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 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bam --METRICS_FILE 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
08:07:18.461 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 08:07:18 GMT 2026] MarkDuplicates --INPUT 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.md.bam --METRICS_FILE 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_2.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 08:07:18 GMT 2026] Executing as ?@nf-fbc3f2ed9e43605873828aaedf9434ad-4efe7-prhf9 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 08:07:18 MarkDuplicates Start of doWork freeMemory: 105493648; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 08:07:18 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 08:07:18 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 08:07:22 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:1,439,346
INFO 2026-06-08 08:07:22 MarkDuplicates Tracking 3062 as yet unmatched pairs. 7 records in RAM.
INFO 2026-06-08 08:07:25 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: chr1:3,787,229
INFO 2026-06-08 08:07:25 MarkDuplicates Tracking 6397 as yet unmatched pairs. 23 records in RAM.
INFO 2026-06-08 08:07:27 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 2s. Last read position: chr1:9,720,206
INFO 2026-06-08 08:07:27 MarkDuplicates Tracking 9453 as yet unmatched pairs. 23 records in RAM.
INFO 2026-06-08 08:07:30 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 2s. Last read position: chr1:13,778,451
INFO 2026-06-08 08:07:30 MarkDuplicates Tracking 12271 as yet unmatched pairs. 34 records in RAM.
INFO 2026-06-08 08:07:31 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: chr1:16,953,322
INFO 2026-06-08 08:07:31 MarkDuplicates Tracking 14949 as yet unmatched pairs. 5 records in RAM.
INFO 2026-06-08 08:07:33 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 2s. Last read position: chr1:21,823,346
INFO 2026-06-08 08:07:33 MarkDuplicates Tracking 18070 as yet unmatched pairs. 202 records in RAM.
INFO 2026-06-08 08:07:36 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr1:23,333,606
INFO 2026-06-08 08:07:36 MarkDuplicates Tracking 21041 as yet unmatched pairs. 55 records in RAM.
INFO 2026-06-08 08:07:38 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 2s. Last read position: chr1:26,863,808
INFO 2026-06-08 08:07:38 MarkDuplicates Tracking 23946 as yet unmatched pairs. 178 records in RAM.
INFO 2026-06-08 08:07:40 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: chr1:30,876,637
INFO 2026-06-08 08:07:40 MarkDuplicates Tracking 26799 as yet unmatched pairs. 122 records in RAM.
INFO 2026-06-08 08:07:42 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 2s. Last read position: chr1:34,785,348
INFO 2026-06-08 08:07:42 MarkDuplicates Tracking 29577 as yet unmatched pairs. 13 records in RAM.
INFO 2026-06-08 08:07:45 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 2s. Last read position: chr1:39,292,005
INFO 2026-06-08 08:07:45 MarkDuplicates Tracking 32638 as yet unmatched pairs. 82 records in RAM.
INFO 2026-06-08 08:07:47 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 1s. Last read position: chr1:40,303,937
INFO 2026-06-08 08:07:47 MarkDuplicates Tracking 35536 as yet unmatched pairs. 398 records in RAM.
INFO 2026-06-08 08:07:49 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 2s. Last read position: chr1:43,588,707
INFO 2026-06-08 08:07:49 MarkDuplicates Tracking 38467 as yet unmatched pairs. 295 records in RAM.
INFO 2026-06-08 08:07:51 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 2s. Last read position: chr1:46,035,131
INFO 2026-06-08 08:07:51 MarkDuplicates Tracking 41123 as yet unmatched pairs. 52 records in RAM.
INFO 2026-06-08 08:07:53 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 1s. Last read position: chr1:61,766,291
INFO 2026-06-08 08:07:53 MarkDuplicates Tracking 43998 as yet unmatched pairs. 15 records in RAM.
INFO 2026-06-08 08:07:55 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 1s. Last read position: chr1:90,027,600
INFO 2026-06-08 08:07:55 MarkDuplicates Tracking 46509 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 08:07:56 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 1s. Last read position: chr1:109,323,008
INFO 2026-06-08 08:07:56 MarkDuplicates Tracking 49104 as yet unmatched pairs. 20 records in RAM.
INFO 2026-06-08 08:07:58 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 1s. Last read position: chr1:113,973,034
INFO 2026-06-08 08:07:58 MarkDuplicates Tracking 51659 as yet unmatched pairs. 9 records in RAM.
INFO 2026-06-08 08:08:01 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 2s. Last read position: chr1:119,925,631
INFO 2026-06-08 08:08:01 MarkDuplicates Tracking 54774 as yet unmatched pairs. 341 records in RAM.
INFO 2026-06-08 08:08:03 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 2s. Last read position: chr1:145,681,012
INFO 2026-06-08 08:08:03 MarkDuplicates Tracking 56115 as yet unmatched pairs. 67 records in RAM.
INFO 2026-06-08 08:08:05 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: chr1:148,540,193
INFO 2026-06-08 08:08:05 MarkDuplicates Tracking 57363 as yet unmatched pairs. 83 records in RAM.
INFO 2026-06-08 08:08:07 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 1s. Last read position: chr1:150,266,626
INFO 2026-06-08 08:08:07 MarkDuplicates Tracking 58407 as yet unmatched pairs. 29 records in RAM.
INFO 2026-06-08 08:08:09 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 1s. Last read position: chr1:152,302,941
INFO 2026-06-08 08:08:09 MarkDuplicates Tracking 61123 as yet unmatched pairs. 12 records in RAM.
INFO 2026-06-08 08:08:10 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 1s. Last read position: chr1:153,093,666
INFO 2026-06-08 08:08:10 MarkDuplicates Tracking 62644 as yet unmatched pairs. 33 records in RAM.
INFO 2026-06-08 08:08:13 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 2s. Last read position: chr1:154,598,419
INFO 2026-06-08 08:08:13 MarkDuplicates Tracking 65153 as yet unmatched pairs. 47 records in RAM.
INFO 2026-06-08 08:08:15 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 2s. Last read position: chr1:155,688,150
INFO 2026-06-08 08:08:15 MarkDuplicates Tracking 67635 as yet unmatched pairs. 69 records in RAM.
INFO 2026-06-08 08:08:16 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 1s. Last read position: chr1:156,135,189
INFO 2026-06-08 08:08:16 MarkDuplicates Tracking 72437 as yet unmatched pairs. 1308 records in RAM.
INFO 2026-06-08 08:08:18 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 1s. Last read position: chr1:156,699,845
INFO 2026-06-08 08:08:18 MarkDuplicates Tracking 74535 as yet unmatched pairs. 94 records in RAM.
INFO 2026-06-08 08:08:20 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 1s. Last read position: chr1:161,589,603
INFO 2026-06-08 08:08:20 MarkDuplicates Tracking 77246 as yet unmatched pairs. 106 records in RAM.
INFO 2026-06-08 08:08:22 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 2s. Last read position: chr1:178,233,576
INFO 2026-06-08 08:08:22 MarkDuplicates Tracking 79481 as yet unmatched pairs. 21 records in RAM.
INFO 2026-06-08 08:08:23 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 1s. Last read position: chr1:186,333,122
INFO 2026-06-08 08:08:23 MarkDuplicates Tracking 82333 as yet unmatched pairs. 155 records in RAM.
INFO 2026-06-08 08:08:25 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 1s. Last read position: chr1:202,764,124
INFO 2026-06-08 08:08:25 MarkDuplicates Tracking 84724 as yet unmatched pairs. 14 records in RAM.
INFO 2026-06-08 08:08:27 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 1s. Last read position: chr1:206,333,315
INFO 2026-06-08 08:08:27 MarkDuplicates Tracking 87323 as yet unmatched pairs. 7 records in RAM.
INFO 2026-06-08 08:08:29 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 2s. Last read position: chr1:213,742,463
INFO 2026-06-08 08:08:29 MarkDuplicates Tracking 90249 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 08:08:31 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 1s. Last read position: chr1:226,735,867
INFO 2026-06-08 08:08:31 MarkDuplicates Tracking 92686 as yet unmatched pairs. 45 records in RAM.
INFO 2026-06-08 08:08:32 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 1s. Last read position: chr1:228,372,983
INFO 2026-06-08 08:08:32 MarkDuplicates Tracking 96109 as yet unmatched pairs. 38 records in RAM.
INFO 2026-06-08 08:08:34 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 2s. Last read position: chr1:236,048,707
INFO 2026-06-08 08:08:34 MarkDuplicates Tracking 99241 as yet unmatched pairs. 134 records in RAM.
INFO 2026-06-08 08:08:37 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 2s. Last read position: chr2:8,730,949
INFO 2026-06-08 08:08:37 MarkDuplicates Tracking 101955 as yet unmatched pairs. 101716 records in RAM.
INFO 2026-06-08 08:08:39 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 1s. Last read position: chr2:24,310,293
INFO 2026-06-08 08:08:39 MarkDuplicates Tracking 104704 as yet unmatched pairs. 104458 records in RAM.
INFO 2026-06-08 08:08:41 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 2s. Last read position: chr2:28,412,310
INFO 2026-06-08 08:08:41 MarkDuplicates Tracking 107592 as yet unmatched pairs. 107342 records in RAM.
INFO 2026-06-08 08:08:43 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,263
INFO 2026-06-08 08:08:43 MarkDuplicates Tracking 162813 as yet unmatched pairs. 103807 records in RAM.
INFO 2026-06-08 08:08:45 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,264
INFO 2026-06-08 08:08:45 MarkDuplicates Tracking 773536 as yet unmatched pairs. 60735 records in RAM.
INFO 2026-06-08 08:08:48 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,406
INFO 2026-06-08 08:08:48 MarkDuplicates Tracking 858805 as yet unmatched pairs. 54430 records in RAM.
INFO 2026-06-08 08:08:50 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 1s. Last read position: chr2:37,344,735
INFO 2026-06-08 08:08:50 MarkDuplicates Tracking 922077 as yet unmatched pairs. 48957 records in RAM.
INFO 2026-06-08 08:08:52 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 2s. Last read position: chr2:54,626,091
INFO 2026-06-08 08:08:52 MarkDuplicates Tracking 919490 as yet unmatched pairs. 46364 records in RAM.
INFO 2026-06-08 08:08:54 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 1s. Last read position: chr2:64,635,986
INFO 2026-06-08 08:08:54 MarkDuplicates Tracking 916622 as yet unmatched pairs. 43495 records in RAM.
INFO 2026-06-08 08:08:56 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 1s. Last read position: chr2:74,047,081
INFO 2026-06-08 08:08:56 MarkDuplicates Tracking 914134 as yet unmatched pairs. 40991 records in RAM.
INFO 2026-06-08 08:08:57 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 1s. Last read position: chr2:86,987,112
INFO 2026-06-08 08:08:57 MarkDuplicates Tracking 911289 as yet unmatched pairs. 38140 records in RAM.
INFO 2026-06-08 08:08:59 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 1s. Last read position: chr2:97,113,799
INFO 2026-06-08 08:08:59 MarkDuplicates Tracking 908773 as yet unmatched pairs. 35615 records in RAM.
INFO 2026-06-08 08:09:01 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 1s. Last read position: chr2:108,763,449
INFO 2026-06-08 08:09:01 MarkDuplicates Tracking 907038 as yet unmatched pairs. 33873 records in RAM.
INFO 2026-06-08 08:09:03 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 1s. Last read position: chr2:113,121,548
INFO 2026-06-08 08:09:03 MarkDuplicates Tracking 905315 as yet unmatched pairs. 32141 records in RAM.
INFO 2026-06-08 08:09:05 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 2s. Last read position: chr2:131,484,119
INFO 2026-06-08 08:09:05 MarkDuplicates Tracking 902594 as yet unmatched pairs. 29404 records in RAM.
INFO 2026-06-08 08:09:07 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 1s. Last read position: chr2:159,430,958
INFO 2026-06-08 08:09:07 MarkDuplicates Tracking 900158 as yet unmatched pairs. 26962 records in RAM.
INFO 2026-06-08 08:09:09 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 1s. Last read position: chr2:174,720,073
INFO 2026-06-08 08:09:09 MarkDuplicates Tracking 897601 as yet unmatched pairs. 24402 records in RAM.
INFO 2026-06-08 08:09:11 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 1s. Last read position: chr2:189,007,579
INFO 2026-06-08 08:09:11 MarkDuplicates Tracking 895259 as yet unmatched pairs. 22058 records in RAM.
INFO 2026-06-08 08:09:12 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 1s. Last read position: chr2:202,036,097
INFO 2026-06-08 08:09:12 MarkDuplicates Tracking 892176 as yet unmatched pairs. 18967 records in RAM.
INFO 2026-06-08 08:09:14 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 1s. Last read position: chr2:215,361,544
INFO 2026-06-08 08:09:14 MarkDuplicates Tracking 890172 as yet unmatched pairs. 16952 records in RAM.
INFO 2026-06-08 08:09:16 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 1s. Last read position: chr2:215,384,033
INFO 2026-06-08 08:09:16 MarkDuplicates Tracking 887405 as yet unmatched pairs. 14183 records in RAM.
INFO 2026-06-08 08:09:18 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 1s. Last read position: chr2:215,422,149
INFO 2026-06-08 08:09:18 MarkDuplicates Tracking 884985 as yet unmatched pairs. 11763 records in RAM.
INFO 2026-06-08 08:09:19 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 1s. Last read position: chr2:218,569,019
INFO 2026-06-08 08:09:19 MarkDuplicates Tracking 881698 as yet unmatched pairs. 8466 records in RAM.
INFO 2026-06-08 08:09:21 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 1s. Last read position: chr2:229,803,985
INFO 2026-06-08 08:09:21 MarkDuplicates Tracking 878704 as yet unmatched pairs. 5413 records in RAM.
INFO 2026-06-08 08:09:23 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 2s. Last read position: chr2:237,381,021
INFO 2026-06-08 08:09:23 MarkDuplicates Tracking 876232 as yet unmatched pairs. 2938 records in RAM.
INFO 2026-06-08 08:09:25 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 2s. Last read position: chr3:3,845,451
INFO 2026-06-08 08:09:25 MarkDuplicates Tracking 873180 as yet unmatched pairs. 53046 records in RAM.
INFO 2026-06-08 08:09:27 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 1s. Last read position: chr3:12,600,266
INFO 2026-06-08 08:09:27 MarkDuplicates Tracking 870843 as yet unmatched pairs. 50706 records in RAM.
INFO 2026-06-08 08:09:29 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 1s. Last read position: chr3:33,696,883
INFO 2026-06-08 08:09:29 MarkDuplicates Tracking 867582 as yet unmatched pairs. 47434 records in RAM.
INFO 2026-06-08 08:09:30 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 1s. Last read position: chr3:42,223,136
INFO 2026-06-08 08:09:30 MarkDuplicates Tracking 864958 as yet unmatched pairs. 44803 records in RAM.
INFO 2026-06-08 08:09:32 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 1s. Last read position: chr3:47,417,606
INFO 2026-06-08 08:09:32 MarkDuplicates Tracking 862063 as yet unmatched pairs. 41904 records in RAM.
INFO 2026-06-08 08:09:34 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 1s. Last read position: chr3:48,567,169
INFO 2026-06-08 08:09:34 MarkDuplicates Tracking 859177 as yet unmatched pairs. 39018 records in RAM.
INFO 2026-06-08 08:09:36 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 1s. Last read position: chr3:48,584,749
INFO 2026-06-08 08:09:36 MarkDuplicates Tracking 856591 as yet unmatched pairs. 36429 records in RAM.
INFO 2026-06-08 08:09:37 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 1s. Last read position: chr3:49,012,229
INFO 2026-06-08 08:09:37 MarkDuplicates Tracking 852664 as yet unmatched pairs. 32495 records in RAM.
INFO 2026-06-08 08:09:39 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 1s. Last read position: chr3:49,967,819
INFO 2026-06-08 08:09:39 MarkDuplicates Tracking 849589 as yet unmatched pairs. 29419 records in RAM.
INFO 2026-06-08 08:09:41 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 1s. Last read position: chr3:52,489,594
INFO 2026-06-08 08:09:41 MarkDuplicates Tracking 846745 as yet unmatched pairs. 26573 records in RAM.
INFO 2026-06-08 08:09:42 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr3:58,170,643
INFO 2026-06-08 08:09:42 MarkDuplicates Tracking 843796 as yet unmatched pairs. 23624 records in RAM.
INFO 2026-06-08 08:09:44 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 1s. Last read position: chr3:98,901,177
INFO 2026-06-08 08:09:44 MarkDuplicates Tracking 841128 as yet unmatched pairs. 20949 records in RAM.
INFO 2026-06-08 08:09:46 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 1s. Last read position: chr3:114,339,305
INFO 2026-06-08 08:09:46 MarkDuplicates Tracking 838433 as yet unmatched pairs. 18245 records in RAM.
INFO 2026-06-08 08:09:48 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 2s. Last read position: chr3:127,014,494
INFO 2026-06-08 08:09:48 MarkDuplicates Tracking 835584 as yet unmatched pairs. 15394 records in RAM.
INFO 2026-06-08 08:09:49 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 1s. Last read position: chr3:136,359,176
INFO 2026-06-08 08:09:49 MarkDuplicates Tracking 832783 as yet unmatched pairs. 12583 records in RAM.
INFO 2026-06-08 08:09:51 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 1s. Last read position: chr3:158,646,854
INFO 2026-06-08 08:09:51 MarkDuplicates Tracking 829995 as yet unmatched pairs. 9791 records in RAM.
INFO 2026-06-08 08:09:53 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 1s. Last read position: chr3:184,135,546
INFO 2026-06-08 08:09:53 MarkDuplicates Tracking 827517 as yet unmatched pairs. 7306 records in RAM.
INFO 2026-06-08 08:09:54 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 1s. Last read position: chr3:188,484,592
INFO 2026-06-08 08:09:54 MarkDuplicates Tracking 825042 as yet unmatched pairs. 4828 records in RAM.
INFO 2026-06-08 08:09:56 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 1s. Last read position: chr3:195,782,355
INFO 2026-06-08 08:09:56 MarkDuplicates Tracking 822599 as yet unmatched pairs. 2378 records in RAM.
INFO 2026-06-08 08:09:58 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 2s. Last read position: chr4:851,885
INFO 2026-06-08 08:09:58 MarkDuplicates Tracking 819888 as yet unmatched pairs. 23662 records in RAM.
INFO 2026-06-08 08:10:00 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 1s. Last read position: chr4:3,416,000
INFO 2026-06-08 08:10:00 MarkDuplicates Tracking 816698 as yet unmatched pairs. 20469 records in RAM.
INFO 2026-06-08 08:10:02 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 1s. Last read position: chr4:15,984,332
INFO 2026-06-08 08:10:02 MarkDuplicates Tracking 813755 as yet unmatched pairs. 17517 records in RAM.
INFO 2026-06-08 08:10:03 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 1s. Last read position: chr4:54,267,292
INFO 2026-06-08 08:10:03 MarkDuplicates Tracking 811467 as yet unmatched pairs. 15210 records in RAM.
INFO 2026-06-08 08:10:05 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 2s. Last read position: chr4:77,055,295
INFO 2026-06-08 08:10:05 MarkDuplicates Tracking 808601 as yet unmatched pairs. 12339 records in RAM.
INFO 2026-06-08 08:10:07 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 1s. Last read position: chr4:102,533,854
INFO 2026-06-08 08:10:07 MarkDuplicates Tracking 805917 as yet unmatched pairs. 9646 records in RAM.
INFO 2026-06-08 08:10:09 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 1s. Last read position: chr4:127,805,681
INFO 2026-06-08 08:10:09 MarkDuplicates Tracking 803453 as yet unmatched pairs. 7174 records in RAM.
INFO 2026-06-08 08:10:11 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 2s. Last read position: chr4:158,868,209
INFO 2026-06-08 08:10:11 MarkDuplicates Tracking 801054 as yet unmatched pairs. 4766 records in RAM.
INFO 2026-06-08 08:10:12 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 1s. Last read position: chr4:186,603,858
INFO 2026-06-08 08:10:12 MarkDuplicates Tracking 798131 as yet unmatched pairs. 1838 records in RAM.
INFO 2026-06-08 08:10:15 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 2s. Last read position: chr5:1,059,744
INFO 2026-06-08 08:10:15 MarkDuplicates Tracking 795265 as yet unmatched pairs. 38491 records in RAM.
INFO 2026-06-08 08:10:16 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 1s. Last read position: chr5:14,488,108
INFO 2026-06-08 08:10:16 MarkDuplicates Tracking 792409 as yet unmatched pairs. 35630 records in RAM.
INFO 2026-06-08 08:10:18 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 1s. Last read position: chr5:39,394,235
INFO 2026-06-08 08:10:18 MarkDuplicates Tracking 789732 as yet unmatched pairs. 32944 records in RAM.
INFO 2026-06-08 08:10:19 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 1s. Last read position: chr5:68,296,146
INFO 2026-06-08 08:10:19 MarkDuplicates Tracking 787122 as yet unmatched pairs. 30322 records in RAM.
INFO 2026-06-08 08:10:21 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 1s. Last read position: chr5:81,312,562
INFO 2026-06-08 08:10:21 MarkDuplicates Tracking 785121 as yet unmatched pairs. 28311 records in RAM.
INFO 2026-06-08 08:10:23 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 1s. Last read position: chr5:103,007,463
INFO 2026-06-08 08:10:23 MarkDuplicates Tracking 782646 as yet unmatched pairs. 25834 records in RAM.
INFO 2026-06-08 08:10:24 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 1s. Last read position: chr5:134,661,219
INFO 2026-06-08 08:10:24 MarkDuplicates Tracking 780046 as yet unmatched pairs. 23229 records in RAM.
INFO 2026-06-08 08:10:26 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 1s. Last read position: chr5:138,904,429
INFO 2026-06-08 08:10:26 MarkDuplicates Tracking 777275 as yet unmatched pairs. 20458 records in RAM.
INFO 2026-06-08 08:10:28 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 1s. Last read position: chr5:141,247,085
INFO 2026-06-08 08:10:28 MarkDuplicates Tracking 774813 as yet unmatched pairs. 17860 records in RAM.
INFO 2026-06-08 08:10:29 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 1s. Last read position: chr5:146,120,421
INFO 2026-06-08 08:10:29 MarkDuplicates Tracking 771847 as yet unmatched pairs. 14891 records in RAM.
INFO 2026-06-08 08:10:31 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 2s. Last read position: chr5:150,406,888
INFO 2026-06-08 08:10:31 MarkDuplicates Tracking 769760 as yet unmatched pairs. 12798 records in RAM.
INFO 2026-06-08 08:10:33 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 1s. Last read position: chr5:151,673,193
INFO 2026-06-08 08:10:33 MarkDuplicates Tracking 766174 as yet unmatched pairs. 9212 records in RAM.
INFO 2026-06-08 08:10:35 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 1s. Last read position: chr5:172,394,607
INFO 2026-06-08 08:10:35 MarkDuplicates Tracking 763378 as yet unmatched pairs. 6409 records in RAM.
INFO 2026-06-08 08:10:37 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 1s. Last read position: chr5:177,536,665
INFO 2026-06-08 08:10:37 MarkDuplicates Tracking 760515 as yet unmatched pairs. 3545 records in RAM.
INFO 2026-06-08 08:10:39 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 2s. Last read position: chr5:180,849,937
INFO 2026-06-08 08:10:39 MarkDuplicates Tracking 757581 as yet unmatched pairs. 609 records in RAM.
INFO 2026-06-08 08:10:41 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 2s. Last read position: chr6:7,231,193
INFO 2026-06-08 08:10:41 MarkDuplicates Tracking 754717 as yet unmatched pairs. 48268 records in RAM.
INFO 2026-06-08 08:10:43 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 1s. Last read position: chr6:7,584,833
INFO 2026-06-08 08:10:43 MarkDuplicates Tracking 752001 as yet unmatched pairs. 45550 records in RAM.
INFO 2026-06-08 08:10:45 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 2s. Last read position: chr6:24,403,042
INFO 2026-06-08 08:10:45 MarkDuplicates Tracking 748768 as yet unmatched pairs. 42298 records in RAM.
INFO 2026-06-08 08:10:47 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 1s. Last read position: chr6:30,722,547
INFO 2026-06-08 08:10:47 MarkDuplicates Tracking 746290 as yet unmatched pairs. 39820 records in RAM.
INFO 2026-06-08 08:10:49 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 2s. Last read position: chr6:31,662,491
INFO 2026-06-08 08:10:49 MarkDuplicates Tracking 743303 as yet unmatched pairs. 36831 records in RAM.
INFO 2026-06-08 08:10:51 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 1s. Last read position: chr6:31,817,337
INFO 2026-06-08 08:10:51 MarkDuplicates Tracking 742571 as yet unmatched pairs. 36096 records in RAM.
INFO 2026-06-08 08:10:52 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 1s. Last read position: chr6:31,829,790
INFO 2026-06-08 08:10:52 MarkDuplicates Tracking 740160 as yet unmatched pairs. 33679 records in RAM.
INFO 2026-06-08 08:10:54 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 1s. Last read position: chr6:33,305,044
INFO 2026-06-08 08:10:54 MarkDuplicates Tracking 737190 as yet unmatched pairs. 30705 records in RAM.
INFO 2026-06-08 08:10:56 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 1s. Last read position: chr6:36,684,144
INFO 2026-06-08 08:10:56 MarkDuplicates Tracking 734151 as yet unmatched pairs. 27657 records in RAM.
INFO 2026-06-08 08:10:57 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 1s. Last read position: chr6:43,355,276
INFO 2026-06-08 08:10:57 MarkDuplicates Tracking 731458 as yet unmatched pairs. 24960 records in RAM.
INFO 2026-06-08 08:10:59 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 1s. Last read position: chr6:56,573,725
INFO 2026-06-08 08:10:59 MarkDuplicates Tracking 728404 as yet unmatched pairs. 21906 records in RAM.
INFO 2026-06-08 08:11:01 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 1s. Last read position: chr6:70,254,967
INFO 2026-06-08 08:11:01 MarkDuplicates Tracking 726035 as yet unmatched pairs. 19536 records in RAM.
INFO 2026-06-08 08:11:03 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 1s. Last read position: chr6:89,081,185
INFO 2026-06-08 08:11:03 MarkDuplicates Tracking 723267 as yet unmatched pairs. 16767 records in RAM.
INFO 2026-06-08 08:11:04 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 1s. Last read position: chr6:111,367,721
INFO 2026-06-08 08:11:04 MarkDuplicates Tracking 720471 as yet unmatched pairs. 13968 records in RAM.
INFO 2026-06-08 08:11:06 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 1s. Last read position: chr6:131,950,848
INFO 2026-06-08 08:11:06 MarkDuplicates Tracking 717716 as yet unmatched pairs. 11210 records in RAM.
INFO 2026-06-08 08:11:08 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 1s. Last read position: chr6:138,405,252
INFO 2026-06-08 08:11:08 MarkDuplicates Tracking 714932 as yet unmatched pairs. 8421 records in RAM.
INFO 2026-06-08 08:11:10 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 1s. Last read position: chr6:151,348,967
INFO 2026-06-08 08:11:10 MarkDuplicates Tracking 712252 as yet unmatched pairs. 5732 records in RAM.
INFO 2026-06-08 08:11:11 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 1s. Last read position: chr6:159,232,996
INFO 2026-06-08 08:11:11 MarkDuplicates Tracking 709231 as yet unmatched pairs. 2707 records in RAM.
INFO 2026-06-08 08:11:13 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 1s. Last read position: chr6:170,318,780
INFO 2026-06-08 08:11:13 MarkDuplicates Tracking 706701 as yet unmatched pairs. 172 records in RAM.
INFO 2026-06-08 08:11:15 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 2s. Last read position: chr7:5,313,677
INFO 2026-06-08 08:11:15 MarkDuplicates Tracking 703536 as yet unmatched pairs. 46160 records in RAM.
INFO 2026-06-08 08:11:17 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 1s. Last read position: chr7:5,529,272
INFO 2026-06-08 08:11:17 MarkDuplicates Tracking 701238 as yet unmatched pairs. 43860 records in RAM.
INFO 2026-06-08 08:11:20 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 2s. Last read position: chr7:27,895,384
INFO 2026-06-08 08:11:20 MarkDuplicates Tracking 697491 as yet unmatched pairs. 40106 records in RAM.
INFO 2026-06-08 08:11:22 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 1s. Last read position: chr7:44,110,312
INFO 2026-06-08 08:11:22 MarkDuplicates Tracking 694841 as yet unmatched pairs. 37449 records in RAM.
INFO 2026-06-08 08:11:24 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 1s. Last read position: chr7:55,146,651
INFO 2026-06-08 08:11:24 MarkDuplicates Tracking 692622 as yet unmatched pairs. 35222 records in RAM.
INFO 2026-06-08 08:11:25 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 1s. Last read position: chr7:67,238,331
INFO 2026-06-08 08:11:25 MarkDuplicates Tracking 689276 as yet unmatched pairs. 31871 records in RAM.
INFO 2026-06-08 08:11:27 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 2s. Last read position: chr7:73,195,993
INFO 2026-06-08 08:11:27 MarkDuplicates Tracking 687732 as yet unmatched pairs. 30324 records in RAM.
INFO 2026-06-08 08:11:29 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 1s. Last read position: chr7:75,366,362
INFO 2026-06-08 08:11:29 MarkDuplicates Tracking 686318 as yet unmatched pairs. 28910 records in RAM.
INFO 2026-06-08 08:11:30 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 1s. Last read position: chr7:76,505,538
INFO 2026-06-08 08:11:30 MarkDuplicates Tracking 683924 as yet unmatched pairs. 26509 records in RAM.
INFO 2026-06-08 08:11:32 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 1s. Last read position: chr7:92,012,591
INFO 2026-06-08 08:11:32 MarkDuplicates Tracking 681762 as yet unmatched pairs. 24343 records in RAM.
INFO 2026-06-08 08:11:34 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 1s. Last read position: chr7:97,024,550
INFO 2026-06-08 08:11:34 MarkDuplicates Tracking 679218 as yet unmatched pairs. 21799 records in RAM.
INFO 2026-06-08 08:11:36 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 1s. Last read position: chr7:100,358,257
INFO 2026-06-08 08:11:36 MarkDuplicates Tracking 677593 as yet unmatched pairs. 20170 records in RAM.
INFO 2026-06-08 08:11:37 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 1s. Last read position: chr7:102,178,550
INFO 2026-06-08 08:11:37 MarkDuplicates Tracking 673266 as yet unmatched pairs. 15841 records in RAM.
INFO 2026-06-08 08:11:39 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 1s. Last read position: chr7:104,668,894
INFO 2026-06-08 08:11:39 MarkDuplicates Tracking 671797 as yet unmatched pairs. 14364 records in RAM.
INFO 2026-06-08 08:11:40 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 1s. Last read position: chr7:116,700,170
INFO 2026-06-08 08:11:40 MarkDuplicates Tracking 669386 as yet unmatched pairs. 11943 records in RAM.
INFO 2026-06-08 08:11:42 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 1s. Last read position: chr7:130,070,701
INFO 2026-06-08 08:11:42 MarkDuplicates Tracking 666731 as yet unmatched pairs. 9284 records in RAM.
INFO 2026-06-08 08:11:43 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 1s. Last read position: chr7:139,261,534
INFO 2026-06-08 08:11:43 MarkDuplicates Tracking 664281 as yet unmatched pairs. 6831 records in RAM.
INFO 2026-06-08 08:11:45 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 1s. Last read position: chr7:144,284,237
INFO 2026-06-08 08:11:45 MarkDuplicates Tracking 662020 as yet unmatched pairs. 4568 records in RAM.
INFO 2026-06-08 08:11:46 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr7:151,066,064
INFO 2026-06-08 08:11:46 MarkDuplicates Tracking 659961 as yet unmatched pairs. 2505 records in RAM.
INFO 2026-06-08 08:11:48 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr8:7,289,648
INFO 2026-06-08 08:11:48 MarkDuplicates Tracking 657169 as yet unmatched pairs. 34418 records in RAM.
INFO 2026-06-08 08:11:50 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 1s. Last read position: chr8:22,140,622
INFO 2026-06-08 08:11:50 MarkDuplicates Tracking 654581 as yet unmatched pairs. 31827 records in RAM.
INFO 2026-06-08 08:11:52 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 2s. Last read position: chr8:30,544,543
INFO 2026-06-08 08:11:52 MarkDuplicates Tracking 652065 as yet unmatched pairs. 29307 records in RAM.
INFO 2026-06-08 08:11:53 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 1s. Last read position: chr8:38,424,541
INFO 2026-06-08 08:11:53 MarkDuplicates Tracking 649239 as yet unmatched pairs. 26475 records in RAM.
INFO 2026-06-08 08:11:55 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 1s. Last read position: chr8:47,737,467
INFO 2026-06-08 08:11:55 MarkDuplicates Tracking 646296 as yet unmatched pairs. 23521 records in RAM.
INFO 2026-06-08 08:11:56 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 1s. Last read position: chr8:74,244,561
INFO 2026-06-08 08:11:56 MarkDuplicates Tracking 643610 as yet unmatched pairs. 20829 records in RAM.
INFO 2026-06-08 08:11:59 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 2s. Last read position: chr8:100,712,721
INFO 2026-06-08 08:11:59 MarkDuplicates Tracking 641223 as yet unmatched pairs. 18437 records in RAM.
INFO 2026-06-08 08:12:01 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 1s. Last read position: chr8:125,431,040
INFO 2026-06-08 08:12:01 MarkDuplicates Tracking 638536 as yet unmatched pairs. 15738 records in RAM.
INFO 2026-06-08 08:12:02 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 1s. Last read position: chr8:143,310,025
INFO 2026-06-08 08:12:02 MarkDuplicates Tracking 635490 as yet unmatched pairs. 12688 records in RAM.
INFO 2026-06-08 08:12:04 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 1s. Last read position: chr8:143,859,532
INFO 2026-06-08 08:12:04 MarkDuplicates Tracking 633091 as yet unmatched pairs. 10288 records in RAM.
INFO 2026-06-08 08:12:05 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 1s. Last read position: chr8:143,862,444
INFO 2026-06-08 08:12:05 MarkDuplicates Tracking 632743 as yet unmatched pairs. 9940 records in RAM.
INFO 2026-06-08 08:12:07 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 1s. Last read position: chr8:143,865,508
INFO 2026-06-08 08:12:07 MarkDuplicates Tracking 631157 as yet unmatched pairs. 8352 records in RAM.
INFO 2026-06-08 08:12:08 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 1s. Last read position: chr8:143,919,290
INFO 2026-06-08 08:12:08 MarkDuplicates Tracking 630264 as yet unmatched pairs. 7459 records in RAM.
INFO 2026-06-08 08:12:10 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 1s. Last read position: chr8:144,085,947
INFO 2026-06-08 08:12:10 MarkDuplicates Tracking 625089 as yet unmatched pairs. 2280 records in RAM.
INFO 2026-06-08 08:12:11 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 1s. Last read position: chr9:712,086
INFO 2026-06-08 08:12:11 MarkDuplicates Tracking 622304 as yet unmatched pairs. 42806 records in RAM.
INFO 2026-06-08 08:12:13 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 1s. Last read position: chr9:14,150,135
INFO 2026-06-08 08:12:13 MarkDuplicates Tracking 619927 as yet unmatched pairs. 40428 records in RAM.
INFO 2026-06-08 08:12:15 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 1s. Last read position: chr9:35,056,971
INFO 2026-06-08 08:12:15 MarkDuplicates Tracking 617162 as yet unmatched pairs. 37660 records in RAM.
INFO 2026-06-08 08:12:16 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 1s. Last read position: chr9:61,330,937
INFO 2026-06-08 08:12:16 MarkDuplicates Tracking 614424 as yet unmatched pairs. 34889 records in RAM.
INFO 2026-06-08 08:12:18 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 1s. Last read position: chr9:91,737,391
INFO 2026-06-08 08:12:18 MarkDuplicates Tracking 612188 as yet unmatched pairs. 32650 records in RAM.
INFO 2026-06-08 08:12:19 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 1s. Last read position: chr9:97,998,556
INFO 2026-06-08 08:12:19 MarkDuplicates Tracking 609278 as yet unmatched pairs. 29729 records in RAM.
INFO 2026-06-08 08:12:21 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 1s. Last read position: chr9:110,244,141
INFO 2026-06-08 08:12:21 MarkDuplicates Tracking 606614 as yet unmatched pairs. 27057 records in RAM.
INFO 2026-06-08 08:12:22 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 1s. Last read position: chr9:114,205,119
INFO 2026-06-08 08:12:22 MarkDuplicates Tracking 604383 as yet unmatched pairs. 24821 records in RAM.
INFO 2026-06-08 08:12:24 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 1s. Last read position: chr9:115,023,972
INFO 2026-06-08 08:12:24 MarkDuplicates Tracking 600584 as yet unmatched pairs. 21018 records in RAM.
INFO 2026-06-08 08:12:25 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 1s. Last read position: chr9:123,452,238
INFO 2026-06-08 08:12:25 MarkDuplicates Tracking 597859 as yet unmatched pairs. 18292 records in RAM.
INFO 2026-06-08 08:12:27 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 1s. Last read position: chr9:128,584,317
INFO 2026-06-08 08:12:27 MarkDuplicates Tracking 595041 as yet unmatched pairs. 15466 records in RAM.
INFO 2026-06-08 08:12:28 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 1s. Last read position: chr9:131,464,870
INFO 2026-06-08 08:12:28 MarkDuplicates Tracking 592220 as yet unmatched pairs. 12639 records in RAM.
INFO 2026-06-08 08:12:30 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 1s. Last read position: chr9:134,050,445
INFO 2026-06-08 08:12:30 MarkDuplicates Tracking 589471 as yet unmatched pairs. 9889 records in RAM.
INFO 2026-06-08 08:12:31 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 1s. Last read position: chr9:136,476,440
INFO 2026-06-08 08:12:31 MarkDuplicates Tracking 586191 as yet unmatched pairs. 6606 records in RAM.
INFO 2026-06-08 08:12:33 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 1s. Last read position: chr9:136,672,012
INFO 2026-06-08 08:12:33 MarkDuplicates Tracking 582644 as yet unmatched pairs. 3057 records in RAM.
INFO 2026-06-08 08:12:36 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 2s. Last read position: chr10:817,758
INFO 2026-06-08 08:12:36 MarkDuplicates Tracking 579316 as yet unmatched pairs. 33922 records in RAM.
INFO 2026-06-08 08:12:38 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 1s. Last read position: chr10:17,229,612
INFO 2026-06-08 08:12:38 MarkDuplicates Tracking 577364 as yet unmatched pairs. 31968 records in RAM.
INFO 2026-06-08 08:12:39 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 1s. Last read position: chr10:26,770,279
INFO 2026-06-08 08:12:39 MarkDuplicates Tracking 573781 as yet unmatched pairs. 28375 records in RAM.
INFO 2026-06-08 08:12:41 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 1s. Last read position: chr10:38,016,987
INFO 2026-06-08 08:12:41 MarkDuplicates Tracking 571401 as yet unmatched pairs. 25995 records in RAM.
INFO 2026-06-08 08:12:42 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 1s. Last read position: chr10:48,011,577
INFO 2026-06-08 08:12:42 MarkDuplicates Tracking 569813 as yet unmatched pairs. 24396 records in RAM.
INFO 2026-06-08 08:12:44 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 1s. Last read position: chr10:63,521,482
INFO 2026-06-08 08:12:44 MarkDuplicates Tracking 567284 as yet unmatched pairs. 21860 records in RAM.
INFO 2026-06-08 08:12:46 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 1s. Last read position: chr10:73,792,340
INFO 2026-06-08 08:12:46 MarkDuplicates Tracking 564702 as yet unmatched pairs. 19272 records in RAM.
INFO 2026-06-08 08:12:47 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 1s. Last read position: chr10:84,417,796
INFO 2026-06-08 08:12:47 MarkDuplicates Tracking 561920 as yet unmatched pairs. 16484 records in RAM.
INFO 2026-06-08 08:12:48 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 1s. Last read position: chr10:95,628,460
INFO 2026-06-08 08:12:48 MarkDuplicates Tracking 559468 as yet unmatched pairs. 14031 records in RAM.
INFO 2026-06-08 08:12:50 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 1s. Last read position: chr10:101,847,596
INFO 2026-06-08 08:12:50 MarkDuplicates Tracking 556747 as yet unmatched pairs. 11309 records in RAM.
INFO 2026-06-08 08:12:51 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 1s. Last read position: chr10:104,039,460
INFO 2026-06-08 08:12:51 MarkDuplicates Tracking 554146 as yet unmatched pairs. 8706 records in RAM.
INFO 2026-06-08 08:12:53 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 1s. Last read position: chr10:104,074,195
INFO 2026-06-08 08:12:53 MarkDuplicates Tracking 551494 as yet unmatched pairs. 6054 records in RAM.
INFO 2026-06-08 08:12:55 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 1s. Last read position: chr10:121,480,003
INFO 2026-06-08 08:12:55 MarkDuplicates Tracking 549203 as yet unmatched pairs. 3761 records in RAM.
INFO 2026-06-08 08:12:56 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 1s. Last read position: chr10:132,397,250
INFO 2026-06-08 08:12:56 MarkDuplicates Tracking 546015 as yet unmatched pairs. 562 records in RAM.
INFO 2026-06-08 08:12:58 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 1s. Last read position: chr11:727,533
INFO 2026-06-08 08:12:58 MarkDuplicates Tracking 543120 as yet unmatched pairs. 54383 records in RAM.
INFO 2026-06-08 08:12:59 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 1s. Last read position: chr11:3,092,972
INFO 2026-06-08 08:12:59 MarkDuplicates Tracking 539997 as yet unmatched pairs. 51255 records in RAM.
INFO 2026-06-08 08:13:01 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 1s. Last read position: chr11:9,021,004
INFO 2026-06-08 08:13:01 MarkDuplicates Tracking 537161 as yet unmatched pairs. 48415 records in RAM.
INFO 2026-06-08 08:13:03 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:05:43s. Time for last 1,000,000: 1s. Last read position: chr11:18,308,990
INFO 2026-06-08 08:13:03 MarkDuplicates Tracking 534596 as yet unmatched pairs. 45845 records in RAM.
INFO 2026-06-08 08:13:04 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 1s. Last read position: chr11:33,710,294
INFO 2026-06-08 08:13:04 MarkDuplicates Tracking 532284 as yet unmatched pairs. 43529 records in RAM.
INFO 2026-06-08 08:13:05 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 1s. Last read position: chr11:46,417,907
INFO 2026-06-08 08:13:05 MarkDuplicates Tracking 529343 as yet unmatched pairs. 40574 records in RAM.
INFO 2026-06-08 08:13:08 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 2s. Last read position: chr11:57,785,708
INFO 2026-06-08 08:13:08 MarkDuplicates Tracking 526631 as yet unmatched pairs. 37857 records in RAM.
INFO 2026-06-08 08:13:09 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 1s. Last read position: chr11:62,518,457
INFO 2026-06-08 08:13:09 MarkDuplicates Tracking 524288 as yet unmatched pairs. 35499 records in RAM.
INFO 2026-06-08 08:13:11 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 1s. Last read position: chr11:62,531,195
INFO 2026-06-08 08:13:11 MarkDuplicates Tracking 522225 as yet unmatched pairs. 33436 records in RAM.
INFO 2026-06-08 08:13:12 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 1s. Last read position: chr11:64,195,730
INFO 2026-06-08 08:13:12 MarkDuplicates Tracking 519088 as yet unmatched pairs. 30293 records in RAM.
INFO 2026-06-08 08:13:14 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 2s. Last read position: chr11:65,539,328
INFO 2026-06-08 08:13:14 MarkDuplicates Tracking 516093 as yet unmatched pairs. 27291 records in RAM.
INFO 2026-06-08 08:13:16 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 1s. Last read position: chr11:66,287,511
INFO 2026-06-08 08:13:16 MarkDuplicates Tracking 512756 as yet unmatched pairs. 23953 records in RAM.
INFO 2026-06-08 08:13:18 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 1s. Last read position: chr11:68,348,040
INFO 2026-06-08 08:13:18 MarkDuplicates Tracking 509755 as yet unmatched pairs. 20952 records in RAM.
INFO 2026-06-08 08:13:20 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 1s. Last read position: chr11:72,001,525
INFO 2026-06-08 08:13:20 MarkDuplicates Tracking 506920 as yet unmatched pairs. 18115 records in RAM.
INFO 2026-06-08 08:13:22 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 1s. Last read position: chr11:75,165,818
INFO 2026-06-08 08:13:22 MarkDuplicates Tracking 503957 as yet unmatched pairs. 15148 records in RAM.
INFO 2026-06-08 08:13:23 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 1s. Last read position: chr11:95,799,345
INFO 2026-06-08 08:13:23 MarkDuplicates Tracking 501075 as yet unmatched pairs. 12266 records in RAM.
INFO 2026-06-08 08:13:25 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 1s. Last read position: chr11:111,723,667
INFO 2026-06-08 08:13:25 MarkDuplicates Tracking 498488 as yet unmatched pairs. 9676 records in RAM.
INFO 2026-06-08 08:13:27 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 1s. Last read position: chr11:118,625,016
INFO 2026-06-08 08:13:27 MarkDuplicates Tracking 495997 as yet unmatched pairs. 7185 records in RAM.
INFO 2026-06-08 08:13:28 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 1s. Last read position: chr11:120,112,373
INFO 2026-06-08 08:13:28 MarkDuplicates Tracking 493444 as yet unmatched pairs. 4626 records in RAM.
INFO 2026-06-08 08:13:30 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 1s. Last read position: chr11:128,758,276
INFO 2026-06-08 08:13:30 MarkDuplicates Tracking 490150 as yet unmatched pairs. 1332 records in RAM.
INFO 2026-06-08 08:13:32 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 1s. Last read position: chr12:2,120,341
INFO 2026-06-08 08:13:32 MarkDuplicates Tracking 487465 as yet unmatched pairs. 52908 records in RAM.
INFO 2026-06-08 08:13:34 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 1s. Last read position: chr12:6,839,071
INFO 2026-06-08 08:13:34 MarkDuplicates Tracking 484622 as yet unmatched pairs. 50063 records in RAM.
INFO 2026-06-08 08:13:36 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 1s. Last read position: chr12:10,704,133
INFO 2026-06-08 08:13:36 MarkDuplicates Tracking 482053 as yet unmatched pairs. 47493 records in RAM.
INFO 2026-06-08 08:13:37 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 1s. Last read position: chr12:26,188,859
INFO 2026-06-08 08:13:37 MarkDuplicates Tracking 479236 as yet unmatched pairs. 44668 records in RAM.
INFO 2026-06-08 08:13:39 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 2s. Last read position: chr12:48,074,738
INFO 2026-06-08 08:13:39 MarkDuplicates Tracking 476597 as yet unmatched pairs. 42026 records in RAM.
INFO 2026-06-08 08:13:40 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 1s. Last read position: chr12:49,600,070
INFO 2026-06-08 08:13:40 MarkDuplicates Tracking 474044 as yet unmatched pairs. 39472 records in RAM.
INFO 2026-06-08 08:13:43 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 2s. Last read position: chr12:52,057,449
INFO 2026-06-08 08:13:43 MarkDuplicates Tracking 471351 as yet unmatched pairs. 36776 records in RAM.
INFO 2026-06-08 08:13:44 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 1s. Last read position: chr12:52,473,461
INFO 2026-06-08 08:13:44 MarkDuplicates Tracking 469748 as yet unmatched pairs. 35173 records in RAM.
INFO 2026-06-08 08:13:46 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 1s. Last read position: chr12:52,493,134
INFO 2026-06-08 08:13:46 MarkDuplicates Tracking 467004 as yet unmatched pairs. 32429 records in RAM.
INFO 2026-06-08 08:13:48 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 1s. Last read position: chr12:52,901,196
INFO 2026-06-08 08:13:48 MarkDuplicates Tracking 464103 as yet unmatched pairs. 29522 records in RAM.
INFO 2026-06-08 08:13:49 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 1s. Last read position: chr12:54,284,266
INFO 2026-06-08 08:13:49 MarkDuplicates Tracking 461642 as yet unmatched pairs. 27060 records in RAM.
INFO 2026-06-08 08:13:51 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:06:31s. Time for last 1,000,000: 1s. Last read position: chr12:56,469,166
INFO 2026-06-08 08:13:51 MarkDuplicates Tracking 458801 as yet unmatched pairs. 24217 records in RAM.
INFO 2026-06-08 08:13:53 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 1s. Last read position: chr12:57,173,249
INFO 2026-06-08 08:13:53 MarkDuplicates Tracking 456175 as yet unmatched pairs. 21589 records in RAM.
INFO 2026-06-08 08:13:54 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 1s. Last read position: chr12:66,248,961
INFO 2026-06-08 08:13:54 MarkDuplicates Tracking 453530 as yet unmatched pairs. 18943 records in RAM.
INFO 2026-06-08 08:13:56 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 1s. Last read position: chr12:95,494,192
INFO 2026-06-08 08:13:56 MarkDuplicates Tracking 451130 as yet unmatched pairs. 16539 records in RAM.
INFO 2026-06-08 08:13:58 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 1s. Last read position: chr12:109,983,489
INFO 2026-06-08 08:13:58 MarkDuplicates Tracking 448518 as yet unmatched pairs. 13918 records in RAM.
INFO 2026-06-08 08:13:59 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 1s. Last read position: chr12:115,983,318
INFO 2026-06-08 08:13:59 MarkDuplicates Tracking 445478 as yet unmatched pairs. 10876 records in RAM.
INFO 2026-06-08 08:14:01 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 1s. Last read position: chr12:122,127,253
INFO 2026-06-08 08:14:01 MarkDuplicates Tracking 442657 as yet unmatched pairs. 8050 records in RAM.
INFO 2026-06-08 08:14:02 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 1s. Last read position: chr12:124,314,379
INFO 2026-06-08 08:14:02 MarkDuplicates Tracking 439799 as yet unmatched pairs. 5190 records in RAM.
INFO 2026-06-08 08:14:04 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:06:44s. Time for last 1,000,000: 1s. Last read position: chr12:131,961,558
INFO 2026-06-08 08:14:04 MarkDuplicates Tracking 436952 as yet unmatched pairs. 2341 records in RAM.
INFO 2026-06-08 08:14:06 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:06:46s. Time for last 1,000,000: 1s. Last read position: chr13:20,188,041
INFO 2026-06-08 08:14:06 MarkDuplicates Tracking 434001 as yet unmatched pairs. 13449 records in RAM.
INFO 2026-06-08 08:14:08 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 1s. Last read position: chr13:41,132,419
INFO 2026-06-08 08:14:08 MarkDuplicates Tracking 431445 as yet unmatched pairs. 10888 records in RAM.
INFO 2026-06-08 08:14:10 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 2s. Last read position: chr13:73,813,180
INFO 2026-06-08 08:14:10 MarkDuplicates Tracking 428945 as yet unmatched pairs. 8383 records in RAM.
INFO 2026-06-08 08:14:12 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 1s. Last read position: chr13:109,783,781
INFO 2026-06-08 08:14:12 MarkDuplicates Tracking 426318 as yet unmatched pairs. 5737 records in RAM.
INFO 2026-06-08 08:14:14 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 2s. Last read position: chr13:110,511,958
INFO 2026-06-08 08:14:14 MarkDuplicates Tracking 423249 as yet unmatched pairs. 2668 records in RAM.
INFO 2026-06-08 08:14:16 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 1s. Last read position: chr14:21,022,373
INFO 2026-06-08 08:14:16 MarkDuplicates Tracking 420044 as yet unmatched pairs. 28422 records in RAM.
INFO 2026-06-08 08:14:18 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:06:57s. Time for last 1,000,000: 1s. Last read position: chr14:23,359,507
INFO 2026-06-08 08:14:18 MarkDuplicates Tracking 417444 as yet unmatched pairs. 25814 records in RAM.
INFO 2026-06-08 08:14:19 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 1s. Last read position: chr14:32,093,600
INFO 2026-06-08 08:14:19 MarkDuplicates Tracking 414429 as yet unmatched pairs. 22799 records in RAM.
INFO 2026-06-08 08:14:21 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 1s. Last read position: chr14:55,062,798
INFO 2026-06-08 08:14:21 MarkDuplicates Tracking 411920 as yet unmatched pairs. 20288 records in RAM.
INFO 2026-06-08 08:14:22 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 1s. Last read position: chr14:67,653,479
INFO 2026-06-08 08:14:22 MarkDuplicates Tracking 409256 as yet unmatched pairs. 17623 records in RAM.
INFO 2026-06-08 08:14:24 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:07:04s. Time for last 1,000,000: 1s. Last read position: chr14:71,672,347
INFO 2026-06-08 08:14:24 MarkDuplicates Tracking 406617 as yet unmatched pairs. 14983 records in RAM.
INFO 2026-06-08 08:14:26 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 1s. Last read position: chr14:75,280,007
INFO 2026-06-08 08:14:26 MarkDuplicates Tracking 404406 as yet unmatched pairs. 12772 records in RAM.
INFO 2026-06-08 08:14:27 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:07:07s. Time for last 1,000,000: 1s. Last read position: chr14:91,273,305
INFO 2026-06-08 08:14:27 MarkDuplicates Tracking 401095 as yet unmatched pairs. 9456 records in RAM.
INFO 2026-06-08 08:14:29 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:07:09s. Time for last 1,000,000: 1s. Last read position: chr14:101,906,408
INFO 2026-06-08 08:14:29 MarkDuplicates Tracking 398165 as yet unmatched pairs. 6503 records in RAM.
INFO 2026-06-08 08:14:31 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 1s. Last read position: chr14:104,884,142
INFO 2026-06-08 08:14:31 MarkDuplicates Tracking 395129 as yet unmatched pairs. 3467 records in RAM.
INFO 2026-06-08 08:14:32 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:07:12s. Time for last 1,000,000: 1s. Last read position: chr14:105,624,517
INFO 2026-06-08 08:14:32 MarkDuplicates Tracking 392384 as yet unmatched pairs. 722 records in RAM.
INFO 2026-06-08 08:14:34 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:07:14s. Time for last 1,000,000: 1s. Last read position: chr15:30,143,644
INFO 2026-06-08 08:14:34 MarkDuplicates Tracking 390163 as yet unmatched pairs. 25937 records in RAM.
INFO 2026-06-08 08:14:36 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:07:16s. Time for last 1,000,000: 1s. Last read position: chr15:39,593,397
INFO 2026-06-08 08:14:36 MarkDuplicates Tracking 388228 as yet unmatched pairs. 24000 records in RAM.
INFO 2026-06-08 08:14:38 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:07:18s. Time for last 1,000,000: 2s. Last read position: chr15:42,402,841
INFO 2026-06-08 08:14:38 MarkDuplicates Tracking 385246 as yet unmatched pairs. 21012 records in RAM.
INFO 2026-06-08 08:14:40 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:07:20s. Time for last 1,000,000: 1s. Last read position: chr15:48,962,771
INFO 2026-06-08 08:14:40 MarkDuplicates Tracking 382796 as yet unmatched pairs. 18562 records in RAM.
INFO 2026-06-08 08:14:42 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:07:22s. Time for last 1,000,000: 2s. Last read position: chr15:61,869,538
INFO 2026-06-08 08:14:42 MarkDuplicates Tracking 380104 as yet unmatched pairs. 15867 records in RAM.
INFO 2026-06-08 08:14:44 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:07:24s. Time for last 1,000,000: 1s. Last read position: chr15:69,268,484
INFO 2026-06-08 08:14:44 MarkDuplicates Tracking 377349 as yet unmatched pairs. 13110 records in RAM.
INFO 2026-06-08 08:14:46 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:07:26s. Time for last 1,000,000: 1s. Last read position: chr15:74,035,487
INFO 2026-06-08 08:14:46 MarkDuplicates Tracking 374553 as yet unmatched pairs. 10312 records in RAM.
INFO 2026-06-08 08:14:48 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 1s. Last read position: chr15:79,845,232
INFO 2026-06-08 08:14:48 MarkDuplicates Tracking 371358 as yet unmatched pairs. 7115 records in RAM.
INFO 2026-06-08 08:14:49 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:07:29s. Time for last 1,000,000: 1s. Last read position: chr15:88,032,900
INFO 2026-06-08 08:14:49 MarkDuplicates Tracking 370132 as yet unmatched pairs. 5886 records in RAM.
INFO 2026-06-08 08:14:51 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:07:31s. Time for last 1,000,000: 1s. Last read position: chr15:90,918,741
INFO 2026-06-08 08:14:51 MarkDuplicates Tracking 366583 as yet unmatched pairs. 2336 records in RAM.
INFO 2026-06-08 08:14:54 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:07:33s. Time for last 1,000,000: 2s. Last read position: chr16:297,918
INFO 2026-06-08 08:14:54 MarkDuplicates Tracking 363730 as yet unmatched pairs. 51016 records in RAM.
INFO 2026-06-08 08:15:59 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:08:39s. Time for last 1,000,000: 65s. Last read position: chr16:1,964,524
INFO 2026-06-08 08:15:59 MarkDuplicates Tracking 360184 as yet unmatched pairs. 47469 records in RAM.
INFO 2026-06-08 08:16:01 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 1s. Last read position: chr16:2,557,687
INFO 2026-06-08 08:16:01 MarkDuplicates Tracking 357104 as yet unmatched pairs. 44389 records in RAM.
INFO 2026-06-08 08:16:02 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:08:42s. Time for last 1,000,000: 1s. Last read position: chr16:3,288,455
INFO 2026-06-08 08:16:02 MarkDuplicates Tracking 354252 as yet unmatched pairs. 41537 records in RAM.
INFO 2026-06-08 08:16:04 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:08:44s. Time for last 1,000,000: 2s. Last read position: chr16:8,915,459
INFO 2026-06-08 08:16:04 MarkDuplicates Tracking 351310 as yet unmatched pairs. 38594 records in RAM.
INFO 2026-06-08 08:16:06 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:08:46s. Time for last 1,000,000: 1s. Last read position: chr16:14,919,040
INFO 2026-06-08 08:16:06 MarkDuplicates Tracking 349350 as yet unmatched pairs. 36632 records in RAM.
INFO 2026-06-08 08:16:08 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 1s. Last read position: chr16:15,757,857
INFO 2026-06-08 08:16:08 MarkDuplicates Tracking 347992 as yet unmatched pairs. 35274 records in RAM.
INFO 2026-06-08 08:16:09 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 1s. Last read position: chr16:16,360,998
INFO 2026-06-08 08:16:09 MarkDuplicates Tracking 347358 as yet unmatched pairs. 34638 records in RAM.
INFO 2026-06-08 08:16:11 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 1s. Last read position: chr16:18,358,329
INFO 2026-06-08 08:16:11 MarkDuplicates Tracking 346307 as yet unmatched pairs. 33587 records in RAM.
INFO 2026-06-08 08:16:12 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:08:52s. Time for last 1,000,000: 1s. Last read position: chr16:21,402,497
INFO 2026-06-08 08:16:12 MarkDuplicates Tracking 344628 as yet unmatched pairs. 31908 records in RAM.
INFO 2026-06-08 08:16:14 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 1s. Last read position: chr16:21,836,451
INFO 2026-06-08 08:16:14 MarkDuplicates Tracking 343721 as yet unmatched pairs. 30996 records in RAM.
INFO 2026-06-08 08:16:15 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:08:55s. Time for last 1,000,000: 1s. Last read position: chr16:22,534,535
INFO 2026-06-08 08:16:15 MarkDuplicates Tracking 343406 as yet unmatched pairs. 30681 records in RAM.
INFO 2026-06-08 08:16:16 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:08:56s. Time for last 1,000,000: 1s. Last read position: chr16:28,390,540
INFO 2026-06-08 08:16:16 MarkDuplicates Tracking 341115 as yet unmatched pairs. 28386 records in RAM.
INFO 2026-06-08 08:16:18 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:08:58s. Time for last 1,000,000: 1s. Last read position: chr16:29,381,957
INFO 2026-06-08 08:16:18 MarkDuplicates Tracking 339231 as yet unmatched pairs. 26501 records in RAM.
INFO 2026-06-08 08:16:19 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:08:59s. Time for last 1,000,000: 1s. Last read position: chr16:29,835,780
INFO 2026-06-08 08:16:19 MarkDuplicates Tracking 337967 as yet unmatched pairs. 25237 records in RAM.
INFO 2026-06-08 08:16:21 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:09:01s. Time for last 1,000,000: 1s. Last read position: chr16:30,582,904
INFO 2026-06-08 08:16:21 MarkDuplicates Tracking 335962 as yet unmatched pairs. 23231 records in RAM.
INFO 2026-06-08 08:16:23 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:09:03s. Time for last 1,000,000: 2s. Last read position: chr16:31,189,591
INFO 2026-06-08 08:16:23 MarkDuplicates Tracking 333393 as yet unmatched pairs. 20650 records in RAM.
INFO 2026-06-08 08:16:25 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 2s. Last read position: chr16:54,285,431
INFO 2026-06-08 08:16:25 MarkDuplicates Tracking 330878 as yet unmatched pairs. 18134 records in RAM.
INFO 2026-06-08 08:16:27 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:09:07s. Time for last 1,000,000: 1s. Last read position: chr16:66,517,810
INFO 2026-06-08 08:16:27 MarkDuplicates Tracking 327582 as yet unmatched pairs. 14835 records in RAM.
INFO 2026-06-08 08:16:28 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 1s. Last read position: chr16:68,808,785
INFO 2026-06-08 08:16:28 MarkDuplicates Tracking 324715 as yet unmatched pairs. 11968 records in RAM.
INFO 2026-06-08 08:16:30 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:09:10s. Time for last 1,000,000: 1s. Last read position: chr16:71,850,731
INFO 2026-06-08 08:16:30 MarkDuplicates Tracking 322160 as yet unmatched pairs. 9411 records in RAM.
INFO 2026-06-08 08:16:32 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:09:12s. Time for last 1,000,000: 1s. Last read position: chr16:84,497,980
INFO 2026-06-08 08:16:32 MarkDuplicates Tracking 319450 as yet unmatched pairs. 6692 records in RAM.
INFO 2026-06-08 08:16:34 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:09:13s. Time for last 1,000,000: 1s. Last read position: chr16:88,437,218
INFO 2026-06-08 08:16:34 MarkDuplicates Tracking 316499 as yet unmatched pairs. 3735 records in RAM.
INFO 2026-06-08 08:16:35 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:09:15s. Time for last 1,000,000: 1s. Last read position: chr16:89,737,838
INFO 2026-06-08 08:16:35 MarkDuplicates Tracking 313258 as yet unmatched pairs. 494 records in RAM.
INFO 2026-06-08 08:16:38 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:09:18s. Time for last 1,000,000: 2s. Last read position: chr17:1,737,487
INFO 2026-06-08 08:16:38 MarkDuplicates Tracking 310528 as yet unmatched pairs. 98231 records in RAM.
INFO 2026-06-08 08:16:40 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 1s. Last read position: chr17:4,892,399
INFO 2026-06-08 08:16:40 MarkDuplicates Tracking 307521 as yet unmatched pairs. 95223 records in RAM.
INFO 2026-06-08 08:16:42 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:09:21s. Time for last 1,000,000: 1s. Last read position: chr17:7,393,683
INFO 2026-06-08 08:16:42 MarkDuplicates Tracking 304605 as yet unmatched pairs. 92306 records in RAM.
INFO 2026-06-08 08:16:43 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:09:23s. Time for last 1,000,000: 1s. Last read position: chr17:7,851,179
INFO 2026-06-08 08:16:43 MarkDuplicates Tracking 301843 as yet unmatched pairs. 89544 records in RAM.
INFO 2026-06-08 08:16:45 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 1s. Last read position: chr17:13,000,256
INFO 2026-06-08 08:16:45 MarkDuplicates Tracking 298773 as yet unmatched pairs. 86471 records in RAM.
INFO 2026-06-08 08:16:46 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:09:26s. Time for last 1,000,000: 1s. Last read position: chr17:17,816,229
INFO 2026-06-08 08:16:46 MarkDuplicates Tracking 296253 as yet unmatched pairs. 83950 records in RAM.
INFO 2026-06-08 08:16:48 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:09:28s. Time for last 1,000,000: 1s. Last read position: chr17:20,517,465
INFO 2026-06-08 08:16:48 MarkDuplicates Tracking 294142 as yet unmatched pairs. 81838 records in RAM.
INFO 2026-06-08 08:16:50 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:09:30s. Time for last 1,000,000: 1s. Last read position: chr17:30,185,080
INFO 2026-06-08 08:16:50 MarkDuplicates Tracking 291489 as yet unmatched pairs. 79184 records in RAM.
INFO 2026-06-08 08:16:51 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:09:31s. Time for last 1,000,000: 1s. Last read position: chr17:36,587,168
INFO 2026-06-08 08:16:51 MarkDuplicates Tracking 289132 as yet unmatched pairs. 76825 records in RAM.
INFO 2026-06-08 08:16:53 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:09:33s. Time for last 1,000,000: 1s. Last read position: chr17:39,627,445
INFO 2026-06-08 08:16:53 MarkDuplicates Tracking 286888 as yet unmatched pairs. 74580 records in RAM.
INFO 2026-06-08 08:16:55 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 2s. Last read position: chr17:40,133,045
INFO 2026-06-08 08:16:55 MarkDuplicates Tracking 283860 as yet unmatched pairs. 71552 records in RAM.
INFO 2026-06-08 08:16:57 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 1s. Last read position: chr17:40,496,185
INFO 2026-06-08 08:16:57 MarkDuplicates Tracking 282609 as yet unmatched pairs. 70295 records in RAM.
INFO 2026-06-08 08:16:59 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:09:39s. Time for last 1,000,000: 1s. Last read position: chr17:41,583,375
INFO 2026-06-08 08:16:59 MarkDuplicates Tracking 279865 as yet unmatched pairs. 67551 records in RAM.
INFO 2026-06-08 08:17:00 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:09:40s. Time for last 1,000,000: 1s. Last read position: chr17:41,586,391
INFO 2026-06-08 08:17:00 MarkDuplicates Tracking 276729 as yet unmatched pairs. 64415 records in RAM.
INFO 2026-06-08 08:17:02 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:09:42s. Time for last 1,000,000: 1s. Last read position: chr17:41,612,486
INFO 2026-06-08 08:17:02 MarkDuplicates Tracking 272903 as yet unmatched pairs. 60589 records in RAM.
INFO 2026-06-08 08:17:04 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 1s. Last read position: chr17:41,621,685
INFO 2026-06-08 08:17:04 MarkDuplicates Tracking 270678 as yet unmatched pairs. 58360 records in RAM.
INFO 2026-06-08 08:17:05 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:09:45s. Time for last 1,000,000: 1s. Last read position: chr17:41,624,474
INFO 2026-06-08 08:17:05 MarkDuplicates Tracking 266678 as yet unmatched pairs. 54360 records in RAM.
INFO 2026-06-08 08:17:07 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:09:47s. Time for last 1,000,000: 1s. Last read position: chr17:42,727,644
INFO 2026-06-08 08:17:07 MarkDuplicates Tracking 263928 as yet unmatched pairs. 51609 records in RAM.
INFO 2026-06-08 08:17:09 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:09:49s. Time for last 1,000,000: 2s. Last read position: chr17:45,547,865
INFO 2026-06-08 08:17:09 MarkDuplicates Tracking 261237 as yet unmatched pairs. 48918 records in RAM.
INFO 2026-06-08 08:17:11 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:09:51s. Time for last 1,000,000: 1s. Last read position: chr17:50,078,061
INFO 2026-06-08 08:17:11 MarkDuplicates Tracking 259228 as yet unmatched pairs. 46907 records in RAM.
INFO 2026-06-08 08:17:13 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:09:53s. Time for last 1,000,000: 2s. Last read position: chr17:50,187,882
INFO 2026-06-08 08:17:13 MarkDuplicates Tracking 261236 as yet unmatched pairs. 48915 records in RAM.
INFO 2026-06-08 08:17:15 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:09:55s. Time for last 1,000,000: 2s. Last read position: chr17:50,189,425
INFO 2026-06-08 08:17:15 MarkDuplicates Tracking 256273 as yet unmatched pairs. 43952 records in RAM.
INFO 2026-06-08 08:17:17 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:09:57s. Time for last 1,000,000: 1s. Last read position: chr17:50,190,817
INFO 2026-06-08 08:17:17 MarkDuplicates Tracking 251044 as yet unmatched pairs. 38723 records in RAM.
INFO 2026-06-08 08:17:19 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 1s. Last read position: chr17:50,193,986
INFO 2026-06-08 08:17:19 MarkDuplicates Tracking 249657 as yet unmatched pairs. 37336 records in RAM.
INFO 2026-06-08 08:17:20 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:10:00s. Time for last 1,000,000: 1s. Last read position: chr17:50,195,598
INFO 2026-06-08 08:17:20 MarkDuplicates Tracking 248204 as yet unmatched pairs. 35883 records in RAM.
INFO 2026-06-08 08:17:22 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:10:02s. Time for last 1,000,000: 1s. Last read position: chr17:50,197,753
INFO 2026-06-08 08:17:22 MarkDuplicates Tracking 243495 as yet unmatched pairs. 31174 records in RAM.
INFO 2026-06-08 08:17:24 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:10:04s. Time for last 1,000,000: 1s. Last read position: chr17:50,531,279
INFO 2026-06-08 08:17:24 MarkDuplicates Tracking 238026 as yet unmatched pairs. 25704 records in RAM.
INFO 2026-06-08 08:17:26 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:10:05s. Time for last 1,000,000: 1s. Last read position: chr17:59,666,488
INFO 2026-06-08 08:17:26 MarkDuplicates Tracking 235390 as yet unmatched pairs. 23063 records in RAM.
INFO 2026-06-08 08:17:27 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:10:07s. Time for last 1,000,000: 1s. Last read position: chr17:64,496,864
INFO 2026-06-08 08:17:27 MarkDuplicates Tracking 232368 as yet unmatched pairs. 20041 records in RAM.
INFO 2026-06-08 08:17:29 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 1s. Last read position: chr17:73,338,615
INFO 2026-06-08 08:17:29 MarkDuplicates Tracking 229856 as yet unmatched pairs. 17526 records in RAM.
INFO 2026-06-08 08:17:30 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:10:10s. Time for last 1,000,000: 1s. Last read position: chr17:75,629,147
INFO 2026-06-08 08:17:30 MarkDuplicates Tracking 226916 as yet unmatched pairs. 14584 records in RAM.
INFO 2026-06-08 08:17:32 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 1s. Last read position: chr17:75,756,994
INFO 2026-06-08 08:17:32 MarkDuplicates Tracking 224231 as yet unmatched pairs. 11899 records in RAM.
INFO 2026-06-08 08:17:34 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:10:14s. Time for last 1,000,000: 1s. Last read position: chr17:77,402,346
INFO 2026-06-08 08:17:34 MarkDuplicates Tracking 220548 as yet unmatched pairs. 8216 records in RAM.
INFO 2026-06-08 08:17:36 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:10:15s. Time for last 1,000,000: 1s. Last read position: chr17:80,319,291
INFO 2026-06-08 08:17:36 MarkDuplicates Tracking 217618 as yet unmatched pairs. 5286 records in RAM.
INFO 2026-06-08 08:17:38 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:10:18s. Time for last 1,000,000: 2s. Last read position: chr17:81,859,194
INFO 2026-06-08 08:17:38 MarkDuplicates Tracking 214524 as yet unmatched pairs. 2188 records in RAM.
INFO 2026-06-08 08:17:40 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:10:20s. Time for last 1,000,000: 2s. Last read position: chr18:3,457,802
INFO 2026-06-08 08:17:40 MarkDuplicates Tracking 211540 as yet unmatched pairs. 10919 records in RAM.
INFO 2026-06-08 08:17:42 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:10:22s. Time for last 1,000,000: 1s. Last read position: chr18:23,881,934
INFO 2026-06-08 08:17:42 MarkDuplicates Tracking 208862 as yet unmatched pairs. 8239 records in RAM.
INFO 2026-06-08 08:17:44 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:10:24s. Time for last 1,000,000: 1s. Last read position: chr18:41,990,463
INFO 2026-06-08 08:17:44 MarkDuplicates Tracking 206244 as yet unmatched pairs. 5620 records in RAM.
INFO 2026-06-08 08:17:45 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:10:25s. Time for last 1,000,000: 1s. Last read position: chr18:62,221,034
INFO 2026-06-08 08:17:45 MarkDuplicates Tracking 203608 as yet unmatched pairs. 2981 records in RAM.
INFO 2026-06-08 08:17:48 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:10:28s. Time for last 1,000,000: 2s. Last read position: chr19:572,609
INFO 2026-06-08 08:17:48 MarkDuplicates Tracking 200481 as yet unmatched pairs. 86552 records in RAM.
INFO 2026-06-08 08:17:50 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:10:29s. Time for last 1,000,000: 1s. Last read position: chr19:2,046,215
INFO 2026-06-08 08:17:50 MarkDuplicates Tracking 196921 as yet unmatched pairs. 82992 records in RAM.
INFO 2026-06-08 08:17:51 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:10:31s. Time for last 1,000,000: 1s. Last read position: chr19:3,574,571
INFO 2026-06-08 08:17:51 MarkDuplicates Tracking 193559 as yet unmatched pairs. 79630 records in RAM.
INFO 2026-06-08 08:17:53 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:10:33s. Time for last 1,000,000: 1s. Last read position: chr19:5,211,751
INFO 2026-06-08 08:17:53 MarkDuplicates Tracking 190332 as yet unmatched pairs. 76403 records in RAM.
INFO 2026-06-08 08:17:55 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:10:35s. Time for last 1,000,000: 1s. Last read position: chr19:6,735,908
INFO 2026-06-08 08:17:55 MarkDuplicates Tracking 186945 as yet unmatched pairs. 73014 records in RAM.
INFO 2026-06-08 08:17:57 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:10:36s. Time for last 1,000,000: 1s. Last read position: chr19:8,811,535
INFO 2026-06-08 08:17:57 MarkDuplicates Tracking 183640 as yet unmatched pairs. 69709 records in RAM.
INFO 2026-06-08 08:17:58 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:10:38s. Time for last 1,000,000: 1s. Last read position: chr19:10,681,234
INFO 2026-06-08 08:17:58 MarkDuplicates Tracking 180734 as yet unmatched pairs. 66803 records in RAM.
INFO 2026-06-08 08:18:00 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:10:40s. Time for last 1,000,000: 1s. Last read position: chr19:11,061,802
INFO 2026-06-08 08:18:00 MarkDuplicates Tracking 177866 as yet unmatched pairs. 63934 records in RAM.
INFO 2026-06-08 08:18:02 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:10:42s. Time for last 1,000,000: 2s. Last read position: chr19:12,646,599
INFO 2026-06-08 08:18:02 MarkDuplicates Tracking 175056 as yet unmatched pairs. 61123 records in RAM.
INFO 2026-06-08 08:18:04 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:10:44s. Time for last 1,000,000: 1s. Last read position: chr19:13,153,478
INFO 2026-06-08 08:18:04 MarkDuplicates Tracking 171817 as yet unmatched pairs. 57881 records in RAM.
INFO 2026-06-08 08:18:06 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 1s. Last read position: chr19:14,516,762
INFO 2026-06-08 08:18:06 MarkDuplicates Tracking 168926 as yet unmatched pairs. 54990 records in RAM.
INFO 2026-06-08 08:18:08 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:10:48s. Time for last 1,000,000: 2s. Last read position: chr19:15,264,750
INFO 2026-06-08 08:18:08 MarkDuplicates Tracking 165906 as yet unmatched pairs. 51965 records in RAM.
INFO 2026-06-08 08:18:10 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:10:50s. Time for last 1,000,000: 1s. Last read position: chr19:17,323,594
INFO 2026-06-08 08:18:10 MarkDuplicates Tracking 162610 as yet unmatched pairs. 48668 records in RAM.
INFO 2026-06-08 08:18:12 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:10:51s. Time for last 1,000,000: 1s. Last read position: chr19:18,775,684
INFO 2026-06-08 08:18:12 MarkDuplicates Tracking 159466 as yet unmatched pairs. 45518 records in RAM.
INFO 2026-06-08 08:18:13 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:10:53s. Time for last 1,000,000: 1s. Last read position: chr19:34,300,644
INFO 2026-06-08 08:18:13 MarkDuplicates Tracking 156621 as yet unmatched pairs. 42673 records in RAM.
INFO 2026-06-08 08:18:15 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:10:55s. Time for last 1,000,000: 1s. Last read position: chr19:35,944,944
INFO 2026-06-08 08:18:15 MarkDuplicates Tracking 153257 as yet unmatched pairs. 39309 records in RAM.
INFO 2026-06-08 08:18:17 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:10:57s. Time for last 1,000,000: 1s. Last read position: chr19:38,724,311
INFO 2026-06-08 08:18:17 MarkDuplicates Tracking 150759 as yet unmatched pairs. 36811 records in RAM.
INFO 2026-06-08 08:18:18 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 1s. Last read position: chr19:39,425,105
INFO 2026-06-08 08:18:18 MarkDuplicates Tracking 147526 as yet unmatched pairs. 33578 records in RAM.
INFO 2026-06-08 08:18:20 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:11:00s. Time for last 1,000,000: 1s. Last read position: chr19:41,219,398
INFO 2026-06-08 08:18:20 MarkDuplicates Tracking 144466 as yet unmatched pairs. 30518 records in RAM.
INFO 2026-06-08 08:18:22 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:11:02s. Time for last 1,000,000: 1s. Last read position: chr19:42,273,571
INFO 2026-06-08 08:18:22 MarkDuplicates Tracking 142094 as yet unmatched pairs. 28145 records in RAM.
INFO 2026-06-08 08:18:24 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:11:03s. Time for last 1,000,000: 1s. Last read position: chr19:42,293,986
INFO 2026-06-08 08:18:24 MarkDuplicates Tracking 138735 as yet unmatched pairs. 24785 records in RAM.
INFO 2026-06-08 08:18:26 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:11:05s. Time for last 1,000,000: 1s. Last read position: chr19:45,361,575
INFO 2026-06-08 08:18:26 MarkDuplicates Tracking 135374 as yet unmatched pairs. 21410 records in RAM.
INFO 2026-06-08 08:18:28 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:11:08s. Time for last 1,000,000: 2s. Last read position: chr19:45,765,823
INFO 2026-06-08 08:18:28 MarkDuplicates Tracking 132334 as yet unmatched pairs. 18366 records in RAM.
INFO 2026-06-08 08:18:30 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:11:09s. Time for last 1,000,000: 1s. Last read position: chr19:47,701,588
INFO 2026-06-08 08:18:30 MarkDuplicates Tracking 128938 as yet unmatched pairs. 14970 records in RAM.
INFO 2026-06-08 08:18:31 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:11:11s. Time for last 1,000,000: 1s. Last read position: chr19:49,108,347
INFO 2026-06-08 08:18:31 MarkDuplicates Tracking 127120 as yet unmatched pairs. 13151 records in RAM.
INFO 2026-06-08 08:18:33 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:11:13s. Time for last 1,000,000: 1s. Last read position: chr19:49,888,217
INFO 2026-06-08 08:18:33 MarkDuplicates Tracking 122860 as yet unmatched pairs. 8890 records in RAM.
INFO 2026-06-08 08:18:34 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:11:14s. Time for last 1,000,000: 1s. Last read position: chr19:54,149,600
INFO 2026-06-08 08:18:34 MarkDuplicates Tracking 119859 as yet unmatched pairs. 5889 records in RAM.
INFO 2026-06-08 08:18:36 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:11:16s. Time for last 1,000,000: 1s. Last read position: chr19:55,616,260
INFO 2026-06-08 08:18:36 MarkDuplicates Tracking 116762 as yet unmatched pairs. 2792 records in RAM.
INFO 2026-06-08 08:18:38 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:11:18s. Time for last 1,000,000: 1s. Last read position: chr20:420,892
INFO 2026-06-08 08:18:38 MarkDuplicates Tracking 113829 as yet unmatched pairs. 23929 records in RAM.
INFO 2026-06-08 08:18:40 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:11:20s. Time for last 1,000,000: 1s. Last read position: chr20:10,648,023
INFO 2026-06-08 08:18:40 MarkDuplicates Tracking 110994 as yet unmatched pairs. 21093 records in RAM.
INFO 2026-06-08 08:18:41 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:11:21s. Time for last 1,000,000: 1s. Last read position: chr20:31,605,601
INFO 2026-06-08 08:18:41 MarkDuplicates Tracking 108025 as yet unmatched pairs. 18120 records in RAM.
INFO 2026-06-08 08:18:43 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:11:23s. Time for last 1,000,000: 1s. Last read position: chr20:36,496,957
INFO 2026-06-08 08:18:43 MarkDuplicates Tracking 105111 as yet unmatched pairs. 15206 records in RAM.
INFO 2026-06-08 08:18:45 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:11:24s. Time for last 1,000,000: 1s. Last read position: chr20:43,548,120
INFO 2026-06-08 08:18:45 MarkDuplicates Tracking 102312 as yet unmatched pairs. 12406 records in RAM.
INFO 2026-06-08 08:18:46 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:11:26s. Time for last 1,000,000: 1s. Last read position: chr20:50,191,832
INFO 2026-06-08 08:18:46 MarkDuplicates Tracking 99438 as yet unmatched pairs. 9530 records in RAM.
INFO 2026-06-08 08:18:48 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:11:28s. Time for last 1,000,000: 1s. Last read position: chr20:59,324,392
INFO 2026-06-08 08:18:48 MarkDuplicates Tracking 96260 as yet unmatched pairs. 6351 records in RAM.
INFO 2026-06-08 08:18:50 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:11:30s. Time for last 1,000,000: 1s. Last read position: chr20:62,827,252
INFO 2026-06-08 08:18:50 MarkDuplicates Tracking 93096 as yet unmatched pairs. 3186 records in RAM.
INFO 2026-06-08 08:18:52 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:11:32s. Time for last 1,000,000: 1s. Last read position: chr21:5,128,267
INFO 2026-06-08 08:18:52 MarkDuplicates Tracking 89718 as yet unmatched pairs. 16424 records in RAM.
INFO 2026-06-08 08:18:53 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:11:33s. Time for last 1,000,000: 1s. Last read position: chr21:8,217,267
INFO 2026-06-08 08:18:53 MarkDuplicates Tracking 88505 as yet unmatched pairs. 15207 records in RAM.
INFO 2026-06-08 08:18:54 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:11:34s. Time for last 1,000,000: 1s. Last read position: chr21:8,260,316
INFO 2026-06-08 08:18:54 MarkDuplicates Tracking 88215 as yet unmatched pairs. 14917 records in RAM.
INFO 2026-06-08 08:18:56 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:11:36s. Time for last 1,000,000: 1s. Last read position: chr21:8,441,950
INFO 2026-06-08 08:18:56 MarkDuplicates Tracking 86578 as yet unmatched pairs. 13270 records in RAM.
INFO 2026-06-08 08:18:57 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:11:37s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,593
INFO 2026-06-08 08:18:57 MarkDuplicates Tracking 85338 as yet unmatched pairs. 12028 records in RAM.
INFO 2026-06-08 08:19:00 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:11:40s. Time for last 1,000,000: 2s. Last read position: chr21:33,751,884
INFO 2026-06-08 08:19:00 MarkDuplicates Tracking 82674 as yet unmatched pairs. 9363 records in RAM.
INFO 2026-06-08 08:19:02 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:11:41s. Time for last 1,000,000: 1s. Last read position: chr21:42,296,330
INFO 2026-06-08 08:19:02 MarkDuplicates Tracking 79630 as yet unmatched pairs. 6318 records in RAM.
INFO 2026-06-08 08:19:03 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:11:43s. Time for last 1,000,000: 1s. Last read position: chr21:45,477,783
INFO 2026-06-08 08:19:03 MarkDuplicates Tracking 77116 as yet unmatched pairs. 3801 records in RAM.
INFO 2026-06-08 08:19:05 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:11:45s. Time for last 1,000,000: 1s. Last read position: chr21:46,444,727
INFO 2026-06-08 08:19:05 MarkDuplicates Tracking 73657 as yet unmatched pairs. 342 records in RAM.
INFO 2026-06-08 08:19:07 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:11:47s. Time for last 1,000,000: 2s. Last read position: chr22:23,263,876
INFO 2026-06-08 08:19:07 MarkDuplicates Tracking 70592 as yet unmatched pairs. 34022 records in RAM.
INFO 2026-06-08 08:19:09 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:11:48s. Time for last 1,000,000: 1s. Last read position: chr22:29,292,498
INFO 2026-06-08 08:19:09 MarkDuplicates Tracking 67938 as yet unmatched pairs. 31368 records in RAM.
INFO 2026-06-08 08:19:10 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:11:50s. Time for last 1,000,000: 1s. Last read position: chr22:31,212,400
INFO 2026-06-08 08:19:10 MarkDuplicates Tracking 64788 as yet unmatched pairs. 28218 records in RAM.
INFO 2026-06-08 08:19:12 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:11:52s. Time for last 1,000,000: 1s. Last read position: chr22:36,285,263
INFO 2026-06-08 08:19:12 MarkDuplicates Tracking 62127 as yet unmatched pairs. 25557 records in RAM.
INFO 2026-06-08 08:19:14 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:11:54s. Time for last 1,000,000: 1s. Last read position: chr22:37,024,742
INFO 2026-06-08 08:19:14 MarkDuplicates Tracking 58941 as yet unmatched pairs. 22371 records in RAM.
INFO 2026-06-08 08:19:15 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:11:55s. Time for last 1,000,000: 1s. Last read position: chr22:37,940,698
INFO 2026-06-08 08:19:15 MarkDuplicates Tracking 56038 as yet unmatched pairs. 19468 records in RAM.
INFO 2026-06-08 08:19:18 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:11:57s. Time for last 1,000,000: 2s. Last read position: chr22:39,225,694
INFO 2026-06-08 08:19:18 MarkDuplicates Tracking 52870 as yet unmatched pairs. 16300 records in RAM.
INFO 2026-06-08 08:19:20 MarkDuplicates Read 368,000,000 records. Elapsed time: 00:12:00s. Time for last 1,000,000: 2s. Last read position: chr22:40,882,076
INFO 2026-06-08 08:19:20 MarkDuplicates Tracking 50051 as yet unmatched pairs. 13481 records in RAM.
INFO 2026-06-08 08:19:22 MarkDuplicates Read 369,000,000 records. Elapsed time: 00:12:01s. Time for last 1,000,000: 1s. Last read position: chr22:41,515,516
INFO 2026-06-08 08:19:22 MarkDuplicates Tracking 47426 as yet unmatched pairs. 10856 records in RAM.
INFO 2026-06-08 08:19:23 MarkDuplicates Read 370,000,000 records. Elapsed time: 00:12:03s. Time for last 1,000,000: 1s. Last read position: chr22:42,602,022
INFO 2026-06-08 08:19:23 MarkDuplicates Tracking 44825 as yet unmatched pairs. 8255 records in RAM.
INFO 2026-06-08 08:19:25 MarkDuplicates Read 371,000,000 records. Elapsed time: 00:12:05s. Time for last 1,000,000: 1s. Last read position: chr22:46,463,833
INFO 2026-06-08 08:19:25 MarkDuplicates Tracking 41623 as yet unmatched pairs. 5053 records in RAM.
INFO 2026-06-08 08:19:27 MarkDuplicates Read 372,000,000 records. Elapsed time: 00:12:06s. Time for last 1,000,000: 1s. Last read position: chr22:50,465,774
INFO 2026-06-08 08:19:27 MarkDuplicates Tracking 38064 as yet unmatched pairs. 1494 records in RAM.
INFO 2026-06-08 08:19:28 MarkDuplicates Read 373,000,000 records. Elapsed time: 00:12:08s. Time for last 1,000,000: 1s. Last read position: chrX:10,567,367
INFO 2026-06-08 08:19:28 MarkDuplicates Tracking 34969 as yet unmatched pairs. 20602 records in RAM.
INFO 2026-06-08 08:19:30 MarkDuplicates Read 374,000,000 records. Elapsed time: 00:12:10s. Time for last 1,000,000: 1s. Last read position: chrX:41,346,912
INFO 2026-06-08 08:19:30 MarkDuplicates Tracking 32400 as yet unmatched pairs. 18006 records in RAM.
INFO 2026-06-08 08:19:32 MarkDuplicates Read 375,000,000 records. Elapsed time: 00:12:12s. Time for last 1,000,000: 2s. Last read position: chrX:49,172,003
INFO 2026-06-08 08:19:32 MarkDuplicates Tracking 29715 as yet unmatched pairs. 15319 records in RAM.
INFO 2026-06-08 08:19:34 MarkDuplicates Read 376,000,000 records. Elapsed time: 00:12:14s. Time for last 1,000,000: 1s. Last read position: chrX:56,737,183
INFO 2026-06-08 08:19:34 MarkDuplicates Tracking 26954 as yet unmatched pairs. 12558 records in RAM.
INFO 2026-06-08 08:19:36 MarkDuplicates Read 377,000,000 records. Elapsed time: 00:12:16s. Time for last 1,000,000: 1s. Last read position: chrX:77,664,692
INFO 2026-06-08 08:19:36 MarkDuplicates Tracking 24452 as yet unmatched pairs. 10054 records in RAM.
INFO 2026-06-08 08:19:38 MarkDuplicates Read 378,000,000 records. Elapsed time: 00:12:18s. Time for last 1,000,000: 1s. Last read position: chrX:123,883,823
INFO 2026-06-08 08:19:38 MarkDuplicates Tracking 22029 as yet unmatched pairs. 7631 records in RAM.
INFO 2026-06-08 08:19:39 MarkDuplicates Read 379,000,000 records. Elapsed time: 00:12:19s. Time for last 1,000,000: 1s. Last read position: chrX:153,774,307
INFO 2026-06-08 08:19:39 MarkDuplicates Tracking 19449 as yet unmatched pairs. 5045 records in RAM.
INFO 2026-06-08 08:19:42 MarkDuplicates Read 380,000,000 records. Elapsed time: 00:12:22s. Time for last 1,000,000: 2s. Last read position: chrX:154,364,075
INFO 2026-06-08 08:19:42 MarkDuplicates Tracking 16632 as yet unmatched pairs. 2228 records in RAM.
INFO 2026-06-08 08:19:44 MarkDuplicates Read 381,000,000 records. Elapsed time: 00:12:23s. Time for last 1,000,000: 1s. Last read position: GL000220.1:114,158
INFO 2026-06-08 08:19:44 MarkDuplicates Tracking 14241 as yet unmatched pairs. 2677 records in RAM.
INFO 2026-06-08 08:19:45 MarkDuplicates Read 382,000,000 records. Elapsed time: 00:12:25s. Time for last 1,000,000: 1s. Last read position: GL000220.1:153,863
INFO 2026-06-08 08:19:45 MarkDuplicates Tracking 11911 as yet unmatched pairs. 346 records in RAM.
INFO 2026-06-08 08:19:46 MarkDuplicates Read 383,000,000 records. Elapsed time: 00:12:26s. Time for last 1,000,000: 1s. Last read position: GL000220.1:160,698
INFO 2026-06-08 08:19:46 MarkDuplicates Tracking 11575 as yet unmatched pairs. 10 records in RAM.
INFO 2026-06-08 08:19:48 MarkDuplicates Read 384,000,000 records. Elapsed time: 00:12:28s. Time for last 1,000,000: 1s. Last read position: KI270733.1:131,072
INFO 2026-06-08 08:19:48 MarkDuplicates Tracking 2089 as yet unmatched pairs. 2072 records in RAM.
INFO 2026-06-08 08:19:49 MarkDuplicates Read 385,000,000 records. Elapsed time: 00:12:29s. Time for last 1,000,000: 1s. Last read position: KI270733.1:176,111
INFO 2026-06-08 08:19:49 MarkDuplicates Tracking 143 as yet unmatched pairs. 126 records in RAM.
INFO 2026-06-08 08:19:50 MarkDuplicates Read 385730900 records. 0 pairs never matched.
INFO 2026-06-08 08:20:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 33285351376; totalMemory: 47546630144; maxMemory: 63585648640
INFO 2026-06-08 08:20:26 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:20:32 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:20:51 OpticalDuplicateFinder Large duplicate set. size = 1472
INFO 2026-06-08 08:20:51 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,409
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder Large duplicate set. size = 1120
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,081
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder Large duplicate set. size = 1299
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,114
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder Large duplicate set. size = 1482
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,305
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder Large duplicate set. size = 1273
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,440
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder Large duplicate set. size = 1143
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,063
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder Large duplicate set. size = 1095
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:31,095
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder Large duplicate set. size = 1122
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:5,870
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder Large duplicate set. size = 1006
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:31,985
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder Large duplicate set. size = 1431
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-25,008
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder Large duplicate set. size = 1048
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,889
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder Large duplicate set. size = 1174
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,687
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder Large duplicate set. size = 1536
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-13,893
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder Large duplicate set. size = 1402
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:25,950
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder Large duplicate set. size = 1365
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,251
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder Large duplicate set. size = 1517
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,305
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder Large duplicate set. size = 1584
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,519
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder Large duplicate set. size = 1220
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:21,961
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder Large duplicate set. size = 4199
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,980
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:8,839
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder compared 3,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,959
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder compared 4,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-19,645
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder Large duplicate set. size = 1737
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,236
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder Large duplicate set. size = 1195
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,815
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder Large duplicate set. size = 1172
INFO 2026-06-08 08:21:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:6,461
INFO 2026-06-08 08:21:05 OpticalDuplicateFinder Large duplicate set. size = 1371
INFO 2026-06-08 08:21:05 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,259
INFO 2026-06-08 08:21:05 OpticalDuplicateFinder Large duplicate set. size = 1685
INFO 2026-06-08 08:21:05 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-13,334
INFO 2026-06-08 08:21:06 OpticalDuplicateFinder Large duplicate set. size = 1136
INFO 2026-06-08 08:21:06 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:23,490
INFO 2026-06-08 08:21:11 OpticalDuplicateFinder Large duplicate set. size = 1092
INFO 2026-06-08 08:21:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:15,813
INFO 2026-06-08 08:21:11 OpticalDuplicateFinder Large duplicate set. size = 1388
INFO 2026-06-08 08:21:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,509
INFO 2026-06-08 08:21:11 OpticalDuplicateFinder Large duplicate set. size = 1505
INFO 2026-06-08 08:21:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,382
INFO 2026-06-08 08:21:11 OpticalDuplicateFinder Large duplicate set. size = 1189
INFO 2026-06-08 08:21:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:4,616
INFO 2026-06-08 08:21:11 OpticalDuplicateFinder Large duplicate set. size = 1073
INFO 2026-06-08 08:21:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:1,809
INFO 2026-06-08 08:21:11 OpticalDuplicateFinder Large duplicate set. size = 1104
INFO 2026-06-08 08:21:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,290
INFO 2026-06-08 08:21:11 OpticalDuplicateFinder Large duplicate set. size = 1089
INFO 2026-06-08 08:21:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,454
INFO 2026-06-08 08:21:11 OpticalDuplicateFinder Large duplicate set. size = 1027
INFO 2026-06-08 08:21:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,050
INFO 2026-06-08 08:21:11 OpticalDuplicateFinder Large duplicate set. size = 1161
INFO 2026-06-08 08:21:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,436
INFO 2026-06-08 08:21:11 OpticalDuplicateFinder Large duplicate set. size = 1125
INFO 2026-06-08 08:21:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-21,610
INFO 2026-06-08 08:21:11 OpticalDuplicateFinder Large duplicate set. size = 1333
INFO 2026-06-08 08:21:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,277
INFO 2026-06-08 08:21:12 OpticalDuplicateFinder Large duplicate set. size = 1129
INFO 2026-06-08 08:21:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:4,576
INFO 2026-06-08 08:21:12 OpticalDuplicateFinder Large duplicate set. size = 1468
INFO 2026-06-08 08:21:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:1,307
INFO 2026-06-08 08:21:12 OpticalDuplicateFinder Large duplicate set. size = 1492
INFO 2026-06-08 08:21:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,887
INFO 2026-06-08 08:21:12 OpticalDuplicateFinder Large duplicate set. size = 1599
INFO 2026-06-08 08:21:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,648
INFO 2026-06-08 08:21:12 OpticalDuplicateFinder Large duplicate set. size = 2097
INFO 2026-06-08 08:21:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,738
INFO 2026-06-08 08:21:12 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:6,372
INFO 2026-06-08 08:21:12 OpticalDuplicateFinder Large duplicate set. size = 1182
INFO 2026-06-08 08:21:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:17,164
INFO 2026-06-08 08:21:12 OpticalDuplicateFinder Large duplicate set. size = 1082
INFO 2026-06-08 08:21:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,510
INFO 2026-06-08 08:21:12 OpticalDuplicateFinder Large duplicate set. size = 1108
INFO 2026-06-08 08:21:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,895
INFO 2026-06-08 08:21:12 OpticalDuplicateFinder Large duplicate set. size = 1116
INFO 2026-06-08 08:21:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:21,718
INFO 2026-06-08 08:21:12 OpticalDuplicateFinder Large duplicate set. size = 1477
INFO 2026-06-08 08:21:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,162
INFO 2026-06-08 08:21:12 MarkDuplicates Traversing fragment information and detecting duplicates.
WARNING 2026-06-08 08:21:12 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
INFO 2026-06-08 08:21:54 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:22:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 31596408088; totalMemory: 47546630144; maxMemory: 63585648640
INFO 2026-06-08 08:22:02 MarkDuplicates Marking 209044688 records as duplicates.
INFO 2026-06-08 08:22:02 MarkDuplicates Found 3379464 optical duplicate clusters.
INFO 2026-06-08 08:22:02 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 08:22:19 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:16s. Time for last 10,000,000: 16s. Last read position: chr1:34,785,348
INFO 2026-06-08 08:22:35 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:32s. Time for last 10,000,000: 16s. Last read position: chr1:145,681,012
INFO 2026-06-08 08:22:51 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:48s. Time for last 10,000,000: 15s. Last read position: chr1:178,233,576
INFO 2026-06-08 08:23:07 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:04s. Time for last 10,000,000: 15s. Last read position: chr2:28,412,310
INFO 2026-06-08 08:23:23 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:20s. Time for last 10,000,000: 15s. Last read position: chr2:108,763,449
INFO 2026-06-08 08:23:38 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:35s. Time for last 10,000,000: 15s. Last read position: chr2:218,569,019
INFO 2026-06-08 08:23:54 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:01:51s. Time for last 10,000,000: 15s. Last read position: chr3:49,012,229
INFO 2026-06-08 08:24:09 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:06s. Time for last 10,000,000: 15s. Last read position: chr3:188,484,592
INFO 2026-06-08 08:24:24 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:21s. Time for last 10,000,000: 15s. Last read position: chr4:186,603,858
INFO 2026-06-08 08:24:40 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:37s. Time for last 10,000,000: 15s. Last read position: chr5:146,120,421
INFO 2026-06-08 08:24:55 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:02:52s. Time for last 10,000,000: 15s. Last read position: chr6:31,662,491
INFO 2026-06-08 08:25:11 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:08s. Time for last 10,000,000: 15s. Last read position: chr6:131,950,848
INFO 2026-06-08 08:25:26 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:23s. Time for last 10,000,000: 15s. Last read position: chr7:67,238,331
INFO 2026-06-08 08:25:42 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:03:39s. Time for last 10,000,000: 15s. Last read position: chr7:130,070,701
INFO 2026-06-08 08:25:57 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:03:54s. Time for last 10,000,000: 15s. Last read position: chr8:100,712,721
INFO 2026-06-08 08:26:12 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:09s. Time for last 10,000,000: 14s. Last read position: chr9:35,056,971
INFO 2026-06-08 08:26:28 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:04:25s. Time for last 10,000,000: 16s. Last read position: chr9:134,050,445
INFO 2026-06-08 08:26:43 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:04:40s. Time for last 10,000,000: 15s. Last read position: chr10:84,417,796
INFO 2026-06-08 08:26:58 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:04:55s. Time for last 10,000,000: 15s. Last read position: chr11:18,308,990
INFO 2026-06-08 08:27:14 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:05:11s. Time for last 10,000,000: 15s. Last read position: chr11:72,001,525
INFO 2026-06-08 08:27:29 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:05:26s. Time for last 10,000,000: 15s. Last read position: chr12:26,188,859
INFO 2026-06-08 08:27:45 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:05:42s. Time for last 10,000,000: 15s. Last read position: chr12:66,248,961
INFO 2026-06-08 08:28:01 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:05:58s. Time for last 10,000,000: 15s. Last read position: chr13:109,783,781
INFO 2026-06-08 08:28:16 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:06:13s. Time for last 10,000,000: 15s. Last read position: chr14:101,906,408
INFO 2026-06-08 08:28:32 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:06:29s. Time for last 10,000,000: 15s. Last read position: chr15:79,845,232
INFO 2026-06-08 08:28:48 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:06:45s. Time for last 10,000,000: 15s. Last read position: chr16:16,360,998
INFO 2026-06-08 08:29:03 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:07:00s. Time for last 10,000,000: 15s. Last read position: chr16:54,285,431
INFO 2026-06-08 08:29:18 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:07:15s. Time for last 10,000,000: 15s. Last read position: chr17:7,851,179
INFO 2026-06-08 08:29:33 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:07:30s. Time for last 10,000,000: 15s. Last read position: chr17:41,586,391
INFO 2026-06-08 08:29:49 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:07:46s. Time for last 10,000,000: 15s. Last read position: chr17:50,193,986
INFO 2026-06-08 08:30:04 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:08:01s. Time for last 10,000,000: 15s. Last read position: chr17:80,319,291
INFO 2026-06-08 08:30:20 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:08:17s. Time for last 10,000,000: 15s. Last read position: chr19:6,735,908
INFO 2026-06-08 08:30:36 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:08:33s. Time for last 10,000,000: 15s. Last read position: chr19:34,300,644
INFO 2026-06-08 08:30:51 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:08:48s. Time for last 10,000,000: 15s. Last read position: chr19:49,108,347
INFO 2026-06-08 08:31:06 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:09:03s. Time for last 10,000,000: 15s. Last read position: chr20:59,324,392
INFO 2026-06-08 08:31:22 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:09:19s. Time for last 10,000,000: 15s. Last read position: chr21:46,444,727
INFO 2026-06-08 08:31:37 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:09:35s. Time for last 10,000,000: 15s. Last read position: chr22:42,602,022
INFO 2026-06-08 08:31:54 MarkDuplicates Written 380,000,000 records. Elapsed time: 00:09:51s. Time for last 10,000,000: 16s. Last read position: chrX:154,364,075
INFO 2026-06-08 08:32:08 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:32:08 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:32:08 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:32:08 MarkDuplicates Before output close freeMemory: 202104760; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:32:08 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:32:08 MarkDuplicates After output close freeMemory: 104131568; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 08:32:08 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 24.84 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory