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 dna_s765.Aligned.sortedByCoord.out.bam --OUTPUT dna_s765.md.bam --METRICS_FILE dna_s765.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:34:33.113 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Jun 08 07:34:33 GMT 2026] MarkDuplicates --INPUT dna_s765.Aligned.sortedByCoord.out.bam --OUTPUT dna_s765.md.bam --METRICS_FILE dna_s765.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 07:34:33 GMT 2026] Executing as ?@nf-5a7a449b7ea94aede466cbd96537ac46-63b89-9blfn on Linux 6.12.88 amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0
INFO 2026-06-08 07:34:33 MarkDuplicates Start of doWork freeMemory: 105829464; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:34:33 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:34:33 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:34:39 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 4s. Last read position: chr1:8,967,652
INFO 2026-06-08 07:34:39 MarkDuplicates Tracking 2988 as yet unmatched pairs. 283 records in RAM.
INFO 2026-06-08 07:34:43 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 3s. Last read position: chr1:15,737,975
INFO 2026-06-08 07:34:43 MarkDuplicates Tracking 6056 as yet unmatched pairs. 462 records in RAM.
INFO 2026-06-08 07:34:46 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 3s. Last read position: chr1:20,637,971
INFO 2026-06-08 07:34:46 MarkDuplicates Tracking 8797 as yet unmatched pairs. 556 records in RAM.
INFO 2026-06-08 07:34:49 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 3s. Last read position: chr1:31,293,333
INFO 2026-06-08 07:34:49 MarkDuplicates Tracking 12167 as yet unmatched pairs. 680 records in RAM.
INFO 2026-06-08 07:34:53 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 3s. Last read position: chr1:39,902,829
INFO 2026-06-08 07:34:53 MarkDuplicates Tracking 16042 as yet unmatched pairs. 1507 records in RAM.
INFO 2026-06-08 07:34:56 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 3s. Last read position: chr1:49,568,489
INFO 2026-06-08 07:34:56 MarkDuplicates Tracking 18653 as yet unmatched pairs. 880 records in RAM.
INFO 2026-06-08 07:34:59 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 2s. Last read position: chr1:67,686,571
INFO 2026-06-08 07:34:59 MarkDuplicates Tracking 23240 as yet unmatched pairs. 1109 records in RAM.
INFO 2026-06-08 07:35:03 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 3s. Last read position: chr1:93,530,832
INFO 2026-06-08 07:35:03 MarkDuplicates Tracking 28677 as yet unmatched pairs. 1220 records in RAM.
INFO 2026-06-08 07:35:06 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 3s. Last read position: chr1:110,517,504
INFO 2026-06-08 07:35:06 MarkDuplicates Tracking 32665 as yet unmatched pairs. 1366 records in RAM.
INFO 2026-06-08 07:35:09 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 3s. Last read position: chr1:121,118,476
INFO 2026-06-08 07:35:09 MarkDuplicates Tracking 36725 as yet unmatched pairs. 1923 records in RAM.
INFO 2026-06-08 07:35:12 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 2s. Last read position: chr1:149,455,404
INFO 2026-06-08 07:35:12 MarkDuplicates Tracking 40251 as yet unmatched pairs. 2174 records in RAM.
INFO 2026-06-08 07:35:15 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 2s. Last read position: chr1:154,499,176
INFO 2026-06-08 07:35:15 MarkDuplicates Tracking 41816 as yet unmatched pairs. 1245 records in RAM.
INFO 2026-06-08 07:35:19 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 3s. Last read position: chr1:159,063,595
INFO 2026-06-08 07:35:19 MarkDuplicates Tracking 44354 as yet unmatched pairs. 1202 records in RAM.
INFO 2026-06-08 07:35:23 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 3s. Last read position: chr1:173,825,218
INFO 2026-06-08 07:35:23 MarkDuplicates Tracking 48255 as yet unmatched pairs. 1176 records in RAM.
INFO 2026-06-08 07:35:26 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 2s. Last read position: chr1:196,726,517
INFO 2026-06-08 07:35:26 MarkDuplicates Tracking 52873 as yet unmatched pairs. 909 records in RAM.
INFO 2026-06-08 07:35:28 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 2s. Last read position: chr1:205,666,467
INFO 2026-06-08 07:35:28 MarkDuplicates Tracking 56292 as yet unmatched pairs. 1152 records in RAM.
INFO 2026-06-08 07:35:32 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 3s. Last read position: chr1:220,754,943
INFO 2026-06-08 07:35:32 MarkDuplicates Tracking 59748 as yet unmatched pairs. 589 records in RAM.
INFO 2026-06-08 07:35:35 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 3s. Last read position: chr1:235,664,486
INFO 2026-06-08 07:35:35 MarkDuplicates Tracking 63430 as yet unmatched pairs. 331 records in RAM.
INFO 2026-06-08 07:35:38 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 2s. Last read position: chr2:5,695,442
INFO 2026-06-08 07:35:38 MarkDuplicates Tracking 68146 as yet unmatched pairs. 17401 records in RAM.
INFO 2026-06-08 07:35:42 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 3s. Last read position: chr2:25,741,063
INFO 2026-06-08 07:35:42 MarkDuplicates Tracking 72581 as yet unmatched pairs. 18306 records in RAM.
INFO 2026-06-08 07:35:45 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 3s. Last read position: chr2:32,916,264
INFO 2026-06-08 07:35:45 MarkDuplicates Tracking 119821 as yet unmatched pairs. 15641 records in RAM.
INFO 2026-06-08 07:35:48 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 3s. Last read position: chr2:46,956,877
INFO 2026-06-08 07:35:48 MarkDuplicates Tracking 180796 as yet unmatched pairs. 12355 records in RAM.
INFO 2026-06-08 07:35:51 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 2s. Last read position: chr2:63,055,687
INFO 2026-06-08 07:35:51 MarkDuplicates Tracking 183152 as yet unmatched pairs. 11504 records in RAM.
INFO 2026-06-08 07:35:54 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 3s. Last read position: chr2:85,637,174
INFO 2026-06-08 07:35:54 MarkDuplicates Tracking 185882 as yet unmatched pairs. 10510 records in RAM.
INFO 2026-06-08 07:35:58 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 3s. Last read position: chr2:96,967,255
INFO 2026-06-08 07:35:58 MarkDuplicates Tracking 187306 as yet unmatched pairs. 9750 records in RAM.
INFO 2026-06-08 07:36:01 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 3s. Last read position: chr2:108,764,057
INFO 2026-06-08 07:36:01 MarkDuplicates Tracking 189718 as yet unmatched pairs. 9523 records in RAM.
INFO 2026-06-08 07:36:04 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 2s. Last read position: chr2:113,228,287
INFO 2026-06-08 07:36:04 MarkDuplicates Tracking 191158 as yet unmatched pairs. 9407 records in RAM.
INFO 2026-06-08 07:36:07 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 3s. Last read position: chr2:131,423,300
INFO 2026-06-08 07:36:07 MarkDuplicates Tracking 192698 as yet unmatched pairs. 7847 records in RAM.
INFO 2026-06-08 07:36:10 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 3s. Last read position: chr2:158,577,326
INFO 2026-06-08 07:36:10 MarkDuplicates Tracking 195365 as yet unmatched pairs. 6375 records in RAM.
INFO 2026-06-08 07:36:13 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 2s. Last read position: chr2:177,220,153
INFO 2026-06-08 07:36:13 MarkDuplicates Tracking 198424 as yet unmatched pairs. 6059 records in RAM.
INFO 2026-06-08 07:36:17 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 3s. Last read position: chr2:189,867,674
INFO 2026-06-08 07:36:17 MarkDuplicates Tracking 199748 as yet unmatched pairs. 4517 records in RAM.
INFO 2026-06-08 07:36:20 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 3s. Last read position: chr2:209,333,462
INFO 2026-06-08 07:36:20 MarkDuplicates Tracking 201967 as yet unmatched pairs. 3142 records in RAM.
INFO 2026-06-08 07:36:23 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 2s. Last read position: chr2:222,206,913
INFO 2026-06-08 07:36:23 MarkDuplicates Tracking 204291 as yet unmatched pairs. 2830 records in RAM.
INFO 2026-06-08 07:36:26 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 3s. Last read position: chr2:233,768,279
INFO 2026-06-08 07:36:26 MarkDuplicates Tracking 205364 as yet unmatched pairs. 1174 records in RAM.
INFO 2026-06-08 07:36:30 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 4s. Last read position: chr3:9,124,750
INFO 2026-06-08 07:36:30 MarkDuplicates Tracking 206965 as yet unmatched pairs. 15304 records in RAM.
INFO 2026-06-08 07:36:34 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 3s. Last read position: chr3:12,346,098
INFO 2026-06-08 07:36:34 MarkDuplicates Tracking 208786 as yet unmatched pairs. 15206 records in RAM.
INFO 2026-06-08 07:36:37 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 3s. Last read position: chr3:23,917,922
INFO 2026-06-08 07:36:37 MarkDuplicates Tracking 209750 as yet unmatched pairs. 13416 records in RAM.
INFO 2026-06-08 07:36:40 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 2s. Last read position: chr3:42,874,492
INFO 2026-06-08 07:36:40 MarkDuplicates Tracking 211744 as yet unmatched pairs. 12296 records in RAM.
INFO 2026-06-08 07:36:43 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 3s. Last read position: chr3:49,720,779
INFO 2026-06-08 07:36:43 MarkDuplicates Tracking 212360 as yet unmatched pairs. 11128 records in RAM.
INFO 2026-06-08 07:36:47 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 3s. Last read position: chr3:58,095,856
INFO 2026-06-08 07:36:47 MarkDuplicates Tracking 213420 as yet unmatched pairs. 9998 records in RAM.
INFO 2026-06-08 07:36:50 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 3s. Last read position: chr3:88,318,901
INFO 2026-06-08 07:36:50 MarkDuplicates Tracking 215993 as yet unmatched pairs. 8367 records in RAM.
INFO 2026-06-08 07:36:54 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 3s. Last read position: chr3:119,831,089
INFO 2026-06-08 07:36:54 MarkDuplicates Tracking 219192 as yet unmatched pairs. 7351 records in RAM.
INFO 2026-06-08 07:36:57 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 2s. Last read position: chr3:131,155,054
INFO 2026-06-08 07:36:57 MarkDuplicates Tracking 219927 as yet unmatched pairs. 5747 records in RAM.
INFO 2026-06-08 07:36:59 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 2s. Last read position: chr3:150,622,381
INFO 2026-06-08 07:36:59 MarkDuplicates Tracking 221643 as yet unmatched pairs. 4318 records in RAM.
INFO 2026-06-08 07:37:02 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 3s. Last read position: chr3:179,721,726
INFO 2026-06-08 07:37:02 MarkDuplicates Tracking 223920 as yet unmatched pairs. 2306 records in RAM.
INFO 2026-06-08 07:37:05 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 2s. Last read position: chr3:186,900,387
INFO 2026-06-08 07:37:05 MarkDuplicates Tracking 224973 as yet unmatched pairs. 1144 records in RAM.
INFO 2026-06-08 07:37:08 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 2s. Last read position: chr4:1,806,929
INFO 2026-06-08 07:37:08 MarkDuplicates Tracking 226465 as yet unmatched pairs. 14032 records in RAM.
INFO 2026-06-08 07:37:12 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 3s. Last read position: chr4:9,249,048
INFO 2026-06-08 07:37:12 MarkDuplicates Tracking 227036 as yet unmatched pairs. 12822 records in RAM.
INFO 2026-06-08 07:37:15 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 3s. Last read position: chr4:38,694,677
INFO 2026-06-08 07:37:15 MarkDuplicates Tracking 228667 as yet unmatched pairs. 10833 records in RAM.
INFO 2026-06-08 07:37:18 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 3s. Last read position: chr4:56,279,628
INFO 2026-06-08 07:37:18 MarkDuplicates Tracking 229612 as yet unmatched pairs. 8986 records in RAM.
INFO 2026-06-08 07:37:21 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 2s. Last read position: chr4:80,730,184
INFO 2026-06-08 07:37:21 MarkDuplicates Tracking 231437 as yet unmatched pairs. 7350 records in RAM.
INFO 2026-06-08 07:37:24 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 2s. Last read position: chr4:105,679,920
INFO 2026-06-08 07:37:24 MarkDuplicates Tracking 233336 as yet unmatched pairs. 5610 records in RAM.
INFO 2026-06-08 07:37:27 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 3s. Last read position: chr4:142,024,440
INFO 2026-06-08 07:37:27 MarkDuplicates Tracking 236384 as yet unmatched pairs. 4226 records in RAM.
INFO 2026-06-08 07:37:30 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 2s. Last read position: chr4:172,333,245
INFO 2026-06-08 07:37:30 MarkDuplicates Tracking 237409 as yet unmatched pairs. 1291 records in RAM.
INFO 2026-06-08 07:37:32 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 2s. Last read position: chr5:1,798,819
INFO 2026-06-08 07:37:32 MarkDuplicates Tracking 238694 as yet unmatched pairs. 15878 records in RAM.
INFO 2026-06-08 07:37:35 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 2s. Last read position: chr5:38,947,426
INFO 2026-06-08 07:37:35 MarkDuplicates Tracking 240817 as yet unmatched pairs. 13797 records in RAM.
INFO 2026-06-08 07:37:38 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 3s. Last read position: chr5:68,216,307
INFO 2026-06-08 07:37:38 MarkDuplicates Tracking 243382 as yet unmatched pairs. 12717 records in RAM.
INFO 2026-06-08 07:37:41 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 3s. Last read position: chr5:81,650,171
INFO 2026-06-08 07:37:41 MarkDuplicates Tracking 242901 as yet unmatched pairs. 10094 records in RAM.
INFO 2026-06-08 07:37:44 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 3s. Last read position: chr5:116,478,549
INFO 2026-06-08 07:37:44 MarkDuplicates Tracking 244559 as yet unmatched pairs. 7700 records in RAM.
INFO 2026-06-08 07:37:47 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 2s. Last read position: chr5:138,827,654
INFO 2026-06-08 07:37:47 MarkDuplicates Tracking 245725 as yet unmatched pairs. 5857 records in RAM.
INFO 2026-06-08 07:37:49 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 2s. Last read position: chr5:149,494,981
INFO 2026-06-08 07:37:49 MarkDuplicates Tracking 246591 as yet unmatched pairs. 4817 records in RAM.
INFO 2026-06-08 07:37:52 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 2s. Last read position: chr5:170,008,372
INFO 2026-06-08 07:37:52 MarkDuplicates Tracking 246456 as yet unmatched pairs. 1952 records in RAM.
INFO 2026-06-08 07:37:54 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 1s. Last read position: chr5:180,612,993
INFO 2026-06-08 07:37:54 MarkDuplicates Tracking 246875 as yet unmatched pairs. 349 records in RAM.
INFO 2026-06-08 07:37:57 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 3s. Last read position: chr6:24,830,460
INFO 2026-06-08 07:37:57 MarkDuplicates Tracking 247677 as yet unmatched pairs. 18818 records in RAM.
INFO 2026-06-08 07:38:01 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 3s. Last read position: chr6:31,358,214
INFO 2026-06-08 07:38:01 MarkDuplicates Tracking 247563 as yet unmatched pairs. 17309 records in RAM.
INFO 2026-06-08 07:38:03 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 2s. Last read position: chr6:33,166,861
INFO 2026-06-08 07:38:03 MarkDuplicates Tracking 247399 as yet unmatched pairs. 16116 records in RAM.
INFO 2026-06-08 07:38:05 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 2s. Last read position: chr6:43,046,756
INFO 2026-06-08 07:38:05 MarkDuplicates Tracking 247405 as yet unmatched pairs. 14452 records in RAM.
INFO 2026-06-08 07:38:08 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 2s. Last read position: chr6:65,490,543
INFO 2026-06-08 07:38:08 MarkDuplicates Tracking 247990 as yet unmatched pairs. 12423 records in RAM.
INFO 2026-06-08 07:38:10 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 2s. Last read position: chr6:93,264,770
INFO 2026-06-08 07:38:10 MarkDuplicates Tracking 248752 as yet unmatched pairs. 10072 records in RAM.
INFO 2026-06-08 07:38:12 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 2s. Last read position: chr6:117,321,643
INFO 2026-06-08 07:38:12 MarkDuplicates Tracking 249725 as yet unmatched pairs. 8120 records in RAM.
INFO 2026-06-08 07:38:14 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 2s. Last read position: chr6:131,860,465
INFO 2026-06-08 07:38:14 MarkDuplicates Tracking 249541 as yet unmatched pairs. 5695 records in RAM.
INFO 2026-06-08 07:38:16 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 2s. Last read position: chr6:149,599,681
INFO 2026-06-08 07:38:16 MarkDuplicates Tracking 249756 as yet unmatched pairs. 3468 records in RAM.
INFO 2026-06-08 07:38:18 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 2s. Last read position: chr6:159,236,070
INFO 2026-06-08 07:38:18 MarkDuplicates Tracking 249559 as yet unmatched pairs. 1467 records in RAM.
INFO 2026-06-08 07:38:21 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 2s. Last read position: chr7:2,937,818
INFO 2026-06-08 07:38:21 MarkDuplicates Tracking 249803 as yet unmatched pairs. 22022 records in RAM.
INFO 2026-06-08 07:38:24 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 2s. Last read position: chr7:13,940,817
INFO 2026-06-08 07:38:24 MarkDuplicates Tracking 249858 as yet unmatched pairs. 20376 records in RAM.
INFO 2026-06-08 07:38:26 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 2s. Last read position: chr7:31,643,352
INFO 2026-06-08 07:38:26 MarkDuplicates Tracking 249656 as yet unmatched pairs. 17978 records in RAM.
INFO 2026-06-08 07:38:28 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 2s. Last read position: chr7:55,019,200
INFO 2026-06-08 07:38:28 MarkDuplicates Tracking 250408 as yet unmatched pairs. 16172 records in RAM.
INFO 2026-06-08 07:38:30 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 2s. Last read position: chr7:72,867,614
INFO 2026-06-08 07:38:30 MarkDuplicates Tracking 249741 as yet unmatched pairs. 13298 records in RAM.
INFO 2026-06-08 07:38:33 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 2s. Last read position: chr7:77,121,577
INFO 2026-06-08 07:38:33 MarkDuplicates Tracking 249675 as yet unmatched pairs. 12501 records in RAM.
INFO 2026-06-08 07:38:35 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 2s. Last read position: chr7:95,592,781
INFO 2026-06-08 07:38:35 MarkDuplicates Tracking 249611 as yet unmatched pairs. 10137 records in RAM.
INFO 2026-06-08 07:38:37 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 2s. Last read position: chr7:102,253,979
INFO 2026-06-08 07:38:37 MarkDuplicates Tracking 250157 as yet unmatched pairs. 9429 records in RAM.
INFO 2026-06-08 07:38:39 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 1s. Last read position: chr7:116,699,868
INFO 2026-06-08 07:38:39 MarkDuplicates Tracking 249744 as yet unmatched pairs. 7084 records in RAM.
INFO 2026-06-08 07:38:41 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 2s. Last read position: chr7:134,306,707
INFO 2026-06-08 07:38:41 MarkDuplicates Tracking 249074 as yet unmatched pairs. 4267 records in RAM.
INFO 2026-06-08 07:38:43 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 2s. Last read position: chr7:143,876,461
INFO 2026-06-08 07:38:43 MarkDuplicates Tracking 248859 as yet unmatched pairs. 2484 records in RAM.
INFO 2026-06-08 07:38:45 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 2s. Last read position: chr7:153,558,684
INFO 2026-06-08 07:38:45 MarkDuplicates Tracking 248422 as yet unmatched pairs. 525 records in RAM.
INFO 2026-06-08 07:38:48 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 2s. Last read position: chr8:7,748,541
INFO 2026-06-08 07:38:48 MarkDuplicates Tracking 248402 as yet unmatched pairs. 20532 records in RAM.
INFO 2026-06-08 07:38:50 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 2s. Last read position: chr8:22,619,183
INFO 2026-06-08 07:38:50 MarkDuplicates Tracking 248072 as yet unmatched pairs. 18662 records in RAM.
INFO 2026-06-08 07:38:52 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 2s. Last read position: chr8:32,644,622
INFO 2026-06-08 07:38:52 MarkDuplicates Tracking 248495 as yet unmatched pairs. 17550 records in RAM.
INFO 2026-06-08 07:38:56 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 3s. Last read position: chr8:32,745,439
INFO 2026-06-08 07:38:56 MarkDuplicates Tracking 247604 as yet unmatched pairs. 15496 records in RAM.
INFO 2026-06-08 07:39:00 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 3s. Last read position: chr8:38,441,475
INFO 2026-06-08 07:39:00 MarkDuplicates Tracking 247318 as yet unmatched pairs. 13875 records in RAM.
INFO 2026-06-08 07:39:02 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr8:54,455,804
INFO 2026-06-08 07:39:02 MarkDuplicates Tracking 246057 as yet unmatched pairs. 10818 records in RAM.
INFO 2026-06-08 07:39:04 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 2s. Last read position: chr8:86,064,310
INFO 2026-06-08 07:39:04 MarkDuplicates Tracking 245545 as yet unmatched pairs. 7554 records in RAM.
INFO 2026-06-08 07:39:06 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 2s. Last read position: chr8:114,179,478
INFO 2026-06-08 07:39:06 MarkDuplicates Tracking 244818 as yet unmatched pairs. 4142 records in RAM.
INFO 2026-06-08 07:39:08 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 2s. Last read position: chr8:143,562,748
INFO 2026-06-08 07:39:08 MarkDuplicates Tracking 244466 as yet unmatched pairs. 1083 records in RAM.
INFO 2026-06-08 07:39:10 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 2s. Last read position: chr9:2,222,579
INFO 2026-06-08 07:39:10 MarkDuplicates Tracking 243600 as yet unmatched pairs. 21613 records in RAM.
INFO 2026-06-08 07:39:13 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 2s. Last read position: chr9:21,935,316
INFO 2026-06-08 07:39:13 MarkDuplicates Tracking 243746 as yet unmatched pairs. 19784 records in RAM.
INFO 2026-06-08 07:39:17 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 3s. Last read position: chr9:37,014,920
INFO 2026-06-08 07:39:17 MarkDuplicates Tracking 242307 as yet unmatched pairs. 16742 records in RAM.
INFO 2026-06-08 07:39:19 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 2s. Last read position: chr9:62,436,927
INFO 2026-06-08 07:39:19 MarkDuplicates Tracking 241715 as yet unmatched pairs. 15236 records in RAM.
INFO 2026-06-08 07:39:21 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 2s. Last read position: chr9:77,716,405
INFO 2026-06-08 07:39:21 MarkDuplicates Tracking 242124 as yet unmatched pairs. 14319 records in RAM.
INFO 2026-06-08 07:39:24 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 2s. Last read position: chr9:84,886,542
INFO 2026-06-08 07:39:24 MarkDuplicates Tracking 241384 as yet unmatched pairs. 12235 records in RAM.
INFO 2026-06-08 07:39:26 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 2s. Last read position: chr9:92,417,063
INFO 2026-06-08 07:39:26 MarkDuplicates Tracking 239728 as yet unmatched pairs. 9293 records in RAM.
INFO 2026-06-08 07:39:28 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 2s. Last read position: chr9:107,485,163
INFO 2026-06-08 07:39:28 MarkDuplicates Tracking 239532 as yet unmatched pairs. 7450 records in RAM.
INFO 2026-06-08 07:39:30 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 2s. Last read position: chr9:127,668,119
INFO 2026-06-08 07:39:30 MarkDuplicates Tracking 238087 as yet unmatched pairs. 4099 records in RAM.
INFO 2026-06-08 07:39:33 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 2s. Last read position: chr9:133,360,255
INFO 2026-06-08 07:39:33 MarkDuplicates Tracking 237004 as yet unmatched pairs. 2056 records in RAM.
INFO 2026-06-08 07:39:36 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 3s. Last read position: chr9:137,464,098
INFO 2026-06-08 07:39:36 MarkDuplicates Tracking 236001 as yet unmatched pairs. 242 records in RAM.
INFO 2026-06-08 07:39:41 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 4s. Last read position: chr10:26,419,016
INFO 2026-06-08 07:39:41 MarkDuplicates Tracking 234914 as yet unmatched pairs. 18182 records in RAM.
INFO 2026-06-08 07:39:44 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 3s. Last read position: chr10:44,293,840
INFO 2026-06-08 07:39:44 MarkDuplicates Tracking 233880 as yet unmatched pairs. 15558 records in RAM.
INFO 2026-06-08 07:39:47 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 2s. Last read position: chr10:62,087,319
INFO 2026-06-08 07:39:47 MarkDuplicates Tracking 232825 as yet unmatched pairs. 13095 records in RAM.
INFO 2026-06-08 07:39:50 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 2s. Last read position: chr10:79,532,466
INFO 2026-06-08 07:39:50 MarkDuplicates Tracking 231567 as yet unmatched pairs. 10257 records in RAM.
INFO 2026-06-08 07:39:52 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 2s. Last read position: chr10:93,333,788
INFO 2026-06-08 07:39:52 MarkDuplicates Tracking 230502 as yet unmatched pairs. 7780 records in RAM.
INFO 2026-06-08 07:39:55 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 2s. Last read position: chr10:103,400,544
INFO 2026-06-08 07:39:55 MarkDuplicates Tracking 229357 as yet unmatched pairs. 5462 records in RAM.
INFO 2026-06-08 07:39:58 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 2s. Last read position: chr10:121,575,608
INFO 2026-06-08 07:39:58 MarkDuplicates Tracking 228096 as yet unmatched pairs. 2488 records in RAM.
INFO 2026-06-08 07:40:01 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 3s. Last read position: chr11:197,528
INFO 2026-06-08 07:40:01 MarkDuplicates Tracking 226791 as yet unmatched pairs. 25543 records in RAM.
INFO 2026-06-08 07:40:04 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 2s. Last read position: chr11:5,610,693
INFO 2026-06-08 07:40:04 MarkDuplicates Tracking 225737 as yet unmatched pairs. 23755 records in RAM.
INFO 2026-06-08 07:40:07 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 2s. Last read position: chr11:20,043,987
INFO 2026-06-08 07:40:07 MarkDuplicates Tracking 224523 as yet unmatched pairs. 21227 records in RAM.
INFO 2026-06-08 07:40:10 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 2s. Last read position: chr11:47,835,662
INFO 2026-06-08 07:40:10 MarkDuplicates Tracking 222950 as yet unmatched pairs. 17776 records in RAM.
INFO 2026-06-08 07:40:13 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 3s. Last read position: chr11:62,708,248
INFO 2026-06-08 07:40:13 MarkDuplicates Tracking 221662 as yet unmatched pairs. 15373 records in RAM.
INFO 2026-06-08 07:40:16 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 3s. Last read position: chr11:67,405,354
INFO 2026-06-08 07:40:16 MarkDuplicates Tracking 220556 as yet unmatched pairs. 13535 records in RAM.
INFO 2026-06-08 07:40:20 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 3s. Last read position: chr11:77,328,340
INFO 2026-06-08 07:40:20 MarkDuplicates Tracking 218987 as yet unmatched pairs. 10979 records in RAM.
INFO 2026-06-08 07:40:24 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 4s. Last read position: chr11:101,129,364
INFO 2026-06-08 07:40:24 MarkDuplicates Tracking 218393 as yet unmatched pairs. 8649 records in RAM.
INFO 2026-06-08 07:40:27 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 3s. Last read position: chr11:117,181,792
INFO 2026-06-08 07:40:27 MarkDuplicates Tracking 215678 as yet unmatched pairs. 4481 records in RAM.
INFO 2026-06-08 07:40:30 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 2s. Last read position: chr11:124,185,900
INFO 2026-06-08 07:40:30 MarkDuplicates Tracking 214070 as yet unmatched pairs. 1906 records in RAM.
INFO 2026-06-08 07:40:34 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 3s. Last read position: chr12:4,288,761
INFO 2026-06-08 07:40:34 MarkDuplicates Tracking 212707 as yet unmatched pairs. 29344 records in RAM.
INFO 2026-06-08 07:40:37 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 3s. Last read position: chr12:11,756,650
INFO 2026-06-08 07:40:37 MarkDuplicates Tracking 211854 as yet unmatched pairs. 27665 records in RAM.
INFO 2026-06-08 07:40:40 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 3s. Last read position: chr12:11,837,536
INFO 2026-06-08 07:40:40 MarkDuplicates Tracking 210393 as yet unmatched pairs. 25537 records in RAM.
INFO 2026-06-08 07:40:43 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 3s. Last read position: chr12:22,201,963
INFO 2026-06-08 07:40:43 MarkDuplicates Tracking 207840 as yet unmatched pairs. 21990 records in RAM.
INFO 2026-06-08 07:40:47 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 3s. Last read position: chr12:47,975,331
INFO 2026-06-08 07:40:47 MarkDuplicates Tracking 206308 as yet unmatched pairs. 18819 records in RAM.
INFO 2026-06-08 07:40:50 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 3s. Last read position: chr12:52,403,782
INFO 2026-06-08 07:40:50 MarkDuplicates Tracking 204430 as yet unmatched pairs. 16334 records in RAM.
INFO 2026-06-08 07:40:53 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 3s. Last read position: chr12:57,234,248
INFO 2026-06-08 07:40:53 MarkDuplicates Tracking 202910 as yet unmatched pairs. 14132 records in RAM.
INFO 2026-06-08 07:40:55 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 2s. Last read position: chr12:76,347,078
INFO 2026-06-08 07:40:55 MarkDuplicates Tracking 200947 as yet unmatched pairs. 10813 records in RAM.
INFO 2026-06-08 07:40:58 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 2s. Last read position: chr12:104,886,292
INFO 2026-06-08 07:40:58 MarkDuplicates Tracking 198277 as yet unmatched pairs. 6434 records in RAM.
INFO 2026-06-08 07:41:01 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 2s. Last read position: chr12:117,280,723
INFO 2026-06-08 07:41:01 MarkDuplicates Tracking 196355 as yet unmatched pairs. 3539 records in RAM.
INFO 2026-06-08 07:41:04 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 2s. Last read position: chr12:132,077,325
INFO 2026-06-08 07:41:04 MarkDuplicates Tracking 194469 as yet unmatched pairs. 564 records in RAM.
INFO 2026-06-08 07:41:07 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:06:31s. Time for last 1,000,000: 3s. Last read position: chr13:28,321,530
INFO 2026-06-08 07:41:07 MarkDuplicates Tracking 192770 as yet unmatched pairs. 12922 records in RAM.
INFO 2026-06-08 07:41:09 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 2s. Last read position: chr13:48,367,190
INFO 2026-06-08 07:41:09 MarkDuplicates Tracking 190186 as yet unmatched pairs. 9068 records in RAM.
INFO 2026-06-08 07:41:12 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 2s. Last read position: chr13:94,597,255
INFO 2026-06-08 07:41:12 MarkDuplicates Tracking 186922 as yet unmatched pairs. 3551 records in RAM.
INFO 2026-06-08 07:41:14 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 2s. Last read position: chr14:18,698,995
INFO 2026-06-08 07:41:14 MarkDuplicates Tracking 184502 as yet unmatched pairs. 16121 records in RAM.
INFO 2026-06-08 07:41:17 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 3s. Last read position: chr14:34,663,758
INFO 2026-06-08 07:41:17 MarkDuplicates Tracking 182267 as yet unmatched pairs. 12984 records in RAM.
INFO 2026-06-08 07:41:21 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 3s. Last read position: chr14:61,695,785
INFO 2026-06-08 07:41:21 MarkDuplicates Tracking 179362 as yet unmatched pairs. 8690 records in RAM.
INFO 2026-06-08 07:41:24 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 3s. Last read position: chr14:79,697,877
INFO 2026-06-08 07:41:24 MarkDuplicates Tracking 177008 as yet unmatched pairs. 5291 records in RAM.
INFO 2026-06-08 07:41:27 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 3s. Last read position: chr14:102,891,217
INFO 2026-06-08 07:41:27 MarkDuplicates Tracking 174219 as yet unmatched pairs. 1380 records in RAM.
INFO 2026-06-08 07:41:31 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 3s. Last read position: chr15:24,977,723
INFO 2026-06-08 07:41:31 MarkDuplicates Tracking 172533 as yet unmatched pairs. 24751 records in RAM.
INFO 2026-06-08 07:41:34 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 3s. Last read position: chr15:34,356,304
INFO 2026-06-08 07:41:34 MarkDuplicates Tracking 171309 as yet unmatched pairs. 23011 records in RAM.
INFO 2026-06-08 07:41:38 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:07:03s. Time for last 1,000,000: 4s. Last read position: chr15:43,456,594
INFO 2026-06-08 07:41:38 MarkDuplicates Tracking 169361 as yet unmatched pairs. 20444 records in RAM.
INFO 2026-06-08 07:41:42 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 3s. Last read position: chr15:59,663,159
INFO 2026-06-08 07:41:42 MarkDuplicates Tracking 166251 as yet unmatched pairs. 16469 records in RAM.
INFO 2026-06-08 07:41:45 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 3s. Last read position: chr15:75,207,676
INFO 2026-06-08 07:41:45 MarkDuplicates Tracking 163880 as yet unmatched pairs. 13259 records in RAM.
INFO 2026-06-08 07:41:48 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 3s. Last read position: chr15:87,871,947
INFO 2026-06-08 07:41:48 MarkDuplicates Tracking 162469 as yet unmatched pairs. 11169 records in RAM.
INFO 2026-06-08 07:41:52 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:07:16s. Time for last 1,000,000: 3s. Last read position: chr15:88,014,831
INFO 2026-06-08 07:41:52 MarkDuplicates Tracking 160737 as yet unmatched pairs. 9011 records in RAM.
INFO 2026-06-08 07:41:55 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:07:20s. Time for last 1,000,000: 3s. Last read position: chr15:88,079,058
INFO 2026-06-08 07:41:55 MarkDuplicates Tracking 158829 as yet unmatched pairs. 6660 records in RAM.
INFO 2026-06-08 07:41:58 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:07:23s. Time for last 1,000,000: 3s. Last read position: chr15:88,856,396
INFO 2026-06-08 07:41:58 MarkDuplicates Tracking 155831 as yet unmatched pairs. 3210 records in RAM.
INFO 2026-06-08 07:42:01 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:07:26s. Time for last 1,000,000: 3s. Last read position: chr15:101,976,172
INFO 2026-06-08 07:42:01 MarkDuplicates Tracking 153529 as yet unmatched pairs. 151 records in RAM.
INFO 2026-06-08 07:42:05 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:07:30s. Time for last 1,000,000: 3s. Last read position: chr16:2,599,629
INFO 2026-06-08 07:42:05 MarkDuplicates Tracking 153243 as yet unmatched pairs. 22766 records in RAM.
INFO 2026-06-08 07:42:07 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:07:32s. Time for last 1,000,000: 2s. Last read position: chr16:11,267,849
INFO 2026-06-08 07:42:07 MarkDuplicates Tracking 149279 as yet unmatched pairs. 18313 records in RAM.
INFO 2026-06-08 07:42:10 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:07:35s. Time for last 1,000,000: 2s. Last read position: chr16:20,348,839
INFO 2026-06-08 07:42:10 MarkDuplicates Tracking 147842 as yet unmatched pairs. 16439 records in RAM.
INFO 2026-06-08 07:42:13 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:07:38s. Time for last 1,000,000: 2s. Last read position: chr16:29,398,395
INFO 2026-06-08 07:42:13 MarkDuplicates Tracking 145861 as yet unmatched pairs. 14056 records in RAM.
INFO 2026-06-08 07:42:16 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:07:41s. Time for last 1,000,000: 3s. Last read position: chr16:33,459,734
INFO 2026-06-08 07:42:16 MarkDuplicates Tracking 144370 as yet unmatched pairs. 12339 records in RAM.
INFO 2026-06-08 07:42:19 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:07:43s. Time for last 1,000,000: 2s. Last read position: chr16:60,006,977
INFO 2026-06-08 07:42:19 MarkDuplicates Tracking 141078 as yet unmatched pairs. 8136 records in RAM.
INFO 2026-06-08 07:42:21 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:07:46s. Time for last 1,000,000: 2s. Last read position: chr16:71,738,943
INFO 2026-06-08 07:42:21 MarkDuplicates Tracking 138756 as yet unmatched pairs. 5250 records in RAM.
INFO 2026-06-08 07:42:24 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:07:49s. Time for last 1,000,000: 2s. Last read position: chr16:87,689,841
INFO 2026-06-08 07:42:24 MarkDuplicates Tracking 135934 as yet unmatched pairs. 1744 records in RAM.
INFO 2026-06-08 07:42:28 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:07:53s. Time for last 1,000,000: 4s. Last read position: chr17:2,041,603
INFO 2026-06-08 07:42:28 MarkDuplicates Tracking 133948 as yet unmatched pairs. 31188 records in RAM.
INFO 2026-06-08 07:42:32 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:07:56s. Time for last 1,000,000: 3s. Last read position: chr17:7,686,483
INFO 2026-06-08 07:42:32 MarkDuplicates Tracking 132621 as yet unmatched pairs. 29546 records in RAM.
INFO 2026-06-08 07:42:35 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:07:59s. Time for last 1,000,000: 2s. Last read position: chr17:16,422,607
INFO 2026-06-08 07:42:35 MarkDuplicates Tracking 129121 as yet unmatched pairs. 25649 records in RAM.
INFO 2026-06-08 07:42:37 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:08:02s. Time for last 1,000,000: 2s. Last read position: chr17:28,701,366
INFO 2026-06-08 07:42:37 MarkDuplicates Tracking 126737 as yet unmatched pairs. 22896 records in RAM.
INFO 2026-06-08 07:42:41 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 3s. Last read position: chr17:36,173,356
INFO 2026-06-08 07:42:41 MarkDuplicates Tracking 124083 as yet unmatched pairs. 19839 records in RAM.
INFO 2026-06-08 07:42:44 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:08:08s. Time for last 1,000,000: 3s. Last read position: chr17:40,331,970
INFO 2026-06-08 07:42:44 MarkDuplicates Tracking 123531 as yet unmatched pairs. 19011 records in RAM.
INFO 2026-06-08 07:42:48 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:08:13s. Time for last 1,000,000: 4s. Last read position: chr17:42,311,238
INFO 2026-06-08 07:42:48 MarkDuplicates Tracking 121238 as yet unmatched pairs. 16400 records in RAM.
INFO 2026-06-08 07:42:52 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 3s. Last read position: chr17:44,926,081
INFO 2026-06-08 07:42:52 MarkDuplicates Tracking 118088 as yet unmatched pairs. 12941 records in RAM.
INFO 2026-06-08 07:42:55 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:08:20s. Time for last 1,000,000: 3s. Last read position: chr17:50,606,923
INFO 2026-06-08 07:42:55 MarkDuplicates Tracking 116036 as yet unmatched pairs. 10614 records in RAM.
INFO 2026-06-08 07:42:58 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 3s. Last read position: chr17:62,788,283
INFO 2026-06-08 07:42:58 MarkDuplicates Tracking 113062 as yet unmatched pairs. 7155 records in RAM.
INFO 2026-06-08 07:43:01 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:08:26s. Time for last 1,000,000: 3s. Last read position: chr17:74,352,237
INFO 2026-06-08 07:43:01 MarkDuplicates Tracking 110189 as yet unmatched pairs. 3873 records in RAM.
INFO 2026-06-08 07:43:05 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 3s. Last read position: chr17:80,922,915
INFO 2026-06-08 07:43:05 MarkDuplicates Tracking 107782 as yet unmatched pairs. 1151 records in RAM.
INFO 2026-06-08 07:43:08 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:08:33s. Time for last 1,000,000: 3s. Last read position: chr18:14,818,593
INFO 2026-06-08 07:43:08 MarkDuplicates Tracking 104409 as yet unmatched pairs. 12264 records in RAM.
INFO 2026-06-08 07:43:12 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:08:36s. Time for last 1,000,000: 3s. Last read position: chr18:46,560,250
INFO 2026-06-08 07:43:12 MarkDuplicates Tracking 100014 as yet unmatched pairs. 7210 records in RAM.
INFO 2026-06-08 07:43:15 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 3s. Last read position: chr18:59,900,454
INFO 2026-06-08 07:43:15 MarkDuplicates Tracking 97639 as yet unmatched pairs. 4429 records in RAM.
INFO 2026-06-08 07:43:19 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:08:44s. Time for last 1,000,000: 3s. Last read position: chr19:1,610,382
INFO 2026-06-08 07:43:19 MarkDuplicates Tracking 94076 as yet unmatched pairs. 26232 records in RAM.
INFO 2026-06-08 07:43:23 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:08:47s. Time for last 1,000,000: 3s. Last read position: chr19:5,844,051
INFO 2026-06-08 07:43:23 MarkDuplicates Tracking 90709 as yet unmatched pairs. 22683 records in RAM.
INFO 2026-06-08 07:43:26 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:08:50s. Time for last 1,000,000: 3s. Last read position: chr19:9,610,252
INFO 2026-06-08 07:43:26 MarkDuplicates Tracking 88182 as yet unmatched pairs. 19994 records in RAM.
INFO 2026-06-08 07:43:29 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:08:53s. Time for last 1,000,000: 2s. Last read position: chr19:14,410,880
INFO 2026-06-08 07:43:29 MarkDuplicates Tracking 85697 as yet unmatched pairs. 17320 records in RAM.
INFO 2026-06-08 07:43:31 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:08:56s. Time for last 1,000,000: 2s. Last read position: chr19:18,170,240
INFO 2026-06-08 07:43:31 MarkDuplicates Tracking 83717 as yet unmatched pairs. 15157 records in RAM.
INFO 2026-06-08 07:43:34 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:08:59s. Time for last 1,000,000: 2s. Last read position: chr19:36,071,740
INFO 2026-06-08 07:43:34 MarkDuplicates Tracking 79646 as yet unmatched pairs. 10796 records in RAM.
INFO 2026-06-08 07:43:37 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:09:02s. Time for last 1,000,000: 3s. Last read position: chr19:41,761,216
INFO 2026-06-08 07:43:37 MarkDuplicates Tracking 77152 as yet unmatched pairs. 8081 records in RAM.
INFO 2026-06-08 07:43:41 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 3s. Last read position: chr19:47,001,871
INFO 2026-06-08 07:43:41 MarkDuplicates Tracking 75642 as yet unmatched pairs. 6390 records in RAM.
INFO 2026-06-08 07:43:44 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 3s. Last read position: chr19:52,095,254
INFO 2026-06-08 07:43:44 MarkDuplicates Tracking 72488 as yet unmatched pairs. 3047 records in RAM.
INFO 2026-06-08 07:43:46 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:09:11s. Time for last 1,000,000: 2s. Last read position: chr19:58,347,237
INFO 2026-06-08 07:43:46 MarkDuplicates Tracking 69905 as yet unmatched pairs. 203 records in RAM.
INFO 2026-06-08 07:43:49 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 3s. Last read position: chr20:23,493,002
INFO 2026-06-08 07:43:49 MarkDuplicates Tracking 65512 as yet unmatched pairs. 11789 records in RAM.
INFO 2026-06-08 07:43:53 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:09:17s. Time for last 1,000,000: 3s. Last read position: chr20:36,816,215
INFO 2026-06-08 07:43:53 MarkDuplicates Tracking 62229 as yet unmatched pairs. 8281 records in RAM.
INFO 2026-06-08 07:43:56 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 2s. Last read position: chr20:47,651,242
INFO 2026-06-08 07:43:56 MarkDuplicates Tracking 59039 as yet unmatched pairs. 4898 records in RAM.
INFO 2026-06-08 07:43:58 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:09:23s. Time for last 1,000,000: 2s. Last read position: chr20:62,909,643
INFO 2026-06-08 07:43:58 MarkDuplicates Tracking 55187 as yet unmatched pairs. 837 records in RAM.
INFO 2026-06-08 07:44:01 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:09:26s. Time for last 1,000,000: 3s. Last read position: chr21:8,471,079
INFO 2026-06-08 07:44:01 MarkDuplicates Tracking 53440 as yet unmatched pairs. 9954 records in RAM.
INFO 2026-06-08 07:44:05 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:09:29s. Time for last 1,000,000: 3s. Last read position: chr21:36,232,864
INFO 2026-06-08 07:44:05 MarkDuplicates Tracking 48523 as yet unmatched pairs. 4712 records in RAM.
INFO 2026-06-08 07:44:08 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:09:33s. Time for last 1,000,000: 3s. Last read position: chr21:44,216,139
INFO 2026-06-08 07:44:08 MarkDuplicates Tracking 45291 as yet unmatched pairs. 1306 records in RAM.
INFO 2026-06-08 07:44:12 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:09:36s. Time for last 1,000,000: 3s. Last read position: chr22:18,852,978
INFO 2026-06-08 07:44:12 MarkDuplicates Tracking 42996 as yet unmatched pairs. 15003 records in RAM.
INFO 2026-06-08 07:44:15 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:09:40s. Time for last 1,000,000: 3s. Last read position: chr22:22,629,764
INFO 2026-06-08 07:44:15 MarkDuplicates Tracking 41408 as yet unmatched pairs. 13354 records in RAM.
INFO 2026-06-08 07:44:18 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:09:43s. Time for last 1,000,000: 3s. Last read position: chr22:24,000,099
INFO 2026-06-08 07:44:18 MarkDuplicates Tracking 37983 as yet unmatched pairs. 9875 records in RAM.
INFO 2026-06-08 07:44:21 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:09:46s. Time for last 1,000,000: 3s. Last read position: chr22:30,525,492
INFO 2026-06-08 07:44:21 MarkDuplicates Tracking 35378 as yet unmatched pairs. 7178 records in RAM.
INFO 2026-06-08 07:44:24 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:09:49s. Time for last 1,000,000: 2s. Last read position: chr22:41,127,501
INFO 2026-06-08 07:44:24 MarkDuplicates Tracking 31743 as yet unmatched pairs. 3433 records in RAM.
INFO 2026-06-08 07:44:28 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:09:52s. Time for last 1,000,000: 3s. Last read position: chrX:1,356,327
INFO 2026-06-08 07:44:28 MarkDuplicates Tracking 28170 as yet unmatched pairs. 20587 records in RAM.
INFO 2026-06-08 07:44:31 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:09:56s. Time for last 1,000,000: 3s. Last read position: chrX:45,028,379
INFO 2026-06-08 07:44:31 MarkDuplicates Tracking 23274 as yet unmatched pairs. 15637 records in RAM.
INFO 2026-06-08 07:44:34 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 3s. Last read position: chrX:64,601,877
INFO 2026-06-08 07:44:34 MarkDuplicates Tracking 20337 as yet unmatched pairs. 12668 records in RAM.
INFO 2026-06-08 07:44:38 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:10:02s. Time for last 1,000,000: 3s. Last read position: chrX:83,872,894
INFO 2026-06-08 07:44:38 MarkDuplicates Tracking 16793 as yet unmatched pairs. 9081 records in RAM.
INFO 2026-06-08 07:44:41 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 3s. Last read position: chrX:124,371,935
INFO 2026-06-08 07:44:41 MarkDuplicates Tracking 12460 as yet unmatched pairs. 4711 records in RAM.
INFO 2026-06-08 07:44:44 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 2s. Last read position: chrX:154,233,618
INFO 2026-06-08 07:44:44 MarkDuplicates Tracking 9239 as yet unmatched pairs. 1463 records in RAM.
INFO 2026-06-08 07:44:47 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 2s. Last read position: chrY:22,417,282
INFO 2026-06-08 07:44:47 MarkDuplicates Tracking 5732 as yet unmatched pairs. 1032 records in RAM.
INFO 2026-06-08 07:44:50 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:10:14s. Time for last 1,000,000: 2s. Last read position: KI270713.1:5,166
INFO 2026-06-08 07:44:50 MarkDuplicates Tracking 3461 as yet unmatched pairs. 1413 records in RAM.
INFO 2026-06-08 07:44:52 MarkDuplicates Read 204776311 records. 0 pairs never matched.
INFO 2026-06-08 07:45:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 32026832016; totalMemory: 56002347008; maxMemory: 63585648640
INFO 2026-06-08 07:45:07 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 07:45:14 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 07:45:44 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 07:46:03 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 07:46:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300896208; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-08 07:46:05 MarkDuplicates Marking 32519726 records as duplicates.
INFO 2026-06-08 07:46:05 MarkDuplicates Found 6701544 optical duplicate clusters.
INFO 2026-06-08 07:46:05 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 07:46:36 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:30s. Time for last 10,000,000: 30s. Last read position: chr1:121,118,476
INFO 2026-06-08 07:47:07 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:01:01s. Time for last 10,000,000: 31s. Last read position: chr2:25,741,063
INFO 2026-06-08 07:47:39 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:34s. Time for last 10,000,000: 32s. Last read position: chr2:177,220,153
INFO 2026-06-08 07:48:13 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:02:07s. Time for last 10,000,000: 33s. Last read position: chr3:58,095,856
INFO 2026-06-08 07:48:46 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:02:40s. Time for last 10,000,000: 32s. Last read position: chr4:56,279,628
INFO 2026-06-08 07:49:19 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:03:13s. Time for last 10,000,000: 33s. Last read position: chr5:138,827,654
INFO 2026-06-08 07:49:51 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:03:45s. Time for last 10,000,000: 31s. Last read position: chr6:117,321,643
INFO 2026-06-08 07:50:24 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:04:18s. Time for last 10,000,000: 32s. Last read position: chr7:95,592,781
INFO 2026-06-08 07:50:55 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:04:49s. Time for last 10,000,000: 31s. Last read position: chr8:38,441,475
INFO 2026-06-08 07:51:27 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:05:21s. Time for last 10,000,000: 32s. Last read position: chr9:84,886,542
INFO 2026-06-08 07:52:00 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:05:54s. Time for last 10,000,000: 32s. Last read position: chr10:93,333,788
INFO 2026-06-08 07:52:32 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:06:27s. Time for last 10,000,000: 32s. Last read position: chr11:101,129,364
INFO 2026-06-08 07:53:04 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:06:58s. Time for last 10,000,000: 31s. Last read position: chr12:76,347,078
INFO 2026-06-08 07:53:37 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:07:31s. Time for last 10,000,000: 32s. Last read position: chr14:79,697,877
INFO 2026-06-08 07:54:09 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:08:04s. Time for last 10,000,000: 32s. Last read position: chr15:88,856,396
INFO 2026-06-08 07:54:40 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:08:35s. Time for last 10,000,000: 30s. Last read position: chr17:2,041,603
INFO 2026-06-08 07:55:12 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:09:07s. Time for last 10,000,000: 32s. Last read position: chr17:74,352,237
INFO 2026-06-08 07:55:45 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:09:39s. Time for last 10,000,000: 32s. Last read position: chr19:36,071,740
INFO 2026-06-08 07:56:18 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:10:12s. Time for last 10,000,000: 33s. Last read position: chr21:36,232,864
INFO 2026-06-08 07:56:50 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:10:45s. Time for last 10,000,000: 32s. Last read position: chrX:83,872,894
INFO 2026-06-08 07:57:15 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 07:57:15 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 07:57:15 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 07:57:16 MarkDuplicates Before output close freeMemory: 202215328; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 07:57:16 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 07:57:16 MarkDuplicates After output close freeMemory: 104380568; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 07:57:16 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 22.72 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory