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 BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.md.bam --METRICS_FILE BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
20:22:09.392 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
[Thu May 28 20:22:09 GMT 2026] MarkDuplicates --INPUT BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.md.bam --METRICS_FILE BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_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
[Thu May 28 20:22:09 GMT 2026] Executing as ?@nf-98685047f4a0aba86afdcd8c1512ecb8-5d01d-h9vrv on Linux 6.12.83 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 2026-05-28 20:22:09 MarkDuplicates Start of doWork freeMemory: 105828880; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-05-28 20:22:09 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-05-28 20:22:09 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-05-28 20:22:15 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 4s. Last read position: chr1:11,099,736
INFO 2026-05-28 20:22:15 MarkDuplicates Tracking 1764 as yet unmatched pairs. 5 records in RAM.
INFO 2026-05-28 20:22:18 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 3s. Last read position: chr1:24,654,932
INFO 2026-05-28 20:22:18 MarkDuplicates Tracking 3558 as yet unmatched pairs. 5 records in RAM.
INFO 2026-05-28 20:22:21 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 2s. Last read position: chr1:35,841,527
INFO 2026-05-28 20:22:21 MarkDuplicates Tracking 5674 as yet unmatched pairs. 5 records in RAM.
INFO 2026-05-28 20:22:25 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 3s. Last read position: chr1:58,782,296
INFO 2026-05-28 20:22:25 MarkDuplicates Tracking 7377 as yet unmatched pairs. 55 records in RAM.
INFO 2026-05-28 20:22:27 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr1:119,948,519
INFO 2026-05-28 20:22:27 MarkDuplicates Tracking 9062 as yet unmatched pairs. 7 records in RAM.
INFO 2026-05-28 20:22:29 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: chr1:150,557,933
INFO 2026-05-28 20:22:29 MarkDuplicates Tracking 9766 as yet unmatched pairs. 8 records in RAM.
INFO 2026-05-28 20:22:31 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 2s. Last read position: chr1:155,751,817
INFO 2026-05-28 20:22:31 MarkDuplicates Tracking 11144 as yet unmatched pairs. 6 records in RAM.
INFO 2026-05-28 20:22:34 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 2s. Last read position: chr1:185,120,109
INFO 2026-05-28 20:22:34 MarkDuplicates Tracking 12611 as yet unmatched pairs. 6 records in RAM.
INFO 2026-05-28 20:22:37 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 3s. Last read position: chr1:226,736,010
INFO 2026-05-28 20:22:37 MarkDuplicates Tracking 14532 as yet unmatched pairs. 2 records in RAM.
INFO 2026-05-28 20:22:40 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 2s. Last read position: chr2:24,081,008
INFO 2026-05-28 20:22:40 MarkDuplicates Tracking 16481 as yet unmatched pairs. 16283 records in RAM.
INFO 2026-05-28 20:22:42 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,406
INFO 2026-05-28 20:22:42 MarkDuplicates Tracking 166178 as yet unmatched pairs. 11913 records in RAM.
INFO 2026-05-28 20:22:45 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 2s. Last read position: chr2:72,515,092
INFO 2026-05-28 20:22:45 MarkDuplicates Tracking 179539 as yet unmatched pairs. 9658 records in RAM.
INFO 2026-05-28 20:22:47 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 2s. Last read position: chr2:108,762,131
INFO 2026-05-28 20:22:47 MarkDuplicates Tracking 177687 as yet unmatched pairs. 7791 records in RAM.
INFO 2026-05-28 20:22:50 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 2s. Last read position: chr2:161,341,138
INFO 2026-05-28 20:22:50 MarkDuplicates Tracking 176750 as yet unmatched pairs. 6839 records in RAM.
INFO 2026-05-28 20:22:53 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chr2:189,005,382
INFO 2026-05-28 20:22:53 MarkDuplicates Tracking 174860 as yet unmatched pairs. 4943 records in RAM.
INFO 2026-05-28 20:22:57 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 3s. Last read position: chr2:215,434,754
INFO 2026-05-28 20:22:57 MarkDuplicates Tracking 172638 as yet unmatched pairs. 2716 records in RAM.
INFO 2026-05-28 20:23:01 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 4s. Last read position: chr2:237,493,429
INFO 2026-05-28 20:23:01 MarkDuplicates Tracking 170773 as yet unmatched pairs. 773 records in RAM.
INFO 2026-05-28 20:23:04 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 2s. Last read position: chr3:37,261,017
INFO 2026-05-28 20:23:04 MarkDuplicates Tracking 168867 as yet unmatched pairs. 7064 records in RAM.
INFO 2026-05-28 20:23:06 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 2s. Last read position: chr3:49,691,422
INFO 2026-05-28 20:23:06 MarkDuplicates Tracking 166833 as yet unmatched pairs. 5029 records in RAM.
INFO 2026-05-28 20:23:09 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 2s. Last read position: chr3:101,664,975
INFO 2026-05-28 20:23:09 MarkDuplicates Tracking 165183 as yet unmatched pairs. 3364 records in RAM.
INFO 2026-05-28 20:23:11 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 1s. Last read position: chr3:150,546,052
INFO 2026-05-28 20:23:11 MarkDuplicates Tracking 163389 as yet unmatched pairs. 1550 records in RAM.
INFO 2026-05-28 20:23:13 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 2s. Last read position: chr3:195,996,661
INFO 2026-05-28 20:23:13 MarkDuplicates Tracking 161904 as yet unmatched pairs. 53 records in RAM.
INFO 2026-05-28 20:23:15 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 2s. Last read position: chr4:41,990,661
INFO 2026-05-28 20:23:15 MarkDuplicates Tracking 160610 as yet unmatched pairs. 2680 records in RAM.
INFO 2026-05-28 20:23:17 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 2s. Last read position: chr4:140,662,030
INFO 2026-05-28 20:23:17 MarkDuplicates Tracking 158854 as yet unmatched pairs. 898 records in RAM.
INFO 2026-05-28 20:23:19 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 2s. Last read position: chr5:14,488,041
INFO 2026-05-28 20:23:19 MarkDuplicates Tracking 157049 as yet unmatched pairs. 5611 records in RAM.
INFO 2026-05-28 20:23:21 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 1s. Last read position: chr5:83,537,602
INFO 2026-05-28 20:23:21 MarkDuplicates Tracking 155744 as yet unmatched pairs. 4294 records in RAM.
INFO 2026-05-28 20:23:24 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 2s. Last read position: chr5:141,215,586
INFO 2026-05-28 20:23:24 MarkDuplicates Tracking 154695 as yet unmatched pairs. 2879 records in RAM.
INFO 2026-05-28 20:23:26 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 2s. Last read position: chr5:170,718,774
INFO 2026-05-28 20:23:26 MarkDuplicates Tracking 153007 as yet unmatched pairs. 1185 records in RAM.
INFO 2026-05-28 20:23:29 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 3s. Last read position: chr6:7,231,444
INFO 2026-05-28 20:23:29 MarkDuplicates Tracking 151712 as yet unmatched pairs. 7200 records in RAM.
INFO 2026-05-28 20:23:32 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 2s. Last read position: chr6:31,816,662
INFO 2026-05-28 20:23:32 MarkDuplicates Tracking 149999 as yet unmatched pairs. 5453 records in RAM.
INFO 2026-05-28 20:23:35 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 3s. Last read position: chr6:36,211,295
INFO 2026-05-28 20:23:35 MarkDuplicates Tracking 148514 as yet unmatched pairs. 3964 records in RAM.
INFO 2026-05-28 20:23:37 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 2s. Last read position: chr6:89,750,349
INFO 2026-05-28 20:23:37 MarkDuplicates Tracking 146959 as yet unmatched pairs. 2402 records in RAM.
INFO 2026-05-28 20:23:40 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 2s. Last read position: chr6:150,936,829
INFO 2026-05-28 20:23:40 MarkDuplicates Tracking 145394 as yet unmatched pairs. 818 records in RAM.
INFO 2026-05-28 20:23:43 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 3s. Last read position: chr7:5,388,222
INFO 2026-05-28 20:23:43 MarkDuplicates Tracking 143799 as yet unmatched pairs. 8169 records in RAM.
INFO 2026-05-28 20:23:47 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 3s. Last read position: chr7:55,019,114
INFO 2026-05-28 20:23:47 MarkDuplicates Tracking 142066 as yet unmatched pairs. 6427 records in RAM.
INFO 2026-05-28 20:23:50 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 3s. Last read position: chr7:79,186,053
INFO 2026-05-28 20:23:50 MarkDuplicates Tracking 140815 as yet unmatched pairs. 5171 records in RAM.
INFO 2026-05-28 20:23:53 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 3s. Last read position: chr7:100,157,903
INFO 2026-05-28 20:23:53 MarkDuplicates Tracking 139321 as yet unmatched pairs. 3671 records in RAM.
INFO 2026-05-28 20:23:56 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 3s. Last read position: chr7:130,666,848
INFO 2026-05-28 20:23:56 MarkDuplicates Tracking 137586 as yet unmatched pairs. 1917 records in RAM.
INFO 2026-05-28 20:23:59 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 2s. Last read position: chr7:151,376,730
INFO 2026-05-28 20:23:59 MarkDuplicates Tracking 136080 as yet unmatched pairs. 406 records in RAM.
INFO 2026-05-28 20:24:01 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 2s. Last read position: chr8:37,698,301
INFO 2026-05-28 20:24:01 MarkDuplicates Tracking 134727 as yet unmatched pairs. 4773 records in RAM.
INFO 2026-05-28 20:24:04 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 2s. Last read position: chr8:97,686,684
INFO 2026-05-28 20:24:04 MarkDuplicates Tracking 132729 as yet unmatched pairs. 2761 records in RAM.
INFO 2026-05-28 20:24:07 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 3s. Last read position: chr8:143,864,767
INFO 2026-05-28 20:24:07 MarkDuplicates Tracking 131391 as yet unmatched pairs. 1396 records in RAM.
INFO 2026-05-28 20:24:10 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 2s. Last read position: chr9:19,378,895
INFO 2026-05-28 20:24:10 MarkDuplicates Tracking 129325 as yet unmatched pairs. 6079 records in RAM.
INFO 2026-05-28 20:24:13 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 3s. Last read position: chr9:96,819,104
INFO 2026-05-28 20:24:13 MarkDuplicates Tracking 127753 as yet unmatched pairs. 4375 records in RAM.
INFO 2026-05-28 20:24:15 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 2s. Last read position: chr9:128,180,469
INFO 2026-05-28 20:24:15 MarkDuplicates Tracking 125740 as yet unmatched pairs. 2354 records in RAM.
INFO 2026-05-28 20:24:18 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 2s. Last read position: chr9:135,938,230
INFO 2026-05-28 20:24:18 MarkDuplicates Tracking 124155 as yet unmatched pairs. 761 records in RAM.
INFO 2026-05-28 20:24:21 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 3s. Last read position: chr10:24,619,805
INFO 2026-05-28 20:24:21 MarkDuplicates Tracking 122542 as yet unmatched pairs. 3728 records in RAM.
INFO 2026-05-28 20:24:23 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 2s. Last read position: chr10:63,473,839
INFO 2026-05-28 20:24:23 MarkDuplicates Tracking 121429 as yet unmatched pairs. 2603 records in RAM.
INFO 2026-05-28 20:24:26 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 3s. Last read position: chr10:98,435,340
INFO 2026-05-28 20:24:26 MarkDuplicates Tracking 120039 as yet unmatched pairs. 1199 records in RAM.
INFO 2026-05-28 20:24:29 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 2s. Last read position: chr11:294,616
INFO 2026-05-28 20:24:29 MarkDuplicates Tracking 118885 as yet unmatched pairs. 9738 records in RAM.
INFO 2026-05-28 20:24:32 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 2s. Last read position: chr11:9,437,918
INFO 2026-05-28 20:24:32 MarkDuplicates Tracking 117280 as yet unmatched pairs. 8128 records in RAM.
INFO 2026-05-28 20:24:34 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 2s. Last read position: chr11:61,329,558
INFO 2026-05-28 20:24:34 MarkDuplicates Tracking 115712 as yet unmatched pairs. 6550 records in RAM.
INFO 2026-05-28 20:24:37 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 2s. Last read position: chr11:65,502,752
INFO 2026-05-28 20:24:37 MarkDuplicates Tracking 113733 as yet unmatched pairs. 4540 records in RAM.
INFO 2026-05-28 20:24:40 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 3s. Last read position: chr11:72,003,420
INFO 2026-05-28 20:24:40 MarkDuplicates Tracking 112526 as yet unmatched pairs. 3331 records in RAM.
INFO 2026-05-28 20:24:42 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 2s. Last read position: chr11:111,723,570
INFO 2026-05-28 20:24:42 MarkDuplicates Tracking 110500 as yet unmatched pairs. 1293 records in RAM.
INFO 2026-05-28 20:24:44 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 2s. Last read position: chr12:3,274,017
INFO 2026-05-28 20:24:44 MarkDuplicates Tracking 108930 as yet unmatched pairs. 8777 records in RAM.
INFO 2026-05-28 20:24:47 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 2s. Last read position: chr12:45,850,803
INFO 2026-05-28 20:24:47 MarkDuplicates Tracking 107494 as yet unmatched pairs. 7334 records in RAM.
INFO 2026-05-28 20:24:49 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 2s. Last read position: chr12:54,282,631
INFO 2026-05-28 20:24:49 MarkDuplicates Tracking 105416 as yet unmatched pairs. 5252 records in RAM.
INFO 2026-05-28 20:24:52 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 3s. Last read position: chr12:65,326,905
INFO 2026-05-28 20:24:52 MarkDuplicates Tracking 103804 as yet unmatched pairs. 3634 records in RAM.
INFO 2026-05-28 20:24:54 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 1s. Last read position: chr12:116,019,848
INFO 2026-05-28 20:24:54 MarkDuplicates Tracking 102138 as yet unmatched pairs. 1955 records in RAM.
INFO 2026-05-28 20:24:56 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 2s. Last read position: chr12:132,640,312
INFO 2026-05-28 20:24:56 MarkDuplicates Tracking 100354 as yet unmatched pairs. 166 records in RAM.
INFO 2026-05-28 20:24:58 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 2s. Last read position: chr13:106,534,843
INFO 2026-05-28 20:24:58 MarkDuplicates Tracking 98680 as yet unmatched pairs. 788 records in RAM.
INFO 2026-05-28 20:25:00 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 1s. Last read position: chr14:28,767,471
INFO 2026-05-28 20:25:00 MarkDuplicates Tracking 96675 as yet unmatched pairs. 3336 records in RAM.
INFO 2026-05-28 20:25:02 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 2s. Last read position: chr14:73,612,845
INFO 2026-05-28 20:25:02 MarkDuplicates Tracking 95577 as yet unmatched pairs. 2228 records in RAM.
INFO 2026-05-28 20:25:04 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 1s. Last read position: chr14:103,700,708
INFO 2026-05-28 20:25:04 MarkDuplicates Tracking 94100 as yet unmatched pairs. 707 records in RAM.
INFO 2026-05-28 20:25:06 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 1s. Last read position: chr15:34,529,974
INFO 2026-05-28 20:25:06 MarkDuplicates Tracking 92831 as yet unmatched pairs. 4304 records in RAM.
INFO 2026-05-28 20:25:08 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 2s. Last read position: chr15:63,770,843
INFO 2026-05-28 20:25:08 MarkDuplicates Tracking 90965 as yet unmatched pairs. 2432 records in RAM.
INFO 2026-05-28 20:25:10 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 1s. Last read position: chr15:84,433,221
INFO 2026-05-28 20:25:10 MarkDuplicates Tracking 89720 as yet unmatched pairs. 1170 records in RAM.
INFO 2026-05-28 20:25:12 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 1s. Last read position: chr16:1,379,273
INFO 2026-05-28 20:25:12 MarkDuplicates Tracking 88100 as yet unmatched pairs. 9143 records in RAM.
INFO 2026-05-28 20:25:15 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 3s. Last read position: chr16:2,767,014
INFO 2026-05-28 20:25:15 MarkDuplicates Tracking 86626 as yet unmatched pairs. 7662 records in RAM.
INFO 2026-05-28 20:25:17 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 2s. Last read position: chr16:15,131,500
INFO 2026-05-28 20:25:17 MarkDuplicates Tracking 84871 as yet unmatched pairs. 5904 records in RAM.
INFO 2026-05-28 20:25:18 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 1s. Last read position: chr16:18,531,100
INFO 2026-05-28 20:25:18 MarkDuplicates Tracking 84234 as yet unmatched pairs. 5265 records in RAM.
INFO 2026-05-28 20:25:20 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 1s. Last read position: chr16:22,527,494
INFO 2026-05-28 20:25:20 MarkDuplicates Tracking 83986 as yet unmatched pairs. 5015 records in RAM.
INFO 2026-05-28 20:25:22 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 1s. Last read position: chr16:29,382,853
INFO 2026-05-28 20:25:22 MarkDuplicates Tracking 83315 as yet unmatched pairs. 4338 records in RAM.
INFO 2026-05-28 20:25:24 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 1s. Last read position: chr16:30,704,208
INFO 2026-05-28 20:25:24 MarkDuplicates Tracking 82699 as yet unmatched pairs. 3722 records in RAM.
INFO 2026-05-28 20:25:26 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 2s. Last read position: chr16:68,191,539
INFO 2026-05-28 20:25:26 MarkDuplicates Tracking 81078 as yet unmatched pairs. 2082 records in RAM.
INFO 2026-05-28 20:25:27 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 1s. Last read position: chr16:88,806,610
INFO 2026-05-28 20:25:27 MarkDuplicates Tracking 79571 as yet unmatched pairs. 558 records in RAM.
INFO 2026-05-28 20:25:30 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 2s. Last read position: chr17:7,311,634
INFO 2026-05-28 20:25:30 MarkDuplicates Tracking 77910 as yet unmatched pairs. 25317 records in RAM.
INFO 2026-05-28 20:25:32 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 2s. Last read position: chr17:18,671,108
INFO 2026-05-28 20:25:32 MarkDuplicates Tracking 76145 as yet unmatched pairs. 23547 records in RAM.
INFO 2026-05-28 20:25:34 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: chr17:39,415,260
INFO 2026-05-28 20:25:34 MarkDuplicates Tracking 74549 as yet unmatched pairs. 21939 records in RAM.
INFO 2026-05-28 20:25:36 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 2s. Last read position: chr17:45,097,209
INFO 2026-05-28 20:25:36 MarkDuplicates Tracking 72471 as yet unmatched pairs. 19857 records in RAM.
INFO 2026-05-28 20:25:38 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 2s. Last read position: chr17:50,186,341
INFO 2026-05-28 20:25:38 MarkDuplicates Tracking 71025 as yet unmatched pairs. 18409 records in RAM.
INFO 2026-05-28 20:25:40 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 1s. Last read position: chr17:50,188,123
INFO 2026-05-28 20:25:40 MarkDuplicates Tracking 69852 as yet unmatched pairs. 17236 records in RAM.
INFO 2026-05-28 20:25:42 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 1s. Last read position: chr17:50,189,526
INFO 2026-05-28 20:25:42 MarkDuplicates Tracking 69396 as yet unmatched pairs. 16780 records in RAM.
INFO 2026-05-28 20:25:45 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 3s. Last read position: chr17:50,191,995
INFO 2026-05-28 20:25:45 MarkDuplicates Tracking 65124 as yet unmatched pairs. 12508 records in RAM.
INFO 2026-05-28 20:25:47 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 1s. Last read position: chr17:50,194,730
INFO 2026-05-28 20:25:47 MarkDuplicates Tracking 63477 as yet unmatched pairs. 10861 records in RAM.
INFO 2026-05-28 20:25:49 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 2s. Last read position: chr17:50,196,517
INFO 2026-05-28 20:25:49 MarkDuplicates Tracking 62154 as yet unmatched pairs. 9538 records in RAM.
INFO 2026-05-28 20:25:51 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 2s. Last read position: chr17:50,199,318
INFO 2026-05-28 20:25:51 MarkDuplicates Tracking 58597 as yet unmatched pairs. 5980 records in RAM.
INFO 2026-05-28 20:25:53 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 1s. Last read position: chr17:63,550,686
INFO 2026-05-28 20:25:53 MarkDuplicates Tracking 56645 as yet unmatched pairs. 4027 records in RAM.
INFO 2026-05-28 20:25:55 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 2s. Last read position: chr17:78,049,372
INFO 2026-05-28 20:25:55 MarkDuplicates Tracking 54641 as yet unmatched pairs. 2017 records in RAM.
INFO 2026-05-28 20:25:58 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 2s. Last read position: chr17:82,273,373
INFO 2026-05-28 20:25:58 MarkDuplicates Tracking 52789 as yet unmatched pairs. 164 records in RAM.
INFO 2026-05-28 20:26:00 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 1s. Last read position: chr18:67,512,995
INFO 2026-05-28 20:26:00 MarkDuplicates Tracking 50425 as yet unmatched pairs. 273 records in RAM.
INFO 2026-05-28 20:26:02 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 2s. Last read position: chr19:4,054,321
INFO 2026-05-28 20:26:02 MarkDuplicates Tracking 48111 as yet unmatched pairs. 13368 records in RAM.
INFO 2026-05-28 20:26:04 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 2s. Last read position: chr19:10,797,097
INFO 2026-05-28 20:26:04 MarkDuplicates Tracking 45780 as yet unmatched pairs. 11034 records in RAM.
INFO 2026-05-28 20:26:06 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 1s. Last read position: chr19:15,432,575
INFO 2026-05-28 20:26:06 MarkDuplicates Tracking 44258 as yet unmatched pairs. 9507 records in RAM.
INFO 2026-05-28 20:26:08 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 2s. Last read position: chr19:35,545,891
INFO 2026-05-28 20:26:08 MarkDuplicates Tracking 41898 as yet unmatched pairs. 7115 records in RAM.
INFO 2026-05-28 20:26:11 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 2s. Last read position: chr19:42,117,290
INFO 2026-05-28 20:26:11 MarkDuplicates Tracking 40611 as yet unmatched pairs. 5823 records in RAM.
INFO 2026-05-28 20:26:12 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 1s. Last read position: chr19:46,693,882
INFO 2026-05-28 20:26:12 MarkDuplicates Tracking 38616 as yet unmatched pairs. 3785 records in RAM.
INFO 2026-05-28 20:26:14 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 2s. Last read position: chr19:50,268,212
INFO 2026-05-28 20:26:14 MarkDuplicates Tracking 36881 as yet unmatched pairs. 2050 records in RAM.
INFO 2026-05-28 20:26:16 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 1s. Last read position: chr19:58,549,802
INFO 2026-05-28 20:26:16 MarkDuplicates Tracking 34996 as yet unmatched pairs. 162 records in RAM.
INFO 2026-05-28 20:26:18 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 1s. Last read position: chr20:35,271,601
INFO 2026-05-28 20:26:18 MarkDuplicates Tracking 33362 as yet unmatched pairs. 2601 records in RAM.
INFO 2026-05-28 20:26:20 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 1s. Last read position: chr20:62,006,679
INFO 2026-05-28 20:26:20 MarkDuplicates Tracking 31723 as yet unmatched pairs. 950 records in RAM.
INFO 2026-05-28 20:26:22 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 1s. Last read position: chr21:8,214,717
INFO 2026-05-28 20:26:22 MarkDuplicates Tracking 30241 as yet unmatched pairs. 9893 records in RAM.
INFO 2026-05-28 20:26:24 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 1s. Last read position: chr21:8,217,073
INFO 2026-05-28 20:26:24 MarkDuplicates Tracking 28429 as yet unmatched pairs. 8042 records in RAM.
INFO 2026-05-28 20:26:25 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 1s. Last read position: chr21:8,258,927
INFO 2026-05-28 20:26:25 MarkDuplicates Tracking 28087 as yet unmatched pairs. 7699 records in RAM.
INFO 2026-05-28 20:26:26 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 1s. Last read position: chr21:8,397,746
INFO 2026-05-28 20:26:26 MarkDuplicates Tracking 27509 as yet unmatched pairs. 7119 records in RAM.
INFO 2026-05-28 20:26:28 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 1s. Last read position: chr21:8,400,295
INFO 2026-05-28 20:26:28 MarkDuplicates Tracking 25529 as yet unmatched pairs. 5125 records in RAM.
INFO 2026-05-28 20:26:30 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 1s. Last read position: chr21:8,441,966
INFO 2026-05-28 20:26:30 MarkDuplicates Tracking 23838 as yet unmatched pairs. 3424 records in RAM.
INFO 2026-05-28 20:26:31 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,142
INFO 2026-05-28 20:26:31 MarkDuplicates Tracking 22956 as yet unmatched pairs. 2540 records in RAM.
INFO 2026-05-28 20:26:33 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 1s. Last read position: chr21:36,937,035
INFO 2026-05-28 20:26:33 MarkDuplicates Tracking 22039 as yet unmatched pairs. 1620 records in RAM.
INFO 2026-05-28 20:26:35 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 1s. Last read position: chr22:19,137,354
INFO 2026-05-28 20:26:35 MarkDuplicates Tracking 20181 as yet unmatched pairs. 4906 records in RAM.
INFO 2026-05-28 20:26:37 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 2s. Last read position: chr22:31,748,833
INFO 2026-05-28 20:26:37 MarkDuplicates Tracking 17762 as yet unmatched pairs. 2485 records in RAM.
INFO 2026-05-28 20:26:39 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 1s. Last read position: chr22:44,736,907
INFO 2026-05-28 20:26:39 MarkDuplicates Tracking 16431 as yet unmatched pairs. 1154 records in RAM.
INFO 2026-05-28 20:26:40 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 1s. Last read position: chrX:40,057,154
INFO 2026-05-28 20:26:40 MarkDuplicates Tracking 14552 as yet unmatched pairs. 3324 records in RAM.
INFO 2026-05-28 20:26:42 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 1s. Last read position: chrX:85,255,717
INFO 2026-05-28 20:26:42 MarkDuplicates Tracking 12832 as yet unmatched pairs. 1599 records in RAM.
INFO 2026-05-28 20:26:45 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 2s. Last read position: chrX:156,025,080
INFO 2026-05-28 20:26:45 MarkDuplicates Tracking 11241 as yet unmatched pairs. 0 records in RAM.
INFO 2026-05-28 20:26:46 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 1s. Last read position: GL000220.1:114,202
INFO 2026-05-28 20:26:46 MarkDuplicates Tracking 11012 as yet unmatched pairs. 2433 records in RAM.
INFO 2026-05-28 20:26:48 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 1s. Last read position: GL000220.1:116,763
INFO 2026-05-28 20:26:48 MarkDuplicates Tracking 8729 as yet unmatched pairs. 150 records in RAM.
INFO 2026-05-28 20:26:49 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 1s. Last read position: GL000220.1:158,157
INFO 2026-05-28 20:26:49 MarkDuplicates Tracking 8730 as yet unmatched pairs. 151 records in RAM.
INFO 2026-05-28 20:26:50 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 1s. Last read position: GL000220.1:160,614
INFO 2026-05-28 20:26:50 MarkDuplicates Tracking 8596 as yet unmatched pairs. 17 records in RAM.
INFO 2026-05-28 20:26:52 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 1s. Last read position: KI270733.1:131,014
INFO 2026-05-28 20:26:52 MarkDuplicates Tracking 5897 as yet unmatched pairs. 5840 records in RAM.
INFO 2026-05-28 20:26:53 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 1s. Last read position: KI270733.1:133,174
INFO 2026-05-28 20:26:53 MarkDuplicates Tracking 1385 as yet unmatched pairs. 1328 records in RAM.
INFO 2026-05-28 20:26:55 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 1s. Last read position: KI270733.1:175,851
INFO 2026-05-28 20:26:55 MarkDuplicates Tracking 289 as yet unmatched pairs. 232 records in RAM.
INFO 2026-05-28 20:26:56 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 1s. Last read position: KI270733.1:177,486
INFO 2026-05-28 20:26:56 MarkDuplicates Tracking 134 as yet unmatched pairs. 77 records in RAM.
INFO 2026-05-28 20:26:57 MarkDuplicates Read 124967583 records. 0 pairs never matched.
INFO 2026-05-28 20:27:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 33348390960; totalMemory: 47647293440; maxMemory: 63585648640
INFO 2026-05-28 20:27:01 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-05-28 20:27:03 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-05-28 20:27:24 OpticalDuplicateFinder Large duplicate set. size = 1156
INFO 2026-05-28 20:27:24 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,207
INFO 2026-05-28 20:27:25 OpticalDuplicateFinder Large duplicate set. size = 1154
INFO 2026-05-28 20:27:25 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,598
INFO 2026-05-28 20:27:28 OpticalDuplicateFinder Large duplicate set. size = 1688
INFO 2026-05-28 20:27:28 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,054
INFO 2026-05-28 20:27:28 OpticalDuplicateFinder Large duplicate set. size = 1048
INFO 2026-05-28 20:27:28 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,691
INFO 2026-05-28 20:27:28 OpticalDuplicateFinder Large duplicate set. size = 2575
INFO 2026-05-28 20:27:28 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,442
INFO 2026-05-28 20:27:28 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,570
INFO 2026-05-28 20:27:29 OpticalDuplicateFinder Large duplicate set. size = 1086
INFO 2026-05-28 20:27:29 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:1,874
INFO 2026-05-28 20:27:29 OpticalDuplicateFinder Large duplicate set. size = 1034
INFO 2026-05-28 20:27:29 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,979
INFO 2026-05-28 20:27:29 OpticalDuplicateFinder Large duplicate set. size = 1382
INFO 2026-05-28 20:27:29 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:23,377
INFO 2026-05-28 20:27:29 OpticalDuplicateFinder Large duplicate set. size = 1010
INFO 2026-05-28 20:27:29 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,571
INFO 2026-05-28 20:27:30 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-05-28 20:27:38 MarkDuplicates Sorting list of duplicate records.
INFO 2026-05-28 20:27:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300763496; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-05-28 20:27:41 MarkDuplicates Marking 88932548 records as duplicates.
INFO 2026-05-28 20:27:41 MarkDuplicates Found 2264478 optical duplicate clusters.
INFO 2026-05-28 20:27:41 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-05-28 20:27:58 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:17s. Time for last 10,000,000: 17s. Last read position: chr2:24,081,008
INFO 2026-05-28 20:28:17 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:35s. Time for last 10,000,000: 18s. Last read position: chr3:101,664,975
INFO 2026-05-28 20:28:33 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:52s. Time for last 10,000,000: 16s. Last read position: chr6:31,816,662
INFO 2026-05-28 20:28:50 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:08s. Time for last 10,000,000: 16s. Last read position: chr8:37,698,301
INFO 2026-05-28 20:29:15 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:33s. Time for last 10,000,000: 25s. Last read position: chr11:294,616
INFO 2026-05-28 20:29:41 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:59s. Time for last 10,000,000: 26s. Last read position: chr12:116,019,848
INFO 2026-05-28 20:30:04 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:22s. Time for last 10,000,000: 22s. Last read position: chr16:2,767,014
INFO 2026-05-28 20:30:30 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:49s. Time for last 10,000,000: 26s. Last read position: chr17:39,415,260
INFO 2026-05-28 20:30:55 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:03:14s. Time for last 10,000,000: 25s. Last read position: chr17:78,049,372
INFO 2026-05-28 20:31:24 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:03:42s. Time for last 10,000,000: 28s. Last read position: chr19:58,549,802
INFO 2026-05-28 20:31:49 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:04:07s. Time for last 10,000,000: 24s. Last read position: chr21:36,937,035
INFO 2026-05-28 20:32:12 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:04:30s. Time for last 10,000,000: 23s. Last read position: GL000220.1:160,614
INFO 2026-05-28 20:32:29 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-05-28 20:32:29 MarkDuplicates Duplicate Index cleanup.
INFO 2026-05-28 20:32:29 MarkDuplicates Getting Memory Stats.
INFO 2026-05-28 20:32:29 MarkDuplicates Before output close freeMemory: 201612864; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-05-28 20:32:29 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-05-28 20:32:29 MarkDuplicates After output close freeMemory: 104239808; totalMemory: 134217728; maxMemory: 63585648640
[Thu May 28 20:32:29 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 10.34 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory