INFO 2026-06-08 08:56:58 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:11:37s. Time for last 1,000,000: 1s. Last read position: chr19:35,267,175
INFO 2026-06-08 08:56:58 MarkDuplicates Tracking 171107 as yet unmatched pairs. 72632 records in RAM.
INFO 2026-06-08 08:57:00 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:11:39s. Time for last 1,000,000: 1s. Last read position: chr19:38,327,182
INFO 2026-06-08 08:57:00 MarkDuplicates Tracking 164634 as yet unmatched pairs. 66158 records in RAM.
INFO 2026-06-08 08:57:02 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:11:41s. Time for last 1,000,000: 2s. Last read position: chr19:39,422,939
INFO 2026-06-08 08:57:02 MarkDuplicates Tracking 161596 as yet unmatched pairs. 63111 records in RAM.
INFO 2026-06-08 08:57:04 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:11:43s. Time for last 1,000,000: 2s. Last read position: chr19:39,873,420
INFO 2026-06-08 08:57:04 MarkDuplicates Tracking 171299 as yet unmatched pairs. 72814 records in RAM.
INFO 2026-06-08 08:57:06 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:11:45s. Time for last 1,000,000: 2s. Last read position: chr19:39,876,857
INFO 2026-06-08 08:57:06 MarkDuplicates Tracking 156867 as yet unmatched pairs. 58382 records in RAM.
INFO 2026-06-08 08:57:07 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:11:46s. Time for last 1,000,000: 1s. Last read position: chr19:39,877,984
INFO 2026-06-08 08:57:07 MarkDuplicates Tracking 176127 as yet unmatched pairs. 77642 records in RAM.
INFO 2026-06-08 08:57:09 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:11:48s. Time for last 1,000,000: 1s. Last read position: chr19:39,885,751
INFO 2026-06-08 08:57:09 MarkDuplicates Tracking 200207 as yet unmatched pairs. 101722 records in RAM.
INFO 2026-06-08 08:57:11 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:11:50s. Time for last 1,000,000: 1s. Last read position: chr19:39,889,532
INFO 2026-06-08 08:57:11 MarkDuplicates Tracking 178804 as yet unmatched pairs. 80319 records in RAM.
INFO 2026-06-08 08:57:12 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:11:51s. Time for last 1,000,000: 1s. Last read position: chr19:39,891,744
INFO 2026-06-08 08:57:12 MarkDuplicates Tracking 216852 as yet unmatched pairs. 118367 records in RAM.
INFO 2026-06-08 08:57:14 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:11:53s. Time for last 1,000,000: 1s. Last read position: chr19:39,892,971
INFO 2026-06-08 08:57:14 MarkDuplicates Tracking 190660 as yet unmatched pairs. 92174 records in RAM.
INFO 2026-06-08 08:57:16 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:11:55s. Time for last 1,000,000: 1s. Last read position: chr19:39,894,069
INFO 2026-06-08 08:57:16 MarkDuplicates Tracking 172144 as yet unmatched pairs. 73656 records in RAM.
INFO 2026-06-08 08:57:17 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:11:57s. Time for last 1,000,000: 1s. Last read position: chr19:39,901,997
INFO 2026-06-08 08:57:17 MarkDuplicates Tracking 163283 as yet unmatched pairs. 64794 records in RAM.
INFO 2026-06-08 08:57:19 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:11:58s. Time for last 1,000,000: 1s. Last read position: chr19:39,905,992
INFO 2026-06-08 08:57:19 MarkDuplicates Tracking 172714 as yet unmatched pairs. 74224 records in RAM.
INFO 2026-06-08 08:57:21 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:12:00s. Time for last 1,000,000: 1s. Last read position: chr19:39,918,312
INFO 2026-06-08 08:57:21 MarkDuplicates Tracking 153177 as yet unmatched pairs. 54683 records in RAM.
INFO 2026-06-08 08:57:23 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:12:03s. Time for last 1,000,000: 2s. Last read position: chr19:40,235,954
INFO 2026-06-08 08:57:23 MarkDuplicates Tracking 132048 as yet unmatched pairs. 33554 records in RAM.
INFO 2026-06-08 08:57:25 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:12:04s. Time for last 1,000,000: 1s. Last read position: chr19:41,709,715
INFO 2026-06-08 08:57:25 MarkDuplicates Tracking 144935 as yet unmatched pairs. 46439 records in RAM.
INFO 2026-06-08 08:57:27 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:12:06s. Time for last 1,000,000: 1s. Last read position: chr19:41,720,926
INFO 2026-06-08 08:57:27 MarkDuplicates Tracking 132875 as yet unmatched pairs. 34379 records in RAM.
INFO 2026-06-08 08:57:29 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:12:08s. Time for last 1,000,000: 1s. Last read position: chr19:42,287,694
INFO 2026-06-08 08:57:29 MarkDuplicates Tracking 123773 as yet unmatched pairs. 25267 records in RAM.
INFO 2026-06-08 08:57:30 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:12:10s. Time for last 1,000,000: 1s. Last read position: chr19:45,040,270
INFO 2026-06-08 08:57:30 MarkDuplicates Tracking 120342 as yet unmatched pairs. 21828 records in RAM.
INFO 2026-06-08 08:57:32 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:12:11s. Time for last 1,000,000: 1s. Last read position: chr19:46,921,006
INFO 2026-06-08 08:57:32 MarkDuplicates Tracking 116458 as yet unmatched pairs. 17942 records in RAM.
INFO 2026-06-08 08:57:34 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:12:13s. Time for last 1,000,000: 1s. Last read position: chr19:48,987,362
INFO 2026-06-08 08:57:34 MarkDuplicates Tracking 113238 as yet unmatched pairs. 14712 records in RAM.
INFO 2026-06-08 08:57:36 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:12:15s. Time for last 1,000,000: 1s. Last read position: chr19:49,664,680
INFO 2026-06-08 08:57:36 MarkDuplicates Tracking 110641 as yet unmatched pairs. 12115 records in RAM.
INFO 2026-06-08 08:57:38 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:12:17s. Time for last 1,000,000: 1s. Last read position: chr19:51,346,915
INFO 2026-06-08 08:57:38 MarkDuplicates Tracking 107036 as yet unmatched pairs. 8510 records in RAM.
INFO 2026-06-08 08:57:39 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:12:18s. Time for last 1,000,000: 1s. Last read position: chr19:54,458,692
INFO 2026-06-08 08:57:39 MarkDuplicates Tracking 105013 as yet unmatched pairs. 6487 records in RAM.
INFO 2026-06-08 08:57:41 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:12:20s. Time for last 1,000,000: 1s. Last read position: chr19:56,088,072
INFO 2026-06-08 08:57:41 MarkDuplicates Tracking 100548 as yet unmatched pairs. 2022 records in RAM.
INFO 2026-06-08 08:57:43 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:12:22s. Time for last 1,000,000: 2s. Last read position: chr20:1,464,342
INFO 2026-06-08 08:57:43 MarkDuplicates Tracking 97675 as yet unmatched pairs. 24674 records in RAM.
INFO 2026-06-08 08:57:45 MarkDuplicates Read 368,000,000 records. Elapsed time: 00:12:24s. Time for last 1,000,000: 1s. Last read position: chr20:10,622,720
INFO 2026-06-08 08:57:45 MarkDuplicates Tracking 94436 as yet unmatched pairs. 21435 records in RAM.
INFO 2026-06-08 08:57:48 MarkDuplicates Read 369,000,000 records. Elapsed time: 00:12:27s. Time for last 1,000,000: 2s. Last read position: chr20:24,970,270
INFO 2026-06-08 08:57:48 MarkDuplicates Tracking 92109 as yet unmatched pairs. 19108 records in RAM.
INFO 2026-06-08 08:57:49 MarkDuplicates Read 370,000,000 records. Elapsed time: 00:12:29s. Time for last 1,000,000: 1s. Last read position: chr20:34,750,500
INFO 2026-06-08 08:57:49 MarkDuplicates Tracking 88938 as yet unmatched pairs. 15934 records in RAM.
INFO 2026-06-08 08:57:51 MarkDuplicates Read 371,000,000 records. Elapsed time: 00:12:30s. Time for last 1,000,000: 1s. Last read position: chr20:38,138,252
INFO 2026-06-08 08:57:51 MarkDuplicates Tracking 86251 as yet unmatched pairs. 13245 records in RAM.
INFO 2026-06-08 08:57:53 MarkDuplicates Read 372,000,000 records. Elapsed time: 00:12:32s. Time for last 1,000,000: 1s. Last read position: chr20:45,803,340
INFO 2026-06-08 08:57:53 MarkDuplicates Tracking 83349 as yet unmatched pairs. 10342 records in RAM.
INFO 2026-06-08 08:57:54 MarkDuplicates Read 373,000,000 records. Elapsed time: 00:12:34s. Time for last 1,000,000: 1s. Last read position: chr20:50,579,807
INFO 2026-06-08 08:57:54 MarkDuplicates Tracking 80555 as yet unmatched pairs. 7548 records in RAM.
INFO 2026-06-08 08:57:56 MarkDuplicates Read 374,000,000 records. Elapsed time: 00:12:35s. Time for last 1,000,000: 1s. Last read position: chr20:62,283,999
INFO 2026-06-08 08:57:56 MarkDuplicates Tracking 77532 as yet unmatched pairs. 4512 records in RAM.
INFO 2026-06-08 08:57:58 MarkDuplicates Read 375,000,000 records. Elapsed time: 00:12:37s. Time for last 1,000,000: 1s. Last read position: chr20:63,701,848
INFO 2026-06-08 08:57:58 MarkDuplicates Tracking 74479 as yet unmatched pairs. 1459 records in RAM.
INFO 2026-06-08 08:58:00 MarkDuplicates Read 376,000,000 records. Elapsed time: 00:12:39s. Time for last 1,000,000: 1s. Last read position: chr21:8,258,917
INFO 2026-06-08 08:58:00 MarkDuplicates Tracking 71888 as yet unmatched pairs. 14004 records in RAM.
INFO 2026-06-08 08:58:02 MarkDuplicates Read 377,000,000 records. Elapsed time: 00:12:41s. Time for last 1,000,000: 1s. Last read position: chr21:9,325,130
INFO 2026-06-08 08:58:02 MarkDuplicates Tracking 70320 as yet unmatched pairs. 12433 records in RAM.
INFO 2026-06-08 08:58:03 MarkDuplicates Read 378,000,000 records. Elapsed time: 00:12:43s. Time for last 1,000,000: 1s. Last read position: chr21:33,554,297
INFO 2026-06-08 08:58:03 MarkDuplicates Tracking 67953 as yet unmatched pairs. 10065 records in RAM.
INFO 2026-06-08 08:58:05 MarkDuplicates Read 379,000,000 records. Elapsed time: 00:12:44s. Time for last 1,000,000: 1s. Last read position: chr21:41,471,815
INFO 2026-06-08 08:58:05 MarkDuplicates Tracking 66928 as yet unmatched pairs. 9035 records in RAM.
INFO 2026-06-08 08:58:07 MarkDuplicates Read 380,000,000 records. Elapsed time: 00:12:46s. Time for last 1,000,000: 1s. Last read position: chr21:44,313,011
INFO 2026-06-08 08:58:07 MarkDuplicates Tracking 62586 as yet unmatched pairs. 4692 records in RAM.
INFO 2026-06-08 08:58:09 MarkDuplicates Read 381,000,000 records. Elapsed time: 00:12:48s. Time for last 1,000,000: 1s. Last read position: chr21:46,260,820
INFO 2026-06-08 08:58:09 MarkDuplicates Tracking 58943 as yet unmatched pairs. 1049 records in RAM.
INFO 2026-06-08 08:58:12 MarkDuplicates Read 382,000,000 records. Elapsed time: 00:12:51s. Time for last 1,000,000: 3s. Last read position: chr22:20,585,212
INFO 2026-06-08 08:58:12 MarkDuplicates Tracking 56670 as yet unmatched pairs. 28982 records in RAM.
INFO 2026-06-08 08:58:14 MarkDuplicates Read 383,000,000 records. Elapsed time: 00:12:53s. Time for last 1,000,000: 2s. Last read position: chr22:24,056,233
INFO 2026-06-08 08:58:14 MarkDuplicates Tracking 52643 as yet unmatched pairs. 24953 records in RAM.
INFO 2026-06-08 08:58:16 MarkDuplicates Read 384,000,000 records. Elapsed time: 00:12:55s. Time for last 1,000,000: 1s. Last read position: chr22:29,298,881
INFO 2026-06-08 08:58:16 MarkDuplicates Tracking 53271 as yet unmatched pairs. 25581 records in RAM.
INFO 2026-06-08 08:58:18 MarkDuplicates Read 385,000,000 records. Elapsed time: 00:12:57s. Time for last 1,000,000: 1s. Last read position: chr22:32,110,016
INFO 2026-06-08 08:58:18 MarkDuplicates Tracking 47161 as yet unmatched pairs. 19469 records in RAM.
INFO 2026-06-08 08:58:20 MarkDuplicates Read 386,000,000 records. Elapsed time: 00:12:59s. Time for last 1,000,000: 1s. Last read position: chr22:36,526,001
INFO 2026-06-08 08:58:20 MarkDuplicates Tracking 44584 as yet unmatched pairs. 16892 records in RAM.
INFO 2026-06-08 08:58:21 MarkDuplicates Read 387,000,000 records. Elapsed time: 00:13:01s. Time for last 1,000,000: 1s. Last read position: chr22:38,485,992
INFO 2026-06-08 08:58:21 MarkDuplicates Tracking 42502 as yet unmatched pairs. 14810 records in RAM.
INFO 2026-06-08 08:58:23 MarkDuplicates Read 388,000,000 records. Elapsed time: 00:13:02s. Time for last 1,000,000: 1s. Last read position: chr22:41,160,705
INFO 2026-06-08 08:58:23 MarkDuplicates Tracking 38343 as yet unmatched pairs. 10651 records in RAM.
INFO 2026-06-08 08:58:25 MarkDuplicates Read 389,000,000 records. Elapsed time: 00:13:04s. Time for last 1,000,000: 1s. Last read position: chr22:44,189,186
INFO 2026-06-08 08:58:25 MarkDuplicates Tracking 35482 as yet unmatched pairs. 7790 records in RAM.
INFO 2026-06-08 08:58:27 MarkDuplicates Read 390,000,000 records. Elapsed time: 00:13:06s. Time for last 1,000,000: 2s. Last read position: chr22:50,284,573
INFO 2026-06-08 08:58:27 MarkDuplicates Tracking 33008 as yet unmatched pairs. 5316 records in RAM.
INFO 2026-06-08 08:58:29 MarkDuplicates Read 391,000,000 records. Elapsed time: 00:13:09s. Time for last 1,000,000: 2s. Last read position: chr22:50,627,276
INFO 2026-06-08 08:58:29 MarkDuplicates Tracking 28811 as yet unmatched pairs. 1119 records in RAM.
INFO 2026-06-08 08:58:32 MarkDuplicates Read 392,000,000 records. Elapsed time: 00:13:11s. Time for last 1,000,000: 2s. Last read position: chrX:19,746,317
INFO 2026-06-08 08:58:32 MarkDuplicates Tracking 25369 as yet unmatched pairs. 19969 records in RAM.
INFO 2026-06-08 08:58:34 MarkDuplicates Read 393,000,000 records. Elapsed time: 00:13:13s. Time for last 1,000,000: 2s. Last read position: chrX:47,142,621
INFO 2026-06-08 08:58:34 MarkDuplicates Tracking 23866 as yet unmatched pairs. 18466 records in RAM.
INFO 2026-06-08 08:58:36 MarkDuplicates Read 394,000,000 records. Elapsed time: 00:13:15s. Time for last 1,000,000: 2s. Last read position: chrX:49,250,150
INFO 2026-06-08 08:58:36 MarkDuplicates Tracking 19747 as yet unmatched pairs. 14347 records in RAM.
INFO 2026-06-08 08:58:38 MarkDuplicates Read 395,000,000 records. Elapsed time: 00:13:17s. Time for last 1,000,000: 2s. Last read position: chrX:65,737,228
INFO 2026-06-08 08:58:38 MarkDuplicates Tracking 18230 as yet unmatched pairs. 12830 records in RAM.
INFO 2026-06-08 08:58:40 MarkDuplicates Read 396,000,000 records. Elapsed time: 00:13:19s. Time for last 1,000,000: 1s. Last read position: chrX:77,857,481
INFO 2026-06-08 08:58:40 MarkDuplicates Tracking 14817 as yet unmatched pairs. 9417 records in RAM.
INFO 2026-06-08 08:58:42 MarkDuplicates Read 397,000,000 records. Elapsed time: 00:13:21s. Time for last 1,000,000: 2s. Last read position: chrX:119,637,142
INFO 2026-06-08 08:58:42 MarkDuplicates Tracking 12323 as yet unmatched pairs. 6923 records in RAM.
INFO 2026-06-08 08:58:44 MarkDuplicates Read 398,000,000 records. Elapsed time: 00:13:23s. Time for last 1,000,000: 2s. Last read position: chrX:153,797,547
INFO 2026-06-08 08:58:44 MarkDuplicates Tracking 10487 as yet unmatched pairs. 5087 records in RAM.
INFO 2026-06-08 08:58:47 MarkDuplicates Read 399,000,000 records. Elapsed time: 00:13:26s. Time for last 1,000,000: 2s. Last read position: chrX:154,450,425
INFO 2026-06-08 08:58:47 MarkDuplicates Tracking 6394 as yet unmatched pairs. 994 records in RAM.
INFO 2026-06-08 08:58:48 MarkDuplicates Read 400,000,000 records. Elapsed time: 00:13:28s. Time for last 1,000,000: 1s. Last read position: GL000220.1:158,119
INFO 2026-06-08 08:58:48 MarkDuplicates Tracking 3414 as yet unmatched pairs. 61 records in RAM.
INFO 2026-06-08 08:58:50 MarkDuplicates Read 401,000,000 records. Elapsed time: 00:13:29s. Time for last 1,000,000: 1s. Last read position: KI270733.1:176,090
INFO 2026-06-08 08:58:50 MarkDuplicates Tracking 57 as yet unmatched pairs. 47 records in RAM.
INFO 2026-06-08 08:58:50 MarkDuplicates Read 401307024 records. 0 pairs never matched.
INFO 2026-06-08 08:59:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 34871453064; totalMemory: 49794777088; maxMemory: 63585648640
INFO 2026-06-08 08:59:36 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 09:00:01 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 09:00:21 OpticalDuplicateFinder Large duplicate set. size = 1104
INFO 2026-06-08 09:00:21 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,577
INFO 2026-06-08 09:00:24 OpticalDuplicateFinder Large duplicate set. size = 1045
INFO 2026-06-08 09:00:24 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:1,607
INFO 2026-06-08 09:00:45 MarkDuplicates Traversing fragment information and detecting duplicates.
WARNING 2026-06-08 09:00:45 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
INFO 2026-06-08 09:01:40 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 09:01:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 33711072072; totalMemory: 49660559360; maxMemory: 63585648640
INFO 2026-06-08 09:01:47 MarkDuplicates Marking 163274816 records as duplicates.
INFO 2026-06-08 09:01:47 MarkDuplicates Found 20403574 optical duplicate clusters.
INFO 2026-06-08 09:01:47 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 09:02:08 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:20s. Time for last 10,000,000: 20s. Last read position: chr1:36,178,549
INFO 2026-06-08 09:02:30 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:43s. Time for last 10,000,000: 22s. Last read position: chr1:148,558,355
INFO 2026-06-08 09:02:50 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:03s. Time for last 10,000,000: 20s. Last read position: chr1:201,649,267
INFO 2026-06-08 09:03:12 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:25s. Time for last 10,000,000: 21s. Last read position: chr2:27,040,070
INFO 2026-06-08 09:03:33 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:46s. Time for last 10,000,000: 21s. Last read position: chr2:95,906,649
INFO 2026-06-08 09:03:53 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:05s. Time for last 10,000,000: 19s. Last read position: chr2:219,539,789
INFO 2026-06-08 09:04:13 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:25s. Time for last 10,000,000: 20s. Last read position: chr3:52,292,291
INFO 2026-06-08 09:04:33 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:45s. Time for last 10,000,000: 19s. Last read position: chr3:195,778,936
INFO 2026-06-08 09:04:52 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:03:05s. Time for last 10,000,000: 19s. Last read position: chr4:39,458,210
INFO 2026-06-08 09:05:15 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:03:28s. Time for last 10,000,000: 22s. Last read position: chr5:69,894,594
INFO 2026-06-08 09:05:34 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:03:47s. Time for last 10,000,000: 18s. Last read position: chr5:176,238,477
INFO 2026-06-08 09:05:53 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:04:05s. Time for last 10,000,000: 18s. Last read position: chr6:31,874,956
INFO 2026-06-08 09:06:11 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:04:24s. Time for last 10,000,000: 18s. Last read position: chr6:144,447,670
INFO 2026-06-08 09:06:30 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:04:42s. Time for last 10,000,000: 18s. Last read position: chr7:93,994,342
INFO 2026-06-08 09:06:49 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:05:02s. Time for last 10,000,000: 19s. Last read position: chr7:101,001,187
INFO 2026-06-08 09:07:10 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:05:23s. Time for last 10,000,000: 20s. Last read position: chr8:23,328,429
INFO 2026-06-08 09:07:30 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:05:42s. Time for last 10,000,000: 19s. Last read position: chr8:143,984,662
INFO 2026-06-08 09:07:50 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:06:02s. Time for last 10,000,000: 20s. Last read position: chr9:128,151,929
INFO 2026-06-08 09:08:12 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:06:24s. Time for last 10,000,000: 21s. Last read position: chr10:76,058,733
INFO 2026-06-08 09:08:29 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:06:41s. Time for last 10,000,000: 17s. Last read position: chr10:122,640,219
INFO 2026-06-08 09:08:50 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:07:02s. Time for last 10,000,000: 21s. Last read position: chr11:32,934,941
INFO 2026-06-08 09:09:14 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:07:26s. Time for last 10,000,000: 23s. Last read position: chr11:72,013,724
INFO 2026-06-08 09:09:37 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:07:49s. Time for last 10,000,000: 22s. Last read position: chr12:29,311,047
INFO 2026-06-08 09:09:58 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:08:10s. Time for last 10,000,000: 21s. Last read position: chr12:110,492,065
INFO 2026-06-08 09:10:19 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:08:32s. Time for last 10,000,000: 21s. Last read position: chr13:112,881,783
INFO 2026-06-08 09:10:40 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:08:52s. Time for last 10,000,000: 20s. Last read position: chr14:104,883,931
INFO 2026-06-08 09:11:00 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:09:12s. Time for last 10,000,000: 20s. Last read position: chr15:58,888,524
INFO 2026-06-08 09:11:20 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:09:32s. Time for last 10,000,000: 19s. Last read position: chr16:5,025,594
INFO 2026-06-08 09:11:38 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:09:50s. Time for last 10,000,000: 18s. Last read position: chr16:31,078,194
INFO 2026-06-08 09:11:56 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:10:08s. Time for last 10,000,000: 17s. Last read position: chr17:4,895,801
INFO 2026-06-08 09:12:14 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:10:26s. Time for last 10,000,000: 17s. Last read position: chr17:42,838,788
INFO 2026-06-08 09:12:34 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:10:46s. Time for last 10,000,000: 20s. Last read position: chr17:75,778,661
INFO 2026-06-08 09:12:53 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:11:06s. Time for last 10,000,000: 19s. Last read position: chr19:1,300,590
INFO 2026-06-08 09:13:23 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:11:35s. Time for last 10,000,000: 29s. Last read position: chr19:18,083,464
INFO 2026-06-08 09:13:51 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:12:03s. Time for last 10,000,000: 28s. Last read position: chr19:39,891,744
INFO 2026-06-08 09:14:17 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:12:30s. Time for last 10,000,000: 26s. Last read position: chr19:45,040,270
INFO 2026-06-08 09:14:39 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:12:51s. Time for last 10,000,000: 21s. Last read position: chr20:34,750,500
INFO 2026-06-08 09:15:02 MarkDuplicates Written 380,000,000 records. Elapsed time: 00:13:14s. Time for last 10,000,000: 22s. Last read position: chr21:44,313,011
INFO 2026-06-08 09:15:21 MarkDuplicates Written 390,000,000 records. Elapsed time: 00:13:33s. Time for last 10,000,000: 18s. Last read position: chr22:50,284,573
INFO 2026-06-08 09:15:38 MarkDuplicates Written 400,000,000 records. Elapsed time: 00:13:51s. Time for last 10,000,000: 17s. Last read position: GL000220.1:158,119
INFO 2026-06-08 09:15:50 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 09:15:50 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 09:15:50 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 09:15:50 MarkDuplicates Before output close freeMemory: 202555880; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 09:15:50 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 09:15:50 MarkDuplicates After output close freeMemory: 104866920; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 09:15:50 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 30.53 minutes.
Tool returned:
0
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory