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_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam --METRICS_FILE BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT 20:54:05.063 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 20:54:05 GMT 2026] MarkDuplicates --INPUT BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam --METRICS_FILE BreastNB_FFPE_L03_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 --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 20:54:05 GMT 2026] Executing as ?@nf-e346cb1e6c507644a5e13c6a27819c8c-f24e1-bz8jw 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 20:54:05 MarkDuplicates Start of doWork freeMemory: 105826608; totalMemory: 134217728; maxMemory: 63585648640 INFO 2026-05-28 20:54:05 MarkDuplicates Reading input file and constructing read end information. INFO 2026-05-28 20:54:05 MarkDuplicates Will retain up to 230382784 data points before spilling to disk. INFO 2026-05-28 20:54:10 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:8,358,604 INFO 2026-05-28 20:54:10 MarkDuplicates Tracking 1693 as yet unmatched pairs. 49 records in RAM. INFO 2026-05-28 20:54:13 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 3s. Last read position: chr1:16,953,304 INFO 2026-05-28 20:54:13 MarkDuplicates Tracking 3728 as yet unmatched pairs. 4 records in RAM. INFO 2026-05-28 20:54:16 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 2s. Last read position: chr1:24,661,325 INFO 2026-05-28 20:54:16 MarkDuplicates Tracking 5633 as yet unmatched pairs. 50 records in RAM. INFO 2026-05-28 20:54:19 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 2s. Last read position: chr1:32,204,578 INFO 2026-05-28 20:54:19 MarkDuplicates Tracking 7424 as yet unmatched pairs. 4 records in RAM. INFO 2026-05-28 20:54:22 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 3s. Last read position: chr1:40,314,204 INFO 2026-05-28 20:54:22 MarkDuplicates Tracking 8857 as yet unmatched pairs. 55 records in RAM. INFO 2026-05-28 20:54:25 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 3s. Last read position: chr1:55,071,877 INFO 2026-05-28 20:54:25 MarkDuplicates Tracking 10567 as yet unmatched pairs. 81 records in RAM. INFO 2026-05-28 20:54:28 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 2s. Last read position: chr1:109,262,915 INFO 2026-05-28 20:54:28 MarkDuplicates Tracking 12057 as yet unmatched pairs. 8 records in RAM. INFO 2026-05-28 20:54:31 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 3s. Last read position: chr1:143,599,120 INFO 2026-05-28 20:54:31 MarkDuplicates Tracking 13873 as yet unmatched pairs. 8 records in RAM. INFO 2026-05-28 20:54:33 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 2s. Last read position: chr1:149,935,299 INFO 2026-05-28 20:54:33 MarkDuplicates Tracking 14634 as yet unmatched pairs. 1 records in RAM. INFO 2026-05-28 20:54:36 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 2s. Last read position: chr1:154,489,268 INFO 2026-05-28 20:54:36 MarkDuplicates Tracking 16674 as yet unmatched pairs. 1 records in RAM. INFO 2026-05-28 20:54:39 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 3s. Last read position: chr1:156,138,686 INFO 2026-05-28 20:54:39 MarkDuplicates Tracking 18763 as yet unmatched pairs. 141 records in RAM. INFO 2026-05-28 20:54:41 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 2s. Last read position: chr1:171,557,636 INFO 2026-05-28 20:54:41 MarkDuplicates Tracking 20580 as yet unmatched pairs. 112 records in RAM. INFO 2026-05-28 20:54:44 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 2s. Last read position: chr1:202,746,142 INFO 2026-05-28 20:54:44 MarkDuplicates Tracking 22253 as yet unmatched pairs. 1 records in RAM. INFO 2026-05-28 20:54:47 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 3s. Last read position: chr1:225,828,834 INFO 2026-05-28 20:54:47 MarkDuplicates Tracking 24033 as yet unmatched pairs. 1 records in RAM. INFO 2026-05-28 20:54:50 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chr1:248,850,288 INFO 2026-05-28 20:54:50 MarkDuplicates Tracking 25756 as yet unmatched pairs. 0 records in RAM. INFO 2026-05-28 20:54:53 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 3s. Last read position: chr2:29,193,418 INFO 2026-05-28 20:54:53 MarkDuplicates Tracking 27743 as yet unmatched pairs. 27449 records in RAM. INFO 2026-05-28 20:54:57 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 3s. Last read position: chr2:32,916,406 INFO 2026-05-28 20:54:57 MarkDuplicates Tracking 258366 as yet unmatched pairs. 16473 records in RAM. INFO 2026-05-28 20:55:00 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 2s. Last read position: chr2:55,049,873 INFO 2026-05-28 20:55:00 MarkDuplicates Tracking 275417 as yet unmatched pairs. 14206 records in RAM. INFO 2026-05-28 20:55:02 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 2s. Last read position: chr2:85,361,743 INFO 2026-05-28 20:55:02 MarkDuplicates Tracking 273529 as yet unmatched pairs. 12309 records in RAM. INFO 2026-05-28 20:55:05 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 2s. Last read position: chr2:106,073,968 INFO 2026-05-28 20:55:05 MarkDuplicates Tracking 272115 as yet unmatched pairs. 10885 records in RAM. INFO 2026-05-28 20:55:08 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 2s. Last read position: chr2:130,657,166 INFO 2026-05-28 20:55:08 MarkDuplicates Tracking 271026 as yet unmatched pairs. 9785 records in RAM. INFO 2026-05-28 20:55:10 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 2s. Last read position: chr2:178,537,855 INFO 2026-05-28 20:55:10 MarkDuplicates Tracking 269292 as yet unmatched pairs. 8044 records in RAM. INFO 2026-05-28 20:55:13 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 3s. Last read position: chr2:189,009,105 INFO 2026-05-28 20:55:13 MarkDuplicates Tracking 267647 as yet unmatched pairs. 6399 records in RAM. INFO 2026-05-28 20:55:15 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 2s. Last read position: chr2:215,386,766 INFO 2026-05-28 20:55:15 MarkDuplicates Tracking 265281 as yet unmatched pairs. 4025 records in RAM. INFO 2026-05-28 20:55:18 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 2s. Last read position: chr2:225,817,142 INFO 2026-05-28 20:55:18 MarkDuplicates Tracking 263628 as yet unmatched pairs. 2311 records in RAM. INFO 2026-05-28 20:55:21 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 2s. Last read position: chr2:240,014,816 INFO 2026-05-28 20:55:21 MarkDuplicates Tracking 261929 as yet unmatched pairs. 607 records in RAM. INFO 2026-05-28 20:55:23 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 2s. Last read position: chr3:15,074,272 INFO 2026-05-28 20:55:23 MarkDuplicates Tracking 260203 as yet unmatched pairs. 13147 records in RAM. INFO 2026-05-28 20:55:25 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 2s. Last read position: chr3:46,995,966 INFO 2026-05-28 20:55:25 MarkDuplicates Tracking 258576 as yet unmatched pairs. 11508 records in RAM. INFO 2026-05-28 20:55:27 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 2s. Last read position: chr3:49,962,668 INFO 2026-05-28 20:55:27 MarkDuplicates Tracking 256195 as yet unmatched pairs. 9126 records in RAM. INFO 2026-05-28 20:55:29 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 2s. Last read position: chr3:58,170,690 INFO 2026-05-28 20:55:29 MarkDuplicates Tracking 254284 as yet unmatched pairs. 7213 records in RAM. INFO 2026-05-28 20:55:31 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 1s. Last read position: chr3:114,351,087 INFO 2026-05-28 20:55:31 MarkDuplicates Tracking 252476 as yet unmatched pairs. 5395 records in RAM. INFO 2026-05-28 20:55:34 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 2s. Last read position: chr3:138,010,188 INFO 2026-05-28 20:55:34 MarkDuplicates Tracking 250522 as yet unmatched pairs. 3419 records in RAM. INFO 2026-05-28 20:55:37 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 3s. Last read position: chr3:184,458,786 INFO 2026-05-28 20:55:37 MarkDuplicates Tracking 248564 as yet unmatched pairs. 1450 records in RAM. INFO 2026-05-28 20:55:40 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 3s. Last read position: chr4:1,212,219 INFO 2026-05-28 20:55:40 MarkDuplicates Tracking 246745 as yet unmatched pairs. 5482 records in RAM. INFO 2026-05-28 20:55:42 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 2s. Last read position: chr4:39,321,287 INFO 2026-05-28 20:55:42 MarkDuplicates Tracking 245304 as yet unmatched pairs. 4030 records in RAM. INFO 2026-05-28 20:55:45 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 2s. Last read position: chr4:88,523,499 INFO 2026-05-28 20:55:45 MarkDuplicates Tracking 243579 as yet unmatched pairs. 2271 records in RAM. INFO 2026-05-28 20:55:47 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 2s. Last read position: chr4:150,817,217 INFO 2026-05-28 20:55:47 MarkDuplicates Tracking 242251 as yet unmatched pairs. 915 records in RAM. INFO 2026-05-28 20:55:50 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 2s. Last read position: chr5:14,316,647 INFO 2026-05-28 20:55:50 MarkDuplicates Tracking 240805 as yet unmatched pairs. 10689 records in RAM. INFO 2026-05-28 20:55:52 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 2s. Last read position: chr5:67,163,379 INFO 2026-05-28 20:55:52 MarkDuplicates Tracking 238709 as yet unmatched pairs. 8577 records in RAM. INFO 2026-05-28 20:55:54 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 1s. Last read position: chr5:114,362,648 INFO 2026-05-28 20:55:54 MarkDuplicates Tracking 237185 as yet unmatched pairs. 7039 records in RAM. INFO 2026-05-28 20:55:56 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 2s. Last read position: chr5:139,561,737 INFO 2026-05-28 20:55:56 MarkDuplicates Tracking 235618 as yet unmatched pairs. 5469 records in RAM. INFO 2026-05-28 20:56:00 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 3s. Last read position: chr5:150,123,180 INFO 2026-05-28 20:56:00 MarkDuplicates Tracking 234443 as yet unmatched pairs. 4073 records in RAM. INFO 2026-05-28 20:56:03 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 2s. Last read position: chr5:168,616,430 INFO 2026-05-28 20:56:03 MarkDuplicates Tracking 232961 as yet unmatched pairs. 2589 records in RAM. INFO 2026-05-28 20:56:06 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 3s. Last read position: chr5:179,822,965 INFO 2026-05-28 20:56:06 MarkDuplicates Tracking 231354 as yet unmatched pairs. 975 records in RAM. INFO 2026-05-28 20:56:08 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 2s. Last read position: chr6:17,735,968 INFO 2026-05-28 20:56:08 MarkDuplicates Tracking 229355 as yet unmatched pairs. 11967 records in RAM. INFO 2026-05-28 20:56:11 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 3s. Last read position: chr6:31,632,916 INFO 2026-05-28 20:56:11 MarkDuplicates Tracking 228071 as yet unmatched pairs. 10679 records in RAM. INFO 2026-05-28 20:56:13 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 2s. Last read position: chr6:32,195,892 INFO 2026-05-28 20:56:13 MarkDuplicates Tracking 226225 as yet unmatched pairs. 8832 records in RAM. INFO 2026-05-28 20:56:17 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 3s. Last read position: chr6:42,262,470 INFO 2026-05-28 20:56:17 MarkDuplicates Tracking 224580 as yet unmatched pairs. 7181 records in RAM. INFO 2026-05-28 20:56:21 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 4s. Last read position: chr6:81,555,345 INFO 2026-05-28 20:56:21 MarkDuplicates Tracking 222430 as yet unmatched pairs. 5022 records in RAM. INFO 2026-05-28 20:56:24 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 2s. Last read position: chr6:129,791,548 INFO 2026-05-28 20:56:24 MarkDuplicates Tracking 220612 as yet unmatched pairs. 3190 records in RAM. INFO 2026-05-28 20:56:26 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 1s. Last read position: chr6:152,060,989 INFO 2026-05-28 20:56:26 MarkDuplicates Tracking 218724 as yet unmatched pairs. 1299 records in RAM. INFO 2026-05-28 20:56:28 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 2s. Last read position: chr7:2,433,473 INFO 2026-05-28 20:56:28 MarkDuplicates Tracking 216761 as yet unmatched pairs. 13579 records in RAM. INFO 2026-05-28 20:56:31 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 2s. Last read position: chr7:23,512,963 INFO 2026-05-28 20:56:31 MarkDuplicates Tracking 214848 as yet unmatched pairs. 11658 records in RAM. INFO 2026-05-28 20:56:35 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 3s. Last read position: chr7:55,201,279 INFO 2026-05-28 20:56:35 MarkDuplicates Tracking 213194 as yet unmatched pairs. 9997 records in RAM. INFO 2026-05-28 20:56:37 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 2s. Last read position: chr7:75,340,724 INFO 2026-05-28 20:56:37 MarkDuplicates Tracking 212057 as yet unmatched pairs. 8849 records in RAM. INFO 2026-05-28 20:56:40 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 2s. Last read position: chr7:94,408,212 INFO 2026-05-28 20:56:40 MarkDuplicates Tracking 210572 as yet unmatched pairs. 7361 records in RAM. INFO 2026-05-28 20:56:42 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 1s. Last read position: chr7:100,430,873 INFO 2026-05-28 20:56:42 MarkDuplicates Tracking 208519 as yet unmatched pairs. 5302 records in RAM. INFO 2026-05-28 20:56:43 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 1s. Last read position: chr7:107,261,316 INFO 2026-05-28 20:56:43 MarkDuplicates Tracking 206780 as yet unmatched pairs. 3556 records in RAM. INFO 2026-05-28 20:56:45 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 2s. Last read position: chr7:139,583,979 INFO 2026-05-28 20:56:45 MarkDuplicates Tracking 205186 as yet unmatched pairs. 1939 records in RAM. INFO 2026-05-28 20:56:47 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 1s. Last read position: chr7:151,142,603 INFO 2026-05-28 20:56:47 MarkDuplicates Tracking 203864 as yet unmatched pairs. 613 records in RAM. INFO 2026-05-28 20:56:49 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 1s. Last read position: chr8:22,556,875 INFO 2026-05-28 20:56:49 MarkDuplicates Tracking 202237 as yet unmatched pairs. 9112 records in RAM. INFO 2026-05-28 20:56:51 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 2s. Last read position: chr8:38,429,886 INFO 2026-05-28 20:56:51 MarkDuplicates Tracking 200405 as yet unmatched pairs. 7273 records in RAM. INFO 2026-05-28 20:56:54 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 2s. Last read position: chr8:93,719,056 INFO 2026-05-28 20:56:54 MarkDuplicates Tracking 198290 as yet unmatched pairs. 5143 records in RAM. INFO 2026-05-28 20:56:56 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 2s. Last read position: chr8:140,152,291 INFO 2026-05-28 20:56:56 MarkDuplicates Tracking 196471 as yet unmatched pairs. 3315 records in RAM. INFO 2026-05-28 20:56:58 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 2s. Last read position: chr8:143,924,181 INFO 2026-05-28 20:56:58 MarkDuplicates Tracking 194498 as yet unmatched pairs. 1306 records in RAM. INFO 2026-05-28 20:57:02 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 3s. Last read position: chr9:14,307,087 INFO 2026-05-28 20:57:02 MarkDuplicates Tracking 193002 as yet unmatched pairs. 10836 records in RAM. INFO 2026-05-28 20:57:04 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 2s. Last read position: chr9:66,920,522 INFO 2026-05-28 20:57:04 MarkDuplicates Tracking 191259 as yet unmatched pairs. 8956 records in RAM. INFO 2026-05-28 20:57:06 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 1s. Last read position: chr9:99,062,260 INFO 2026-05-28 20:57:06 MarkDuplicates Tracking 189340 as yet unmatched pairs. 7029 records in RAM. INFO 2026-05-28 20:57:07 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 1s. Last read position: chr9:122,204,686 INFO 2026-05-28 20:57:07 MarkDuplicates Tracking 187753 as yet unmatched pairs. 5441 records in RAM. INFO 2026-05-28 20:57:10 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 2s. Last read position: chr9:130,878,444 INFO 2026-05-28 20:57:10 MarkDuplicates Tracking 185799 as yet unmatched pairs. 3481 records in RAM. INFO 2026-05-28 20:57:12 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 2s. Last read position: chr9:136,545,731 INFO 2026-05-28 20:57:12 MarkDuplicates Tracking 183304 as yet unmatched pairs. 977 records in RAM. INFO 2026-05-28 20:57:14 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 1s. Last read position: chr10:13,610,098 INFO 2026-05-28 20:57:14 MarkDuplicates Tracking 181215 as yet unmatched pairs. 8420 records in RAM. INFO 2026-05-28 20:57:16 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 1s. Last read position: chr10:37,176,206 INFO 2026-05-28 20:57:16 MarkDuplicates Tracking 179846 as yet unmatched pairs. 7042 records in RAM. INFO 2026-05-28 20:57:18 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 1s. Last read position: chr10:59,792,929 INFO 2026-05-28 20:57:18 MarkDuplicates Tracking 178201 as yet unmatched pairs. 5389 records in RAM. INFO 2026-05-28 20:57:21 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 3s. Last read position: chr10:80,157,688 INFO 2026-05-28 20:57:21 MarkDuplicates Tracking 176689 as yet unmatched pairs. 3873 records in RAM. INFO 2026-05-28 20:57:24 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 2s. Last read position: chr10:102,139,555 INFO 2026-05-28 20:57:24 MarkDuplicates Tracking 174705 as yet unmatched pairs. 1882 records in RAM. INFO 2026-05-28 20:57:26 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 2s. Last read position: chr10:128,069,721 INFO 2026-05-28 20:57:26 MarkDuplicates Tracking 173168 as yet unmatched pairs. 296 records in RAM. INFO 2026-05-28 20:57:29 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 2s. Last read position: chr11:1,757,323 INFO 2026-05-28 20:57:29 MarkDuplicates Tracking 171146 as yet unmatched pairs. 15524 records in RAM. INFO 2026-05-28 20:57:31 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 2s. Last read position: chr11:17,288,881 INFO 2026-05-28 20:57:31 MarkDuplicates Tracking 169323 as yet unmatched pairs. 13692 records in RAM. INFO 2026-05-28 20:57:34 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 2s. Last read position: chr11:57,313,676 INFO 2026-05-28 20:57:34 MarkDuplicates Tracking 167480 as yet unmatched pairs. 11838 records in RAM. INFO 2026-05-28 20:57:37 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 2s. Last read position: chr11:62,529,844 INFO 2026-05-28 20:57:37 MarkDuplicates Tracking 165723 as yet unmatched pairs. 10059 records in RAM. INFO 2026-05-28 20:57:39 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 2s. Last read position: chr11:65,424,585 INFO 2026-05-28 20:57:39 MarkDuplicates Tracking 163751 as yet unmatched pairs. 8085 records in RAM. INFO 2026-05-28 20:57:41 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 1s. Last read position: chr11:67,286,378 INFO 2026-05-28 20:57:41 MarkDuplicates Tracking 162165 as yet unmatched pairs. 6499 records in RAM. INFO 2026-05-28 20:57:43 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 2s. Last read position: chr11:73,309,317 INFO 2026-05-28 20:57:43 MarkDuplicates Tracking 160237 as yet unmatched pairs. 4567 records in RAM. INFO 2026-05-28 20:57:46 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 2s. Last read position: chr11:103,909,785 INFO 2026-05-28 20:57:46 MarkDuplicates Tracking 158332 as yet unmatched pairs. 2644 records in RAM. INFO 2026-05-28 20:57:49 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 2s. Last read position: chr11:119,744,039 INFO 2026-05-28 20:57:49 MarkDuplicates Tracking 156514 as yet unmatched pairs. 823 records in RAM. INFO 2026-05-28 20:57:51 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 1s. Last read position: chr12:6,573,095 INFO 2026-05-28 20:57:51 MarkDuplicates Tracking 154924 as yet unmatched pairs. 13321 records in RAM. INFO 2026-05-28 20:57:52 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 1s. Last read position: chr12:14,947,899 INFO 2026-05-28 20:57:52 MarkDuplicates Tracking 153588 as yet unmatched pairs. 11983 records in RAM. INFO 2026-05-28 20:57:54 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 1s. Last read position: chr12:49,055,014 INFO 2026-05-28 20:57:54 MarkDuplicates Tracking 152266 as yet unmatched pairs. 10652 records in RAM. INFO 2026-05-28 20:57:56 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 1s. Last read position: chr12:53,063,243 INFO 2026-05-28 20:57:56 MarkDuplicates Tracking 150290 as yet unmatched pairs. 8674 records in RAM. INFO 2026-05-28 20:57:58 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 2s. Last read position: chr12:56,721,309 INFO 2026-05-28 20:57:58 MarkDuplicates Tracking 148676 as yet unmatched pairs. 7059 records in RAM. INFO 2026-05-28 20:58:01 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 2s. Last read position: chr12:68,689,534 INFO 2026-05-28 20:58:01 MarkDuplicates Tracking 146798 as yet unmatched pairs. 5175 records in RAM. INFO 2026-05-28 20:58:03 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 2s. Last read position: chr12:110,028,511 INFO 2026-05-28 20:58:03 MarkDuplicates Tracking 145277 as yet unmatched pairs. 3645 records in RAM. INFO 2026-05-28 20:58:05 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 1s. Last read position: chr12:122,133,659 INFO 2026-05-28 20:58:05 MarkDuplicates Tracking 143398 as yet unmatched pairs. 1763 records in RAM. INFO 2026-05-28 20:58:07 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 2s. Last read position: chr12:132,748,176 INFO 2026-05-28 20:58:07 MarkDuplicates Tracking 141805 as yet unmatched pairs. 164 records in RAM. INFO 2026-05-28 20:58:10 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 3s. Last read position: chr13:52,029,323 INFO 2026-05-28 20:58:10 MarkDuplicates Tracking 139646 as yet unmatched pairs. 1888 records in RAM. INFO 2026-05-28 20:58:12 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 2s. Last read position: chr14:20,380,259 INFO 2026-05-28 20:58:12 MarkDuplicates Tracking 137728 as yet unmatched pairs. 8749 records in RAM. INFO 2026-05-28 20:58:14 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 1s. Last read position: chr14:34,612,995 INFO 2026-05-28 20:58:14 MarkDuplicates Tracking 135680 as yet unmatched pairs. 6697 records in RAM. INFO 2026-05-28 20:58:16 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 1s. Last read position: chr14:67,691,183 INFO 2026-05-28 20:58:16 MarkDuplicates Tracking 133990 as yet unmatched pairs. 5003 records in RAM. INFO 2026-05-28 20:58:18 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 1s. Last read position: chr14:75,783,330 INFO 2026-05-28 20:58:18 MarkDuplicates Tracking 132378 as yet unmatched pairs. 3389 records in RAM. INFO 2026-05-28 20:58:21 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 2s. Last read position: chr14:102,903,277 INFO 2026-05-28 20:58:21 MarkDuplicates Tracking 130605 as yet unmatched pairs. 1565 records in RAM. INFO 2026-05-28 20:58:23 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 2s. Last read position: chr15:25,779,094 INFO 2026-05-28 20:58:23 MarkDuplicates Tracking 128858 as yet unmatched pairs. 7984 records in RAM. INFO 2026-05-28 20:58:26 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 2s. Last read position: chr15:41,835,065 INFO 2026-05-28 20:58:26 MarkDuplicates Tracking 127341 as yet unmatched pairs. 6458 records in RAM. INFO 2026-05-28 20:58:28 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 2s. Last read position: chr15:61,907,327 INFO 2026-05-28 20:58:28 MarkDuplicates Tracking 125806 as yet unmatched pairs. 4922 records in RAM. INFO 2026-05-28 20:58:31 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 2s. Last read position: chr15:74,043,075 INFO 2026-05-28 20:58:31 MarkDuplicates Tracking 123907 as yet unmatched pairs. 3017 records in RAM. INFO 2026-05-28 20:58:32 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 1s. Last read position: chr15:85,579,623 INFO 2026-05-28 20:58:32 MarkDuplicates Tracking 122226 as yet unmatched pairs. 1323 records in RAM. INFO 2026-05-28 20:58:35 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 2s. Last read position: chr16:381,792 INFO 2026-05-28 20:58:35 MarkDuplicates Tracking 120523 as yet unmatched pairs. 14092 records in RAM. INFO 2026-05-28 20:58:36 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 1s. Last read position: chr16:2,757,556 INFO 2026-05-28 20:58:36 MarkDuplicates Tracking 118679 as yet unmatched pairs. 12245 records in RAM. INFO 2026-05-28 20:58:38 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 1s. Last read position: chr16:4,652,016 INFO 2026-05-28 20:58:38 MarkDuplicates Tracking 117256 as yet unmatched pairs. 10818 records in RAM. INFO 2026-05-28 20:58:40 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 1s. Last read position: chr16:15,363,810 INFO 2026-05-28 20:58:40 MarkDuplicates Tracking 116150 as yet unmatched pairs. 9711 records in RAM. INFO 2026-05-28 20:58:41 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 1s. Last read position: chr16:18,351,271 INFO 2026-05-28 20:58:41 MarkDuplicates Tracking 115594 as yet unmatched pairs. 9153 records in RAM. INFO 2026-05-28 20:58:43 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 1s. Last read position: chr16:21,404,973 INFO 2026-05-28 20:58:43 MarkDuplicates Tracking 115066 as yet unmatched pairs. 8625 records in RAM. INFO 2026-05-28 20:58:45 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 1s. Last read position: chr16:22,527,565 INFO 2026-05-28 20:58:45 MarkDuplicates Tracking 114546 as yet unmatched pairs. 8104 records in RAM. INFO 2026-05-28 20:58:47 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 2s. Last read position: chr16:27,776,901 INFO 2026-05-28 20:58:47 MarkDuplicates Tracking 113856 as yet unmatched pairs. 7414 records in RAM. INFO 2026-05-28 20:58:49 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 1s. Last read position: chr16:29,485,485 INFO 2026-05-28 20:58:49 MarkDuplicates Tracking 113333 as yet unmatched pairs. 6889 records in RAM. INFO 2026-05-28 20:58:51 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 2s. Last read position: chr16:30,664,846 INFO 2026-05-28 20:58:51 MarkDuplicates Tracking 112246 as yet unmatched pairs. 5796 records in RAM. INFO 2026-05-28 20:58:53 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 2s. Last read position: chr16:56,502,329 INFO 2026-05-28 20:58:53 MarkDuplicates Tracking 110534 as yet unmatched pairs. 4069 records in RAM. INFO 2026-05-28 20:58:56 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 2s. Last read position: chr16:70,664,597 INFO 2026-05-28 20:58:56 MarkDuplicates Tracking 108783 as yet unmatched pairs. 2309 records in RAM. INFO 2026-05-28 20:58:59 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 2s. Last read position: chr16:88,624,045 INFO 2026-05-28 20:58:59 MarkDuplicates Tracking 107354 as yet unmatched pairs. 863 records in RAM. INFO 2026-05-28 20:59:02 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 3s. Last read position: chr17:3,577,628 INFO 2026-05-28 20:59:02 MarkDuplicates Tracking 105362 as yet unmatched pairs. 30545 records in RAM. INFO 2026-05-28 20:59:05 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 3s. Last read position: chr17:7,513,489 INFO 2026-05-28 20:59:05 MarkDuplicates Tracking 103794 as yet unmatched pairs. 28973 records in RAM. INFO 2026-05-28 20:59:08 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 2s. Last read position: chr17:17,217,159 INFO 2026-05-28 20:59:08 MarkDuplicates Tracking 101876 as yet unmatched pairs. 27051 records in RAM. INFO 2026-05-28 20:59:11 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 2s. Last read position: chr17:31,865,385 INFO 2026-05-28 20:59:11 MarkDuplicates Tracking 99809 as yet unmatched pairs. 24981 records in RAM. INFO 2026-05-28 20:59:12 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 1s. Last read position: chr17:39,710,346 INFO 2026-05-28 20:59:12 MarkDuplicates Tracking 98226 as yet unmatched pairs. 23395 records in RAM. INFO 2026-05-28 20:59:14 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 1s. Last read position: chr17:42,991,465 INFO 2026-05-28 20:59:14 MarkDuplicates Tracking 95937 as yet unmatched pairs. 21105 records in RAM. INFO 2026-05-28 20:59:16 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr17:50,149,167 INFO 2026-05-28 20:59:16 MarkDuplicates Tracking 94611 as yet unmatched pairs. 19774 records in RAM. INFO 2026-05-28 20:59:18 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 1s. Last read position: chr17:50,186,913 INFO 2026-05-28 20:59:18 MarkDuplicates Tracking 93875 as yet unmatched pairs. 19038 records in RAM. INFO 2026-05-28 20:59:21 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 2s. Last read position: chr17:50,188,930 INFO 2026-05-28 20:59:21 MarkDuplicates Tracking 91904 as yet unmatched pairs. 17067 records in RAM. INFO 2026-05-28 20:59:24 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 2s. Last read position: chr17:50,190,077 INFO 2026-05-28 20:59:24 MarkDuplicates Tracking 90510 as yet unmatched pairs. 15673 records in RAM. INFO 2026-05-28 20:59:27 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 2s. Last read position: chr17:50,193,992 INFO 2026-05-28 20:59:27 MarkDuplicates Tracking 88737 as yet unmatched pairs. 13900 records in RAM. INFO 2026-05-28 20:59:29 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 2s. Last read position: chr17:50,195,960 INFO 2026-05-28 20:59:29 MarkDuplicates Tracking 87352 as yet unmatched pairs. 12515 records in RAM. INFO 2026-05-28 20:59:32 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 2s. Last read position: chr17:50,199,226 INFO 2026-05-28 20:59:32 MarkDuplicates Tracking 83688 as yet unmatched pairs. 8851 records in RAM. INFO 2026-05-28 20:59:35 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 2s. Last read position: chr17:56,981,182 INFO 2026-05-28 20:59:35 MarkDuplicates Tracking 81663 as yet unmatched pairs. 6824 records in RAM. INFO 2026-05-28 20:59:38 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 2s. Last read position: chr17:68,528,864 INFO 2026-05-28 20:59:38 MarkDuplicates Tracking 79706 as yet unmatched pairs. 4862 records in RAM. INFO 2026-05-28 20:59:41 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 3s. Last read position: chr17:78,091,504 INFO 2026-05-28 20:59:41 MarkDuplicates Tracking 77559 as yet unmatched pairs. 2710 records in RAM. INFO 2026-05-28 20:59:44 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 2s. Last read position: chr17:82,079,185 INFO 2026-05-28 20:59:44 MarkDuplicates Tracking 75654 as yet unmatched pairs. 803 records in RAM. INFO 2026-05-28 20:59:46 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 2s. Last read position: chr18:36,198,901 INFO 2026-05-28 20:59:46 MarkDuplicates Tracking 73397 as yet unmatched pairs. 1805 records in RAM. INFO 2026-05-28 20:59:49 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 3s. Last read position: chr19:860,683 INFO 2026-05-28 20:59:49 MarkDuplicates Tracking 71437 as yet unmatched pairs. 26894 records in RAM. INFO 2026-05-28 20:59:52 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 2s. Last read position: chr19:3,387,249 INFO 2026-05-28 20:59:52 MarkDuplicates Tracking 68899 as yet unmatched pairs. 24353 records in RAM. INFO 2026-05-28 20:59:55 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 2s. Last read position: chr19:6,415,018 INFO 2026-05-28 20:59:55 MarkDuplicates Tracking 66778 as yet unmatched pairs. 22227 records in RAM. INFO 2026-05-28 20:59:57 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 2s. Last read position: chr19:10,986,954 INFO 2026-05-28 20:59:57 MarkDuplicates Tracking 65042 as yet unmatched pairs. 20486 records in RAM. INFO 2026-05-28 21:00:00 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 2s. Last read position: chr19:15,161,606 INFO 2026-05-28 21:00:00 MarkDuplicates Tracking 62569 as yet unmatched pairs. 18012 records in RAM. INFO 2026-05-28 21:00:02 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 2s. Last read position: chr19:17,862,161 INFO 2026-05-28 21:00:02 MarkDuplicates Tracking 60613 as yet unmatched pairs. 16041 records in RAM. INFO 2026-05-28 21:00:04 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 2s. Last read position: chr19:35,267,234 INFO 2026-05-28 21:00:04 MarkDuplicates Tracking 58294 as yet unmatched pairs. 13719 records in RAM. INFO 2026-05-28 21:00:07 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 2s. Last read position: chr19:39,408,339 INFO 2026-05-28 21:00:07 MarkDuplicates Tracking 56077 as yet unmatched pairs. 11502 records in RAM. INFO 2026-05-28 21:00:09 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 2s. Last read position: chr19:42,273,799 INFO 2026-05-28 21:00:09 MarkDuplicates Tracking 54202 as yet unmatched pairs. 9625 records in RAM. INFO 2026-05-28 21:00:12 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 2s. Last read position: chr19:45,472,915 INFO 2026-05-28 21:00:12 MarkDuplicates Tracking 51963 as yet unmatched pairs. 7352 records in RAM. INFO 2026-05-28 21:00:15 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 2s. Last read position: chr19:49,061,352 INFO 2026-05-28 21:00:15 MarkDuplicates Tracking 49359 as yet unmatched pairs. 4748 records in RAM. INFO 2026-05-28 21:00:16 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:06:09s. Time for last 1,000,000: 1s. Last read position: chr19:52,415,139 INFO 2026-05-28 21:00:16 MarkDuplicates Tracking 47211 as yet unmatched pairs. 2600 records in RAM. INFO 2026-05-28 21:00:18 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 1s. Last read position: chr19:57,390,017 INFO 2026-05-28 21:00:18 MarkDuplicates Tracking 45267 as yet unmatched pairs. 652 records in RAM. INFO 2026-05-28 21:00:21 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 2s. Last read position: chr20:17,659,071 INFO 2026-05-28 21:00:21 MarkDuplicates Tracking 43743 as yet unmatched pairs. 6149 records in RAM. INFO 2026-05-28 21:00:23 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:06:16s. Time for last 1,000,000: 2s. Last read position: chr20:36,786,551 INFO 2026-05-28 21:00:23 MarkDuplicates Tracking 41762 as yet unmatched pairs. 4165 records in RAM. INFO 2026-05-28 21:00:25 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 1s. Last read position: chr20:53,254,486 INFO 2026-05-28 21:00:25 MarkDuplicates Tracking 39995 as yet unmatched pairs. 2397 records in RAM. INFO 2026-05-28 21:00:28 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 3s. Last read position: chr20:64,069,360 INFO 2026-05-28 21:00:28 MarkDuplicates Tracking 37615 as yet unmatched pairs. 13 records in RAM. INFO 2026-05-28 21:00:30 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 2s. Last read position: chr21:8,216,836 INFO 2026-05-28 21:00:30 MarkDuplicates Tracking 36661 as yet unmatched pairs. 11407 records in RAM. INFO 2026-05-28 21:00:32 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 1s. Last read position: chr21:8,258,898 INFO 2026-05-28 21:00:32 MarkDuplicates Tracking 35733 as yet unmatched pairs. 10478 records in RAM. INFO 2026-05-28 21:00:33 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 1s. Last read position: chr21:8,389,269 INFO 2026-05-28 21:00:33 MarkDuplicates Tracking 35658 as yet unmatched pairs. 10403 records in RAM. INFO 2026-05-28 21:00:35 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 1s. Last read position: chr21:8,399,886 INFO 2026-05-28 21:00:35 MarkDuplicates Tracking 32751 as yet unmatched pairs. 7488 records in RAM. INFO 2026-05-28 21:00:36 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 1s. Last read position: chr21:8,441,948 INFO 2026-05-28 21:00:36 MarkDuplicates Tracking 30645 as yet unmatched pairs. 5372 records in RAM. INFO 2026-05-28 21:00:37 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:06:30s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,101 INFO 2026-05-28 21:00:37 MarkDuplicates Tracking 29431 as yet unmatched pairs. 4156 records in RAM. INFO 2026-05-28 21:00:39 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 1s. Last read position: chr21:25,954,623 INFO 2026-05-28 21:00:39 MarkDuplicates Tracking 29173 as yet unmatched pairs. 3897 records in RAM. INFO 2026-05-28 21:00:42 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:06:35s. Time for last 1,000,000: 2s. Last read position: chr21:44,773,540 INFO 2026-05-28 21:00:42 MarkDuplicates Tracking 27683 as yet unmatched pairs. 2407 records in RAM. INFO 2026-05-28 21:00:45 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 3s. Last read position: chr21:46,132,030 INFO 2026-05-28 21:00:45 MarkDuplicates Tracking 25637 as yet unmatched pairs. 360 records in RAM. INFO 2026-05-28 21:00:47 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 2s. Last read position: chr22:24,269,405 INFO 2026-05-28 21:00:47 MarkDuplicates Tracking 23631 as yet unmatched pairs. 6611 records in RAM. INFO 2026-05-28 21:00:49 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 2s. Last read position: chr22:36,145,516 INFO 2026-05-28 21:00:49 MarkDuplicates Tracking 22119 as yet unmatched pairs. 5098 records in RAM. INFO 2026-05-28 21:00:52 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 2s. Last read position: chr22:40,266,160 INFO 2026-05-28 21:00:52 MarkDuplicates Tracking 19910 as yet unmatched pairs. 2887 records in RAM. INFO 2026-05-28 21:00:54 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:06:47s. Time for last 1,000,000: 2s. Last read position: chr22:50,437,507 INFO 2026-05-28 21:00:54 MarkDuplicates Tracking 17728 as yet unmatched pairs. 704 records in RAM. INFO 2026-05-28 21:00:56 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 2s. Last read position: chrX:32,644,979 INFO 2026-05-28 21:00:56 MarkDuplicates Tracking 16030 as yet unmatched pairs. 5290 records in RAM. INFO 2026-05-28 21:00:58 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:06:51s. Time for last 1,000,000: 2s. Last read position: chrX:54,930,279 INFO 2026-05-28 21:00:58 MarkDuplicates Tracking 14206 as yet unmatched pairs. 3460 records in RAM. INFO 2026-05-28 21:01:00 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 1s. Last read position: chrX:118,907,494 INFO 2026-05-28 21:01:00 MarkDuplicates Tracking 12661 as yet unmatched pairs. 1909 records in RAM. INFO 2026-05-28 21:01:02 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 1s. Last read position: chrX:154,368,047 INFO 2026-05-28 21:01:02 MarkDuplicates Tracking 11080 as yet unmatched pairs. 324 records in RAM. INFO 2026-05-28 21:01:04 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:06:57s. Time for last 1,000,000: 1s. Last read position: GL000220.1:114,176 INFO 2026-05-28 21:01:04 MarkDuplicates Tracking 10531 as yet unmatched pairs. 2460 records in RAM. INFO 2026-05-28 21:01:05 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 1s. Last read position: GL000220.1:116,328 INFO 2026-05-28 21:01:05 MarkDuplicates Tracking 8196 as yet unmatched pairs. 122 records in RAM. INFO 2026-05-28 21:01:06 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 1s. Last read position: GL000220.1:158,127 INFO 2026-05-28 21:01:06 MarkDuplicates Tracking 8216 as yet unmatched pairs. 142 records in RAM. INFO 2026-05-28 21:01:08 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:07:00s. Time for last 1,000,000: 1s. Last read position: GL000220.1:160,284 INFO 2026-05-28 21:01:08 MarkDuplicates Tracking 8099 as yet unmatched pairs. 25 records in RAM. INFO 2026-05-28 21:01:09 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 1s. Last read position: KI270733.1:129,682 INFO 2026-05-28 21:01:09 MarkDuplicates Tracking 7986 as yet unmatched pairs. 7980 records in RAM. INFO 2026-05-28 21:01:11 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:07:03s. Time for last 1,000,000: 1s. Last read position: KI270733.1:132,335 INFO 2026-05-28 21:01:11 MarkDuplicates Tracking 2513 as yet unmatched pairs. 2507 records in RAM. INFO 2026-05-28 21:01:12 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 1s. Last read position: KI270733.1:148,214 INFO 2026-05-28 21:01:12 MarkDuplicates Tracking 367 as yet unmatched pairs. 361 records in RAM. INFO 2026-05-28 21:01:13 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 1s. Last read position: KI270733.1:176,187 INFO 2026-05-28 21:01:13 MarkDuplicates Tracking 120 as yet unmatched pairs. 114 records in RAM. INFO 2026-05-28 21:01:15 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:07:07s. Time for last 1,000,000: 1s. Last read position: KI270733.1:178,729 INFO 2026-05-28 21:01:15 MarkDuplicates Tracking 11 as yet unmatched pairs. 5 records in RAM. INFO 2026-05-28 21:01:15 MarkDuplicates Read 180139752 records. 0 pairs never matched. INFO 2026-05-28 21:01:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 42655377344; totalMemory: 62176362496; maxMemory: 63585648640 INFO 2026-05-28 21:01:27 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk. INFO 2026-05-28 21:01:36 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2026-05-28 21:01:44 OpticalDuplicateFinder Large duplicate set. size = 1158 INFO 2026-05-28 21:01:44 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:4,883 INFO 2026-05-28 21:02:12 OpticalDuplicateFinder Large duplicate set. size = 1355 INFO 2026-05-28 21:02:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,554 INFO 2026-05-28 21:02:14 OpticalDuplicateFinder Large duplicate set. size = 1033 INFO 2026-05-28 21:02:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,883 INFO 2026-05-28 21:02:14 OpticalDuplicateFinder Large duplicate set. size = 1037 INFO 2026-05-28 21:02:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,231 INFO 2026-05-28 21:02:14 OpticalDuplicateFinder Large duplicate set. size = 1249 INFO 2026-05-28 21:02:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,353 INFO 2026-05-28 21:02:14 OpticalDuplicateFinder Large duplicate set. size = 1042 INFO 2026-05-28 21:02:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,806 INFO 2026-05-28 21:02:15 OpticalDuplicateFinder Large duplicate set. size = 1124 INFO 2026-05-28 21:02:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,604 INFO 2026-05-28 21:02:20 OpticalDuplicateFinder Large duplicate set. size = 1091 INFO 2026-05-28 21:02:20 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,878 INFO 2026-05-28 21:02:20 OpticalDuplicateFinder Large duplicate set. size = 1630 INFO 2026-05-28 21:02:20 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 21:02:20 OpticalDuplicateFinder Large duplicate set. size = 1137 INFO 2026-05-28 21:02:20 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:21,411 INFO 2026-05-28 21:02:20 OpticalDuplicateFinder Large duplicate set. size = 1143 INFO 2026-05-28 21:02:20 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,070 INFO 2026-05-28 21:02:20 OpticalDuplicateFinder Large duplicate set. size = 1935 INFO 2026-05-28 21:02:20 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:23,612 INFO 2026-05-28 21:02:20 OpticalDuplicateFinder Large duplicate set. size = 1610 INFO 2026-05-28 21:02:20 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:26,508 INFO 2026-05-28 21:02:20 OpticalDuplicateFinder Large duplicate set. size = 1015 INFO 2026-05-28 21:02:20 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:23,401 INFO 2026-05-28 21:02:23 OpticalDuplicateFinder Large duplicate set. size = 1018 INFO 2026-05-28 21:02:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,990 INFO 2026-05-28 21:02:23 OpticalDuplicateFinder Large duplicate set. size = 1257 INFO 2026-05-28 21:02:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,889 INFO 2026-05-28 21:02:23 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2026-05-28 21:02:37 MarkDuplicates Sorting list of duplicate records. INFO 2026-05-28 21:02:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300758976; totalMemory: 53250883584; maxMemory: 63585648640 INFO 2026-05-28 21:02:44 MarkDuplicates Marking 133365941 records as duplicates. INFO 2026-05-28 21:02:44 MarkDuplicates Found 3000938 optical duplicate clusters. INFO 2026-05-28 21:02:44 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2026-05-28 21:03:09 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:25s. Time for last 10,000,000: 25s. Last read position: chr1:154,489,268 INFO 2026-05-28 21:03:35 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:50s. Time for last 10,000,000: 25s. Last read position: chr2:106,073,968 INFO 2026-05-28 21:04:00 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:15s. Time for last 10,000,000: 25s. Last read position: chr3:58,170,690 INFO 2026-05-28 21:04:25 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:40s. Time for last 10,000,000: 24s. Last read position: chr5:114,362,648 INFO 2026-05-28 21:04:49 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:02:04s. Time for last 10,000,000: 24s. Last read position: chr6:129,791,548 INFO 2026-05-28 21:05:14 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:29s. Time for last 10,000,000: 24s. Last read position: chr7:151,142,603 INFO 2026-05-28 21:05:38 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:54s. Time for last 10,000,000: 24s. Last read position: chr9:130,878,444 INFO 2026-05-28 21:06:02 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:03:17s. Time for last 10,000,000: 23s. Last read position: chr11:57,313,676 INFO 2026-05-28 21:06:27 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:03:42s. Time for last 10,000,000: 24s. Last read position: chr12:53,063,243 INFO 2026-05-28 21:06:52 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:04:07s. Time for last 10,000,000: 25s. Last read position: chr14:75,783,330 INFO 2026-05-28 21:07:16 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:04:31s. Time for last 10,000,000: 23s. Last read position: chr16:15,363,810 INFO 2026-05-28 21:07:40 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:04:55s. Time for last 10,000,000: 23s. Last read position: chr17:3,577,628 INFO 2026-05-28 21:08:05 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:05:20s. Time for last 10,000,000: 25s. Last read position: chr17:50,193,992 INFO 2026-05-28 21:08:30 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:05:45s. Time for last 10,000,000: 24s. Last read position: chr19:6,415,018 INFO 2026-05-28 21:08:54 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:06:09s. Time for last 10,000,000: 24s. Last read position: chr19:57,390,017 INFO 2026-05-28 21:09:18 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:06:33s. Time for last 10,000,000: 24s. Last read position: chr21:8,444,101 INFO 2026-05-28 21:09:42 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:06:57s. Time for last 10,000,000: 24s. Last read position: chrX:118,907,494 INFO 2026-05-28 21:10:06 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:07:21s. Time for last 10,000,000: 23s. Last read position: KI270733.1:178,729 INFO 2026-05-28 21:10:14 MarkDuplicates Writing complete. Closing input iterator. INFO 2026-05-28 21:10:14 MarkDuplicates Duplicate Index cleanup. INFO 2026-05-28 21:10:14 MarkDuplicates Getting Memory Stats. INFO 2026-05-28 21:10:14 MarkDuplicates Before output close freeMemory: 201541488; totalMemory: 234881024; maxMemory: 63585648640 INFO 2026-05-28 21:10:14 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2026-05-28 21:10:14 MarkDuplicates After output close freeMemory: 104232504; totalMemory: 134217728; maxMemory: 63585648640 [Thu May 28 21:10:14 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 16.16 minutes. Runtime.totalMemory()=134217728 ls: *cram: No such file or directory ls: *.crai: No such file or directory