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 659_bCu-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bam --METRICS_FILE 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:45:46.666 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 07:45:46 GMT 2026] MarkDuplicates --INPUT 659_bCu-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bam --METRICS_FILE 659_bCu-T1-TRNA-1_B23WHTKLT4_1.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 07:45:46 GMT 2026] Executing as ?@nf-1dce393d6c57309e5285ad2026222f1c-3bccb-jdxpc 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 07:45:46 MarkDuplicates Start of doWork freeMemory: 105849936; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:45:46 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:45:46 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:45:53 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:16,587,205
INFO 2026-06-08 07:45:53 MarkDuplicates Tracking 2275 as yet unmatched pairs. 82 records in RAM.
INFO 2026-06-08 07:45:57 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 4s. Last read position: chr1:27,109,721
INFO 2026-06-08 07:45:57 MarkDuplicates Tracking 4236 as yet unmatched pairs. 86 records in RAM.
INFO 2026-06-08 07:46:00 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 2s. Last read position: chr1:41,513,525
INFO 2026-06-08 07:46:00 MarkDuplicates Tracking 6310 as yet unmatched pairs. 0 records in RAM.
INFO 2026-06-08 07:46:03 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 3s. Last read position: chr1:110,041,494
INFO 2026-06-08 07:46:03 MarkDuplicates Tracking 8355 as yet unmatched pairs. 32 records in RAM.
INFO 2026-06-08 07:46:06 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 2s. Last read position: chr1:145,394,977
INFO 2026-06-08 07:46:06 MarkDuplicates Tracking 9644 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 07:46:09 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 3s. Last read position: chr1:148,563,807
INFO 2026-06-08 07:46:09 MarkDuplicates Tracking 10557 as yet unmatched pairs. 203 records in RAM.
INFO 2026-06-08 07:46:11 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 2s. Last read position: chr1:150,511,107
INFO 2026-06-08 07:46:11 MarkDuplicates Tracking 11239 as yet unmatched pairs. 119 records in RAM.
INFO 2026-06-08 07:46:14 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 2s. Last read position: chr1:153,811,755
INFO 2026-06-08 07:46:14 MarkDuplicates Tracking 13234 as yet unmatched pairs. 25 records in RAM.
INFO 2026-06-08 07:46:16 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 2s. Last read position: chr1:155,765,148
INFO 2026-06-08 07:46:16 MarkDuplicates Tracking 15135 as yet unmatched pairs. 99 records in RAM.
INFO 2026-06-08 07:46:20 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 3s. Last read position: chr1:156,671,583
INFO 2026-06-08 07:46:20 MarkDuplicates Tracking 17588 as yet unmatched pairs. 129 records in RAM.
INFO 2026-06-08 07:46:23 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 3s. Last read position: chr1:171,557,634
INFO 2026-06-08 07:46:23 MarkDuplicates Tracking 19694 as yet unmatched pairs. 91 records in RAM.
INFO 2026-06-08 07:46:25 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 2s. Last read position: chr1:201,200,337
INFO 2026-06-08 07:46:25 MarkDuplicates Tracking 21897 as yet unmatched pairs. 258 records in RAM.
INFO 2026-06-08 07:46:29 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 3s. Last read position: chr1:201,712,816
INFO 2026-06-08 07:46:29 MarkDuplicates Tracking 23642 as yet unmatched pairs. 172 records in RAM.
INFO 2026-06-08 07:46:32 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 3s. Last read position: chr1:212,619,513
INFO 2026-06-08 07:46:32 MarkDuplicates Tracking 25381 as yet unmatched pairs. 10 records in RAM.
INFO 2026-06-08 07:46:35 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 2s. Last read position: chr1:234,608,764
INFO 2026-06-08 07:46:35 MarkDuplicates Tracking 27964 as yet unmatched pairs. 181 records in RAM.
INFO 2026-06-08 07:46:38 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 3s. Last read position: chr2:28,776,853
INFO 2026-06-08 07:46:38 MarkDuplicates Tracking 30240 as yet unmatched pairs. 30186 records in RAM.
INFO 2026-06-08 07:46:42 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 4s. Last read position: chr2:32,916,264
INFO 2026-06-08 07:46:42 MarkDuplicates Tracking 67542 as yet unmatched pairs. 28470 records in RAM.
INFO 2026-06-08 07:46:45 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 2s. Last read position: chr2:33,398,363
INFO 2026-06-08 07:46:45 MarkDuplicates Tracking 272952 as yet unmatched pairs. 16810 records in RAM.
INFO 2026-06-08 07:46:47 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 1s. Last read position: chr2:61,348,174
INFO 2026-06-08 07:46:47 MarkDuplicates Tracking 270644 as yet unmatched pairs. 14500 records in RAM.
INFO 2026-06-08 07:46:49 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 2s. Last read position: chr2:74,880,502
INFO 2026-06-08 07:46:49 MarkDuplicates Tracking 268715 as yet unmatched pairs. 12571 records in RAM.
INFO 2026-06-08 07:46:52 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 2s. Last read position: chr2:110,535,666
INFO 2026-06-08 07:46:52 MarkDuplicates Tracking 267034 as yet unmatched pairs. 10886 records in RAM.
INFO 2026-06-08 07:46:54 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 2s. Last read position: chr2:188,999,476
INFO 2026-06-08 07:46:54 MarkDuplicates Tracking 265173 as yet unmatched pairs. 9019 records in RAM.
INFO 2026-06-08 07:46:57 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 2s. Last read position: chr2:205,716,245
INFO 2026-06-08 07:46:57 MarkDuplicates Tracking 263229 as yet unmatched pairs. 7073 records in RAM.
INFO 2026-06-08 07:46:59 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 1s. Last read position: chr2:215,406,351
INFO 2026-06-08 07:46:59 MarkDuplicates Tracking 261779 as yet unmatched pairs. 5623 records in RAM.
INFO 2026-06-08 07:47:01 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 2s. Last read position: chr2:217,897,942
INFO 2026-06-08 07:47:01 MarkDuplicates Tracking 259994 as yet unmatched pairs. 3838 records in RAM.
INFO 2026-06-08 07:47:04 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 2s. Last read position: chr2:238,194,735
INFO 2026-06-08 07:47:04 MarkDuplicates Tracking 256942 as yet unmatched pairs. 781 records in RAM.
INFO 2026-06-08 07:47:06 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 2s. Last read position: chr3:33,114,416
INFO 2026-06-08 07:47:06 MarkDuplicates Tracking 254940 as yet unmatched pairs. 13538 records in RAM.
INFO 2026-06-08 07:47:09 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 2s. Last read position: chr3:48,469,123
INFO 2026-06-08 07:47:09 MarkDuplicates Tracking 252800 as yet unmatched pairs. 11397 records in RAM.
INFO 2026-06-08 07:47:12 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 2s. Last read position: chr3:51,386,237
INFO 2026-06-08 07:47:12 MarkDuplicates Tracking 250259 as yet unmatched pairs. 8856 records in RAM.
INFO 2026-06-08 07:47:14 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 2s. Last read position: chr3:72,378,616
INFO 2026-06-08 07:47:14 MarkDuplicates Tracking 248137 as yet unmatched pairs. 6733 records in RAM.
INFO 2026-06-08 07:47:16 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 2s. Last read position: chr3:123,700,553
INFO 2026-06-08 07:47:16 MarkDuplicates Tracking 247719 as yet unmatched pairs. 6313 records in RAM.
INFO 2026-06-08 07:47:19 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 3s. Last read position: chr3:143,985,631
INFO 2026-06-08 07:47:19 MarkDuplicates Tracking 244063 as yet unmatched pairs. 2656 records in RAM.
INFO 2026-06-08 07:47:23 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 3s. Last read position: chr3:194,441,399
INFO 2026-06-08 07:47:23 MarkDuplicates Tracking 241889 as yet unmatched pairs. 480 records in RAM.
INFO 2026-06-08 07:47:26 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 3s. Last read position: chr4:7,043,629
INFO 2026-06-08 07:47:26 MarkDuplicates Tracking 239721 as yet unmatched pairs. 5068 records in RAM.
INFO 2026-06-08 07:47:29 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 2s. Last read position: chr4:67,681,562
INFO 2026-06-08 07:47:29 MarkDuplicates Tracking 237290 as yet unmatched pairs. 2635 records in RAM.
INFO 2026-06-08 07:47:31 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 1s. Last read position: chr4:139,698,176
INFO 2026-06-08 07:47:31 MarkDuplicates Tracking 235409 as yet unmatched pairs. 753 records in RAM.
INFO 2026-06-08 07:47:32 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 1s. Last read position: chr5:17,275,360
INFO 2026-06-08 07:47:32 MarkDuplicates Tracking 232986 as yet unmatched pairs. 11035 records in RAM.
INFO 2026-06-08 07:47:36 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 3s. Last read position: chr5:83,512,102
INFO 2026-06-08 07:47:36 MarkDuplicates Tracking 231877 as yet unmatched pairs. 9925 records in RAM.
INFO 2026-06-08 07:47:38 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 2s. Last read position: chr5:134,826,947
INFO 2026-06-08 07:47:38 MarkDuplicates Tracking 229292 as yet unmatched pairs. 7339 records in RAM.
INFO 2026-06-08 07:47:40 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 1s. Last read position: chr5:141,491,380
INFO 2026-06-08 07:47:40 MarkDuplicates Tracking 227862 as yet unmatched pairs. 5898 records in RAM.
INFO 2026-06-08 07:47:42 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 1s. Last read position: chr5:151,042,658
INFO 2026-06-08 07:47:42 MarkDuplicates Tracking 225803 as yet unmatched pairs. 3839 records in RAM.
INFO 2026-06-08 07:47:44 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 2s. Last read position: chr5:177,483,681
INFO 2026-06-08 07:47:44 MarkDuplicates Tracking 224368 as yet unmatched pairs. 2400 records in RAM.
INFO 2026-06-08 07:47:47 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 2s. Last read position: chr6:7,231,811
INFO 2026-06-08 07:47:47 MarkDuplicates Tracking 221574 as yet unmatched pairs. 14842 records in RAM.
INFO 2026-06-08 07:47:50 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 2s. Last read position: chr6:31,540,358
INFO 2026-06-08 07:47:50 MarkDuplicates Tracking 219957 as yet unmatched pairs. 13223 records in RAM.
INFO 2026-06-08 07:47:52 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 2s. Last read position: chr6:32,079,110
INFO 2026-06-08 07:47:52 MarkDuplicates Tracking 218004 as yet unmatched pairs. 11268 records in RAM.
INFO 2026-06-08 07:47:55 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 2s. Last read position: chr6:35,245,230
INFO 2026-06-08 07:47:55 MarkDuplicates Tracking 215557 as yet unmatched pairs. 8820 records in RAM.
INFO 2026-06-08 07:47:57 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 2s. Last read position: chr6:56,482,833
INFO 2026-06-08 07:47:57 MarkDuplicates Tracking 213363 as yet unmatched pairs. 6624 records in RAM.
INFO 2026-06-08 07:48:00 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 2s. Last read position: chr6:113,896,782
INFO 2026-06-08 07:48:00 MarkDuplicates Tracking 211250 as yet unmatched pairs. 4506 records in RAM.
INFO 2026-06-08 07:48:03 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 2s. Last read position: chr6:151,944,410
INFO 2026-06-08 07:48:03 MarkDuplicates Tracking 209162 as yet unmatched pairs. 2418 records in RAM.
INFO 2026-06-08 07:48:07 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 4s. Last read position: chr7:1,444,998
INFO 2026-06-08 07:48:07 MarkDuplicates Tracking 206772 as yet unmatched pairs. 13093 records in RAM.
INFO 2026-06-08 07:48:11 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 3s. Last read position: chr7:44,756,925
INFO 2026-06-08 07:48:11 MarkDuplicates Tracking 204284 as yet unmatched pairs. 10603 records in RAM.
INFO 2026-06-08 07:48:14 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 2s. Last read position: chr7:76,304,058
INFO 2026-06-08 07:48:14 MarkDuplicates Tracking 202841 as yet unmatched pairs. 9159 records in RAM.
INFO 2026-06-08 07:48:16 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 2s. Last read position: chr7:99,908,761
INFO 2026-06-08 07:48:16 MarkDuplicates Tracking 200567 as yet unmatched pairs. 6883 records in RAM.
INFO 2026-06-08 07:48:18 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 1s. Last read position: chr7:102,567,010
INFO 2026-06-08 07:48:18 MarkDuplicates Tracking 199171 as yet unmatched pairs. 5486 records in RAM.
INFO 2026-06-08 07:48:20 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 2s. Last read position: chr7:128,854,672
INFO 2026-06-08 07:48:20 MarkDuplicates Tracking 197219 as yet unmatched pairs. 3532 records in RAM.
INFO 2026-06-08 07:48:23 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 2s. Last read position: chr7:149,266,515
INFO 2026-06-08 07:48:23 MarkDuplicates Tracking 195515 as yet unmatched pairs. 1825 records in RAM.
INFO 2026-06-08 07:48:26 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 3s. Last read position: chr8:18,872,057
INFO 2026-06-08 07:48:26 MarkDuplicates Tracking 193078 as yet unmatched pairs. 11751 records in RAM.
INFO 2026-06-08 07:48:29 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 3s. Last read position: chr8:38,331,501
INFO 2026-06-08 07:48:29 MarkDuplicates Tracking 190837 as yet unmatched pairs. 9509 records in RAM.
INFO 2026-06-08 07:48:32 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 2s. Last read position: chr8:69,658,530
INFO 2026-06-08 07:48:32 MarkDuplicates Tracking 188827 as yet unmatched pairs. 7496 records in RAM.
INFO 2026-06-08 07:48:35 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 2s. Last read position: chr8:133,238,788
INFO 2026-06-08 07:48:35 MarkDuplicates Tracking 187182 as yet unmatched pairs. 5850 records in RAM.
INFO 2026-06-08 07:48:38 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 3s. Last read position: chr8:143,922,940
INFO 2026-06-08 07:48:38 MarkDuplicates Tracking 184248 as yet unmatched pairs. 2910 records in RAM.
INFO 2026-06-08 07:48:41 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 2s. Last read position: chr9:4,719,195
INFO 2026-06-08 07:48:41 MarkDuplicates Tracking 181083 as yet unmatched pairs. 13133 records in RAM.
INFO 2026-06-08 07:48:43 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 2s. Last read position: chr9:76,399,489
INFO 2026-06-08 07:48:43 MarkDuplicates Tracking 179037 as yet unmatched pairs. 11087 records in RAM.
INFO 2026-06-08 07:48:46 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 2s. Last read position: chr9:111,484,061
INFO 2026-06-08 07:48:46 MarkDuplicates Tracking 176688 as yet unmatched pairs. 8738 records in RAM.
INFO 2026-06-08 07:48:48 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 1s. Last read position: chr9:122,984,569
INFO 2026-06-08 07:48:48 MarkDuplicates Tracking 174277 as yet unmatched pairs. 6327 records in RAM.
INFO 2026-06-08 07:48:50 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 1s. Last read position: chr9:129,831,034
INFO 2026-06-08 07:48:50 MarkDuplicates Tracking 171945 as yet unmatched pairs. 3993 records in RAM.
INFO 2026-06-08 07:48:52 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 2s. Last read position: chr9:136,451,254
INFO 2026-06-08 07:48:52 MarkDuplicates Tracking 169698 as yet unmatched pairs. 1745 records in RAM.
INFO 2026-06-08 07:48:53 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 1s. Last read position: chr10:17,229,421
INFO 2026-06-08 07:48:53 MarkDuplicates Tracking 168543 as yet unmatched pairs. 9891 records in RAM.
INFO 2026-06-08 07:48:56 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 2s. Last read position: chr10:45,757,029
INFO 2026-06-08 07:48:56 MarkDuplicates Tracking 165295 as yet unmatched pairs. 6642 records in RAM.
INFO 2026-06-08 07:48:58 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 1s. Last read position: chr10:73,794,538
INFO 2026-06-08 07:48:58 MarkDuplicates Tracking 163379 as yet unmatched pairs. 4725 records in RAM.
INFO 2026-06-08 07:49:00 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 1s. Last read position: chr10:96,158,406
INFO 2026-06-08 07:49:00 MarkDuplicates Tracking 161716 as yet unmatched pairs. 3061 records in RAM.
INFO 2026-06-08 07:49:02 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 1s. Last read position: chr10:119,042,706
INFO 2026-06-08 07:49:02 MarkDuplicates Tracking 159665 as yet unmatched pairs. 1005 records in RAM.
INFO 2026-06-08 07:49:04 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 2s. Last read position: chr11:2,133,101
INFO 2026-06-08 07:49:04 MarkDuplicates Tracking 160627 as yet unmatched pairs. 22569 records in RAM.
INFO 2026-06-08 07:49:08 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 3s. Last read position: chr11:6,640,539
INFO 2026-06-08 07:49:08 MarkDuplicates Tracking 155152 as yet unmatched pairs. 17094 records in RAM.
INFO 2026-06-08 07:49:11 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 2s. Last read position: chr11:19,934,066
INFO 2026-06-08 07:49:11 MarkDuplicates Tracking 155233 as yet unmatched pairs. 17174 records in RAM.
INFO 2026-06-08 07:49:13 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 2s. Last read position: chr11:57,310,064
INFO 2026-06-08 07:49:13 MarkDuplicates Tracking 151172 as yet unmatched pairs. 13113 records in RAM.
INFO 2026-06-08 07:49:16 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 2s. Last read position: chr11:62,529,723
INFO 2026-06-08 07:49:16 MarkDuplicates Tracking 149628 as yet unmatched pairs. 11567 records in RAM.
INFO 2026-06-08 07:49:19 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 2s. Last read position: chr11:65,532,768
INFO 2026-06-08 07:49:19 MarkDuplicates Tracking 147239 as yet unmatched pairs. 9178 records in RAM.
INFO 2026-06-08 07:49:21 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 2s. Last read position: chr11:67,398,579
INFO 2026-06-08 07:49:21 MarkDuplicates Tracking 144698 as yet unmatched pairs. 6635 records in RAM.
INFO 2026-06-08 07:49:24 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 2s. Last read position: chr11:74,085,756
INFO 2026-06-08 07:49:24 MarkDuplicates Tracking 142208 as yet unmatched pairs. 4145 records in RAM.
INFO 2026-06-08 07:49:28 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 3s. Last read position: chr11:117,315,603
INFO 2026-06-08 07:49:28 MarkDuplicates Tracking 140245 as yet unmatched pairs. 2181 records in RAM.
INFO 2026-06-08 07:49:31 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 3s. Last read position: chr12:753,536
INFO 2026-06-08 07:49:31 MarkDuplicates Tracking 138013 as yet unmatched pairs. 16441 records in RAM.
INFO 2026-06-08 07:49:33 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 2s. Last read position: chr12:8,655,415
INFO 2026-06-08 07:49:33 MarkDuplicates Tracking 135759 as yet unmatched pairs. 14186 records in RAM.
INFO 2026-06-08 07:49:35 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 2s. Last read position: chr12:48,837,989
INFO 2026-06-08 07:49:35 MarkDuplicates Tracking 133997 as yet unmatched pairs. 12423 records in RAM.
INFO 2026-06-08 07:49:38 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 2s. Last read position: chr12:53,465,942
INFO 2026-06-08 07:49:38 MarkDuplicates Tracking 132665 as yet unmatched pairs. 11091 records in RAM.
INFO 2026-06-08 07:49:41 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 2s. Last read position: chr12:57,092,913
INFO 2026-06-08 07:49:41 MarkDuplicates Tracking 131120 as yet unmatched pairs. 9546 records in RAM.
INFO 2026-06-08 07:49:43 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 2s. Last read position: chr12:57,516,870
INFO 2026-06-08 07:49:43 MarkDuplicates Tracking 128753 as yet unmatched pairs. 7179 records in RAM.
INFO 2026-06-08 07:49:45 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 1s. Last read position: chr12:104,265,766
INFO 2026-06-08 07:49:45 MarkDuplicates Tracking 126311 as yet unmatched pairs. 4734 records in RAM.
INFO 2026-06-08 07:49:47 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 2s. Last read position: chr12:121,810,602
INFO 2026-06-08 07:49:47 MarkDuplicates Tracking 124111 as yet unmatched pairs. 2532 records in RAM.
INFO 2026-06-08 07:49:50 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 2s. Last read position: chr12:132,711,025
INFO 2026-06-08 07:49:50 MarkDuplicates Tracking 122006 as yet unmatched pairs. 427 records in RAM.
INFO 2026-06-08 07:49:52 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 1s. Last read position: chr13:110,201,491
INFO 2026-06-08 07:49:52 MarkDuplicates Tracking 120270 as yet unmatched pairs. 1437 records in RAM.
INFO 2026-06-08 07:49:55 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 3s. Last read position: chr14:23,321,784
INFO 2026-06-08 07:49:55 MarkDuplicates Tracking 117823 as yet unmatched pairs. 8317 records in RAM.
INFO 2026-06-08 07:49:58 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 3s. Last read position: chr14:64,427,315
INFO 2026-06-08 07:49:58 MarkDuplicates Tracking 115731 as yet unmatched pairs. 6225 records in RAM.
INFO 2026-06-08 07:50:00 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 2s. Last read position: chr14:74,949,382
INFO 2026-06-08 07:50:00 MarkDuplicates Tracking 113595 as yet unmatched pairs. 4088 records in RAM.
INFO 2026-06-08 07:50:02 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 1s. Last read position: chr14:103,657,608
INFO 2026-06-08 07:50:02 MarkDuplicates Tracking 111824 as yet unmatched pairs. 2309 records in RAM.
INFO 2026-06-08 07:50:04 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 1s. Last read position: chr15:25,781,081
INFO 2026-06-08 07:50:04 MarkDuplicates Tracking 109460 as yet unmatched pairs. 8295 records in RAM.
INFO 2026-06-08 07:50:06 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 1s. Last read position: chr15:43,523,163
INFO 2026-06-08 07:50:06 MarkDuplicates Tracking 107886 as yet unmatched pairs. 6721 records in RAM.
INFO 2026-06-08 07:50:08 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 1s. Last read position: chr15:64,156,841
INFO 2026-06-08 07:50:08 MarkDuplicates Tracking 106239 as yet unmatched pairs. 5074 records in RAM.
INFO 2026-06-08 07:50:10 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 2s. Last read position: chr15:75,206,589
INFO 2026-06-08 07:50:10 MarkDuplicates Tracking 104088 as yet unmatched pairs. 2923 records in RAM.
INFO 2026-06-08 07:50:13 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 2s. Last read position: chr15:89,632,861
INFO 2026-06-08 07:50:13 MarkDuplicates Tracking 101891 as yet unmatched pairs. 726 records in RAM.
INFO 2026-06-08 07:50:16 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 3s. Last read position: chr16:1,764,176
INFO 2026-06-08 07:50:16 MarkDuplicates Tracking 100009 as yet unmatched pairs. 15156 records in RAM.
INFO 2026-06-08 07:50:19 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 2s. Last read position: chr16:2,930,609
INFO 2026-06-08 07:50:19 MarkDuplicates Tracking 97166 as yet unmatched pairs. 12313 records in RAM.
INFO 2026-06-08 07:50:22 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 2s. Last read position: chr16:15,129,977
INFO 2026-06-08 07:50:22 MarkDuplicates Tracking 95132 as yet unmatched pairs. 10277 records in RAM.
INFO 2026-06-08 07:50:24 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 2s. Last read position: chr16:18,390,686
INFO 2026-06-08 07:50:24 MarkDuplicates Tracking 94099 as yet unmatched pairs. 9243 records in RAM.
INFO 2026-06-08 07:50:27 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 2s. Last read position: chr16:27,363,228
INFO 2026-06-08 07:50:27 MarkDuplicates Tracking 93264 as yet unmatched pairs. 8405 records in RAM.
INFO 2026-06-08 07:50:29 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 2s. Last read position: chr16:30,224,649
INFO 2026-06-08 07:50:29 MarkDuplicates Tracking 91638 as yet unmatched pairs. 6778 records in RAM.
INFO 2026-06-08 07:50:32 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 2s. Last read position: chr16:55,479,555
INFO 2026-06-08 07:50:32 MarkDuplicates Tracking 90524 as yet unmatched pairs. 5663 records in RAM.
INFO 2026-06-08 07:50:34 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 2s. Last read position: chr16:70,146,132
INFO 2026-06-08 07:50:34 MarkDuplicates Tracking 87890 as yet unmatched pairs. 3027 records in RAM.
INFO 2026-06-08 07:50:37 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 2s. Last read position: chr16:88,738,059
INFO 2026-06-08 07:50:37 MarkDuplicates Tracking 85605 as yet unmatched pairs. 741 records in RAM.
INFO 2026-06-08 07:50:39 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 1s. Last read position: chr17:4,891,638
INFO 2026-06-08 07:50:39 MarkDuplicates Tracking 83503 as yet unmatched pairs. 20540 records in RAM.
INFO 2026-06-08 07:50:42 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 3s. Last read position: chr17:8,444,339
INFO 2026-06-08 07:50:42 MarkDuplicates Tracking 81359 as yet unmatched pairs. 18396 records in RAM.
INFO 2026-06-08 07:50:45 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 3s. Last read position: chr17:28,689,364
INFO 2026-06-08 07:50:45 MarkDuplicates Tracking 79055 as yet unmatched pairs. 16092 records in RAM.
INFO 2026-06-08 07:50:47 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 2s. Last read position: chr17:38,890,462
INFO 2026-06-08 07:50:47 MarkDuplicates Tracking 77197 as yet unmatched pairs. 14234 records in RAM.
INFO 2026-06-08 07:50:49 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 1s. Last read position: chr17:44,212,826
INFO 2026-06-08 07:50:49 MarkDuplicates Tracking 75306 as yet unmatched pairs. 12343 records in RAM.
INFO 2026-06-08 07:50:51 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 1s. Last read position: chr17:50,187,528
INFO 2026-06-08 07:50:51 MarkDuplicates Tracking 76907 as yet unmatched pairs. 13944 records in RAM.
INFO 2026-06-08 07:50:54 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 2s. Last read position: chr17:50,192,640
INFO 2026-06-08 07:50:54 MarkDuplicates Tracking 73042 as yet unmatched pairs. 10078 records in RAM.
INFO 2026-06-08 07:50:56 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 2s. Last read position: chr17:50,196,646
INFO 2026-06-08 07:50:56 MarkDuplicates Tracking 73593 as yet unmatched pairs. 10629 records in RAM.
INFO 2026-06-08 07:50:58 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr17:63,496,864
INFO 2026-06-08 07:50:58 MarkDuplicates Tracking 66758 as yet unmatched pairs. 3794 records in RAM.
INFO 2026-06-08 07:51:00 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 2s. Last read position: chr17:76,685,129
INFO 2026-06-08 07:51:00 MarkDuplicates Tracking 64744 as yet unmatched pairs. 1780 records in RAM.
INFO 2026-06-08 07:51:02 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 2s. Last read position: chr18:8,796,368
INFO 2026-06-08 07:51:02 MarkDuplicates Tracking 62597 as yet unmatched pairs. 2446 records in RAM.
INFO 2026-06-08 07:51:04 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 1s. Last read position: chr18:76,441,738
INFO 2026-06-08 07:51:04 MarkDuplicates Tracking 60560 as yet unmatched pairs. 407 records in RAM.
INFO 2026-06-08 07:51:06 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 2s. Last read position: chr19:2,726,589
INFO 2026-06-08 07:51:06 MarkDuplicates Tracking 57153 as yet unmatched pairs. 22207 records in RAM.
INFO 2026-06-08 07:51:08 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 1s. Last read position: chr19:7,629,825
INFO 2026-06-08 07:51:08 MarkDuplicates Tracking 55087 as yet unmatched pairs. 20141 records in RAM.
INFO 2026-06-08 07:51:10 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 2s. Last read position: chr19:12,792,683
INFO 2026-06-08 07:51:10 MarkDuplicates Tracking 53466 as yet unmatched pairs. 18520 records in RAM.
INFO 2026-06-08 07:51:12 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 1s. Last read position: chr19:16,086,480
INFO 2026-06-08 07:51:12 MarkDuplicates Tracking 50664 as yet unmatched pairs. 15718 records in RAM.
INFO 2026-06-08 07:51:14 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 1s. Last read position: chr19:33,205,675
INFO 2026-06-08 07:51:14 MarkDuplicates Tracking 47910 as yet unmatched pairs. 12963 records in RAM.
INFO 2026-06-08 07:51:16 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 2s. Last read position: chr19:39,485,699
INFO 2026-06-08 07:51:16 MarkDuplicates Tracking 45282 as yet unmatched pairs. 10334 records in RAM.
INFO 2026-06-08 07:51:20 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 3s. Last read position: chr19:42,274,560
INFO 2026-06-08 07:51:20 MarkDuplicates Tracking 42881 as yet unmatched pairs. 7933 records in RAM.
INFO 2026-06-08 07:51:23 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 3s. Last read position: chr19:47,271,455
INFO 2026-06-08 07:51:23 MarkDuplicates Tracking 40714 as yet unmatched pairs. 5763 records in RAM.
INFO 2026-06-08 07:51:26 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 2s. Last read position: chr19:49,862,257
INFO 2026-06-08 07:51:26 MarkDuplicates Tracking 37987 as yet unmatched pairs. 3035 records in RAM.
INFO 2026-06-08 07:51:28 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 2s. Last read position: chr19:55,661,057
INFO 2026-06-08 07:51:28 MarkDuplicates Tracking 35741 as yet unmatched pairs. 789 records in RAM.
INFO 2026-06-08 07:51:31 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 2s. Last read position: chr20:17,659,158
INFO 2026-06-08 07:51:31 MarkDuplicates Tracking 33571 as yet unmatched pairs. 5856 records in RAM.
INFO 2026-06-08 07:51:34 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 2s. Last read position: chr20:41,098,244
INFO 2026-06-08 07:51:34 MarkDuplicates Tracking 31609 as yet unmatched pairs. 3893 records in RAM.
INFO 2026-06-08 07:51:37 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 2s. Last read position: chr20:58,895,650
INFO 2026-06-08 07:51:37 MarkDuplicates Tracking 29105 as yet unmatched pairs. 1389 records in RAM.
INFO 2026-06-08 07:51:40 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 2s. Last read position: chr21:8,217,348
INFO 2026-06-08 07:51:40 MarkDuplicates Tracking 27080 as yet unmatched pairs. 7165 records in RAM.
INFO 2026-06-08 07:51:42 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 2s. Last read position: chr21:25,976,014
INFO 2026-06-08 07:51:42 MarkDuplicates Tracking 25511 as yet unmatched pairs. 5595 records in RAM.
INFO 2026-06-08 07:51:45 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 3s. Last read position: chr21:45,866,644
INFO 2026-06-08 07:51:45 MarkDuplicates Tracking 23185 as yet unmatched pairs. 3269 records in RAM.
INFO 2026-06-08 07:51:48 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 2s. Last read position: chr21:46,122,147
INFO 2026-06-08 07:51:48 MarkDuplicates Tracking 22672 as yet unmatched pairs. 2756 records in RAM.
INFO 2026-06-08 07:51:51 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 2s. Last read position: chr22:30,344,960
INFO 2026-06-08 07:51:51 MarkDuplicates Tracking 18629 as yet unmatched pairs. 8865 records in RAM.
INFO 2026-06-08 07:51:54 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 2s. Last read position: chr22:37,877,991
INFO 2026-06-08 07:51:54 MarkDuplicates Tracking 16241 as yet unmatched pairs. 6477 records in RAM.
INFO 2026-06-08 07:51:57 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 2s. Last read position: chr22:41,273,592
INFO 2026-06-08 07:51:57 MarkDuplicates Tracking 13961 as yet unmatched pairs. 4197 records in RAM.
INFO 2026-06-08 07:51:59 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 2s. Last read position: chr22:50,244,082
INFO 2026-06-08 07:51:59 MarkDuplicates Tracking 12125 as yet unmatched pairs. 2361 records in RAM.
INFO 2026-06-08 07:52:02 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 2s. Last read position: chrX:12,976,837
INFO 2026-06-08 07:52:02 MarkDuplicates Tracking 9213 as yet unmatched pairs. 5932 records in RAM.
INFO 2026-06-08 07:52:04 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 2s. Last read position: chrX:53,250,495
INFO 2026-06-08 07:52:04 MarkDuplicates Tracking 7570 as yet unmatched pairs. 4286 records in RAM.
INFO 2026-06-08 07:52:08 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 3s. Last read position: chrX:107,714,476
INFO 2026-06-08 07:52:08 MarkDuplicates Tracking 5901 as yet unmatched pairs. 2617 records in RAM.
INFO 2026-06-08 07:52:11 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 2s. Last read position: chrX:154,364,670
INFO 2026-06-08 07:52:11 MarkDuplicates Tracking 4086 as yet unmatched pairs. 802 records in RAM.
INFO 2026-06-08 07:52:13 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 2s. Last read position: GL000220.1:160,636
INFO 2026-06-08 07:52:13 MarkDuplicates Tracking 2605 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 07:52:15 MarkDuplicates Read 147862439 records. 0 pairs never matched.
INFO 2026-06-08 07:52:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 41093641280; totalMemory: 59324235776; maxMemory: 63585648640
INFO 2026-06-08 07:52:24 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 07:52:33 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 07:53:13 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 07:53:29 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 07:53:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300860704; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-08 07:53:37 MarkDuplicates Marking 122307700 records as duplicates.
INFO 2026-06-08 07:53:37 MarkDuplicates Found 2287006 optical duplicate clusters.
INFO 2026-06-08 07:53:37 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 07:54:07 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:30s. Time for last 10,000,000: 30s. Last read position: chr1:156,671,583
INFO 2026-06-08 07:54:37 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:59s. Time for last 10,000,000: 29s. Last read position: chr2:74,880,502
INFO 2026-06-08 07:55:08 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:30s. Time for last 10,000,000: 30s. Last read position: chr3:72,378,616
INFO 2026-06-08 07:55:38 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:02:00s. Time for last 10,000,000: 29s. Last read position: chr5:141,491,380
INFO 2026-06-08 07:56:07 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:02:30s. Time for last 10,000,000: 29s. Last read position: chr7:1,444,998
INFO 2026-06-08 07:56:40 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:03:02s. Time for last 10,000,000: 32s. Last read position: chr8:133,238,788
INFO 2026-06-08 07:57:09 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:03:31s. Time for last 10,000,000: 28s. Last read position: chr10:73,794,538
INFO 2026-06-08 07:57:37 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:03:59s. Time for last 10,000,000: 28s. Last read position: chr11:74,085,756
INFO 2026-06-08 07:58:04 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:04:26s. Time for last 10,000,000: 27s. Last read position: chr12:132,711,025
INFO 2026-06-08 07:58:32 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:04:54s. Time for last 10,000,000: 27s. Last read position: chr15:89,632,861
INFO 2026-06-08 07:59:01 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:05:23s. Time for last 10,000,000: 29s. Last read position: chr17:4,891,638
INFO 2026-06-08 07:59:29 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:05:52s. Time for last 10,000,000: 28s. Last read position: chr18:8,796,368
INFO 2026-06-08 07:59:56 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:06:18s. Time for last 10,000,000: 26s. Last read position: chr19:49,862,257
INFO 2026-06-08 08:00:23 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:06:46s. Time for last 10,000,000: 27s. Last read position: chr22:37,877,991
INFO 2026-06-08 08:00:50 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:00:50 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:00:50 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:00:50 MarkDuplicates Before output close freeMemory: 37314121280; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-08 08:00:50 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:00:51 MarkDuplicates After output close freeMemory: 204024232; totalMemory: 234881024; maxMemory: 63585648640
[Mon Jun 08 08:00:51 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 15.07 minutes.
Runtime.totalMemory()=234881024
ls: *cram: No such file or directory
ls: *.crai: No such file or directory