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/a2/35c0e724ee5ae49cc30c6ed85ccc98/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/35c0e724ee5ae49cc30c6ed85ccc98/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/3a629bdeef588d9d7d8be6eacf91b0/tih_rna_sample_00598_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)
Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT tih_rna_sample_00598_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00598_B23MVV7LT4_1.md.bam --METRICS_FILE tih_rna_sample_00598_B23MVV7LT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
08:13:15.928 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 08:13:15 GMT 2026] MarkDuplicates --INPUT tih_rna_sample_00598_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00598_B23MVV7LT4_1.md.bam --METRICS_FILE tih_rna_sample_00598_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 08:13:15 GMT 2026] Executing as ?@nf-a235c0e724ee5ae49cc30c6ed85ccc98-b0c49-dj7nf 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 08:13:16 MarkDuplicates Start of doWork freeMemory: 105828384; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 08:13:16 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 08:13:16 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 08:13:20 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:1,358,369
INFO 2026-06-08 08:13:20 MarkDuplicates Tracking 2500 as yet unmatched pairs. 39 records in RAM.
INFO 2026-06-08 08:13:24 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 3s. Last read position: chr1:3,625,075
INFO 2026-06-08 08:13:24 MarkDuplicates Tracking 4914 as yet unmatched pairs. 15 records in RAM.
INFO 2026-06-08 08:13:27 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 2s. Last read position: chr1:8,867,147
INFO 2026-06-08 08:13:27 MarkDuplicates Tracking 7627 as yet unmatched pairs. 87 records in RAM.
INFO 2026-06-08 08:13:29 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 2s. Last read position: chr1:12,261,099
INFO 2026-06-08 08:13:29 MarkDuplicates Tracking 10035 as yet unmatched pairs. 149 records in RAM.
INFO 2026-06-08 08:13:32 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: chr1:16,577,333
INFO 2026-06-08 08:13:32 MarkDuplicates Tracking 12228 as yet unmatched pairs. 108 records in RAM.
INFO 2026-06-08 08:13:34 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr1:19,694,527
INFO 2026-06-08 08:13:34 MarkDuplicates Tracking 14395 as yet unmatched pairs. 17 records in RAM.
INFO 2026-06-08 08:13:37 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 2s. Last read position: chr1:22,639,044
INFO 2026-06-08 08:13:37 MarkDuplicates Tracking 16996 as yet unmatched pairs. 418 records in RAM.
INFO 2026-06-08 08:13:38 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: chr1:24,929,828
INFO 2026-06-08 08:13:38 MarkDuplicates Tracking 18788 as yet unmatched pairs. 86 records in RAM.
INFO 2026-06-08 08:13:42 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 3s. Last read position: chr1:27,207,304
INFO 2026-06-08 08:13:42 MarkDuplicates Tracking 21004 as yet unmatched pairs. 23 records in RAM.
INFO 2026-06-08 08:13:44 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 2s. Last read position: chr1:31,434,093
INFO 2026-06-08 08:13:44 MarkDuplicates Tracking 23508 as yet unmatched pairs. 411 records in RAM.
INFO 2026-06-08 08:13:46 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 1s. Last read position: chr1:35,093,951
INFO 2026-06-08 08:13:46 MarkDuplicates Tracking 25327 as yet unmatched pairs. 18 records in RAM.
INFO 2026-06-08 08:13:49 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 2s. Last read position: chr1:37,931,445
INFO 2026-06-08 08:13:49 MarkDuplicates Tracking 27731 as yet unmatched pairs. 65 records in RAM.
INFO 2026-06-08 08:13:52 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 3s. Last read position: chr1:40,059,394
INFO 2026-06-08 08:13:52 MarkDuplicates Tracking 29632 as yet unmatched pairs. 70 records in RAM.
INFO 2026-06-08 08:13:54 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 2s. Last read position: chr1:43,453,615
INFO 2026-06-08 08:13:54 MarkDuplicates Tracking 31949 as yet unmatched pairs. 94 records in RAM.
INFO 2026-06-08 08:13:56 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 1s. Last read position: chr1:46,034,215
INFO 2026-06-08 08:13:56 MarkDuplicates Tracking 34599 as yet unmatched pairs. 371 records in RAM.
INFO 2026-06-08 08:13:58 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 2s. Last read position: chr1:55,068,919
INFO 2026-06-08 08:13:58 MarkDuplicates Tracking 36436 as yet unmatched pairs. 64 records in RAM.
INFO 2026-06-08 08:14:01 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 2s. Last read position: chr1:77,044,209
INFO 2026-06-08 08:14:01 MarkDuplicates Tracking 38672 as yet unmatched pairs. 12 records in RAM.
INFO 2026-06-08 08:14:04 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 2s. Last read position: chr1:95,244,472
INFO 2026-06-08 08:14:04 MarkDuplicates Tracking 40792 as yet unmatched pairs. 93 records in RAM.
INFO 2026-06-08 08:14:07 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 2s. Last read position: chr1:111,476,045
INFO 2026-06-08 08:14:07 MarkDuplicates Tracking 42741 as yet unmatched pairs. 62 records in RAM.
INFO 2026-06-08 08:14:09 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 2s. Last read position: chr1:119,919,459
INFO 2026-06-08 08:14:09 MarkDuplicates Tracking 45130 as yet unmatched pairs. 374 records in RAM.
INFO 2026-06-08 08:14:11 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 2s. Last read position: chr1:145,366,247
INFO 2026-06-08 08:14:11 MarkDuplicates Tracking 46061 as yet unmatched pairs. 18 records in RAM.
INFO 2026-06-08 08:14:13 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 2s. Last read position: chr1:148,124,901
INFO 2026-06-08 08:14:13 MarkDuplicates Tracking 47544 as yet unmatched pairs. 286 records in RAM.
INFO 2026-06-08 08:14:16 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 2s. Last read position: chr1:149,494,113
INFO 2026-06-08 08:14:16 MarkDuplicates Tracking 48120 as yet unmatched pairs. 20 records in RAM.
INFO 2026-06-08 08:14:19 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 3s. Last read position: chr1:150,625,684
INFO 2026-06-08 08:14:19 MarkDuplicates Tracking 50554 as yet unmatched pairs. 398 records in RAM.
INFO 2026-06-08 08:14:22 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 2s. Last read position: chr1:151,811,364
INFO 2026-06-08 08:14:22 MarkDuplicates Tracking 52583 as yet unmatched pairs. 70 records in RAM.
INFO 2026-06-08 08:14:24 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 2s. Last read position: chr1:154,176,184
INFO 2026-06-08 08:14:24 MarkDuplicates Tracking 55158 as yet unmatched pairs. 636 records in RAM.
INFO 2026-06-08 08:14:26 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 1s. Last read position: chr1:155,056,146
INFO 2026-06-08 08:14:26 MarkDuplicates Tracking 57029 as yet unmatched pairs. 169 records in RAM.
INFO 2026-06-08 08:14:28 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 1s. Last read position: chr1:155,478,566
INFO 2026-06-08 08:14:28 MarkDuplicates Tracking 58912 as yet unmatched pairs. 140 records in RAM.
INFO 2026-06-08 08:14:31 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 3s. Last read position: chr1:156,252,427
INFO 2026-06-08 08:14:31 MarkDuplicates Tracking 61131 as yet unmatched pairs. 88 records in RAM.
INFO 2026-06-08 08:14:34 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 2s. Last read position: chr1:160,095,112
INFO 2026-06-08 08:14:34 MarkDuplicates Tracking 63572 as yet unmatched pairs. 181 records in RAM.
INFO 2026-06-08 08:14:37 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 2s. Last read position: chr1:161,542,660
INFO 2026-06-08 08:14:37 MarkDuplicates Tracking 66284 as yet unmatched pairs. 617 records in RAM.
INFO 2026-06-08 08:14:40 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 2s. Last read position: chr1:170,074,360
INFO 2026-06-08 08:14:40 MarkDuplicates Tracking 67844 as yet unmatched pairs. 64 records in RAM.
INFO 2026-06-08 08:14:42 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 1s. Last read position: chr1:179,846,313
INFO 2026-06-08 08:14:42 MarkDuplicates Tracking 69949 as yet unmatched pairs. 94 records in RAM.
INFO 2026-06-08 08:14:44 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 2s. Last read position: chr1:186,353,690
INFO 2026-06-08 08:14:44 MarkDuplicates Tracking 72104 as yet unmatched pairs. 216 records in RAM.
INFO 2026-06-08 08:14:46 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 1s. Last read position: chr1:202,758,454
INFO 2026-06-08 08:14:46 MarkDuplicates Tracking 74147 as yet unmatched pairs. 20 records in RAM.
INFO 2026-06-08 08:14:48 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 1s. Last read position: chr1:206,493,005
INFO 2026-06-08 08:14:48 MarkDuplicates Tracking 76247 as yet unmatched pairs. 50 records in RAM.
INFO 2026-06-08 08:14:50 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 2s. Last read position: chr1:222,523,625
INFO 2026-06-08 08:14:50 MarkDuplicates Tracking 78279 as yet unmatched pairs. 21 records in RAM.
INFO 2026-06-08 08:14:52 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 2s. Last read position: chr1:226,064,376
INFO 2026-06-08 08:14:52 MarkDuplicates Tracking 80443 as yet unmatched pairs. 249 records in RAM.
INFO 2026-06-08 08:14:55 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 2s. Last read position: chr1:228,735,783
INFO 2026-06-08 08:14:55 MarkDuplicates Tracking 82863 as yet unmatched pairs. 30 records in RAM.
INFO 2026-06-08 08:14:58 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 2s. Last read position: chr1:243,165,205
INFO 2026-06-08 08:14:58 MarkDuplicates Tracking 85365 as yet unmatched pairs. 63 records in RAM.
INFO 2026-06-08 08:15:01 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 3s. Last read position: chr2:6,897,803
INFO 2026-06-08 08:15:01 MarkDuplicates Tracking 87877 as yet unmatched pairs. 87669 records in RAM.
INFO 2026-06-08 08:15:03 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 2s. Last read position: chr2:24,758,008
INFO 2026-06-08 08:15:03 MarkDuplicates Tracking 90240 as yet unmatched pairs. 90030 records in RAM.
INFO 2026-06-08 08:15:06 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 2s. Last read position: chr2:28,781,831
INFO 2026-06-08 08:15:06 MarkDuplicates Tracking 92618 as yet unmatched pairs. 92407 records in RAM.
INFO 2026-06-08 08:15:08 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,264
INFO 2026-06-08 08:15:08 MarkDuplicates Tracking 328786 as yet unmatched pairs. 75221 records in RAM.
INFO 2026-06-08 08:15:12 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 3s. Last read position: chr2:32,916,406
INFO 2026-06-08 08:15:12 MarkDuplicates Tracking 716224 as yet unmatched pairs. 46366 records in RAM.
INFO 2026-06-08 08:15:14 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 1s. Last read position: chr2:36,916,125
INFO 2026-06-08 08:15:14 MarkDuplicates Tracking 767613 as yet unmatched pairs. 42948 records in RAM.
INFO 2026-06-08 08:15:16 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 1s. Last read position: chr2:46,010,457
INFO 2026-06-08 08:15:16 MarkDuplicates Tracking 764627 as yet unmatched pairs. 39961 records in RAM.
INFO 2026-06-08 08:15:18 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 1s. Last read position: chr2:60,881,705
INFO 2026-06-08 08:15:18 MarkDuplicates Tracking 762549 as yet unmatched pairs. 37883 records in RAM.
INFO 2026-06-08 08:15:20 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 1s. Last read position: chr2:71,349,788
INFO 2026-06-08 08:15:20 MarkDuplicates Tracking 760056 as yet unmatched pairs. 35390 records in RAM.
INFO 2026-06-08 08:15:22 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 2s. Last read position: chr2:74,556,344
INFO 2026-06-08 08:15:22 MarkDuplicates Tracking 757746 as yet unmatched pairs. 33078 records in RAM.
INFO 2026-06-08 08:15:24 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 1s. Last read position: chr2:88,857,396
INFO 2026-06-08 08:15:24 MarkDuplicates Tracking 755771 as yet unmatched pairs. 31100 records in RAM.
INFO 2026-06-08 08:15:27 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 3s. Last read position: chr2:97,724,349
INFO 2026-06-08 08:15:27 MarkDuplicates Tracking 753915 as yet unmatched pairs. 29244 records in RAM.
INFO 2026-06-08 08:15:30 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 2s. Last read position: chr2:108,755,204
INFO 2026-06-08 08:15:30 MarkDuplicates Tracking 751783 as yet unmatched pairs. 27107 records in RAM.
INFO 2026-06-08 08:15:31 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 1s. Last read position: chr2:113,443,782
INFO 2026-06-08 08:15:31 MarkDuplicates Tracking 749950 as yet unmatched pairs. 25271 records in RAM.
INFO 2026-06-08 08:15:33 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 1s. Last read position: chr2:130,372,440
INFO 2026-06-08 08:15:33 MarkDuplicates Tracking 748405 as yet unmatched pairs. 23726 records in RAM.
INFO 2026-06-08 08:15:35 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 1s. Last read position: chr2:131,591,927
INFO 2026-06-08 08:15:35 MarkDuplicates Tracking 748269 as yet unmatched pairs. 23588 records in RAM.
INFO 2026-06-08 08:15:37 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 1s. Last read position: chr2:157,737,447
INFO 2026-06-08 08:15:37 MarkDuplicates Tracking 744629 as yet unmatched pairs. 19946 records in RAM.
INFO 2026-06-08 08:15:39 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 2s. Last read position: chr2:171,554,550
INFO 2026-06-08 08:15:39 MarkDuplicates Tracking 742462 as yet unmatched pairs. 17777 records in RAM.
INFO 2026-06-08 08:15:41 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 2s. Last read position: chr2:178,652,111
INFO 2026-06-08 08:15:41 MarkDuplicates Tracking 740351 as yet unmatched pairs. 15664 records in RAM.
INFO 2026-06-08 08:15:43 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 2s. Last read position: chr2:190,980,655
INFO 2026-06-08 08:15:43 MarkDuplicates Tracking 738538 as yet unmatched pairs. 13849 records in RAM.
INFO 2026-06-08 08:15:45 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 2s. Last read position: chr2:203,489,832
INFO 2026-06-08 08:15:45 MarkDuplicates Tracking 736007 as yet unmatched pairs. 11316 records in RAM.
INFO 2026-06-08 08:15:47 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 2s. Last read position: chr2:216,500,008
INFO 2026-06-08 08:15:47 MarkDuplicates Tracking 733927 as yet unmatched pairs. 9232 records in RAM.
INFO 2026-06-08 08:15:49 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 1s. Last read position: chr2:219,283,207
INFO 2026-06-08 08:15:49 MarkDuplicates Tracking 731653 as yet unmatched pairs. 6957 records in RAM.
INFO 2026-06-08 08:15:51 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 2s. Last read position: chr2:231,463,233
INFO 2026-06-08 08:15:51 MarkDuplicates Tracking 729957 as yet unmatched pairs. 5231 records in RAM.
INFO 2026-06-08 08:15:53 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 1s. Last read position: chr2:237,542,618
INFO 2026-06-08 08:15:53 MarkDuplicates Tracking 727707 as yet unmatched pairs. 2978 records in RAM.
INFO 2026-06-08 08:15:55 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 2s. Last read position: chr2:241,801,907
INFO 2026-06-08 08:15:55 MarkDuplicates Tracking 724796 as yet unmatched pairs. 63 records in RAM.
INFO 2026-06-08 08:15:58 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 2s. Last read position: chr3:11,564,983
INFO 2026-06-08 08:15:58 MarkDuplicates Tracking 722669 as yet unmatched pairs. 36256 records in RAM.
INFO 2026-06-08 08:16:01 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 2s. Last read position: chr3:22,382,230
INFO 2026-06-08 08:16:01 MarkDuplicates Tracking 720400 as yet unmatched pairs. 33986 records in RAM.
INFO 2026-06-08 08:16:03 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 2s. Last read position: chr3:39,099,364
INFO 2026-06-08 08:16:03 MarkDuplicates Tracking 718399 as yet unmatched pairs. 31982 records in RAM.
INFO 2026-06-08 08:16:05 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 2s. Last read position: chr3:45,981,622
INFO 2026-06-08 08:16:05 MarkDuplicates Tracking 716315 as yet unmatched pairs. 29896 records in RAM.
INFO 2026-06-08 08:16:07 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 2s. Last read position: chr3:47,877,442
INFO 2026-06-08 08:16:07 MarkDuplicates Tracking 714201 as yet unmatched pairs. 27780 records in RAM.
INFO 2026-06-08 08:16:09 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 2s. Last read position: chr3:49,111,138
INFO 2026-06-08 08:16:09 MarkDuplicates Tracking 711994 as yet unmatched pairs. 25571 records in RAM.
INFO 2026-06-08 08:16:12 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 3s. Last read position: chr3:50,188,020
INFO 2026-06-08 08:16:12 MarkDuplicates Tracking 709585 as yet unmatched pairs. 23161 records in RAM.
INFO 2026-06-08 08:16:15 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 2s. Last read position: chr3:52,487,550
INFO 2026-06-08 08:16:15 MarkDuplicates Tracking 707371 as yet unmatched pairs. 20943 records in RAM.
INFO 2026-06-08 08:16:17 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 2s. Last read position: chr3:58,121,334
INFO 2026-06-08 08:16:17 MarkDuplicates Tracking 705196 as yet unmatched pairs. 18759 records in RAM.
INFO 2026-06-08 08:16:19 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 1s. Last read position: chr3:87,240,720
INFO 2026-06-08 08:16:19 MarkDuplicates Tracking 702424 as yet unmatched pairs. 15985 records in RAM.
INFO 2026-06-08 08:16:21 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 1s. Last read position: chr3:114,308,952
INFO 2026-06-08 08:16:21 MarkDuplicates Tracking 700537 as yet unmatched pairs. 14093 records in RAM.
INFO 2026-06-08 08:16:23 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 2s. Last read position: chr3:125,344,497
INFO 2026-06-08 08:16:23 MarkDuplicates Tracking 698301 as yet unmatched pairs. 11847 records in RAM.
INFO 2026-06-08 08:16:26 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 2s. Last read position: chr3:132,700,364
INFO 2026-06-08 08:16:26 MarkDuplicates Tracking 695959 as yet unmatched pairs. 9501 records in RAM.
INFO 2026-06-08 08:16:28 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 1s. Last read position: chr3:151,198,594
INFO 2026-06-08 08:16:28 MarkDuplicates Tracking 693669 as yet unmatched pairs. 7208 records in RAM.
INFO 2026-06-08 08:16:31 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 2s. Last read position: chr3:180,610,370
INFO 2026-06-08 08:16:31 MarkDuplicates Tracking 691787 as yet unmatched pairs. 5321 records in RAM.
INFO 2026-06-08 08:16:34 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 2s. Last read position: chr3:186,857,869
INFO 2026-06-08 08:16:34 MarkDuplicates Tracking 689513 as yet unmatched pairs. 3045 records in RAM.
INFO 2026-06-08 08:16:36 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 2s. Last read position: chr3:195,971,323
INFO 2026-06-08 08:16:36 MarkDuplicates Tracking 687475 as yet unmatched pairs. 1002 records in RAM.
INFO 2026-06-08 08:16:38 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 2s. Last read position: chr4:1,213,401
INFO 2026-06-08 08:16:38 MarkDuplicates Tracking 685407 as yet unmatched pairs. 20659 records in RAM.
INFO 2026-06-08 08:16:40 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: chr4:2,915,004
INFO 2026-06-08 08:16:40 MarkDuplicates Tracking 682580 as yet unmatched pairs. 17828 records in RAM.
INFO 2026-06-08 08:16:42 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 2s. Last read position: chr4:10,078,932
INFO 2026-06-08 08:16:42 MarkDuplicates Tracking 680197 as yet unmatched pairs. 15443 records in RAM.
INFO 2026-06-08 08:16:44 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 1s. Last read position: chr4:39,825,348
INFO 2026-06-08 08:16:44 MarkDuplicates Tracking 677872 as yet unmatched pairs. 13115 records in RAM.
INFO 2026-06-08 08:16:46 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 1s. Last read position: chr4:73,090,793
INFO 2026-06-08 08:16:46 MarkDuplicates Tracking 675817 as yet unmatched pairs. 11055 records in RAM.
INFO 2026-06-08 08:16:48 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 1s. Last read position: chr4:82,427,505
INFO 2026-06-08 08:16:48 MarkDuplicates Tracking 673807 as yet unmatched pairs. 9043 records in RAM.
INFO 2026-06-08 08:16:49 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 1s. Last read position: chr4:98,261,399
INFO 2026-06-08 08:16:49 MarkDuplicates Tracking 671602 as yet unmatched pairs. 6832 records in RAM.
INFO 2026-06-08 08:16:51 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 1s. Last read position: chr4:122,893,004
INFO 2026-06-08 08:16:51 MarkDuplicates Tracking 669359 as yet unmatched pairs. 4581 records in RAM.
INFO 2026-06-08 08:16:53 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 1s. Last read position: chr4:145,902,636
INFO 2026-06-08 08:16:53 MarkDuplicates Tracking 667438 as yet unmatched pairs. 2654 records in RAM.
INFO 2026-06-08 08:16:55 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 1s. Last read position: chr4:186,076,915
INFO 2026-06-08 08:16:55 MarkDuplicates Tracking 665007 as yet unmatched pairs. 220 records in RAM.
INFO 2026-06-08 08:16:57 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 2s. Last read position: chr5:14,394,076
INFO 2026-06-08 08:16:57 MarkDuplicates Tracking 662828 as yet unmatched pairs. 34607 records in RAM.
INFO 2026-06-08 08:17:01 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 3s. Last read position: chr5:39,153,494
INFO 2026-06-08 08:17:01 MarkDuplicates Tracking 660985 as yet unmatched pairs. 32764 records in RAM.
INFO 2026-06-08 08:17:03 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 2s. Last read position: chr5:62,358,280
INFO 2026-06-08 08:17:03 MarkDuplicates Tracking 658586 as yet unmatched pairs. 30363 records in RAM.
INFO 2026-06-08 08:17:05 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 1s. Last read position: chr5:72,989,434
INFO 2026-06-08 08:17:05 MarkDuplicates Tracking 656933 as yet unmatched pairs. 28710 records in RAM.
INFO 2026-06-08 08:17:06 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 1s. Last read position: chr5:95,895,647
INFO 2026-06-08 08:17:06 MarkDuplicates Tracking 654904 as yet unmatched pairs. 26678 records in RAM.
INFO 2026-06-08 08:17:08 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 1s. Last read position: chr5:131,442,405
INFO 2026-06-08 08:17:08 MarkDuplicates Tracking 652706 as yet unmatched pairs. 24476 records in RAM.
INFO 2026-06-08 08:17:10 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 1s. Last read position: chr5:132,898,376
INFO 2026-06-08 08:17:10 MarkDuplicates Tracking 650007 as yet unmatched pairs. 21777 records in RAM.
INFO 2026-06-08 08:17:12 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 1s. Last read position: chr5:135,578,812
INFO 2026-06-08 08:17:12 MarkDuplicates Tracking 653261 as yet unmatched pairs. 25031 records in RAM.
INFO 2026-06-08 08:17:14 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 1s. Last read position: chr5:140,528,427
INFO 2026-06-08 08:17:14 MarkDuplicates Tracking 645769 as yet unmatched pairs. 17440 records in RAM.
INFO 2026-06-08 08:17:16 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 2s. Last read position: chr5:146,229,742
INFO 2026-06-08 08:17:16 MarkDuplicates Tracking 643312 as yet unmatched pairs. 14982 records in RAM.
INFO 2026-06-08 08:17:19 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 2s. Last read position: chr5:150,402,203
INFO 2026-06-08 08:17:19 MarkDuplicates Tracking 650692 as yet unmatched pairs. 22362 records in RAM.
INFO 2026-06-08 08:17:21 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 2s. Last read position: chr5:150,407,183
INFO 2026-06-08 08:17:21 MarkDuplicates Tracking 641834 as yet unmatched pairs. 13504 records in RAM.
INFO 2026-06-08 08:17:23 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 1s. Last read position: chr5:154,875,359
INFO 2026-06-08 08:17:23 MarkDuplicates Tracking 637077 as yet unmatched pairs. 8744 records in RAM.
INFO 2026-06-08 08:17:25 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 1s. Last read position: chr5:172,339,245
INFO 2026-06-08 08:17:25 MarkDuplicates Tracking 634821 as yet unmatched pairs. 6486 records in RAM.
INFO 2026-06-08 08:17:27 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 1s. Last read position: chr5:177,536,385
INFO 2026-06-08 08:17:27 MarkDuplicates Tracking 632901 as yet unmatched pairs. 4564 records in RAM.
INFO 2026-06-08 08:17:29 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 1s. Last read position: chr5:179,824,264
INFO 2026-06-08 08:17:29 MarkDuplicates Tracking 631563 as yet unmatched pairs. 3225 records in RAM.
INFO 2026-06-08 08:17:31 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 2s. Last read position: chr6:3,273,267
INFO 2026-06-08 08:17:31 MarkDuplicates Tracking 627969 as yet unmatched pairs. 44251 records in RAM.
INFO 2026-06-08 08:17:33 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 2s. Last read position: chr6:13,658,778
INFO 2026-06-08 08:17:33 MarkDuplicates Tracking 625420 as yet unmatched pairs. 41701 records in RAM.
INFO 2026-06-08 08:17:35 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 1s. Last read position: chr6:26,199,718
INFO 2026-06-08 08:17:35 MarkDuplicates Tracking 623203 as yet unmatched pairs. 39477 records in RAM.
INFO 2026-06-08 08:17:36 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 1s. Last read position: chr6:29,944,241
INFO 2026-06-08 08:17:36 MarkDuplicates Tracking 622320 as yet unmatched pairs. 38593 records in RAM.
INFO 2026-06-08 08:17:38 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 1s. Last read position: chr6:31,268,971
INFO 2026-06-08 08:17:38 MarkDuplicates Tracking 619481 as yet unmatched pairs. 35752 records in RAM.
INFO 2026-06-08 08:17:40 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 2s. Last read position: chr6:31,643,054
INFO 2026-06-08 08:17:40 MarkDuplicates Tracking 617867 as yet unmatched pairs. 34137 records in RAM.
INFO 2026-06-08 08:17:43 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 2s. Last read position: chr6:31,960,488
INFO 2026-06-08 08:17:43 MarkDuplicates Tracking 615125 as yet unmatched pairs. 31395 records in RAM.
INFO 2026-06-08 08:17:44 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr6:32,192,161
INFO 2026-06-08 08:17:44 MarkDuplicates Tracking 614076 as yet unmatched pairs. 30345 records in RAM.
INFO 2026-06-08 08:17:46 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr6:33,068,663
INFO 2026-06-08 08:17:46 MarkDuplicates Tracking 611861 as yet unmatched pairs. 28129 records in RAM.
INFO 2026-06-08 08:17:48 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 1s. Last read position: chr6:33,446,580
INFO 2026-06-08 08:17:48 MarkDuplicates Tracking 608705 as yet unmatched pairs. 24973 records in RAM.
INFO 2026-06-08 08:17:50 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 1s. Last read position: chr6:38,592,595
INFO 2026-06-08 08:17:50 MarkDuplicates Tracking 606388 as yet unmatched pairs. 22656 records in RAM.
INFO 2026-06-08 08:17:52 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 1s. Last read position: chr6:43,355,257
INFO 2026-06-08 08:17:52 MarkDuplicates Tracking 604146 as yet unmatched pairs. 20412 records in RAM.
INFO 2026-06-08 08:17:53 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 1s. Last read position: chr6:56,614,368
INFO 2026-06-08 08:17:53 MarkDuplicates Tracking 601710 as yet unmatched pairs. 17976 records in RAM.
INFO 2026-06-08 08:17:55 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 1s. Last read position: chr6:87,701,540
INFO 2026-06-08 08:17:55 MarkDuplicates Tracking 599619 as yet unmatched pairs. 15883 records in RAM.
INFO 2026-06-08 08:17:57 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 1s. Last read position: chr6:109,446,221
INFO 2026-06-08 08:17:57 MarkDuplicates Tracking 597754 as yet unmatched pairs. 14015 records in RAM.
INFO 2026-06-08 08:17:59 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 2s. Last read position: chr6:130,869,772
INFO 2026-06-08 08:17:59 MarkDuplicates Tracking 595141 as yet unmatched pairs. 11395 records in RAM.
INFO 2026-06-08 08:18:01 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 1s. Last read position: chr6:143,941,886
INFO 2026-06-08 08:18:01 MarkDuplicates Tracking 592802 as yet unmatched pairs. 9054 records in RAM.
INFO 2026-06-08 08:18:03 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 1s. Last read position: chr6:151,808,047
INFO 2026-06-08 08:18:03 MarkDuplicates Tracking 597902 as yet unmatched pairs. 14153 records in RAM.
INFO 2026-06-08 08:18:04 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 1s. Last read position: chr6:156,779,330
INFO 2026-06-08 08:18:04 MarkDuplicates Tracking 588021 as yet unmatched pairs. 4269 records in RAM.
INFO 2026-06-08 08:18:06 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 1s. Last read position: chr6:159,783,981
INFO 2026-06-08 08:18:06 MarkDuplicates Tracking 585352 as yet unmatched pairs. 1599 records in RAM.
INFO 2026-06-08 08:18:08 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 2s. Last read position: chr7:1,487,321
INFO 2026-06-08 08:18:08 MarkDuplicates Tracking 582872 as yet unmatched pairs. 38721 records in RAM.
INFO 2026-06-08 08:18:11 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 2s. Last read position: chr7:5,370,723
INFO 2026-06-08 08:18:11 MarkDuplicates Tracking 580861 as yet unmatched pairs. 36710 records in RAM.
INFO 2026-06-08 08:18:13 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 2s. Last read position: chr7:6,155,098
INFO 2026-06-08 08:18:13 MarkDuplicates Tracking 577783 as yet unmatched pairs. 33631 records in RAM.
INFO 2026-06-08 08:18:15 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 1s. Last read position: chr7:27,828,667
INFO 2026-06-08 08:18:15 MarkDuplicates Tracking 575517 as yet unmatched pairs. 31364 records in RAM.
INFO 2026-06-08 08:18:16 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 1s. Last read position: chr7:44,059,356
INFO 2026-06-08 08:18:16 MarkDuplicates Tracking 573390 as yet unmatched pairs. 29223 records in RAM.
INFO 2026-06-08 08:18:18 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 1s. Last read position: chr7:51,028,712
INFO 2026-06-08 08:18:18 MarkDuplicates Tracking 571078 as yet unmatched pairs. 26910 records in RAM.
INFO 2026-06-08 08:18:20 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 1s. Last read position: chr7:72,965,876
INFO 2026-06-08 08:18:20 MarkDuplicates Tracking 569035 as yet unmatched pairs. 24864 records in RAM.
INFO 2026-06-08 08:18:22 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 1s. Last read position: chr7:75,147,853
INFO 2026-06-08 08:18:22 MarkDuplicates Tracking 567356 as yet unmatched pairs. 23184 records in RAM.
INFO 2026-06-08 08:18:23 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 1s. Last read position: chr7:76,510,741
INFO 2026-06-08 08:18:23 MarkDuplicates Tracking 565509 as yet unmatched pairs. 21337 records in RAM.
INFO 2026-06-08 08:18:25 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 2s. Last read position: chr7:92,581,514
INFO 2026-06-08 08:18:25 MarkDuplicates Tracking 563695 as yet unmatched pairs. 19520 records in RAM.
INFO 2026-06-08 08:18:27 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr7:99,968,339
INFO 2026-06-08 08:18:27 MarkDuplicates Tracking 561228 as yet unmatched pairs. 17050 records in RAM.
INFO 2026-06-08 08:18:29 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 1s. Last read position: chr7:100,678,600
INFO 2026-06-08 08:18:29 MarkDuplicates Tracking 559211 as yet unmatched pairs. 15033 records in RAM.
INFO 2026-06-08 08:18:31 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 1s. Last read position: chr7:102,545,468
INFO 2026-06-08 08:18:31 MarkDuplicates Tracking 557071 as yet unmatched pairs. 12891 records in RAM.
INFO 2026-06-08 08:18:32 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 1s. Last read position: chr7:107,940,039
INFO 2026-06-08 08:18:32 MarkDuplicates Tracking 555465 as yet unmatched pairs. 11283 records in RAM.
INFO 2026-06-08 08:18:34 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 1s. Last read position: chr7:130,990,248
INFO 2026-06-08 08:18:34 MarkDuplicates Tracking 553321 as yet unmatched pairs. 9138 records in RAM.
INFO 2026-06-08 08:18:36 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 1s. Last read position: chr7:140,024,591
INFO 2026-06-08 08:18:36 MarkDuplicates Tracking 551447 as yet unmatched pairs. 7264 records in RAM.
INFO 2026-06-08 08:18:37 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 1s. Last read position: chr7:144,286,433
INFO 2026-06-08 08:18:37 MarkDuplicates Tracking 549281 as yet unmatched pairs. 5098 records in RAM.
INFO 2026-06-08 08:18:39 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 2s. Last read position: chr7:151,044,101
INFO 2026-06-08 08:18:39 MarkDuplicates Tracking 547299 as yet unmatched pairs. 3116 records in RAM.
INFO 2026-06-08 08:18:41 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 1s. Last read position: chr7:156,950,224
INFO 2026-06-08 08:18:41 MarkDuplicates Tracking 544817 as yet unmatched pairs. 630 records in RAM.
INFO 2026-06-08 08:18:43 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 2s. Last read position: chr8:17,955,474
INFO 2026-06-08 08:18:43 MarkDuplicates Tracking 542957 as yet unmatched pairs. 35306 records in RAM.
INFO 2026-06-08 08:18:45 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 2s. Last read position: chr8:25,408,040
INFO 2026-06-08 08:18:45 MarkDuplicates Tracking 540447 as yet unmatched pairs. 32795 records in RAM.
INFO 2026-06-08 08:18:48 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 2s. Last read position: chr8:37,697,406
INFO 2026-06-08 08:18:48 MarkDuplicates Tracking 538402 as yet unmatched pairs. 30746 records in RAM.
INFO 2026-06-08 08:18:49 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 1s. Last read position: chr8:41,724,468
INFO 2026-06-08 08:18:49 MarkDuplicates Tracking 535849 as yet unmatched pairs. 28193 records in RAM.
INFO 2026-06-08 08:18:51 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 1s. Last read position: chr8:58,815,516
INFO 2026-06-08 08:18:51 MarkDuplicates Tracking 533661 as yet unmatched pairs. 26003 records in RAM.
INFO 2026-06-08 08:18:53 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 1s. Last read position: chr8:93,734,176
INFO 2026-06-08 08:18:53 MarkDuplicates Tracking 532008 as yet unmatched pairs. 24348 records in RAM.
INFO 2026-06-08 08:18:55 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 2s. Last read position: chr8:102,836,321
INFO 2026-06-08 08:18:55 MarkDuplicates Tracking 529404 as yet unmatched pairs. 21744 records in RAM.
INFO 2026-06-08 08:18:57 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 1s. Last read position: chr8:124,475,221
INFO 2026-06-08 08:18:57 MarkDuplicates Tracking 527433 as yet unmatched pairs. 19766 records in RAM.
INFO 2026-06-08 08:18:59 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 1s. Last read position: chr8:143,378,724
INFO 2026-06-08 08:18:59 MarkDuplicates Tracking 525267 as yet unmatched pairs. 17598 records in RAM.
INFO 2026-06-08 08:19:00 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 1s. Last read position: chr8:143,858,255
INFO 2026-06-08 08:19:00 MarkDuplicates Tracking 522814 as yet unmatched pairs. 15143 records in RAM.
INFO 2026-06-08 08:19:01 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:05:43s. Time for last 1,000,000: 1s. Last read position: chr8:143,859,121
INFO 2026-06-08 08:19:01 MarkDuplicates Tracking 524843 as yet unmatched pairs. 17172 records in RAM.
INFO 2026-06-08 08:19:03 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 1s. Last read position: chr8:143,860,573
INFO 2026-06-08 08:19:03 MarkDuplicates Tracking 522462 as yet unmatched pairs. 14791 records in RAM.
INFO 2026-06-08 08:19:04 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 1s. Last read position: chr8:143,861,525
INFO 2026-06-08 08:19:04 MarkDuplicates Tracking 520862 as yet unmatched pairs. 13191 records in RAM.
INFO 2026-06-08 08:19:05 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 1s. Last read position: chr8:143,862,415
INFO 2026-06-08 08:19:05 MarkDuplicates Tracking 521867 as yet unmatched pairs. 14196 records in RAM.
INFO 2026-06-08 08:19:07 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 1s. Last read position: chr8:143,863,414
INFO 2026-06-08 08:19:07 MarkDuplicates Tracking 518604 as yet unmatched pairs. 10933 records in RAM.
INFO 2026-06-08 08:19:08 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 1s. Last read position: chr8:143,864,699
INFO 2026-06-08 08:19:08 MarkDuplicates Tracking 520475 as yet unmatched pairs. 12804 records in RAM.
INFO 2026-06-08 08:19:10 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 1s. Last read position: chr8:143,865,636
INFO 2026-06-08 08:19:10 MarkDuplicates Tracking 517129 as yet unmatched pairs. 9456 records in RAM.
INFO 2026-06-08 08:19:11 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 1s. Last read position: chr8:143,867,822
INFO 2026-06-08 08:19:11 MarkDuplicates Tracking 517126 as yet unmatched pairs. 9453 records in RAM.
INFO 2026-06-08 08:19:13 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 2s. Last read position: chr8:143,921,484
INFO 2026-06-08 08:19:13 MarkDuplicates Tracking 514985 as yet unmatched pairs. 7310 records in RAM.
INFO 2026-06-08 08:19:15 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 2s. Last read position: chr8:143,984,704
INFO 2026-06-08 08:19:15 MarkDuplicates Tracking 511699 as yet unmatched pairs. 4024 records in RAM.
INFO 2026-06-08 08:19:17 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 1s. Last read position: chr8:144,512,469
INFO 2026-06-08 08:19:17 MarkDuplicates Tracking 508283 as yet unmatched pairs. 608 records in RAM.
INFO 2026-06-08 08:19:19 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 2s. Last read position: chr9:7,169,819
INFO 2026-06-08 08:19:19 MarkDuplicates Tracking 506107 as yet unmatched pairs. 31550 records in RAM.
INFO 2026-06-08 08:19:21 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 1s. Last read position: chr9:34,647,880
INFO 2026-06-08 08:19:21 MarkDuplicates Tracking 503994 as yet unmatched pairs. 29436 records in RAM.
INFO 2026-06-08 08:19:23 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 1s. Last read position: chr9:37,163,126
INFO 2026-06-08 08:19:23 MarkDuplicates Tracking 501845 as yet unmatched pairs. 27250 records in RAM.
INFO 2026-06-08 08:19:24 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 1s. Last read position: chr9:83,977,042
INFO 2026-06-08 08:19:24 MarkDuplicates Tracking 500098 as yet unmatched pairs. 25502 records in RAM.
INFO 2026-06-08 08:19:26 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 1s. Last read position: chr9:93,335,528
INFO 2026-06-08 08:19:26 MarkDuplicates Tracking 497770 as yet unmatched pairs. 23171 records in RAM.
INFO 2026-06-08 08:19:28 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 1s. Last read position: chr9:105,356,230
INFO 2026-06-08 08:19:28 MarkDuplicates Tracking 495535 as yet unmatched pairs. 20933 records in RAM.
INFO 2026-06-08 08:19:30 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 1s. Last read position: chr9:114,356,863
INFO 2026-06-08 08:19:30 MarkDuplicates Tracking 493762 as yet unmatched pairs. 19158 records in RAM.
INFO 2026-06-08 08:19:31 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 1s. Last read position: chr9:121,328,912
INFO 2026-06-08 08:19:31 MarkDuplicates Tracking 490991 as yet unmatched pairs. 16387 records in RAM.
INFO 2026-06-08 08:19:33 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 1s. Last read position: chr9:127,886,704
INFO 2026-06-08 08:19:33 MarkDuplicates Tracking 488671 as yet unmatched pairs. 14067 records in RAM.
INFO 2026-06-08 08:19:35 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 1s. Last read position: chr9:129,006,474
INFO 2026-06-08 08:19:35 MarkDuplicates Tracking 486538 as yet unmatched pairs. 11934 records in RAM.
INFO 2026-06-08 08:19:37 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 1s. Last read position: chr9:131,467,666
INFO 2026-06-08 08:19:37 MarkDuplicates Tracking 484413 as yet unmatched pairs. 9809 records in RAM.
INFO 2026-06-08 08:19:39 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 1s. Last read position: chr9:134,036,203
INFO 2026-06-08 08:19:39 MarkDuplicates Tracking 481813 as yet unmatched pairs. 7209 records in RAM.
INFO 2026-06-08 08:19:40 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 1s. Last read position: chr9:136,506,615
INFO 2026-06-08 08:19:40 MarkDuplicates Tracking 479396 as yet unmatched pairs. 4792 records in RAM.
INFO 2026-06-08 08:19:42 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 1s. Last read position: chr9:137,110,880
INFO 2026-06-08 08:19:42 MarkDuplicates Tracking 476750 as yet unmatched pairs. 2141 records in RAM.
INFO 2026-06-08 08:19:44 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 1s. Last read position: chr10:3,170,124
INFO 2026-06-08 08:19:44 MarkDuplicates Tracking 474164 as yet unmatched pairs. 25393 records in RAM.
INFO 2026-06-08 08:19:45 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 1s. Last read position: chr10:8,058,580
INFO 2026-06-08 08:19:45 MarkDuplicates Tracking 476428 as yet unmatched pairs. 27656 records in RAM.
INFO 2026-06-08 08:19:47 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 2s. Last read position: chr10:17,695,202
INFO 2026-06-08 08:19:47 MarkDuplicates Tracking 469706 as yet unmatched pairs. 20932 records in RAM.
INFO 2026-06-08 08:19:49 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:06:31s. Time for last 1,000,000: 2s. Last read position: chr10:32,018,536
INFO 2026-06-08 08:19:49 MarkDuplicates Tracking 467822 as yet unmatched pairs. 19047 records in RAM.
INFO 2026-06-08 08:19:52 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 2s. Last read position: chr10:45,755,043
INFO 2026-06-08 08:19:52 MarkDuplicates Tracking 465713 as yet unmatched pairs. 16936 records in RAM.
INFO 2026-06-08 08:19:53 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:06:35s. Time for last 1,000,000: 1s. Last read position: chr10:60,572,468
INFO 2026-06-08 08:19:53 MarkDuplicates Tracking 463558 as yet unmatched pairs. 14781 records in RAM.
INFO 2026-06-08 08:19:55 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 1s. Last read position: chr10:73,125,316
INFO 2026-06-08 08:19:55 MarkDuplicates Tracking 461060 as yet unmatched pairs. 12281 records in RAM.
INFO 2026-06-08 08:19:57 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 1s. Last read position: chr10:77,821,756
INFO 2026-06-08 08:19:57 MarkDuplicates Tracking 459142 as yet unmatched pairs. 10363 records in RAM.
INFO 2026-06-08 08:19:59 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 1s. Last read position: chr10:87,366,382
INFO 2026-06-08 08:19:59 MarkDuplicates Tracking 457218 as yet unmatched pairs. 8439 records in RAM.
INFO 2026-06-08 08:20:00 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 1s. Last read position: chr10:100,498,157
INFO 2026-06-08 08:20:00 MarkDuplicates Tracking 454974 as yet unmatched pairs. 6193 records in RAM.
INFO 2026-06-08 08:20:02 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:06:44s. Time for last 1,000,000: 1s. Last read position: chr10:110,582,071
INFO 2026-06-08 08:20:02 MarkDuplicates Tracking 452637 as yet unmatched pairs. 3854 records in RAM.
INFO 2026-06-08 08:20:04 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:06:46s. Time for last 1,000,000: 1s. Last read position: chr10:122,249,628
INFO 2026-06-08 08:20:04 MarkDuplicates Tracking 450400 as yet unmatched pairs. 1615 records in RAM.
INFO 2026-06-08 08:20:06 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 2s. Last read position: chr11:294,298
INFO 2026-06-08 08:20:06 MarkDuplicates Tracking 449084 as yet unmatched pairs. 56178 records in RAM.
INFO 2026-06-08 08:20:08 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 1s. Last read position: chr11:721,158
INFO 2026-06-08 08:20:08 MarkDuplicates Tracking 445436 as yet unmatched pairs. 52529 records in RAM.
INFO 2026-06-08 08:20:10 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 1s. Last read position: chr11:1,244,378
INFO 2026-06-08 08:20:10 MarkDuplicates Tracking 444327 as yet unmatched pairs. 51419 records in RAM.
INFO 2026-06-08 08:20:11 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 1s. Last read position: chr11:1,248,827
INFO 2026-06-08 08:20:11 MarkDuplicates Tracking 443937 as yet unmatched pairs. 51028 records in RAM.
INFO 2026-06-08 08:20:13 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 1s. Last read position: chr11:1,881,569
INFO 2026-06-08 08:20:13 MarkDuplicates Tracking 441134 as yet unmatched pairs. 48225 records in RAM.
INFO 2026-06-08 08:20:14 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 1s. Last read position: chr11:6,610,496
INFO 2026-06-08 08:20:14 MarkDuplicates Tracking 438510 as yet unmatched pairs. 45600 records in RAM.
INFO 2026-06-08 08:20:16 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 1s. Last read position: chr11:16,794,542
INFO 2026-06-08 08:20:16 MarkDuplicates Tracking 436301 as yet unmatched pairs. 43391 records in RAM.
INFO 2026-06-08 08:20:18 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:07:00s. Time for last 1,000,000: 1s. Last read position: chr11:35,685,233
INFO 2026-06-08 08:20:18 MarkDuplicates Tracking 434232 as yet unmatched pairs. 41320 records in RAM.
INFO 2026-06-08 08:20:20 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 2s. Last read position: chr11:47,295,908
INFO 2026-06-08 08:20:20 MarkDuplicates Tracking 431855 as yet unmatched pairs. 38942 records in RAM.
INFO 2026-06-08 08:20:22 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:07:04s. Time for last 1,000,000: 1s. Last read position: chr11:59,854,774
INFO 2026-06-08 08:20:22 MarkDuplicates Tracking 429567 as yet unmatched pairs. 36654 records in RAM.
INFO 2026-06-08 08:20:24 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 1s. Last read position: chr11:62,517,558
INFO 2026-06-08 08:20:24 MarkDuplicates Tracking 427584 as yet unmatched pairs. 34659 records in RAM.
INFO 2026-06-08 08:20:26 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:07:07s. Time for last 1,000,000: 1s. Last read position: chr11:62,531,092
INFO 2026-06-08 08:20:26 MarkDuplicates Tracking 426147 as yet unmatched pairs. 33221 records in RAM.
INFO 2026-06-08 08:20:27 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:07:09s. Time for last 1,000,000: 1s. Last read position: chr11:62,885,262
INFO 2026-06-08 08:20:27 MarkDuplicates Tracking 423345 as yet unmatched pairs. 30418 records in RAM.
INFO 2026-06-08 08:20:29 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:07:11s. Time for last 1,000,000: 1s. Last read position: chr11:64,765,933
INFO 2026-06-08 08:20:29 MarkDuplicates Tracking 421212 as yet unmatched pairs. 28283 records in RAM.
INFO 2026-06-08 08:20:30 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:07:12s. Time for last 1,000,000: 1s. Last read position: chr11:65,553,512
INFO 2026-06-08 08:20:30 MarkDuplicates Tracking 418628 as yet unmatched pairs. 25689 records in RAM.
INFO 2026-06-08 08:20:32 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:07:14s. Time for last 1,000,000: 1s. Last read position: chr11:65,865,812
INFO 2026-06-08 08:20:32 MarkDuplicates Tracking 416175 as yet unmatched pairs. 23235 records in RAM.
INFO 2026-06-08 08:20:34 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:07:16s. Time for last 1,000,000: 1s. Last read position: chr11:66,844,294
INFO 2026-06-08 08:20:34 MarkDuplicates Tracking 413490 as yet unmatched pairs. 20550 records in RAM.
INFO 2026-06-08 08:20:36 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:07:18s. Time for last 1,000,000: 1s. Last read position: chr11:67,666,318
INFO 2026-06-08 08:20:36 MarkDuplicates Tracking 411067 as yet unmatched pairs. 18124 records in RAM.
INFO 2026-06-08 08:20:37 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:07:19s. Time for last 1,000,000: 1s. Last read position: chr11:69,653,257
INFO 2026-06-08 08:20:37 MarkDuplicates Tracking 408964 as yet unmatched pairs. 16021 records in RAM.
INFO 2026-06-08 08:20:39 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:07:21s. Time for last 1,000,000: 1s. Last read position: chr11:72,229,980
INFO 2026-06-08 08:20:39 MarkDuplicates Tracking 406390 as yet unmatched pairs. 13430 records in RAM.
INFO 2026-06-08 08:20:41 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:07:23s. Time for last 1,000,000: 1s. Last read position: chr11:75,401,716
INFO 2026-06-08 08:20:41 MarkDuplicates Tracking 404728 as yet unmatched pairs. 11768 records in RAM.
INFO 2026-06-08 08:20:43 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:07:24s. Time for last 1,000,000: 1s. Last read position: chr11:93,683,576
INFO 2026-06-08 08:20:43 MarkDuplicates Tracking 401524 as yet unmatched pairs. 8562 records in RAM.
INFO 2026-06-08 08:20:45 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 2s. Last read position: chr11:110,164,585
INFO 2026-06-08 08:20:45 MarkDuplicates Tracking 398919 as yet unmatched pairs. 5955 records in RAM.
INFO 2026-06-08 08:20:47 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:07:29s. Time for last 1,000,000: 2s. Last read position: chr11:118,506,336
INFO 2026-06-08 08:20:47 MarkDuplicates Tracking 397086 as yet unmatched pairs. 4122 records in RAM.
INFO 2026-06-08 08:20:48 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:07:30s. Time for last 1,000,000: 1s. Last read position: chr11:121,615,675
INFO 2026-06-08 08:20:48 MarkDuplicates Tracking 394953 as yet unmatched pairs. 1989 records in RAM.
INFO 2026-06-08 08:20:51 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:07:33s. Time for last 1,000,000: 2s. Last read position: chr12:565,321
INFO 2026-06-08 08:20:51 MarkDuplicates Tracking 392745 as yet unmatched pairs. 42611 records in RAM.
INFO 2026-06-08 08:20:52 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:07:34s. Time for last 1,000,000: 1s. Last read position: chr12:6,453,045
INFO 2026-06-08 08:20:52 MarkDuplicates Tracking 390602 as yet unmatched pairs. 40468 records in RAM.
INFO 2026-06-08 08:20:54 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:07:36s. Time for last 1,000,000: 1s. Last read position: chr12:7,150,996
INFO 2026-06-08 08:20:54 MarkDuplicates Tracking 388404 as yet unmatched pairs. 38270 records in RAM.
INFO 2026-06-08 08:20:56 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:07:38s. Time for last 1,000,000: 1s. Last read position: chr12:14,794,637
INFO 2026-06-08 08:20:56 MarkDuplicates Tracking 386209 as yet unmatched pairs. 36075 records in RAM.
INFO 2026-06-08 08:20:57 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:07:39s. Time for last 1,000,000: 1s. Last read position: chr12:42,446,145
INFO 2026-06-08 08:20:57 MarkDuplicates Tracking 384221 as yet unmatched pairs. 34083 records in RAM.
INFO 2026-06-08 08:20:59 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:07:41s. Time for last 1,000,000: 1s. Last read position: chr12:49,038,300
INFO 2026-06-08 08:20:59 MarkDuplicates Tracking 382543 as yet unmatched pairs. 32403 records in RAM.
INFO 2026-06-08 08:21:01 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:07:43s. Time for last 1,000,000: 1s. Last read position: chr12:49,792,003
INFO 2026-06-08 08:21:01 MarkDuplicates Tracking 379965 as yet unmatched pairs. 29825 records in RAM.
INFO 2026-06-08 08:21:03 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:07:45s. Time for last 1,000,000: 1s. Last read position: chr12:53,172,368
INFO 2026-06-08 08:21:03 MarkDuplicates Tracking 377890 as yet unmatched pairs. 27747 records in RAM.
INFO 2026-06-08 08:21:05 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:07:47s. Time for last 1,000,000: 1s. Last read position: chr12:54,398,607
INFO 2026-06-08 08:21:05 MarkDuplicates Tracking 375584 as yet unmatched pairs. 25440 records in RAM.
INFO 2026-06-08 08:21:06 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:07:48s. Time for last 1,000,000: 1s. Last read position: chr12:56,285,949
INFO 2026-06-08 08:21:06 MarkDuplicates Tracking 373449 as yet unmatched pairs. 23303 records in RAM.
INFO 2026-06-08 08:21:08 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:07:50s. Time for last 1,000,000: 1s. Last read position: chr12:57,099,354
INFO 2026-06-08 08:21:08 MarkDuplicates Tracking 372261 as yet unmatched pairs. 22115 records in RAM.
INFO 2026-06-08 08:21:10 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:07:52s. Time for last 1,000,000: 1s. Last read position: chr12:57,599,126
INFO 2026-06-08 08:21:10 MarkDuplicates Tracking 369105 as yet unmatched pairs. 18959 records in RAM.
INFO 2026-06-08 08:21:12 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:07:54s. Time for last 1,000,000: 1s. Last read position: chr12:71,615,255
INFO 2026-06-08 08:21:12 MarkDuplicates Tracking 366931 as yet unmatched pairs. 16784 records in RAM.
INFO 2026-06-08 08:21:14 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:07:56s. Time for last 1,000,000: 1s. Last read position: chr12:100,334,165
INFO 2026-06-08 08:21:14 MarkDuplicates Tracking 364904 as yet unmatched pairs. 14756 records in RAM.
INFO 2026-06-08 08:21:16 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:07:58s. Time for last 1,000,000: 1s. Last read position: chr12:110,339,559
INFO 2026-06-08 08:21:16 MarkDuplicates Tracking 362857 as yet unmatched pairs. 12709 records in RAM.
INFO 2026-06-08 08:21:18 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:08:00s. Time for last 1,000,000: 1s. Last read position: chr12:113,269,756
INFO 2026-06-08 08:21:18 MarkDuplicates Tracking 360637 as yet unmatched pairs. 10488 records in RAM.
INFO 2026-06-08 08:21:19 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:08:01s. Time for last 1,000,000: 1s. Last read position: chr12:120,534,692
INFO 2026-06-08 08:21:19 MarkDuplicates Tracking 358312 as yet unmatched pairs. 8163 records in RAM.
INFO 2026-06-08 08:21:22 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:08:04s. Time for last 1,000,000: 2s. Last read position: chr12:122,546,620
INFO 2026-06-08 08:21:22 MarkDuplicates Tracking 355672 as yet unmatched pairs. 5522 records in RAM.
INFO 2026-06-08 08:21:24 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:08:06s. Time for last 1,000,000: 2s. Last read position: chr12:124,372,558
INFO 2026-06-08 08:21:24 MarkDuplicates Tracking 353887 as yet unmatched pairs. 3737 records in RAM.
INFO 2026-06-08 08:21:26 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:08:08s. Time for last 1,000,000: 1s. Last read position: chr12:132,583,541
INFO 2026-06-08 08:21:26 MarkDuplicates Tracking 351304 as yet unmatched pairs. 1154 records in RAM.
INFO 2026-06-08 08:21:28 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:08:10s. Time for last 1,000,000: 1s. Last read position: chr13:27,256,449
INFO 2026-06-08 08:21:28 MarkDuplicates Tracking 349066 as yet unmatched pairs. 7831 records in RAM.
INFO 2026-06-08 08:21:30 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:08:12s. Time for last 1,000,000: 1s. Last read position: chr13:44,574,914
INFO 2026-06-08 08:21:30 MarkDuplicates Tracking 347151 as yet unmatched pairs. 5915 records in RAM.
INFO 2026-06-08 08:21:32 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:08:14s. Time for last 1,000,000: 1s. Last read position: chr13:79,365,617
INFO 2026-06-08 08:21:32 MarkDuplicates Tracking 345050 as yet unmatched pairs. 3813 records in RAM.
INFO 2026-06-08 08:21:33 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:08:15s. Time for last 1,000,000: 1s. Last read position: chr13:110,883,672
INFO 2026-06-08 08:21:33 MarkDuplicates Tracking 342510 as yet unmatched pairs. 1271 records in RAM.
INFO 2026-06-08 08:21:35 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:08:17s. Time for last 1,000,000: 2s. Last read position: chr14:21,408,545
INFO 2026-06-08 08:21:35 MarkDuplicates Tracking 340201 as yet unmatched pairs. 23685 records in RAM.
INFO 2026-06-08 08:21:37 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 1s. Last read position: chr14:24,119,218
INFO 2026-06-08 08:21:37 MarkDuplicates Tracking 337817 as yet unmatched pairs. 21300 records in RAM.
INFO 2026-06-08 08:21:39 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 1s. Last read position: chr14:34,713,310
INFO 2026-06-08 08:21:39 MarkDuplicates Tracking 335613 as yet unmatched pairs. 19093 records in RAM.
INFO 2026-06-08 08:21:41 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 1s. Last read position: chr14:51,720,328
INFO 2026-06-08 08:21:41 MarkDuplicates Tracking 333321 as yet unmatched pairs. 16798 records in RAM.
INFO 2026-06-08 08:21:43 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 2s. Last read position: chr14:64,741,416
INFO 2026-06-08 08:21:43 MarkDuplicates Tracking 331212 as yet unmatched pairs. 14688 records in RAM.
INFO 2026-06-08 08:21:45 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:08:27s. Time for last 1,000,000: 2s. Last read position: chr14:73,739,905
INFO 2026-06-08 08:21:45 MarkDuplicates Tracking 328857 as yet unmatched pairs. 12332 records in RAM.
INFO 2026-06-08 08:21:47 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 1s. Last read position: chr14:89,893,046
INFO 2026-06-08 08:21:47 MarkDuplicates Tracking 326352 as yet unmatched pairs. 9824 records in RAM.
INFO 2026-06-08 08:21:49 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:08:31s. Time for last 1,000,000: 1s. Last read position: chr14:96,331,448
INFO 2026-06-08 08:21:49 MarkDuplicates Tracking 323978 as yet unmatched pairs. 7444 records in RAM.
INFO 2026-06-08 08:21:51 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:08:33s. Time for last 1,000,000: 2s. Last read position: chr14:102,034,045
INFO 2026-06-08 08:21:51 MarkDuplicates Tracking 321754 as yet unmatched pairs. 5195 records in RAM.
INFO 2026-06-08 08:21:53 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 1s. Last read position: chr14:104,802,052
INFO 2026-06-08 08:21:53 MarkDuplicates Tracking 319635 as yet unmatched pairs. 3075 records in RAM.
INFO 2026-06-08 08:21:55 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 1s. Last read position: chr14:105,741,486
INFO 2026-06-08 08:21:55 MarkDuplicates Tracking 318144 as yet unmatched pairs. 1566 records in RAM.
INFO 2026-06-08 08:21:57 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:08:39s. Time for last 1,000,000: 2s. Last read position: chr15:28,680,785
INFO 2026-06-08 08:21:57 MarkDuplicates Tracking 315701 as yet unmatched pairs. 24119 records in RAM.
INFO 2026-06-08 08:23:01 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:09:43s. Time for last 1,000,000: 63s. Last read position: chr15:39,600,852
INFO 2026-06-08 08:23:01 MarkDuplicates Tracking 314046 as yet unmatched pairs. 22464 records in RAM.
INFO 2026-06-08 08:23:02 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 1s. Last read position: chr15:42,359,868
INFO 2026-06-08 08:23:02 MarkDuplicates Tracking 311700 as yet unmatched pairs. 20116 records in RAM.
INFO 2026-06-08 08:23:04 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:09:46s. Time for last 1,000,000: 1s. Last read position: chr15:44,615,435
INFO 2026-06-08 08:23:04 MarkDuplicates Tracking 309738 as yet unmatched pairs. 18154 records in RAM.
INFO 2026-06-08 08:23:06 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:09:48s. Time for last 1,000,000: 1s. Last read position: chr15:57,232,396
INFO 2026-06-08 08:23:06 MarkDuplicates Tracking 308031 as yet unmatched pairs. 16445 records in RAM.
INFO 2026-06-08 08:23:08 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:09:50s. Time for last 1,000,000: 2s. Last read position: chr15:64,623,016
INFO 2026-06-08 08:23:08 MarkDuplicates Tracking 305246 as yet unmatched pairs. 13659 records in RAM.
INFO 2026-06-08 08:23:10 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:09:52s. Time for last 1,000,000: 1s. Last read position: chr15:71,242,933
INFO 2026-06-08 08:23:10 MarkDuplicates Tracking 303300 as yet unmatched pairs. 11712 records in RAM.
INFO 2026-06-08 08:23:12 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:09:54s. Time for last 1,000,000: 1s. Last read position: chr15:75,202,035
INFO 2026-06-08 08:23:12 MarkDuplicates Tracking 300357 as yet unmatched pairs. 8769 records in RAM.
INFO 2026-06-08 08:23:14 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:09:56s. Time for last 1,000,000: 1s. Last read position: chr15:81,296,940
INFO 2026-06-08 08:23:14 MarkDuplicates Tracking 298139 as yet unmatched pairs. 6550 records in RAM.
INFO 2026-06-08 08:23:15 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:09:57s. Time for last 1,000,000: 1s. Last read position: chr15:88,913,252
INFO 2026-06-08 08:23:15 MarkDuplicates Tracking 296325 as yet unmatched pairs. 4733 records in RAM.
INFO 2026-06-08 08:23:17 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 1s. Last read position: chr15:90,067,506
INFO 2026-06-08 08:23:17 MarkDuplicates Tracking 294406 as yet unmatched pairs. 2814 records in RAM.
INFO 2026-06-08 08:23:19 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:10:01s. Time for last 1,000,000: 1s. Last read position: chr15:101,251,188
INFO 2026-06-08 08:23:19 MarkDuplicates Tracking 291807 as yet unmatched pairs. 211 records in RAM.
INFO 2026-06-08 08:23:21 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:10:03s. Time for last 1,000,000: 2s. Last read position: chr16:715,926
INFO 2026-06-08 08:23:21 MarkDuplicates Tracking 289602 as yet unmatched pairs. 46131 records in RAM.
INFO 2026-06-08 08:23:23 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:10:05s. Time for last 1,000,000: 1s. Last read position: chr16:1,975,823
INFO 2026-06-08 08:23:23 MarkDuplicates Tracking 286440 as yet unmatched pairs. 42968 records in RAM.
INFO 2026-06-08 08:23:24 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 1s. Last read position: chr16:2,756,497
INFO 2026-06-08 08:23:24 MarkDuplicates Tracking 284637 as yet unmatched pairs. 41165 records in RAM.
INFO 2026-06-08 08:23:26 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:10:08s. Time for last 1,000,000: 1s. Last read position: chr16:2,767,754
INFO 2026-06-08 08:23:26 MarkDuplicates Tracking 283268 as yet unmatched pairs. 39795 records in RAM.
INFO 2026-06-08 08:23:28 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:10:10s. Time for last 1,000,000: 2s. Last read position: chr16:3,773,797
INFO 2026-06-08 08:23:28 MarkDuplicates Tracking 280121 as yet unmatched pairs. 36648 records in RAM.
INFO 2026-06-08 08:23:30 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 1s. Last read position: chr16:10,907,982
INFO 2026-06-08 08:23:30 MarkDuplicates Tracking 277697 as yet unmatched pairs. 34223 records in RAM.
INFO 2026-06-08 08:23:32 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:10:14s. Time for last 1,000,000: 1s. Last read position: chr16:14,929,705
INFO 2026-06-08 08:23:32 MarkDuplicates Tracking 275958 as yet unmatched pairs. 32483 records in RAM.
INFO 2026-06-08 08:23:33 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:10:15s. Time for last 1,000,000: 1s. Last read position: chr16:16,328,998
INFO 2026-06-08 08:23:33 MarkDuplicates Tracking 274831 as yet unmatched pairs. 31356 records in RAM.
INFO 2026-06-08 08:23:35 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:10:16s. Time for last 1,000,000: 1s. Last read position: chr16:18,358,520
INFO 2026-06-08 08:23:35 MarkDuplicates Tracking 274263 as yet unmatched pairs. 30787 records in RAM.
INFO 2026-06-08 08:23:36 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:10:18s. Time for last 1,000,000: 1s. Last read position: chr16:21,402,450
INFO 2026-06-08 08:23:36 MarkDuplicates Tracking 272482 as yet unmatched pairs. 29006 records in RAM.
INFO 2026-06-08 08:23:38 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:10:20s. Time for last 1,000,000: 1s. Last read position: chr16:21,405,242
INFO 2026-06-08 08:23:38 MarkDuplicates Tracking 272812 as yet unmatched pairs. 29335 records in RAM.
INFO 2026-06-08 08:23:40 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:10:22s. Time for last 1,000,000: 1s. Last read position: chr16:21,837,194
INFO 2026-06-08 08:23:40 MarkDuplicates Tracking 271182 as yet unmatched pairs. 27704 records in RAM.
INFO 2026-06-08 08:23:41 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:10:23s. Time for last 1,000,000: 1s. Last read position: chr16:22,533,746
INFO 2026-06-08 08:23:41 MarkDuplicates Tracking 270712 as yet unmatched pairs. 27234 records in RAM.
INFO 2026-06-08 08:23:42 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:10:24s. Time for last 1,000,000: 1s. Last read position: chr16:22,536,073
INFO 2026-06-08 08:23:42 MarkDuplicates Tracking 270148 as yet unmatched pairs. 26670 records in RAM.
INFO 2026-06-08 08:23:44 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 1s. Last read position: chr16:28,538,209
INFO 2026-06-08 08:23:44 MarkDuplicates Tracking 267963 as yet unmatched pairs. 24485 records in RAM.
INFO 2026-06-08 08:23:46 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:10:28s. Time for last 1,000,000: 1s. Last read position: chr16:29,383,883
INFO 2026-06-08 08:23:46 MarkDuplicates Tracking 267176 as yet unmatched pairs. 23697 records in RAM.
INFO 2026-06-08 08:23:47 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:10:29s. Time for last 1,000,000: 1s. Last read position: chr16:29,537,312
INFO 2026-06-08 08:23:47 MarkDuplicates Tracking 266005 as yet unmatched pairs. 22526 records in RAM.
INFO 2026-06-08 08:23:49 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:10:31s. Time for last 1,000,000: 1s. Last read position: chr16:30,188,192
INFO 2026-06-08 08:23:49 MarkDuplicates Tracking 263974 as yet unmatched pairs. 20494 records in RAM.
INFO 2026-06-08 08:23:50 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:10:32s. Time for last 1,000,000: 1s. Last read position: chr16:30,494,225
INFO 2026-06-08 08:23:50 MarkDuplicates Tracking 262554 as yet unmatched pairs. 19073 records in RAM.
INFO 2026-06-08 08:23:52 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:10:34s. Time for last 1,000,000: 1s. Last read position: chr16:30,930,502
INFO 2026-06-08 08:23:52 MarkDuplicates Tracking 260306 as yet unmatched pairs. 16825 records in RAM.
INFO 2026-06-08 08:23:54 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:10:36s. Time for last 1,000,000: 1s. Last read position: chr16:48,296,056
INFO 2026-06-08 08:23:54 MarkDuplicates Tracking 257672 as yet unmatched pairs. 14190 records in RAM.
INFO 2026-06-08 08:23:56 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:10:38s. Time for last 1,000,000: 1s. Last read position: chr16:57,363,894
INFO 2026-06-08 08:23:56 MarkDuplicates Tracking 255572 as yet unmatched pairs. 12080 records in RAM.
INFO 2026-06-08 08:23:57 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:10:39s. Time for last 1,000,000: 1s. Last read position: chr16:67,883,035
INFO 2026-06-08 08:23:57 MarkDuplicates Tracking 253204 as yet unmatched pairs. 9712 records in RAM.
INFO 2026-06-08 08:23:59 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:10:41s. Time for last 1,000,000: 1s. Last read position: chr16:71,850,320
INFO 2026-06-08 08:23:59 MarkDuplicates Tracking 251132 as yet unmatched pairs. 7640 records in RAM.
INFO 2026-06-08 08:24:02 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:10:44s. Time for last 1,000,000: 2s. Last read position: chr16:84,178,874
INFO 2026-06-08 08:24:02 MarkDuplicates Tracking 248921 as yet unmatched pairs. 5428 records in RAM.
INFO 2026-06-08 08:24:03 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:10:45s. Time for last 1,000,000: 1s. Last read position: chr16:88,706,168
INFO 2026-06-08 08:24:03 MarkDuplicates Tracking 246335 as yet unmatched pairs. 2839 records in RAM.
INFO 2026-06-08 08:24:05 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:10:47s. Time for last 1,000,000: 1s. Last read position: chr16:89,896,069
INFO 2026-06-08 08:24:05 MarkDuplicates Tracking 243938 as yet unmatched pairs. 442 records in RAM.
INFO 2026-06-08 08:24:08 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:10:49s. Time for last 1,000,000: 2s. Last read position: chr17:2,372,973
INFO 2026-06-08 08:24:08 MarkDuplicates Tracking 241411 as yet unmatched pairs. 55975 records in RAM.
INFO 2026-06-08 08:24:09 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:10:51s. Time for last 1,000,000: 1s. Last read position: chr17:4,974,471
INFO 2026-06-08 08:24:09 MarkDuplicates Tracking 239155 as yet unmatched pairs. 53719 records in RAM.
INFO 2026-06-08 08:24:11 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:10:53s. Time for last 1,000,000: 1s. Last read position: chr17:7,463,194
INFO 2026-06-08 08:24:11 MarkDuplicates Tracking 237290 as yet unmatched pairs. 51852 records in RAM.
INFO 2026-06-08 08:24:13 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:10:55s. Time for last 1,000,000: 1s. Last read position: chr17:7,894,971
INFO 2026-06-08 08:24:13 MarkDuplicates Tracking 235192 as yet unmatched pairs. 49754 records in RAM.
INFO 2026-06-08 08:24:15 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:10:57s. Time for last 1,000,000: 1s. Last read position: chr17:16,382,148
INFO 2026-06-08 08:24:15 MarkDuplicates Tracking 233245 as yet unmatched pairs. 47806 records in RAM.
INFO 2026-06-08 08:24:17 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:10:59s. Time for last 1,000,000: 1s. Last read position: chr17:19,283,399
INFO 2026-06-08 08:24:17 MarkDuplicates Tracking 230751 as yet unmatched pairs. 45312 records in RAM.
INFO 2026-06-08 08:24:19 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:11:01s. Time for last 1,000,000: 2s. Last read position: chr17:28,758,811
INFO 2026-06-08 08:24:19 MarkDuplicates Tracking 228550 as yet unmatched pairs. 43110 records in RAM.
INFO 2026-06-08 08:24:21 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:11:03s. Time for last 1,000,000: 2s. Last read position: chr17:31,886,040
INFO 2026-06-08 08:24:21 MarkDuplicates Tracking 226310 as yet unmatched pairs. 40870 records in RAM.
INFO 2026-06-08 08:24:23 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:11:05s. Time for last 1,000,000: 1s. Last read position: chr17:36,430,578
INFO 2026-06-08 08:24:23 MarkDuplicates Tracking 224644 as yet unmatched pairs. 39203 records in RAM.
INFO 2026-06-08 08:24:24 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:11:06s. Time for last 1,000,000: 1s. Last read position: chr17:38,721,897
INFO 2026-06-08 08:24:24 MarkDuplicates Tracking 223304 as yet unmatched pairs. 37863 records in RAM.
INFO 2026-06-08 08:24:26 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:11:08s. Time for last 1,000,000: 1s. Last read position: chr17:39,725,072
INFO 2026-06-08 08:24:26 MarkDuplicates Tracking 220852 as yet unmatched pairs. 35411 records in RAM.
INFO 2026-06-08 08:24:28 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:11:10s. Time for last 1,000,000: 2s. Last read position: chr17:41,690,835
INFO 2026-06-08 08:24:28 MarkDuplicates Tracking 218889 as yet unmatched pairs. 33447 records in RAM.
INFO 2026-06-08 08:24:31 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:11:13s. Time for last 1,000,000: 2s. Last read position: chr17:43,177,986
INFO 2026-06-08 08:24:31 MarkDuplicates Tracking 216174 as yet unmatched pairs. 30732 records in RAM.
INFO 2026-06-08 08:24:33 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:11:15s. Time for last 1,000,000: 1s. Last read position: chr17:45,437,948
INFO 2026-06-08 08:24:33 MarkDuplicates Tracking 213796 as yet unmatched pairs. 28354 records in RAM.
INFO 2026-06-08 08:24:34 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:11:16s. Time for last 1,000,000: 1s. Last read position: chr17:47,674,733
INFO 2026-06-08 08:24:34 MarkDuplicates Tracking 212387 as yet unmatched pairs. 26945 records in RAM.
INFO 2026-06-08 08:24:36 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:11:18s. Time for last 1,000,000: 1s. Last read position: chr17:48,943,940
INFO 2026-06-08 08:24:36 MarkDuplicates Tracking 209770 as yet unmatched pairs. 24328 records in RAM.
INFO 2026-06-08 08:24:38 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:11:20s. Time for last 1,000,000: 1s. Last read position: chr17:50,190,099
INFO 2026-06-08 08:24:38 MarkDuplicates Tracking 209104 as yet unmatched pairs. 23662 records in RAM.
INFO 2026-06-08 08:24:40 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:11:22s. Time for last 1,000,000: 1s. Last read position: chr17:50,199,419
INFO 2026-06-08 08:24:40 MarkDuplicates Tracking 205429 as yet unmatched pairs. 19987 records in RAM.
INFO 2026-06-08 08:24:42 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:11:24s. Time for last 1,000,000: 1s. Last read position: chr17:57,974,573
INFO 2026-06-08 08:24:42 MarkDuplicates Tracking 202919 as yet unmatched pairs. 17477 records in RAM.
INFO 2026-06-08 08:24:43 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:11:25s. Time for last 1,000,000: 1s. Last read position: chr17:63,421,757
INFO 2026-06-08 08:24:43 MarkDuplicates Tracking 200784 as yet unmatched pairs. 15342 records in RAM.
INFO 2026-06-08 08:24:45 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:11:27s. Time for last 1,000,000: 1s. Last read position: chr17:67,366,440
INFO 2026-06-08 08:24:45 MarkDuplicates Tracking 198450 as yet unmatched pairs. 13006 records in RAM.
INFO 2026-06-08 08:24:47 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:11:29s. Time for last 1,000,000: 1s. Last read position: chr17:75,339,034
INFO 2026-06-08 08:24:47 MarkDuplicates Tracking 196399 as yet unmatched pairs. 10951 records in RAM.
INFO 2026-06-08 08:24:49 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:11:31s. Time for last 1,000,000: 2s. Last read position: chr17:76,736,434
INFO 2026-06-08 08:24:49 MarkDuplicates Tracking 194816 as yet unmatched pairs. 9367 records in RAM.
INFO 2026-06-08 08:24:51 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:11:33s. Time for last 1,000,000: 1s. Last read position: chr17:80,210,660
INFO 2026-06-08 08:24:51 MarkDuplicates Tracking 191480 as yet unmatched pairs. 6028 records in RAM.
INFO 2026-06-08 08:24:53 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:11:35s. Time for last 1,000,000: 1s. Last read position: chr17:80,730,631
INFO 2026-06-08 08:24:53 MarkDuplicates Tracking 189241 as yet unmatched pairs. 3788 records in RAM.
INFO 2026-06-08 08:24:55 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:11:37s. Time for last 1,000,000: 1s. Last read position: chr17:82,091,364
INFO 2026-06-08 08:24:55 MarkDuplicates Tracking 186558 as yet unmatched pairs. 1103 records in RAM.
INFO 2026-06-08 08:24:57 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:11:39s. Time for last 1,000,000: 1s. Last read position: chr18:9,610,557
INFO 2026-06-08 08:24:57 MarkDuplicates Tracking 184275 as yet unmatched pairs. 6345 records in RAM.
INFO 2026-06-08 08:24:58 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:11:40s. Time for last 1,000,000: 1s. Last read position: chr18:36,796,979
INFO 2026-06-08 08:24:58 MarkDuplicates Tracking 182347 as yet unmatched pairs. 4416 records in RAM.
INFO 2026-06-08 08:25:00 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:11:42s. Time for last 1,000,000: 1s. Last read position: chr18:58,256,479
INFO 2026-06-08 08:25:00 MarkDuplicates Tracking 180345 as yet unmatched pairs. 2412 records in RAM.
INFO 2026-06-08 08:25:03 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:11:45s. Time for last 1,000,000: 2s. Last read position: chr19:572,616
INFO 2026-06-08 08:25:03 MarkDuplicates Tracking 177938 as yet unmatched pairs. 79079 records in RAM.
INFO 2026-06-08 08:25:04 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:11:46s. Time for last 1,000,000: 1s. Last read position: chr19:1,106,584
INFO 2026-06-08 08:25:04 MarkDuplicates Tracking 176392 as yet unmatched pairs. 77533 records in RAM.
INFO 2026-06-08 08:25:06 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:11:48s. Time for last 1,000,000: 2s. Last read position: chr19:1,622,329
INFO 2026-06-08 08:25:06 MarkDuplicates Tracking 172574 as yet unmatched pairs. 73715 records in RAM.
INFO 2026-06-08 08:25:08 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:11:50s. Time for last 1,000,000: 1s. Last read position: chr19:3,015,668
INFO 2026-06-08 08:25:08 MarkDuplicates Tracking 170073 as yet unmatched pairs. 71214 records in RAM.
INFO 2026-06-08 08:25:10 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:11:52s. Time for last 1,000,000: 2s. Last read position: chr19:4,454,075
INFO 2026-06-08 08:25:10 MarkDuplicates Tracking 167439 as yet unmatched pairs. 68579 records in RAM.
INFO 2026-06-08 08:25:13 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:11:55s. Time for last 1,000,000: 2s. Last read position: chr19:5,692,198
INFO 2026-06-08 08:25:13 MarkDuplicates Tracking 165110 as yet unmatched pairs. 66249 records in RAM.
INFO 2026-06-08 08:25:15 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:11:57s. Time for last 1,000,000: 1s. Last read position: chr19:7,550,584
INFO 2026-06-08 08:25:15 MarkDuplicates Tracking 162771 as yet unmatched pairs. 63909 records in RAM.
INFO 2026-06-08 08:25:17 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:11:59s. Time for last 1,000,000: 1s. Last read position: chr19:8,902,106
INFO 2026-06-08 08:25:17 MarkDuplicates Tracking 160400 as yet unmatched pairs. 61538 records in RAM.
INFO 2026-06-08 08:25:19 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:12:01s. Time for last 1,000,000: 1s. Last read position: chr19:10,350,859
INFO 2026-06-08 08:25:19 MarkDuplicates Tracking 158034 as yet unmatched pairs. 59172 records in RAM.
INFO 2026-06-08 08:25:20 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:12:02s. Time for last 1,000,000: 1s. Last read position: chr19:11,345,264
INFO 2026-06-08 08:25:20 MarkDuplicates Tracking 155700 as yet unmatched pairs. 56837 records in RAM.
INFO 2026-06-08 08:25:22 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:12:04s. Time for last 1,000,000: 1s. Last read position: chr19:12,953,053
INFO 2026-06-08 08:25:22 MarkDuplicates Tracking 153196 as yet unmatched pairs. 54333 records in RAM.
INFO 2026-06-08 08:25:24 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:12:06s. Time for last 1,000,000: 1s. Last read position: chr19:14,719,198
INFO 2026-06-08 08:25:24 MarkDuplicates Tracking 150680 as yet unmatched pairs. 51815 records in RAM.
INFO 2026-06-08 08:25:26 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:12:08s. Time for last 1,000,000: 1s. Last read position: chr19:15,403,580
INFO 2026-06-08 08:25:26 MarkDuplicates Tracking 148549 as yet unmatched pairs. 49684 records in RAM.
INFO 2026-06-08 08:25:29 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:12:11s. Time for last 1,000,000: 2s. Last read position: chr19:17,211,678
INFO 2026-06-08 08:25:29 MarkDuplicates Tracking 146389 as yet unmatched pairs. 47522 records in RAM.
INFO 2026-06-08 08:25:31 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:12:13s. Time for last 1,000,000: 1s. Last read position: chr19:18,280,683
INFO 2026-06-08 08:25:31 MarkDuplicates Tracking 143733 as yet unmatched pairs. 44860 records in RAM.
INFO 2026-06-08 08:25:32 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:12:14s. Time for last 1,000,000: 1s. Last read position: chr19:19,528,060
INFO 2026-06-08 08:25:32 MarkDuplicates Tracking 140707 as yet unmatched pairs. 41834 records in RAM.
INFO 2026-06-08 08:25:34 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:12:16s. Time for last 1,000,000: 1s. Last read position: chr19:35,021,846
INFO 2026-06-08 08:25:34 MarkDuplicates Tracking 138839 as yet unmatched pairs. 39963 records in RAM.
INFO 2026-06-08 08:25:36 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:12:18s. Time for last 1,000,000: 1s. Last read position: chr19:35,907,517
INFO 2026-06-08 08:25:36 MarkDuplicates Tracking 135763 as yet unmatched pairs. 36886 records in RAM.
INFO 2026-06-08 08:25:38 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:12:20s. Time for last 1,000,000: 1s. Last read position: chr19:39,172,995
INFO 2026-06-08 08:25:38 MarkDuplicates Tracking 133189 as yet unmatched pairs. 34310 records in RAM.
INFO 2026-06-08 08:25:39 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:12:21s. Time for last 1,000,000: 1s. Last read position: chr19:40,376,743
INFO 2026-06-08 08:25:39 MarkDuplicates Tracking 130715 as yet unmatched pairs. 31836 records in RAM.
INFO 2026-06-08 08:25:41 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:12:23s. Time for last 1,000,000: 1s. Last read position: chr19:41,715,798
INFO 2026-06-08 08:25:41 MarkDuplicates Tracking 128084 as yet unmatched pairs. 29205 records in RAM.
INFO 2026-06-08 08:25:43 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:12:25s. Time for last 1,000,000: 1s. Last read position: chr19:42,273,012
INFO 2026-06-08 08:25:43 MarkDuplicates Tracking 126143 as yet unmatched pairs. 27264 records in RAM.
INFO 2026-06-08 08:25:45 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:12:27s. Time for last 1,000,000: 2s. Last read position: chr19:44,032,130
INFO 2026-06-08 08:25:45 MarkDuplicates Tracking 123092 as yet unmatched pairs. 24197 records in RAM.
INFO 2026-06-08 08:25:47 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:12:29s. Time for last 1,000,000: 1s. Last read position: chr19:45,251,491
INFO 2026-06-08 08:25:47 MarkDuplicates Tracking 120362 as yet unmatched pairs. 21467 records in RAM.
INFO 2026-06-08 08:25:49 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:12:31s. Time for last 1,000,000: 1s. Last read position: chr19:46,920,259
INFO 2026-06-08 08:25:49 MarkDuplicates Tracking 118136 as yet unmatched pairs. 19239 records in RAM.
INFO 2026-06-08 08:25:50 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:12:32s. Time for last 1,000,000: 1s. Last read position: chr19:48,493,699
INFO 2026-06-08 08:25:50 MarkDuplicates Tracking 115247 as yet unmatched pairs. 16350 records in RAM.
INFO 2026-06-08 08:25:53 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:12:35s. Time for last 1,000,000: 2s. Last read position: chr19:49,196,773
INFO 2026-06-08 08:25:53 MarkDuplicates Tracking 112880 as yet unmatched pairs. 13983 records in RAM.
INFO 2026-06-08 08:25:54 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:12:36s. Time for last 1,000,000: 1s. Last read position: chr19:49,653,503
INFO 2026-06-08 08:25:54 MarkDuplicates Tracking 110158 as yet unmatched pairs. 11260 records in RAM.
INFO 2026-06-08 08:25:56 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:12:38s. Time for last 1,000,000: 1s. Last read position: chr19:50,482,682
INFO 2026-06-08 08:25:56 MarkDuplicates Tracking 107659 as yet unmatched pairs. 8761 records in RAM.
INFO 2026-06-08 08:25:59 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:12:41s. Time for last 1,000,000: 2s. Last read position: chr19:54,242,103
INFO 2026-06-08 08:25:59 MarkDuplicates Tracking 105660 as yet unmatched pairs. 6762 records in RAM.
INFO 2026-06-08 08:26:01 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:12:43s. Time for last 1,000,000: 1s. Last read position: chr19:55,347,217
INFO 2026-06-08 08:26:01 MarkDuplicates Tracking 103658 as yet unmatched pairs. 4760 records in RAM.
INFO 2026-06-08 08:26:02 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:12:44s. Time for last 1,000,000: 1s. Last read position: chr19:57,808,785
INFO 2026-06-08 08:26:02 MarkDuplicates Tracking 101116 as yet unmatched pairs. 2216 records in RAM.
INFO 2026-06-08 08:26:04 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:12:46s. Time for last 1,000,000: 1s. Last read position: chr20:427,363
INFO 2026-06-08 08:26:04 MarkDuplicates Tracking 98694 as yet unmatched pairs. 20139 records in RAM.
INFO 2026-06-08 08:26:06 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:12:48s. Time for last 1,000,000: 1s. Last read position: chr20:6,009,777
INFO 2026-06-08 08:26:06 MarkDuplicates Tracking 96005 as yet unmatched pairs. 17450 records in RAM.
INFO 2026-06-08 08:26:08 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:12:50s. Time for last 1,000,000: 1s. Last read position: chr20:25,469,972
INFO 2026-06-08 08:26:08 MarkDuplicates Tracking 93783 as yet unmatched pairs. 15228 records in RAM.
INFO 2026-06-08 08:26:09 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:12:51s. Time for last 1,000,000: 1s. Last read position: chr20:35,303,983
INFO 2026-06-08 08:26:09 MarkDuplicates Tracking 91678 as yet unmatched pairs. 13123 records in RAM.
INFO 2026-06-08 08:26:11 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:12:53s. Time for last 1,000,000: 1s. Last read position: chr20:40,688,450
INFO 2026-06-08 08:26:11 MarkDuplicates Tracking 89875 as yet unmatched pairs. 11319 records in RAM.
INFO 2026-06-08 08:26:14 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:12:55s. Time for last 1,000,000: 2s. Last read position: chr20:45,963,812
INFO 2026-06-08 08:26:14 MarkDuplicates Tracking 87663 as yet unmatched pairs. 9106 records in RAM.
INFO 2026-06-08 08:26:15 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:12:57s. Time for last 1,000,000: 1s. Last read position: chr20:51,523,413
INFO 2026-06-08 08:26:15 MarkDuplicates Tracking 87240 as yet unmatched pairs. 8680 records in RAM.
INFO 2026-06-08 08:26:17 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:12:59s. Time for last 1,000,000: 1s. Last read position: chr20:62,012,872
INFO 2026-06-08 08:26:17 MarkDuplicates Tracking 83266 as yet unmatched pairs. 4706 records in RAM.
INFO 2026-06-08 08:26:18 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:13:00s. Time for last 1,000,000: 1s. Last read position: chr20:63,520,861
INFO 2026-06-08 08:26:18 MarkDuplicates Tracking 82182 as yet unmatched pairs. 3622 records in RAM.
INFO 2026-06-08 08:26:20 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:13:02s. Time for last 1,000,000: 1s. Last read position: chr21:6,452,258
INFO 2026-06-08 08:26:20 MarkDuplicates Tracking 78407 as yet unmatched pairs. 12782 records in RAM.
INFO 2026-06-08 08:26:22 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:13:04s. Time for last 1,000,000: 1s. Last read position: chr21:8,258,888
INFO 2026-06-08 08:26:22 MarkDuplicates Tracking 76992 as yet unmatched pairs. 11356 records in RAM.
INFO 2026-06-08 08:26:23 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:13:05s. Time for last 1,000,000: 1s. Last read position: chr21:8,397,769
INFO 2026-06-08 08:26:23 MarkDuplicates Tracking 76746 as yet unmatched pairs. 11110 records in RAM.
INFO 2026-06-08 08:26:24 MarkDuplicates Read 368,000,000 records. Elapsed time: 00:13:06s. Time for last 1,000,000: 1s. Last read position: chr21:8,441,951
INFO 2026-06-08 08:26:24 MarkDuplicates Tracking 75031 as yet unmatched pairs. 9387 records in RAM.
INFO 2026-06-08 08:26:26 MarkDuplicates Read 369,000,000 records. Elapsed time: 00:13:08s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,553
INFO 2026-06-08 08:26:26 MarkDuplicates Tracking 73393 as yet unmatched pairs. 7749 records in RAM.
INFO 2026-06-08 08:26:27 MarkDuplicates Read 370,000,000 records. Elapsed time: 00:13:09s. Time for last 1,000,000: 1s. Last read position: chr21:34,419,120
INFO 2026-06-08 08:26:27 MarkDuplicates Tracking 71261 as yet unmatched pairs. 5617 records in RAM.
INFO 2026-06-08 08:26:29 MarkDuplicates Read 371,000,000 records. Elapsed time: 00:13:11s. Time for last 1,000,000: 1s. Last read position: chr21:44,080,021
INFO 2026-06-08 08:26:29 MarkDuplicates Tracking 68932 as yet unmatched pairs. 3288 records in RAM.
INFO 2026-06-08 08:26:30 MarkDuplicates Read 372,000,000 records. Elapsed time: 00:13:12s. Time for last 1,000,000: 1s. Last read position: chr21:46,122,117
INFO 2026-06-08 08:26:30 MarkDuplicates Tracking 66713 as yet unmatched pairs. 1069 records in RAM.
INFO 2026-06-08 08:26:33 MarkDuplicates Read 373,000,000 records. Elapsed time: 00:13:15s. Time for last 1,000,000: 2s. Last read position: chr22:19,918,196
INFO 2026-06-08 08:26:33 MarkDuplicates Tracking 64441 as yet unmatched pairs. 28749 records in RAM.
INFO 2026-06-08 08:26:35 MarkDuplicates Read 374,000,000 records. Elapsed time: 00:13:17s. Time for last 1,000,000: 2s. Last read position: chr22:23,181,269
INFO 2026-06-08 08:26:35 MarkDuplicates Tracking 62447 as yet unmatched pairs. 26754 records in RAM.
INFO 2026-06-08 08:26:37 MarkDuplicates Read 375,000,000 records. Elapsed time: 00:13:19s. Time for last 1,000,000: 1s. Last read position: chr22:25,112,226
INFO 2026-06-08 08:26:37 MarkDuplicates Tracking 59824 as yet unmatched pairs. 24131 records in RAM.
INFO 2026-06-08 08:26:38 MarkDuplicates Read 376,000,000 records. Elapsed time: 00:13:20s. Time for last 1,000,000: 1s. Last read position: chr22:29,287,020
INFO 2026-06-08 08:26:38 MarkDuplicates Tracking 58313 as yet unmatched pairs. 22620 records in RAM.
INFO 2026-06-08 08:26:40 MarkDuplicates Read 377,000,000 records. Elapsed time: 00:13:22s. Time for last 1,000,000: 1s. Last read position: chr22:31,125,290
INFO 2026-06-08 08:26:40 MarkDuplicates Tracking 55351 as yet unmatched pairs. 19658 records in RAM.
INFO 2026-06-08 08:26:42 MarkDuplicates Read 378,000,000 records. Elapsed time: 00:13:24s. Time for last 1,000,000: 1s. Last read position: chr22:36,285,315
INFO 2026-06-08 08:26:42 MarkDuplicates Tracking 52931 as yet unmatched pairs. 17238 records in RAM.
INFO 2026-06-08 08:26:44 MarkDuplicates Read 379,000,000 records. Elapsed time: 00:13:26s. Time for last 1,000,000: 1s. Last read position: chr22:37,631,005
INFO 2026-06-08 08:26:44 MarkDuplicates Tracking 50362 as yet unmatched pairs. 14669 records in RAM.
INFO 2026-06-08 08:26:45 MarkDuplicates Read 380,000,000 records. Elapsed time: 00:13:27s. Time for last 1,000,000: 1s. Last read position: chr22:38,866,475
INFO 2026-06-08 08:26:45 MarkDuplicates Tracking 48073 as yet unmatched pairs. 12380 records in RAM.
INFO 2026-06-08 08:26:47 MarkDuplicates Read 381,000,000 records. Elapsed time: 00:13:29s. Time for last 1,000,000: 1s. Last read position: chr22:41,172,641
INFO 2026-06-08 08:26:47 MarkDuplicates Tracking 45713 as yet unmatched pairs. 10020 records in RAM.
INFO 2026-06-08 08:26:49 MarkDuplicates Read 382,000,000 records. Elapsed time: 00:13:31s. Time for last 1,000,000: 2s. Last read position: chr22:42,822,378
INFO 2026-06-08 08:26:49 MarkDuplicates Tracking 43331 as yet unmatched pairs. 7638 records in RAM.
INFO 2026-06-08 08:26:51 MarkDuplicates Read 383,000,000 records. Elapsed time: 00:13:33s. Time for last 1,000,000: 2s. Last read position: chr22:49,883,812
INFO 2026-06-08 08:26:51 MarkDuplicates Tracking 40641 as yet unmatched pairs. 4948 records in RAM.
INFO 2026-06-08 08:26:53 MarkDuplicates Read 384,000,000 records. Elapsed time: 00:13:35s. Time for last 1,000,000: 1s. Last read position: chr22:50,505,054
INFO 2026-06-08 08:26:53 MarkDuplicates Tracking 38170 as yet unmatched pairs. 2477 records in RAM.
INFO 2026-06-08 08:26:55 MarkDuplicates Read 385,000,000 records. Elapsed time: 00:13:37s. Time for last 1,000,000: 1s. Last read position: chrX:2,691,381
INFO 2026-06-08 08:26:55 MarkDuplicates Tracking 35163 as yet unmatched pairs. 20570 records in RAM.
INFO 2026-06-08 08:26:57 MarkDuplicates Read 386,000,000 records. Elapsed time: 00:13:39s. Time for last 1,000,000: 1s. Last read position: chrX:23,783,286
INFO 2026-06-08 08:26:57 MarkDuplicates Tracking 33054 as yet unmatched pairs. 18451 records in RAM.
INFO 2026-06-08 08:26:59 MarkDuplicates Read 387,000,000 records. Elapsed time: 00:13:41s. Time for last 1,000,000: 1s. Last read position: chrX:47,182,194
INFO 2026-06-08 08:26:59 MarkDuplicates Tracking 30430 as yet unmatched pairs. 15826 records in RAM.
INFO 2026-06-08 08:27:01 MarkDuplicates Read 388,000,000 records. Elapsed time: 00:13:43s. Time for last 1,000,000: 1s. Last read position: chrX:51,896,549
INFO 2026-06-08 08:27:01 MarkDuplicates Tracking 27912 as yet unmatched pairs. 13308 records in RAM.
INFO 2026-06-08 08:27:02 MarkDuplicates Read 389,000,000 records. Elapsed time: 00:13:44s. Time for last 1,000,000: 1s. Last read position: chrX:56,565,430
INFO 2026-06-08 08:27:02 MarkDuplicates Tracking 25871 as yet unmatched pairs. 11267 records in RAM.
INFO 2026-06-08 08:27:04 MarkDuplicates Read 390,000,000 records. Elapsed time: 00:13:46s. Time for last 1,000,000: 1s. Last read position: chrX:72,273,231
INFO 2026-06-08 08:27:04 MarkDuplicates Tracking 23967 as yet unmatched pairs. 9360 records in RAM.
INFO 2026-06-08 08:27:06 MarkDuplicates Read 391,000,000 records. Elapsed time: 00:13:48s. Time for last 1,000,000: 1s. Last read position: chrX:103,676,383
INFO 2026-06-08 08:27:06 MarkDuplicates Tracking 22078 as yet unmatched pairs. 7471 records in RAM.
INFO 2026-06-08 08:27:07 MarkDuplicates Read 392,000,000 records. Elapsed time: 00:13:49s. Time for last 1,000,000: 1s. Last read position: chrX:132,406,246
INFO 2026-06-08 08:27:07 MarkDuplicates Tracking 19603 as yet unmatched pairs. 4994 records in RAM.
INFO 2026-06-08 08:27:09 MarkDuplicates Read 393,000,000 records. Elapsed time: 00:13:51s. Time for last 1,000,000: 1s. Last read position: chrX:153,958,208
INFO 2026-06-08 08:27:09 MarkDuplicates Tracking 17466 as yet unmatched pairs. 2855 records in RAM.
INFO 2026-06-08 08:27:11 MarkDuplicates Read 394,000,000 records. Elapsed time: 00:13:53s. Time for last 1,000,000: 1s. Last read position: chrX:154,640,088
INFO 2026-06-08 08:27:11 MarkDuplicates Tracking 15031 as yet unmatched pairs. 420 records in RAM.
INFO 2026-06-08 08:27:13 MarkDuplicates Read 395,000,000 records. Elapsed time: 00:13:55s. Time for last 1,000,000: 1s. Last read position: GL000220.1:114,196
INFO 2026-06-08 08:27:13 MarkDuplicates Tracking 14491 as yet unmatched pairs. 3929 records in RAM.
INFO 2026-06-08 08:27:14 MarkDuplicates Read 396,000,000 records. Elapsed time: 00:13:56s. Time for last 1,000,000: 1s. Last read position: GL000220.1:158,121
INFO 2026-06-08 08:27:14 MarkDuplicates Tracking 10722 as yet unmatched pairs. 160 records in RAM.
INFO 2026-06-08 08:27:16 MarkDuplicates Read 397,000,000 records. Elapsed time: 00:13:58s. Time for last 1,000,000: 1s. Last read position: GL000220.1:160,667
INFO 2026-06-08 08:27:16 MarkDuplicates Tracking 10568 as yet unmatched pairs. 6 records in RAM.
INFO 2026-06-08 08:27:17 MarkDuplicates Read 398,000,000 records. Elapsed time: 00:13:59s. Time for last 1,000,000: 1s. Last read position: KI270733.1:131,031
INFO 2026-06-08 08:27:17 MarkDuplicates Tracking 3747 as yet unmatched pairs. 3735 records in RAM.
INFO 2026-06-08 08:27:18 MarkDuplicates Read 399,000,000 records. Elapsed time: 00:14:00s. Time for last 1,000,000: 1s. Last read position: KI270733.1:176,079
INFO 2026-06-08 08:27:18 MarkDuplicates Tracking 146 as yet unmatched pairs. 134 records in RAM.
INFO 2026-06-08 08:27:20 MarkDuplicates Read 400,000,000 records. Elapsed time: 00:14:01s. Time for last 1,000,000: 1s. Last read position: KI270733.1:178,680
INFO 2026-06-08 08:27:20 MarkDuplicates Tracking 21 as yet unmatched pairs. 9 records in RAM.
INFO 2026-06-08 08:27:20 MarkDuplicates Read 400232406 records. 0 pairs never matched.
INFO 2026-06-08 08:28:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 34052228144; totalMemory: 48653926400; maxMemory: 63585648640
INFO 2026-06-08 08:28:03 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:28:14 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:28:36 OpticalDuplicateFinder Large duplicate set. size = 1168
INFO 2026-06-08 08:28:36 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,796
INFO 2026-06-08 08:29:27 OpticalDuplicateFinder Large duplicate set. size = 1185
INFO 2026-06-08 08:29:27 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-22,508
INFO 2026-06-08 08:29:27 OpticalDuplicateFinder Large duplicate set. size = 1674
INFO 2026-06-08 08:29:27 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,704
INFO 2026-06-08 08:29:27 OpticalDuplicateFinder Large duplicate set. size = 1181
INFO 2026-06-08 08:29:27 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,343
INFO 2026-06-08 08:29:27 OpticalDuplicateFinder Large duplicate set. size = 1067
INFO 2026-06-08 08:29:27 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,286
INFO 2026-06-08 08:29:27 OpticalDuplicateFinder Large duplicate set. size = 1180
INFO 2026-06-08 08:29:27 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,421
INFO 2026-06-08 08:29:27 OpticalDuplicateFinder Large duplicate set. size = 1193
INFO 2026-06-08 08:29:27 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,016
INFO 2026-06-08 08:29:27 OpticalDuplicateFinder Large duplicate set. size = 1099
INFO 2026-06-08 08:29:27 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,134
INFO 2026-06-08 08:29:27 OpticalDuplicateFinder Large duplicate set. size = 1041
INFO 2026-06-08 08:29:27 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,088
INFO 2026-06-08 08:29:27 OpticalDuplicateFinder Large duplicate set. size = 1479
INFO 2026-06-08 08:29:27 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-22,152
INFO 2026-06-08 08:29:27 MarkDuplicates Traversing fragment information and detecting duplicates.
WARNING 2026-06-08 08:29:27 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
INFO 2026-06-08 08:30:17 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:30:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 203999168; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:30:18 MarkDuplicates Marking 279306496 records as duplicates.
INFO 2026-06-08 08:30:18 MarkDuplicates Found 12050800 optical duplicate clusters.
INFO 2026-06-08 08:30:18 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 08:30:35 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:16s. Time for last 10,000,000: 16s. Last read position: chr1:31,434,093
INFO 2026-06-08 08:30:50 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:32s. Time for last 10,000,000: 15s. Last read position: chr1:119,919,459
INFO 2026-06-08 08:31:08 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:50s. Time for last 10,000,000: 18s. Last read position: chr1:160,095,112
INFO 2026-06-08 08:31:25 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:07s. Time for last 10,000,000: 16s. Last read position: chr1:243,165,205
INFO 2026-06-08 08:31:44 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:25s. Time for last 10,000,000: 18s. Last read position: chr2:74,556,344
INFO 2026-06-08 08:32:06 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:47s. Time for last 10,000,000: 22s. Last read position: chr2:190,980,655
INFO 2026-06-08 08:32:22 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:03s. Time for last 10,000,000: 15s. Last read position: chr3:45,981,622
INFO 2026-06-08 08:32:37 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:18s. Time for last 10,000,000: 15s. Last read position: chr3:151,198,594
INFO 2026-06-08 08:32:52 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:34s. Time for last 10,000,000: 15s. Last read position: chr4:98,261,399
INFO 2026-06-08 08:33:08 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:50s. Time for last 10,000,000: 15s. Last read position: chr5:132,898,376
INFO 2026-06-08 08:33:24 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:03:06s. Time for last 10,000,000: 16s. Last read position: chr6:3,273,267
INFO 2026-06-08 08:33:44 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:25s. Time for last 10,000,000: 19s. Last read position: chr6:38,592,595
INFO 2026-06-08 08:33:59 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:41s. Time for last 10,000,000: 15s. Last read position: chr7:1,487,321
INFO 2026-06-08 08:34:15 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:03:56s. Time for last 10,000,000: 15s. Last read position: chr7:99,968,339
INFO 2026-06-08 08:34:31 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:04:12s. Time for last 10,000,000: 15s. Last read position: chr8:25,408,040
INFO 2026-06-08 08:34:46 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:27s. Time for last 10,000,000: 15s. Last read position: chr8:143,860,573
INFO 2026-06-08 08:35:00 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:04:42s. Time for last 10,000,000: 14s. Last read position: chr9:7,169,819
INFO 2026-06-08 08:35:16 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:04:57s. Time for last 10,000,000: 15s. Last read position: chr9:131,467,666
INFO 2026-06-08 08:35:30 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:05:12s. Time for last 10,000,000: 14s. Last read position: chr10:73,125,316
INFO 2026-06-08 08:35:45 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:05:27s. Time for last 10,000,000: 14s. Last read position: chr11:1,881,569
INFO 2026-06-08 08:36:01 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:05:42s. Time for last 10,000,000: 15s. Last read position: chr11:65,553,512
INFO 2026-06-08 08:36:16 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:05:58s. Time for last 10,000,000: 15s. Last read position: chr11:121,615,675
INFO 2026-06-08 08:36:32 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:06:13s. Time for last 10,000,000: 15s. Last read position: chr12:56,285,949
INFO 2026-06-08 08:36:47 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:06:29s. Time for last 10,000,000: 15s. Last read position: chr12:132,583,541
INFO 2026-06-08 08:37:02 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:06:44s. Time for last 10,000,000: 14s. Last read position: chr14:73,739,905
INFO 2026-06-08 08:37:17 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:06:59s. Time for last 10,000,000: 14s. Last read position: chr15:57,232,396
INFO 2026-06-08 08:37:32 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:07:14s. Time for last 10,000,000: 14s. Last read position: chr16:2,756,497
INFO 2026-06-08 08:37:47 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:07:29s. Time for last 10,000,000: 14s. Last read position: chr16:22,533,746
INFO 2026-06-08 08:38:02 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:07:44s. Time for last 10,000,000: 15s. Last read position: chr16:67,883,035
INFO 2026-06-08 08:38:18 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:07:59s. Time for last 10,000,000: 15s. Last read position: chr17:19,283,399
INFO 2026-06-08 08:38:33 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:08:14s. Time for last 10,000,000: 15s. Last read position: chr17:48,943,940
INFO 2026-06-08 08:38:48 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:08:29s. Time for last 10,000,000: 15s. Last read position: chr17:82,091,364
INFO 2026-06-08 08:39:03 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:08:45s. Time for last 10,000,000: 15s. Last read position: chr19:7,550,584
INFO 2026-06-08 08:39:19 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:09:00s. Time for last 10,000,000: 15s. Last read position: chr19:35,021,846
INFO 2026-06-08 08:39:33 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:09:15s. Time for last 10,000,000: 14s. Last read position: chr19:49,196,773
INFO 2026-06-08 08:39:48 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:09:30s. Time for last 10,000,000: 14s. Last read position: chr20:40,688,450
INFO 2026-06-08 08:40:02 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:09:44s. Time for last 10,000,000: 13s. Last read position: chr21:34,419,120
INFO 2026-06-08 08:40:16 MarkDuplicates Written 380,000,000 records. Elapsed time: 00:09:58s. Time for last 10,000,000: 14s. Last read position: chr22:38,866,475
INFO 2026-06-08 08:40:30 MarkDuplicates Written 390,000,000 records. Elapsed time: 00:10:12s. Time for last 10,000,000: 14s. Last read position: chrX:72,273,231
INFO 2026-06-08 08:40:44 MarkDuplicates Written 400,000,000 records. Elapsed time: 00:10:25s. Time for last 10,000,000: 13s. Last read position: KI270733.1:178,680
INFO 2026-06-08 08:40:51 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:40:51 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:40:51 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:40:51 MarkDuplicates Before output close freeMemory: 203978856; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:40:51 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:40:51 MarkDuplicates After output close freeMemory: 104214816; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 08:40:51 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 27.59 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory