Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT 659_bGc-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bam --METRICS_FILE 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
08:12:03.920 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Jun 08 08:12:03 GMT 2026] MarkDuplicates --INPUT 659_bGc-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bam --METRICS_FILE 659_bGc-T1-TRNA-1_B23WHTKLT4_1.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 08:12:03 GMT 2026] Executing as ?@nf-ca35d1a9ca8699bcb7c703cbc3b2b841-956a7-r7lvr on Linux 6.12.88 amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0
INFO 2026-06-08 08:12:03 MarkDuplicates Start of doWork freeMemory: 105494112; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 08:12:03 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 08:12:03 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 08:12:07 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:1,512,312
INFO 2026-06-08 08:12:07 MarkDuplicates Tracking 2345 as yet unmatched pairs. 69 records in RAM.
INFO 2026-06-08 08:12:09 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: chr1:6,026,368
INFO 2026-06-08 08:12:09 MarkDuplicates Tracking 4637 as yet unmatched pairs. 202 records in RAM.
INFO 2026-06-08 08:12:11 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: chr1:10,408,081
INFO 2026-06-08 08:12:11 MarkDuplicates Tracking 6324 as yet unmatched pairs. 214 records in RAM.
INFO 2026-06-08 08:12:14 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: chr1:15,933,042
INFO 2026-06-08 08:12:14 MarkDuplicates Tracking 8022 as yet unmatched pairs. 155 records in RAM.
INFO 2026-06-08 08:12:16 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 2s. Last read position: chr1:19,385,515
INFO 2026-06-08 08:12:16 MarkDuplicates Tracking 10500 as yet unmatched pairs. 655 records in RAM.
INFO 2026-06-08 08:12:18 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: chr1:21,846,114
INFO 2026-06-08 08:12:18 MarkDuplicates Tracking 12209 as yet unmatched pairs. 499 records in RAM.
INFO 2026-06-08 08:12:20 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: chr1:22,660,983
INFO 2026-06-08 08:12:20 MarkDuplicates Tracking 14175 as yet unmatched pairs. 763 records in RAM.
INFO 2026-06-08 08:12:21 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: chr1:26,731,257
INFO 2026-06-08 08:12:21 MarkDuplicates Tracking 15240 as yet unmatched pairs. 85 records in RAM.
INFO 2026-06-08 08:12:24 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 2s. Last read position: chr1:29,181,643
INFO 2026-06-08 08:12:24 MarkDuplicates Tracking 17013 as yet unmatched pairs. 56 records in RAM.
INFO 2026-06-08 08:12:26 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 2s. Last read position: chr1:32,964,293
INFO 2026-06-08 08:12:26 MarkDuplicates Tracking 18739 as yet unmatched pairs. 87 records in RAM.
INFO 2026-06-08 08:12:28 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: chr1:39,028,853
INFO 2026-06-08 08:12:28 MarkDuplicates Tracking 20629 as yet unmatched pairs. 214 records in RAM.
INFO 2026-06-08 08:12:29 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: chr1:39,442,878
INFO 2026-06-08 08:12:29 MarkDuplicates Tracking 22674 as yet unmatched pairs. 613 records in RAM.
INFO 2026-06-08 08:12:32 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 2s. Last read position: chr1:43,415,995
INFO 2026-06-08 08:12:32 MarkDuplicates Tracking 24016 as yet unmatched pairs. 91 records in RAM.
INFO 2026-06-08 08:12:33 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 1s. Last read position: chr1:46,286,155
INFO 2026-06-08 08:12:33 MarkDuplicates Tracking 26093 as yet unmatched pairs. 471 records in RAM.
INFO 2026-06-08 08:12:35 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 1s. Last read position: chr1:53,014,949
INFO 2026-06-08 08:12:35 MarkDuplicates Tracking 27644 as yet unmatched pairs. 230 records in RAM.
INFO 2026-06-08 08:12:37 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 1s. Last read position: chr1:64,844,757
INFO 2026-06-08 08:12:37 MarkDuplicates Tracking 29386 as yet unmatched pairs. 309 records in RAM.
INFO 2026-06-08 08:12:39 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 1s. Last read position: chr1:89,188,688
INFO 2026-06-08 08:12:39 MarkDuplicates Tracking 30818 as yet unmatched pairs. 141 records in RAM.
INFO 2026-06-08 08:12:41 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 1s. Last read position: chr1:109,235,330
INFO 2026-06-08 08:12:41 MarkDuplicates Tracking 32504 as yet unmatched pairs. 257 records in RAM.
INFO 2026-06-08 08:12:42 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 1s. Last read position: chr1:113,852,057
INFO 2026-06-08 08:12:42 MarkDuplicates Tracking 34100 as yet unmatched pairs. 129 records in RAM.
INFO 2026-06-08 08:12:44 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 1s. Last read position: chr1:117,623,984
INFO 2026-06-08 08:12:44 MarkDuplicates Tracking 35824 as yet unmatched pairs. 296 records in RAM.
INFO 2026-06-08 08:12:46 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 1s. Last read position: chr1:144,063,205
INFO 2026-06-08 08:12:46 MarkDuplicates Tracking 36793 as yet unmatched pairs. 21 records in RAM.
INFO 2026-06-08 08:12:48 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 1s. Last read position: chr1:146,228,860
INFO 2026-06-08 08:12:48 MarkDuplicates Tracking 37877 as yet unmatched pairs. 17 records in RAM.
INFO 2026-06-08 08:12:50 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 2s. Last read position: chr1:148,979,774
INFO 2026-06-08 08:12:50 MarkDuplicates Tracking 39057 as yet unmatched pairs. 176 records in RAM.
INFO 2026-06-08 08:12:51 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 1s. Last read position: chr1:150,627,490
INFO 2026-06-08 08:12:51 MarkDuplicates Tracking 41295 as yet unmatched pairs. 1002 records in RAM.
INFO 2026-06-08 08:12:53 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 1s. Last read position: chr1:151,983,180
INFO 2026-06-08 08:12:53 MarkDuplicates Tracking 42563 as yet unmatched pairs. 308 records in RAM.
INFO 2026-06-08 08:12:54 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 1s. Last read position: chr1:153,991,585
INFO 2026-06-08 08:12:54 MarkDuplicates Tracking 44375 as yet unmatched pairs. 265 records in RAM.
INFO 2026-06-08 08:12:56 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 1s. Last read position: chr1:155,057,855
INFO 2026-06-08 08:12:56 MarkDuplicates Tracking 46180 as yet unmatched pairs. 310 records in RAM.
INFO 2026-06-08 08:12:57 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 1s. Last read position: chr1:155,190,643
INFO 2026-06-08 08:12:57 MarkDuplicates Tracking 47752 as yet unmatched pairs. 602 records in RAM.
INFO 2026-06-08 08:12:58 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 1s. Last read position: chr1:155,859,631
INFO 2026-06-08 08:12:58 MarkDuplicates Tracking 48446 as yet unmatched pairs. 26 records in RAM.
INFO 2026-06-08 08:13:00 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 2s. Last read position: chr1:156,767,821
INFO 2026-06-08 08:13:00 MarkDuplicates Tracking 50413 as yet unmatched pairs. 190 records in RAM.
INFO 2026-06-08 08:13:03 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 2s. Last read position: chr1:161,209,883
INFO 2026-06-08 08:13:03 MarkDuplicates Tracking 52084 as yet unmatched pairs. 208 records in RAM.
INFO 2026-06-08 08:13:05 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 1s. Last read position: chr1:171,203,987
INFO 2026-06-08 08:13:05 MarkDuplicates Tracking 53949 as yet unmatched pairs. 482 records in RAM.
INFO 2026-06-08 08:13:07 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 1s. Last read position: chr1:180,632,225
INFO 2026-06-08 08:13:07 MarkDuplicates Tracking 55174 as yet unmatched pairs. 235 records in RAM.
INFO 2026-06-08 08:13:09 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 1s. Last read position: chr1:186,145,780
INFO 2026-06-08 08:13:09 MarkDuplicates Tracking 56737 as yet unmatched pairs. 313 records in RAM.
INFO 2026-06-08 08:13:10 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 1s. Last read position: chr1:201,829,306
INFO 2026-06-08 08:13:10 MarkDuplicates Tracking 58031 as yet unmatched pairs. 160 records in RAM.
INFO 2026-06-08 08:13:12 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 1s. Last read position: chr1:205,351,294
INFO 2026-06-08 08:13:12 MarkDuplicates Tracking 59527 as yet unmatched pairs. 0 records in RAM.
INFO 2026-06-08 08:13:13 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 1s. Last read position: chr1:207,114,213
INFO 2026-06-08 08:13:13 MarkDuplicates Tracking 63133 as yet unmatched pairs. 1957 records in RAM.
INFO 2026-06-08 08:13:15 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 1s. Last read position: chr1:214,330,176
INFO 2026-06-08 08:13:15 MarkDuplicates Tracking 62885 as yet unmatched pairs. 50 records in RAM.
INFO 2026-06-08 08:13:16 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 1s. Last read position: chr1:225,810,147
INFO 2026-06-08 08:13:16 MarkDuplicates Tracking 65545 as yet unmatched pairs. 962 records in RAM.
INFO 2026-06-08 08:13:18 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 1s. Last read position: chr1:228,406,380
INFO 2026-06-08 08:13:18 MarkDuplicates Tracking 66778 as yet unmatched pairs. 194 records in RAM.
INFO 2026-06-08 08:13:19 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 1s. Last read position: chr1:236,220,831
INFO 2026-06-08 08:13:19 MarkDuplicates Tracking 68687 as yet unmatched pairs. 28 records in RAM.
INFO 2026-06-08 08:13:21 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 1s. Last read position: chr2:3,651,326
INFO 2026-06-08 08:13:21 MarkDuplicates Tracking 70375 as yet unmatched pairs. 70244 records in RAM.
INFO 2026-06-08 08:13:23 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 1s. Last read position: chr2:20,447,918
INFO 2026-06-08 08:13:23 MarkDuplicates Tracking 73372 as yet unmatched pairs. 73228 records in RAM.
INFO 2026-06-08 08:13:26 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 2s. Last read position: chr2:27,434,736
INFO 2026-06-08 08:13:26 MarkDuplicates Tracking 74181 as yet unmatched pairs. 74029 records in RAM.
INFO 2026-06-08 08:13:28 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,258
INFO 2026-06-08 08:13:28 MarkDuplicates Tracking 113594 as yet unmatched pairs. 73003 records in RAM.
INFO 2026-06-08 08:13:30 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,370
INFO 2026-06-08 08:13:30 MarkDuplicates Tracking 559272 as yet unmatched pairs. 48624 records in RAM.
INFO 2026-06-08 08:13:32 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 1s. Last read position: chr2:33,347,415
INFO 2026-06-08 08:13:32 MarkDuplicates Tracking 629215 as yet unmatched pairs. 45487 records in RAM.
INFO 2026-06-08 08:13:33 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 1s. Last read position: chr2:43,581,874
INFO 2026-06-08 08:13:33 MarkDuplicates Tracking 626770 as yet unmatched pairs. 43042 records in RAM.
INFO 2026-06-08 08:13:35 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 1s. Last read position: chr2:47,800,321
INFO 2026-06-08 08:13:35 MarkDuplicates Tracking 624929 as yet unmatched pairs. 41201 records in RAM.
INFO 2026-06-08 08:13:37 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 1s. Last read position: chr2:55,233,361
INFO 2026-06-08 08:13:37 MarkDuplicates Tracking 623715 as yet unmatched pairs. 39986 records in RAM.
INFO 2026-06-08 08:13:38 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 1s. Last read position: chr2:69,400,517
INFO 2026-06-08 08:13:38 MarkDuplicates Tracking 621706 as yet unmatched pairs. 37975 records in RAM.
INFO 2026-06-08 08:13:40 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 1s. Last read position: chr2:74,529,223
INFO 2026-06-08 08:13:40 MarkDuplicates Tracking 620117 as yet unmatched pairs. 36386 records in RAM.
INFO 2026-06-08 08:13:41 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 1s. Last read position: chr2:85,661,508
INFO 2026-06-08 08:13:41 MarkDuplicates Tracking 638403 as yet unmatched pairs. 54660 records in RAM.
INFO 2026-06-08 08:13:43 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 2s. Last read position: chr2:85,665,306
INFO 2026-06-08 08:13:43 MarkDuplicates Tracking 637149 as yet unmatched pairs. 53406 records in RAM.
INFO 2026-06-08 08:13:45 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 1s. Last read position: chr2:85,667,144
INFO 2026-06-08 08:13:45 MarkDuplicates Tracking 624892 as yet unmatched pairs. 41149 records in RAM.
INFO 2026-06-08 08:13:46 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 1s. Last read position: chr2:96,279,511
INFO 2026-06-08 08:13:46 MarkDuplicates Tracking 612946 as yet unmatched pairs. 29203 records in RAM.
INFO 2026-06-08 08:13:48 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 1s. Last read position: chr2:106,096,802
INFO 2026-06-08 08:13:48 MarkDuplicates Tracking 611290 as yet unmatched pairs. 27539 records in RAM.
INFO 2026-06-08 08:13:50 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 1s. Last read position: chr2:112,106,049
INFO 2026-06-08 08:13:50 MarkDuplicates Tracking 610116 as yet unmatched pairs. 26365 records in RAM.
INFO 2026-06-08 08:13:51 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 1s. Last read position: chr2:127,709,779
INFO 2026-06-08 08:13:51 MarkDuplicates Tracking 608789 as yet unmatched pairs. 25037 records in RAM.
INFO 2026-06-08 08:13:52 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 1s. Last read position: chr2:152,673,641
INFO 2026-06-08 08:13:52 MarkDuplicates Tracking 607241 as yet unmatched pairs. 23489 records in RAM.
INFO 2026-06-08 08:13:55 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 2s. Last read position: chr2:171,553,422
INFO 2026-06-08 08:13:55 MarkDuplicates Tracking 606148 as yet unmatched pairs. 22389 records in RAM.
INFO 2026-06-08 08:13:56 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 1s. Last read position: chr2:181,915,265
INFO 2026-06-08 08:13:56 MarkDuplicates Tracking 604023 as yet unmatched pairs. 20258 records in RAM.
INFO 2026-06-08 08:13:58 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 1s. Last read position: chr2:189,924,007
INFO 2026-06-08 08:13:58 MarkDuplicates Tracking 602019 as yet unmatched pairs. 18252 records in RAM.
INFO 2026-06-08 08:14:00 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 1s. Last read position: chr2:201,380,941
INFO 2026-06-08 08:14:00 MarkDuplicates Tracking 600470 as yet unmatched pairs. 16685 records in RAM.
INFO 2026-06-08 08:14:02 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 1s. Last read position: chr2:215,361,542
INFO 2026-06-08 08:14:02 MarkDuplicates Tracking 605037 as yet unmatched pairs. 21242 records in RAM.
INFO 2026-06-08 08:14:03 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 1s. Last read position: chr2:215,375,249
INFO 2026-06-08 08:14:03 MarkDuplicates Tracking 603685 as yet unmatched pairs. 19885 records in RAM.
INFO 2026-06-08 08:14:06 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 2s. Last read position: chr2:215,386,864
INFO 2026-06-08 08:14:06 MarkDuplicates Tracking 601892 as yet unmatched pairs. 18092 records in RAM.
INFO 2026-06-08 08:14:07 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 1s. Last read position: chr2:215,408,151
INFO 2026-06-08 08:14:07 MarkDuplicates Tracking 600510 as yet unmatched pairs. 16710 records in RAM.
INFO 2026-06-08 08:14:09 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 1s. Last read position: chr2:215,428,320
INFO 2026-06-08 08:14:09 MarkDuplicates Tracking 596283 as yet unmatched pairs. 12480 records in RAM.
INFO 2026-06-08 08:14:10 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 1s. Last read position: chr2:217,818,568
INFO 2026-06-08 08:14:10 MarkDuplicates Tracking 593329 as yet unmatched pairs. 9526 records in RAM.
INFO 2026-06-08 08:14:12 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 1s. Last read position: chr2:219,224,561
INFO 2026-06-08 08:14:12 MarkDuplicates Tracking 590384 as yet unmatched pairs. 6580 records in RAM.
INFO 2026-06-08 08:14:13 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 1s. Last read position: chr2:230,444,327
INFO 2026-06-08 08:14:13 MarkDuplicates Tracking 588753 as yet unmatched pairs. 4942 records in RAM.
INFO 2026-06-08 08:14:15 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 1s. Last read position: chr2:237,368,723
INFO 2026-06-08 08:14:15 MarkDuplicates Tracking 587266 as yet unmatched pairs. 3448 records in RAM.
INFO 2026-06-08 08:14:16 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 1s. Last read position: chr2:241,068,996
INFO 2026-06-08 08:14:16 MarkDuplicates Tracking 584684 as yet unmatched pairs. 866 records in RAM.
INFO 2026-06-08 08:14:18 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 1s. Last read position: chr3:9,909,178
INFO 2026-06-08 08:14:18 MarkDuplicates Tracking 583077 as yet unmatched pairs. 29779 records in RAM.
INFO 2026-06-08 08:14:19 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 1s. Last read position: chr3:15,685,242
INFO 2026-06-08 08:14:19 MarkDuplicates Tracking 581269 as yet unmatched pairs. 27970 records in RAM.
INFO 2026-06-08 08:14:21 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 1s. Last read position: chr3:37,102,930
INFO 2026-06-08 08:14:21 MarkDuplicates Tracking 579740 as yet unmatched pairs. 26421 records in RAM.
INFO 2026-06-08 08:14:22 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 1s. Last read position: chr3:41,663,686
INFO 2026-06-08 08:14:22 MarkDuplicates Tracking 578066 as yet unmatched pairs. 24745 records in RAM.
INFO 2026-06-08 08:14:24 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 1s. Last read position: chr3:47,410,884
INFO 2026-06-08 08:14:24 MarkDuplicates Tracking 576283 as yet unmatched pairs. 22961 records in RAM.
INFO 2026-06-08 08:14:26 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 1s. Last read position: chr3:49,098,386
INFO 2026-06-08 08:14:26 MarkDuplicates Tracking 574596 as yet unmatched pairs. 21274 records in RAM.
INFO 2026-06-08 08:14:27 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr3:50,174,341
INFO 2026-06-08 08:14:27 MarkDuplicates Tracking 572869 as yet unmatched pairs. 19545 records in RAM.
INFO 2026-06-08 08:14:29 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 1s. Last read position: chr3:52,353,132
INFO 2026-06-08 08:14:29 MarkDuplicates Tracking 571144 as yet unmatched pairs. 17818 records in RAM.
INFO 2026-06-08 08:14:30 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 1s. Last read position: chr3:58,098,755
INFO 2026-06-08 08:14:30 MarkDuplicates Tracking 569639 as yet unmatched pairs. 16306 records in RAM.
INFO 2026-06-08 08:14:32 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 1s. Last read position: chr3:78,606,899
INFO 2026-06-08 08:14:32 MarkDuplicates Tracking 567616 as yet unmatched pairs. 14276 records in RAM.
INFO 2026-06-08 08:14:33 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 1s. Last read position: chr3:111,885,269
INFO 2026-06-08 08:14:33 MarkDuplicates Tracking 566170 as yet unmatched pairs. 12829 records in RAM.
INFO 2026-06-08 08:14:35 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 1s. Last read position: chr3:122,879,273
INFO 2026-06-08 08:14:35 MarkDuplicates Tracking 564563 as yet unmatched pairs. 11218 records in RAM.
INFO 2026-06-08 08:14:36 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 1s. Last read position: chr3:128,069,559
INFO 2026-06-08 08:14:36 MarkDuplicates Tracking 563192 as yet unmatched pairs. 9846 records in RAM.
INFO 2026-06-08 08:14:38 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 2s. Last read position: chr3:132,681,955
INFO 2026-06-08 08:14:38 MarkDuplicates Tracking 560860 as yet unmatched pairs. 7514 records in RAM.
INFO 2026-06-08 08:14:40 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 1s. Last read position: chr3:149,542,487
INFO 2026-06-08 08:14:40 MarkDuplicates Tracking 559338 as yet unmatched pairs. 5983 records in RAM.
INFO 2026-06-08 08:14:41 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 1s. Last read position: chr3:170,384,569
INFO 2026-06-08 08:14:41 MarkDuplicates Tracking 557490 as yet unmatched pairs. 4134 records in RAM.
INFO 2026-06-08 08:14:44 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 2s. Last read position: chr3:184,337,597
INFO 2026-06-08 08:14:44 MarkDuplicates Tracking 556003 as yet unmatched pairs. 2647 records in RAM.
INFO 2026-06-08 08:14:45 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 1s. Last read position: chr3:195,381,936
INFO 2026-06-08 08:14:45 MarkDuplicates Tracking 554500 as yet unmatched pairs. 1141 records in RAM.
INFO 2026-06-08 08:14:47 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 1s. Last read position: chr4:1,213,477
INFO 2026-06-08 08:14:47 MarkDuplicates Tracking 553296 as yet unmatched pairs. 21744 records in RAM.
INFO 2026-06-08 08:14:49 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 1s. Last read position: chr4:5,793,622
INFO 2026-06-08 08:14:49 MarkDuplicates Tracking 550800 as yet unmatched pairs. 19248 records in RAM.
INFO 2026-06-08 08:14:51 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 1s. Last read position: chr4:24,576,446
INFO 2026-06-08 08:14:51 MarkDuplicates Tracking 548744 as yet unmatched pairs. 17189 records in RAM.
INFO 2026-06-08 08:14:52 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 1s. Last read position: chr4:25,673,240
INFO 2026-06-08 08:14:52 MarkDuplicates Tracking 553101 as yet unmatched pairs. 21546 records in RAM.
INFO 2026-06-08 08:14:54 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 1s. Last read position: chr4:39,446,360
INFO 2026-06-08 08:14:54 MarkDuplicates Tracking 545423 as yet unmatched pairs. 13868 records in RAM.
INFO 2026-06-08 08:14:56 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 1s. Last read position: chr4:54,274,545
INFO 2026-06-08 08:14:56 MarkDuplicates Tracking 545287 as yet unmatched pairs. 13730 records in RAM.
INFO 2026-06-08 08:14:57 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 1s. Last read position: chr4:73,094,084
INFO 2026-06-08 08:14:57 MarkDuplicates Tracking 542350 as yet unmatched pairs. 10790 records in RAM.
INFO 2026-06-08 08:14:59 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 1s. Last read position: chr4:82,851,591
INFO 2026-06-08 08:14:59 MarkDuplicates Tracking 540948 as yet unmatched pairs. 9380 records in RAM.
INFO 2026-06-08 08:15:00 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 1s. Last read position: chr4:88,439,952
INFO 2026-06-08 08:15:00 MarkDuplicates Tracking 539141 as yet unmatched pairs. 7573 records in RAM.
INFO 2026-06-08 08:15:02 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 1s. Last read position: chr4:106,347,618
INFO 2026-06-08 08:15:02 MarkDuplicates Tracking 537555 as yet unmatched pairs. 5986 records in RAM.
INFO 2026-06-08 08:15:03 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 1s. Last read position: chr4:125,450,528
INFO 2026-06-08 08:15:03 MarkDuplicates Tracking 536109 as yet unmatched pairs. 4533 records in RAM.
INFO 2026-06-08 08:15:05 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 1s. Last read position: chr4:151,165,606
INFO 2026-06-08 08:15:05 MarkDuplicates Tracking 534946 as yet unmatched pairs. 3366 records in RAM.
INFO 2026-06-08 08:15:06 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 1s. Last read position: chr4:177,439,609
INFO 2026-06-08 08:15:06 MarkDuplicates Tracking 532898 as yet unmatched pairs. 1314 records in RAM.
INFO 2026-06-08 08:15:08 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 1s. Last read position: chr5:1,470,823
INFO 2026-06-08 08:15:08 MarkDuplicates Tracking 531732 as yet unmatched pairs. 40258 records in RAM.
INFO 2026-06-08 08:15:10 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 1s. Last read position: chr5:14,374,297
INFO 2026-06-08 08:15:10 MarkDuplicates Tracking 530471 as yet unmatched pairs. 38986 records in RAM.
INFO 2026-06-08 08:15:11 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 1s. Last read position: chr5:35,659,029
INFO 2026-06-08 08:15:11 MarkDuplicates Tracking 527092 as yet unmatched pairs. 35606 records in RAM.
INFO 2026-06-08 08:15:13 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 1s. Last read position: chr5:43,529,850
INFO 2026-06-08 08:15:13 MarkDuplicates Tracking 525626 as yet unmatched pairs. 34139 records in RAM.
INFO 2026-06-08 08:15:15 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 1s. Last read position: chr5:67,145,337
INFO 2026-06-08 08:15:15 MarkDuplicates Tracking 524189 as yet unmatched pairs. 32700 records in RAM.
INFO 2026-06-08 08:15:16 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 1s. Last read position: chr5:75,511,289
INFO 2026-06-08 08:15:16 MarkDuplicates Tracking 522507 as yet unmatched pairs. 31018 records in RAM.
INFO 2026-06-08 08:15:17 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 1s. Last read position: chr5:91,150,126
INFO 2026-06-08 08:15:17 MarkDuplicates Tracking 520939 as yet unmatched pairs. 29445 records in RAM.
INFO 2026-06-08 08:15:19 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 1s. Last read position: chr5:112,902,388
INFO 2026-06-08 08:15:19 MarkDuplicates Tracking 519649 as yet unmatched pairs. 28155 records in RAM.
INFO 2026-06-08 08:15:21 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 1s. Last read position: chr5:133,956,918
INFO 2026-06-08 08:15:21 MarkDuplicates Tracking 517591 as yet unmatched pairs. 26089 records in RAM.
INFO 2026-06-08 08:15:22 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 1s. Last read position: chr5:138,932,646
INFO 2026-06-08 08:15:22 MarkDuplicates Tracking 516550 as yet unmatched pairs. 25045 records in RAM.
INFO 2026-06-08 08:15:23 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 1s. Last read position: chr5:141,194,271
INFO 2026-06-08 08:15:23 MarkDuplicates Tracking 514455 as yet unmatched pairs. 22945 records in RAM.
INFO 2026-06-08 08:15:26 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 2s. Last read position: chr5:146,284,625
INFO 2026-06-08 08:15:26 MarkDuplicates Tracking 512829 as yet unmatched pairs. 21319 records in RAM.
INFO 2026-06-08 08:15:27 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: chr5:150,120,010
INFO 2026-06-08 08:15:27 MarkDuplicates Tracking 511829 as yet unmatched pairs. 20319 records in RAM.
INFO 2026-06-08 08:15:29 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 1s. Last read position: chr5:150,402,563
INFO 2026-06-08 08:15:29 MarkDuplicates Tracking 538695 as yet unmatched pairs. 47185 records in RAM.
INFO 2026-06-08 08:15:31 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 2s. Last read position: chr5:150,405,112
INFO 2026-06-08 08:15:31 MarkDuplicates Tracking 530969 as yet unmatched pairs. 39459 records in RAM.
INFO 2026-06-08 08:15:33 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 2s. Last read position: chr5:150,407,157
INFO 2026-06-08 08:15:33 MarkDuplicates Tracking 523457 as yet unmatched pairs. 31947 records in RAM.
INFO 2026-06-08 08:15:35 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 1s. Last read position: chr5:150,656,889
INFO 2026-06-08 08:15:35 MarkDuplicates Tracking 503970 as yet unmatched pairs. 12460 records in RAM.
INFO 2026-06-08 08:15:37 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 1s. Last read position: chr5:158,796,370
INFO 2026-06-08 08:15:37 MarkDuplicates Tracking 501834 as yet unmatched pairs. 10314 records in RAM.
INFO 2026-06-08 08:15:38 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 1s. Last read position: chr5:172,337,155
INFO 2026-06-08 08:15:38 MarkDuplicates Tracking 500173 as yet unmatched pairs. 8650 records in RAM.
INFO 2026-06-08 08:15:40 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 1s. Last read position: chr5:177,468,886
INFO 2026-06-08 08:15:40 MarkDuplicates Tracking 498371 as yet unmatched pairs. 6847 records in RAM.
INFO 2026-06-08 08:15:41 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 1s. Last read position: chr5:179,822,957
INFO 2026-06-08 08:15:41 MarkDuplicates Tracking 498543 as yet unmatched pairs. 7019 records in RAM.
INFO 2026-06-08 08:15:43 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 1s. Last read position: chr5:180,590,216
INFO 2026-06-08 08:15:43 MarkDuplicates Tracking 524572 as yet unmatched pairs. 33048 records in RAM.
INFO 2026-06-08 08:15:44 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 1s. Last read position: chr5:181,238,200
INFO 2026-06-08 08:15:44 MarkDuplicates Tracking 494260 as yet unmatched pairs. 2726 records in RAM.
INFO 2026-06-08 08:15:46 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 1s. Last read position: chr6:7,886,030
INFO 2026-06-08 08:15:46 MarkDuplicates Tracking 490042 as yet unmatched pairs. 36247 records in RAM.
INFO 2026-06-08 08:15:48 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 1s. Last read position: chr6:24,843,292
INFO 2026-06-08 08:15:48 MarkDuplicates Tracking 487964 as yet unmatched pairs. 34169 records in RAM.
INFO 2026-06-08 08:15:49 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 1s. Last read position: chr6:29,944,350
INFO 2026-06-08 08:15:49 MarkDuplicates Tracking 490888 as yet unmatched pairs. 37081 records in RAM.
INFO 2026-06-08 08:15:51 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 1s. Last read position: chr6:31,164,675
INFO 2026-06-08 08:15:51 MarkDuplicates Tracking 484951 as yet unmatched pairs. 31144 records in RAM.
INFO 2026-06-08 08:15:52 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 1s. Last read position: chr6:31,641,863
INFO 2026-06-08 08:15:52 MarkDuplicates Tracking 483359 as yet unmatched pairs. 29552 records in RAM.
INFO 2026-06-08 08:15:54 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 1s. Last read position: chr6:31,983,361
INFO 2026-06-08 08:15:54 MarkDuplicates Tracking 481534 as yet unmatched pairs. 27726 records in RAM.
INFO 2026-06-08 08:15:55 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 1s. Last read position: chr6:32,062,200
INFO 2026-06-08 08:15:55 MarkDuplicates Tracking 480632 as yet unmatched pairs. 26823 records in RAM.
INFO 2026-06-08 08:15:57 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 1s. Last read position: chr6:32,215,269
INFO 2026-06-08 08:15:57 MarkDuplicates Tracking 478360 as yet unmatched pairs. 24551 records in RAM.
INFO 2026-06-08 08:15:58 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 1s. Last read position: chr6:32,980,002
INFO 2026-06-08 08:15:58 MarkDuplicates Tracking 476993 as yet unmatched pairs. 23181 records in RAM.
INFO 2026-06-08 08:15:59 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 1s. Last read position: chr6:33,415,248
INFO 2026-06-08 08:15:59 MarkDuplicates Tracking 475659 as yet unmatched pairs. 21847 records in RAM.
INFO 2026-06-08 08:16:01 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 1s. Last read position: chr6:35,577,222
INFO 2026-06-08 08:16:01 MarkDuplicates Tracking 475246 as yet unmatched pairs. 21434 records in RAM.
INFO 2026-06-08 08:16:03 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 1s. Last read position: chr6:41,740,576
INFO 2026-06-08 08:16:03 MarkDuplicates Tracking 475593 as yet unmatched pairs. 21781 records in RAM.
INFO 2026-06-08 08:16:04 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 1s. Last read position: chr6:43,186,085
INFO 2026-06-08 08:16:04 MarkDuplicates Tracking 469733 as yet unmatched pairs. 15919 records in RAM.
INFO 2026-06-08 08:16:06 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 1s. Last read position: chr6:47,286,400
INFO 2026-06-08 08:16:06 MarkDuplicates Tracking 467948 as yet unmatched pairs. 14133 records in RAM.
INFO 2026-06-08 08:16:07 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 1s. Last read position: chr6:73,500,601
INFO 2026-06-08 08:16:07 MarkDuplicates Tracking 466341 as yet unmatched pairs. 12517 records in RAM.
INFO 2026-06-08 08:16:09 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 1s. Last read position: chr6:100,848,483
INFO 2026-06-08 08:16:09 MarkDuplicates Tracking 464913 as yet unmatched pairs. 11086 records in RAM.
INFO 2026-06-08 08:16:10 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 1s. Last read position: chr6:117,326,224
INFO 2026-06-08 08:16:10 MarkDuplicates Tracking 463339 as yet unmatched pairs. 9512 records in RAM.
INFO 2026-06-08 08:16:12 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 1s. Last read position: chr6:130,869,719
INFO 2026-06-08 08:16:12 MarkDuplicates Tracking 461643 as yet unmatched pairs. 7816 records in RAM.
INFO 2026-06-08 08:16:14 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 2s. Last read position: chr6:142,411,256
INFO 2026-06-08 08:16:14 MarkDuplicates Tracking 459601 as yet unmatched pairs. 5774 records in RAM.
INFO 2026-06-08 08:16:15 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 1s. Last read position: chr6:152,148,364
INFO 2026-06-08 08:16:15 MarkDuplicates Tracking 458196 as yet unmatched pairs. 4367 records in RAM.
INFO 2026-06-08 08:16:17 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 1s. Last read position: chr6:158,783,560
INFO 2026-06-08 08:16:17 MarkDuplicates Tracking 458092 as yet unmatched pairs. 4263 records in RAM.
INFO 2026-06-08 08:16:19 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 1s. Last read position: chr6:168,598,876
INFO 2026-06-08 08:16:19 MarkDuplicates Tracking 454355 as yet unmatched pairs. 526 records in RAM.
INFO 2026-06-08 08:16:21 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 2s. Last read position: chr7:4,791,238
INFO 2026-06-08 08:16:21 MarkDuplicates Tracking 452091 as yet unmatched pairs. 29822 records in RAM.
INFO 2026-06-08 08:16:23 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 1s. Last read position: chr7:5,528,568
INFO 2026-06-08 08:16:23 MarkDuplicates Tracking 453374 as yet unmatched pairs. 31097 records in RAM.
INFO 2026-06-08 08:16:24 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 1s. Last read position: chr7:20,003,010
INFO 2026-06-08 08:16:24 MarkDuplicates Tracking 448329 as yet unmatched pairs. 26052 records in RAM.
INFO 2026-06-08 08:16:26 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 1s. Last read position: chr7:33,002,719
INFO 2026-06-08 08:16:26 MarkDuplicates Tracking 446840 as yet unmatched pairs. 24561 records in RAM.
INFO 2026-06-08 08:16:27 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 1s. Last read position: chr7:44,111,900
INFO 2026-06-08 08:16:27 MarkDuplicates Tracking 445893 as yet unmatched pairs. 23614 records in RAM.
INFO 2026-06-08 08:16:29 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 1s. Last read position: chr7:55,151,310
INFO 2026-06-08 08:16:29 MarkDuplicates Tracking 444159 as yet unmatched pairs. 21880 records in RAM.
INFO 2026-06-08 08:16:30 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 1s. Last read position: chr7:73,195,880
INFO 2026-06-08 08:16:30 MarkDuplicates Tracking 441591 as yet unmatched pairs. 19312 records in RAM.
INFO 2026-06-08 08:16:32 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr7:74,376,224
INFO 2026-06-08 08:16:32 MarkDuplicates Tracking 439339 as yet unmatched pairs. 17059 records in RAM.
INFO 2026-06-08 08:16:33 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr7:77,005,659
INFO 2026-06-08 08:16:33 MarkDuplicates Tracking 438218 as yet unmatched pairs. 15938 records in RAM.
INFO 2026-06-08 08:16:35 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 1s. Last read position: chr7:94,408,362
INFO 2026-06-08 08:16:35 MarkDuplicates Tracking 438582 as yet unmatched pairs. 16302 records in RAM.
INFO 2026-06-08 08:16:37 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 1s. Last read position: chr7:98,953,253
INFO 2026-06-08 08:16:37 MarkDuplicates Tracking 434803 as yet unmatched pairs. 12519 records in RAM.
INFO 2026-06-08 08:16:38 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 1s. Last read position: chr7:100,681,950
INFO 2026-06-08 08:16:38 MarkDuplicates Tracking 433124 as yet unmatched pairs. 10838 records in RAM.
INFO 2026-06-08 08:16:39 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 1s. Last read position: chr7:102,652,435
INFO 2026-06-08 08:16:39 MarkDuplicates Tracking 432118 as yet unmatched pairs. 9831 records in RAM.
INFO 2026-06-08 08:16:41 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 1s. Last read position: chr7:116,250,367
INFO 2026-06-08 08:16:41 MarkDuplicates Tracking 430188 as yet unmatched pairs. 7900 records in RAM.
INFO 2026-06-08 08:16:42 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 1s. Last read position: chr7:128,948,728
INFO 2026-06-08 08:16:42 MarkDuplicates Tracking 428450 as yet unmatched pairs. 6161 records in RAM.
INFO 2026-06-08 08:16:44 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 1s. Last read position: chr7:139,417,608
INFO 2026-06-08 08:16:44 MarkDuplicates Tracking 427087 as yet unmatched pairs. 4798 records in RAM.
INFO 2026-06-08 08:16:45 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 1s. Last read position: chr7:148,787,040
INFO 2026-06-08 08:16:45 MarkDuplicates Tracking 425337 as yet unmatched pairs. 3048 records in RAM.
INFO 2026-06-08 08:16:47 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 1s. Last read position: chr7:152,157,761
INFO 2026-06-08 08:16:47 MarkDuplicates Tracking 423353 as yet unmatched pairs. 1063 records in RAM.
INFO 2026-06-08 08:16:48 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 1s. Last read position: chr8:12,175,618
INFO 2026-06-08 08:16:48 MarkDuplicates Tracking 421360 as yet unmatched pairs. 27388 records in RAM.
INFO 2026-06-08 08:16:51 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 2s. Last read position: chr8:22,162,573
INFO 2026-06-08 08:16:51 MarkDuplicates Tracking 440053 as yet unmatched pairs. 46072 records in RAM.
INFO 2026-06-08 08:16:52 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 1s. Last read position: chr8:22,163,473
INFO 2026-06-08 08:16:52 MarkDuplicates Tracking 440961 as yet unmatched pairs. 46980 records in RAM.
INFO 2026-06-08 08:16:54 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 1s. Last read position: chr8:22,474,960
INFO 2026-06-08 08:16:54 MarkDuplicates Tracking 415661 as yet unmatched pairs. 21680 records in RAM.
INFO 2026-06-08 08:16:56 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 2s. Last read position: chr8:26,643,548
INFO 2026-06-08 08:16:56 MarkDuplicates Tracking 414728 as yet unmatched pairs. 20746 records in RAM.
INFO 2026-06-08 08:16:57 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 1s. Last read position: chr8:37,871,411
INFO 2026-06-08 08:16:57 MarkDuplicates Tracking 412176 as yet unmatched pairs. 18193 records in RAM.
INFO 2026-06-08 08:16:59 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 1s. Last read position: chr8:38,846,794
INFO 2026-06-08 08:16:59 MarkDuplicates Tracking 412137 as yet unmatched pairs. 18154 records in RAM.
INFO 2026-06-08 08:17:01 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 1s. Last read position: chr8:51,861,211
INFO 2026-06-08 08:17:01 MarkDuplicates Tracking 408169 as yet unmatched pairs. 14185 records in RAM.
INFO 2026-06-08 08:17:03 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 1s. Last read position: chr8:73,291,777
INFO 2026-06-08 08:17:03 MarkDuplicates Tracking 407678 as yet unmatched pairs. 13693 records in RAM.
INFO 2026-06-08 08:17:04 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 1s. Last read position: chr8:99,875,387
INFO 2026-06-08 08:17:04 MarkDuplicates Tracking 405062 as yet unmatched pairs. 11075 records in RAM.
INFO 2026-06-08 08:17:06 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 1s. Last read position: chr8:119,208,478
INFO 2026-06-08 08:17:06 MarkDuplicates Tracking 404188 as yet unmatched pairs. 10201 records in RAM.
INFO 2026-06-08 08:17:07 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 1s. Last read position: chr8:141,128,785
INFO 2026-06-08 08:17:07 MarkDuplicates Tracking 401786 as yet unmatched pairs. 7799 records in RAM.
INFO 2026-06-08 08:17:09 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 1s. Last read position: chr8:143,858,963
INFO 2026-06-08 08:17:09 MarkDuplicates Tracking 399788 as yet unmatched pairs. 5801 records in RAM.
INFO 2026-06-08 08:17:10 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 1s. Last read position: chr8:143,865,249
INFO 2026-06-08 08:17:10 MarkDuplicates Tracking 398700 as yet unmatched pairs. 4713 records in RAM.
INFO 2026-06-08 08:17:11 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 1s. Last read position: chr8:143,930,040
INFO 2026-06-08 08:17:11 MarkDuplicates Tracking 397864 as yet unmatched pairs. 3876 records in RAM.
INFO 2026-06-08 08:17:13 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 1s. Last read position: chr8:144,773,496
INFO 2026-06-08 08:17:13 MarkDuplicates Tracking 394252 as yet unmatched pairs. 264 records in RAM.
INFO 2026-06-08 08:17:14 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr9:14,307,423
INFO 2026-06-08 08:17:14 MarkDuplicates Tracking 393354 as yet unmatched pairs. 25744 records in RAM.
INFO 2026-06-08 08:17:16 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 1s. Last read position: chr9:33,953,463
INFO 2026-06-08 08:17:16 MarkDuplicates Tracking 390820 as yet unmatched pairs. 23208 records in RAM.
INFO 2026-06-08 08:17:17 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 1s. Last read position: chr9:35,717,337
INFO 2026-06-08 08:17:17 MarkDuplicates Tracking 389505 as yet unmatched pairs. 21880 records in RAM.
INFO 2026-06-08 08:17:19 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 1s. Last read position: chr9:72,355,946
INFO 2026-06-08 08:17:19 MarkDuplicates Tracking 388206 as yet unmatched pairs. 20577 records in RAM.
INFO 2026-06-08 08:17:20 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 1s. Last read position: chr9:92,047,630
INFO 2026-06-08 08:17:20 MarkDuplicates Tracking 385824 as yet unmatched pairs. 18191 records in RAM.
INFO 2026-06-08 08:17:22 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 1s. Last read position: chr9:99,984,991
INFO 2026-06-08 08:17:22 MarkDuplicates Tracking 384226 as yet unmatched pairs. 16592 records in RAM.
INFO 2026-06-08 08:17:23 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 1s. Last read position: chr9:112,750,973
INFO 2026-06-08 08:17:23 MarkDuplicates Tracking 383428 as yet unmatched pairs. 15794 records in RAM.
INFO 2026-06-08 08:17:25 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:05:20s. Time for last 1,000,000: 1s. Last read position: chr9:121,157,472
INFO 2026-06-08 08:17:25 MarkDuplicates Tracking 380370 as yet unmatched pairs. 12736 records in RAM.
INFO 2026-06-08 08:17:27 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 2s. Last read position: chr9:125,506,261
INFO 2026-06-08 08:17:27 MarkDuplicates Tracking 378829 as yet unmatched pairs. 11187 records in RAM.
INFO 2026-06-08 08:17:29 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 1s. Last read position: chr9:128,273,889
INFO 2026-06-08 08:17:29 MarkDuplicates Tracking 376716 as yet unmatched pairs. 9073 records in RAM.
INFO 2026-06-08 08:17:31 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 1s. Last read position: chr9:130,862,836
INFO 2026-06-08 08:17:31 MarkDuplicates Tracking 375151 as yet unmatched pairs. 7506 records in RAM.
INFO 2026-06-08 08:17:32 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 1s. Last read position: chr9:133,349,934
INFO 2026-06-08 08:17:32 MarkDuplicates Tracking 374147 as yet unmatched pairs. 6500 records in RAM.
INFO 2026-06-08 08:17:34 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 1s. Last read position: chr9:136,381,339
INFO 2026-06-08 08:17:34 MarkDuplicates Tracking 371522 as yet unmatched pairs. 3875 records in RAM.
INFO 2026-06-08 08:17:36 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 1s. Last read position: chr9:136,980,189
INFO 2026-06-08 08:17:36 MarkDuplicates Tracking 371311 as yet unmatched pairs. 3664 records in RAM.
INFO 2026-06-08 08:17:38 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 1s. Last read position: chr10:3,159,848
INFO 2026-06-08 08:17:38 MarkDuplicates Tracking 367388 as yet unmatched pairs. 21113 records in RAM.
INFO 2026-06-08 08:17:39 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 1s. Last read position: chr10:17,229,680
INFO 2026-06-08 08:17:39 MarkDuplicates Tracking 366603 as yet unmatched pairs. 20327 records in RAM.
INFO 2026-06-08 08:17:40 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 1s. Last read position: chr10:32,017,218
INFO 2026-06-08 08:17:40 MarkDuplicates Tracking 364550 as yet unmatched pairs. 18273 records in RAM.
INFO 2026-06-08 08:17:42 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 1s. Last read position: chr10:45,425,030
INFO 2026-06-08 08:17:42 MarkDuplicates Tracking 362686 as yet unmatched pairs. 16406 records in RAM.
INFO 2026-06-08 08:17:43 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 1s. Last read position: chr10:59,352,332
INFO 2026-06-08 08:17:43 MarkDuplicates Tracking 361165 as yet unmatched pairs. 14884 records in RAM.
INFO 2026-06-08 08:17:45 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 1s. Last read position: chr10:71,761,848
INFO 2026-06-08 08:17:45 MarkDuplicates Tracking 359535 as yet unmatched pairs. 13253 records in RAM.
INFO 2026-06-08 08:17:47 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 1s. Last read position: chr10:75,223,270
INFO 2026-06-08 08:17:47 MarkDuplicates Tracking 357819 as yet unmatched pairs. 11537 records in RAM.
INFO 2026-06-08 08:17:48 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 1s. Last read position: chr10:79,611,924
INFO 2026-06-08 08:17:48 MarkDuplicates Tracking 363987 as yet unmatched pairs. 17705 records in RAM.
INFO 2026-06-08 08:17:49 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 1s. Last read position: chr10:87,234,205
INFO 2026-06-08 08:17:49 MarkDuplicates Tracking 354721 as yet unmatched pairs. 8437 records in RAM.
INFO 2026-06-08 08:17:51 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 1s. Last read position: chr10:95,874,058
INFO 2026-06-08 08:17:51 MarkDuplicates Tracking 353285 as yet unmatched pairs. 6998 records in RAM.
INFO 2026-06-08 08:17:53 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 1s. Last read position: chr10:102,133,048
INFO 2026-06-08 08:17:53 MarkDuplicates Tracking 351505 as yet unmatched pairs. 5218 records in RAM.
INFO 2026-06-08 08:17:54 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 1s. Last read position: chr10:114,044,858
INFO 2026-06-08 08:17:54 MarkDuplicates Tracking 349431 as yet unmatched pairs. 3143 records in RAM.
INFO 2026-06-08 08:17:55 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 1s. Last read position: chr10:122,461,855
INFO 2026-06-08 08:17:55 MarkDuplicates Tracking 348167 as yet unmatched pairs. 1873 records in RAM.
INFO 2026-06-08 08:17:57 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 1s. Last read position: chr11:291,040
INFO 2026-06-08 08:17:57 MarkDuplicates Tracking 346592 as yet unmatched pairs. 40585 records in RAM.
INFO 2026-06-08 08:17:59 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 1s. Last read position: chr11:823,792
INFO 2026-06-08 08:17:59 MarkDuplicates Tracking 344403 as yet unmatched pairs. 38396 records in RAM.
INFO 2026-06-08 08:18:00 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 1s. Last read position: chr11:2,377,558
INFO 2026-06-08 08:18:00 MarkDuplicates Tracking 344071 as yet unmatched pairs. 38064 records in RAM.
INFO 2026-06-08 08:18:02 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 1s. Last read position: chr11:6,630,752
INFO 2026-06-08 08:18:02 MarkDuplicates Tracking 340052 as yet unmatched pairs. 34044 records in RAM.
INFO 2026-06-08 08:18:03 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 1s. Last read position: chr11:12,764,214
INFO 2026-06-08 08:18:03 MarkDuplicates Tracking 338407 as yet unmatched pairs. 32398 records in RAM.
INFO 2026-06-08 08:18:05 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 2s. Last read position: chr11:33,717,387
INFO 2026-06-08 08:18:05 MarkDuplicates Tracking 338851 as yet unmatched pairs. 32828 records in RAM.
INFO 2026-06-08 08:18:07 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 1s. Last read position: chr11:46,762,017
INFO 2026-06-08 08:18:07 MarkDuplicates Tracking 335129 as yet unmatched pairs. 29106 records in RAM.
INFO 2026-06-08 08:18:08 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 1s. Last read position: chr11:57,606,419
INFO 2026-06-08 08:18:08 MarkDuplicates Tracking 334673 as yet unmatched pairs. 28649 records in RAM.
INFO 2026-06-08 08:18:10 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 1s. Last read position: chr11:61,965,035
INFO 2026-06-08 08:18:10 MarkDuplicates Tracking 333539 as yet unmatched pairs. 27512 records in RAM.
INFO 2026-06-08 08:18:12 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 1s. Last read position: chr11:62,524,447
INFO 2026-06-08 08:18:12 MarkDuplicates Tracking 331933 as yet unmatched pairs. 25906 records in RAM.
INFO 2026-06-08 08:18:14 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:06:09s. Time for last 1,000,000: 1s. Last read position: chr11:62,533,250
INFO 2026-06-08 08:18:14 MarkDuplicates Tracking 329890 as yet unmatched pairs. 23863 records in RAM.
INFO 2026-06-08 08:18:16 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 1s. Last read position: chr11:63,997,387
INFO 2026-06-08 08:18:16 MarkDuplicates Tracking 327527 as yet unmatched pairs. 21498 records in RAM.
INFO 2026-06-08 08:18:18 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 1s. Last read position: chr11:65,133,012
INFO 2026-06-08 08:18:18 MarkDuplicates Tracking 325706 as yet unmatched pairs. 19676 records in RAM.
INFO 2026-06-08 08:18:19 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 1s. Last read position: chr11:65,855,664
INFO 2026-06-08 08:18:19 MarkDuplicates Tracking 323740 as yet unmatched pairs. 17710 records in RAM.
INFO 2026-06-08 08:18:21 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 1s. Last read position: chr11:67,365,492
INFO 2026-06-08 08:18:21 MarkDuplicates Tracking 321248 as yet unmatched pairs. 15218 records in RAM.
INFO 2026-06-08 08:18:22 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 1s. Last read position: chr11:70,203,619
INFO 2026-06-08 08:18:22 MarkDuplicates Tracking 319426 as yet unmatched pairs. 13396 records in RAM.
INFO 2026-06-08 08:18:24 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 1s. Last read position: chr11:72,817,755
INFO 2026-06-08 08:18:24 MarkDuplicates Tracking 317595 as yet unmatched pairs. 11565 records in RAM.
INFO 2026-06-08 08:18:25 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 1s. Last read position: chr11:78,416,370
INFO 2026-06-08 08:18:25 MarkDuplicates Tracking 315660 as yet unmatched pairs. 9630 records in RAM.
INFO 2026-06-08 08:18:27 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 1s. Last read position: chr11:102,186,054
INFO 2026-06-08 08:18:27 MarkDuplicates Tracking 315058 as yet unmatched pairs. 9021 records in RAM.
INFO 2026-06-08 08:18:28 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 1s. Last read position: chr11:114,064,276
INFO 2026-06-08 08:18:28 MarkDuplicates Tracking 313613 as yet unmatched pairs. 7576 records in RAM.
INFO 2026-06-08 08:18:30 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 1s. Last read position: chr11:117,315,697
INFO 2026-06-08 08:18:30 MarkDuplicates Tracking 310554 as yet unmatched pairs. 4516 records in RAM.
INFO 2026-06-08 08:18:31 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 1s. Last read position: chr11:119,340,348
INFO 2026-06-08 08:18:31 MarkDuplicates Tracking 308904 as yet unmatched pairs. 2866 records in RAM.
INFO 2026-06-08 08:18:33 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 1s. Last read position: chr11:129,873,066
INFO 2026-06-08 08:18:33 MarkDuplicates Tracking 307023 as yet unmatched pairs. 985 records in RAM.
INFO 2026-06-08 08:18:35 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 1s. Last read position: chr12:896,241
INFO 2026-06-08 08:18:35 MarkDuplicates Tracking 305522 as yet unmatched pairs. 36103 records in RAM.
INFO 2026-06-08 08:18:36 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:06:30s. Time for last 1,000,000: 1s. Last read position: chr12:6,064,367
INFO 2026-06-08 08:18:36 MarkDuplicates Tracking 304716 as yet unmatched pairs. 35296 records in RAM.
INFO 2026-06-08 08:18:37 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 1s. Last read position: chr12:6,936,252
INFO 2026-06-08 08:18:37 MarkDuplicates Tracking 302046 as yet unmatched pairs. 32625 records in RAM.
INFO 2026-06-08 08:18:39 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 1s. Last read position: chr12:9,068,757
INFO 2026-06-08 08:18:39 MarkDuplicates Tracking 305701 as yet unmatched pairs. 36280 records in RAM.
INFO 2026-06-08 08:18:41 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 1s. Last read position: chr12:9,099,459
INFO 2026-06-08 08:18:41 MarkDuplicates Tracking 302234 as yet unmatched pairs. 32813 records in RAM.
INFO 2026-06-08 08:18:43 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 1s. Last read position: chr12:12,908,618
INFO 2026-06-08 08:18:43 MarkDuplicates Tracking 298108 as yet unmatched pairs. 28687 records in RAM.
INFO 2026-06-08 08:18:45 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 2s. Last read position: chr12:30,978,602
INFO 2026-06-08 08:18:45 MarkDuplicates Tracking 295828 as yet unmatched pairs. 26407 records in RAM.
INFO 2026-06-08 08:18:47 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 2s. Last read position: chr12:47,798,835
INFO 2026-06-08 08:18:47 MarkDuplicates Tracking 295016 as yet unmatched pairs. 25595 records in RAM.
INFO 2026-06-08 08:18:49 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 1s. Last read position: chr12:49,755,686
INFO 2026-06-08 08:18:49 MarkDuplicates Tracking 293916 as yet unmatched pairs. 24495 records in RAM.
INFO 2026-06-08 08:18:50 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 1s. Last read position: chr12:53,018,924
INFO 2026-06-08 08:18:50 MarkDuplicates Tracking 291245 as yet unmatched pairs. 21819 records in RAM.
INFO 2026-06-08 08:18:52 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:06:47s. Time for last 1,000,000: 1s. Last read position: chr12:53,711,894
INFO 2026-06-08 08:18:52 MarkDuplicates Tracking 289368 as yet unmatched pairs. 19939 records in RAM.
INFO 2026-06-08 08:19:49 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:07:43s. Time for last 1,000,000: 56s. Last read position: chr12:56,158,378
INFO 2026-06-08 08:19:49 MarkDuplicates Tracking 287808 as yet unmatched pairs. 18378 records in RAM.
INFO 2026-06-08 08:19:50 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:07:45s. Time for last 1,000,000: 1s. Last read position: chr12:57,096,915
INFO 2026-06-08 08:19:50 MarkDuplicates Tracking 287327 as yet unmatched pairs. 17897 records in RAM.
INFO 2026-06-08 08:19:52 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:07:46s. Time for last 1,000,000: 1s. Last read position: chr12:57,202,433
INFO 2026-06-08 08:19:52 MarkDuplicates Tracking 284874 as yet unmatched pairs. 15444 records in RAM.
INFO 2026-06-08 08:19:53 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:07:48s. Time for last 1,000,000: 1s. Last read position: chr12:64,729,028
INFO 2026-06-08 08:19:53 MarkDuplicates Tracking 282546 as yet unmatched pairs. 13116 records in RAM.
INFO 2026-06-08 08:19:55 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:07:50s. Time for last 1,000,000: 1s. Last read position: chr12:76,347,098
INFO 2026-06-08 08:19:55 MarkDuplicates Tracking 280760 as yet unmatched pairs. 11329 records in RAM.
INFO 2026-06-08 08:19:57 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:07:51s. Time for last 1,000,000: 1s. Last read position: chr12:96,021,105
INFO 2026-06-08 08:19:57 MarkDuplicates Tracking 279526 as yet unmatched pairs. 10094 records in RAM.
INFO 2026-06-08 08:19:58 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:07:53s. Time for last 1,000,000: 1s. Last read position: chr12:108,788,823
INFO 2026-06-08 08:19:58 MarkDuplicates Tracking 277655 as yet unmatched pairs. 8223 records in RAM.
INFO 2026-06-08 08:20:00 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:07:54s. Time for last 1,000,000: 1s. Last read position: chr12:112,408,251
INFO 2026-06-08 08:20:00 MarkDuplicates Tracking 276488 as yet unmatched pairs. 7056 records in RAM.
INFO 2026-06-08 08:20:02 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:07:56s. Time for last 1,000,000: 1s. Last read position: chr12:120,222,689
INFO 2026-06-08 08:20:02 MarkDuplicates Tracking 274499 as yet unmatched pairs. 5066 records in RAM.
INFO 2026-06-08 08:20:03 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:07:58s. Time for last 1,000,000: 1s. Last read position: chr12:123,671,556
INFO 2026-06-08 08:20:03 MarkDuplicates Tracking 272311 as yet unmatched pairs. 2876 records in RAM.
INFO 2026-06-08 08:20:05 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:07:59s. Time for last 1,000,000: 1s. Last read position: chr12:132,509,218
INFO 2026-06-08 08:20:05 MarkDuplicates Tracking 270880 as yet unmatched pairs. 1444 records in RAM.
INFO 2026-06-08 08:20:06 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:08:00s. Time for last 1,000,000: 1s. Last read position: chr13:28,322,800
INFO 2026-06-08 08:20:06 MarkDuplicates Tracking 268572 as yet unmatched pairs. 10383 records in RAM.
INFO 2026-06-08 08:20:08 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:08:03s. Time for last 1,000,000: 2s. Last read position: chr13:44,574,481
INFO 2026-06-08 08:20:08 MarkDuplicates Tracking 267082 as yet unmatched pairs. 8892 records in RAM.
INFO 2026-06-08 08:20:10 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 1s. Last read position: chr13:75,817,160
INFO 2026-06-08 08:20:10 MarkDuplicates Tracking 265574 as yet unmatched pairs. 7384 records in RAM.
INFO 2026-06-08 08:20:12 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:08:06s. Time for last 1,000,000: 1s. Last read position: chr13:98,888,636
INFO 2026-06-08 08:20:12 MarkDuplicates Tracking 264202 as yet unmatched pairs. 6012 records in RAM.
INFO 2026-06-08 08:20:13 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:08:08s. Time for last 1,000,000: 1s. Last read position: chr13:110,183,264
INFO 2026-06-08 08:20:13 MarkDuplicates Tracking 261920 as yet unmatched pairs. 3727 records in RAM.
INFO 2026-06-08 08:20:15 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:08:09s. Time for last 1,000,000: 1s. Last read position: chr13:112,810,636
INFO 2026-06-08 08:20:15 MarkDuplicates Tracking 260302 as yet unmatched pairs. 2108 records in RAM.
INFO 2026-06-08 08:20:16 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:08:11s. Time for last 1,000,000: 1s. Last read position: chr14:20,801,858
INFO 2026-06-08 08:20:16 MarkDuplicates Tracking 260744 as yet unmatched pairs. 25170 records in RAM.
INFO 2026-06-08 08:20:18 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:08:13s. Time for last 1,000,000: 1s. Last read position: chr14:23,357,626
INFO 2026-06-08 08:20:18 MarkDuplicates Tracking 256148 as yet unmatched pairs. 20574 records in RAM.
INFO 2026-06-08 08:20:20 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:08:14s. Time for last 1,000,000: 1s. Last read position: chr14:32,127,859
INFO 2026-06-08 08:20:20 MarkDuplicates Tracking 254236 as yet unmatched pairs. 18662 records in RAM.
INFO 2026-06-08 08:20:21 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:08:15s. Time for last 1,000,000: 1s. Last read position: chr14:49,862,630
INFO 2026-06-08 08:20:21 MarkDuplicates Tracking 253512 as yet unmatched pairs. 17934 records in RAM.
INFO 2026-06-08 08:20:22 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:08:17s. Time for last 1,000,000: 1s. Last read position: chr14:64,076,029
INFO 2026-06-08 08:20:22 MarkDuplicates Tracking 250937 as yet unmatched pairs. 15358 records in RAM.
INFO 2026-06-08 08:20:24 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 1s. Last read position: chr14:71,724,749
INFO 2026-06-08 08:20:24 MarkDuplicates Tracking 249429 as yet unmatched pairs. 13848 records in RAM.
INFO 2026-06-08 08:20:26 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:08:20s. Time for last 1,000,000: 1s. Last read position: chr14:74,508,706
INFO 2026-06-08 08:20:26 MarkDuplicates Tracking 249839 as yet unmatched pairs. 14258 records in RAM.
INFO 2026-06-08 08:20:27 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:08:22s. Time for last 1,000,000: 1s. Last read position: chr14:75,103,915
INFO 2026-06-08 08:20:27 MarkDuplicates Tracking 246131 as yet unmatched pairs. 10550 records in RAM.
INFO 2026-06-08 08:20:29 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 1s. Last read position: chr14:91,299,937
INFO 2026-06-08 08:20:29 MarkDuplicates Tracking 244238 as yet unmatched pairs. 8655 records in RAM.
INFO 2026-06-08 08:20:30 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 1s. Last read position: chr14:96,039,504
INFO 2026-06-08 08:20:30 MarkDuplicates Tracking 242670 as yet unmatched pairs. 7086 records in RAM.
INFO 2026-06-08 08:20:32 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:08:26s. Time for last 1,000,000: 1s. Last read position: chr14:102,975,748
INFO 2026-06-08 08:20:32 MarkDuplicates Tracking 240898 as yet unmatched pairs. 5312 records in RAM.
INFO 2026-06-08 08:20:33 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:08:27s. Time for last 1,000,000: 1s. Last read position: chr14:105,226,285
INFO 2026-06-08 08:20:33 MarkDuplicates Tracking 238932 as yet unmatched pairs. 3346 records in RAM.
INFO 2026-06-08 08:20:35 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 1s. Last read position: chr14:105,708,000
INFO 2026-06-08 08:20:35 MarkDuplicates Tracking 238661 as yet unmatched pairs. 3075 records in RAM.
INFO 2026-06-08 08:20:36 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:08:31s. Time for last 1,000,000: 1s. Last read position: chr14:105,855,036
INFO 2026-06-08 08:20:36 MarkDuplicates Tracking 237597 as yet unmatched pairs. 2011 records in RAM.
INFO 2026-06-08 08:20:38 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 1s. Last read position: chr15:29,268,829
INFO 2026-06-08 08:20:38 MarkDuplicates Tracking 234733 as yet unmatched pairs. 21448 records in RAM.
INFO 2026-06-08 08:20:39 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 1s. Last read position: chr15:39,819,365
INFO 2026-06-08 08:20:39 MarkDuplicates Tracking 233182 as yet unmatched pairs. 19895 records in RAM.
INFO 2026-06-08 08:20:41 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 1s. Last read position: chr15:42,276,350
INFO 2026-06-08 08:20:41 MarkDuplicates Tracking 231811 as yet unmatched pairs. 18523 records in RAM.
INFO 2026-06-08 08:20:42 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 1s. Last read position: chr15:44,668,329
INFO 2026-06-08 08:20:42 MarkDuplicates Tracking 229827 as yet unmatched pairs. 16539 records in RAM.
INFO 2026-06-08 08:20:44 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:08:38s. Time for last 1,000,000: 1s. Last read position: chr15:48,992,596
INFO 2026-06-08 08:20:44 MarkDuplicates Tracking 228771 as yet unmatched pairs. 15483 records in RAM.
INFO 2026-06-08 08:20:45 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 1s. Last read position: chr15:58,787,917
INFO 2026-06-08 08:20:45 MarkDuplicates Tracking 226871 as yet unmatched pairs. 13574 records in RAM.
INFO 2026-06-08 08:20:47 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:08:41s. Time for last 1,000,000: 1s. Last read position: chr15:64,499,826
INFO 2026-06-08 08:20:47 MarkDuplicates Tracking 225489 as yet unmatched pairs. 12192 records in RAM.
INFO 2026-06-08 08:20:48 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:08:43s. Time for last 1,000,000: 1s. Last read position: chr15:71,757,955
INFO 2026-06-08 08:20:48 MarkDuplicates Tracking 223372 as yet unmatched pairs. 10074 records in RAM.
INFO 2026-06-08 08:20:50 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:08:44s. Time for last 1,000,000: 1s. Last read position: chr15:74,929,134
INFO 2026-06-08 08:20:50 MarkDuplicates Tracking 221952 as yet unmatched pairs. 8653 records in RAM.
INFO 2026-06-08 08:20:51 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:08:46s. Time for last 1,000,000: 1s. Last read position: chr15:78,766,081
INFO 2026-06-08 08:20:51 MarkDuplicates Tracking 219735 as yet unmatched pairs. 6436 records in RAM.
INFO 2026-06-08 08:20:53 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 2s. Last read position: chr15:82,538,947
INFO 2026-06-08 08:20:53 MarkDuplicates Tracking 218470 as yet unmatched pairs. 5169 records in RAM.
INFO 2026-06-08 08:20:55 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 1s. Last read position: chr15:85,664,628
INFO 2026-06-08 08:20:55 MarkDuplicates Tracking 217865 as yet unmatched pairs. 4564 records in RAM.
INFO 2026-06-08 08:20:56 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 1s. Last read position: chr15:90,474,523
INFO 2026-06-08 08:20:56 MarkDuplicates Tracking 215163 as yet unmatched pairs. 1862 records in RAM.
INFO 2026-06-08 08:20:58 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:08:53s. Time for last 1,000,000: 2s. Last read position: chr16:79,441
INFO 2026-06-08 08:20:58 MarkDuplicates Tracking 213546 as yet unmatched pairs. 37799 records in RAM.
INFO 2026-06-08 08:21:00 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:08:55s. Time for last 1,000,000: 1s. Last read position: chr16:1,228,944
INFO 2026-06-08 08:21:00 MarkDuplicates Tracking 211733 as yet unmatched pairs. 35986 records in RAM.
INFO 2026-06-08 08:21:02 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:08:56s. Time for last 1,000,000: 1s. Last read position: chr16:1,964,472
INFO 2026-06-08 08:21:02 MarkDuplicates Tracking 209417 as yet unmatched pairs. 33670 records in RAM.
INFO 2026-06-08 08:21:03 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:08:58s. Time for last 1,000,000: 1s. Last read position: chr16:2,284,915
INFO 2026-06-08 08:21:03 MarkDuplicates Tracking 208603 as yet unmatched pairs. 32856 records in RAM.
INFO 2026-06-08 08:21:05 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:08:59s. Time for last 1,000,000: 1s. Last read position: chr16:2,766,660
INFO 2026-06-08 08:21:05 MarkDuplicates Tracking 206015 as yet unmatched pairs. 30268 records in RAM.
INFO 2026-06-08 08:21:06 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:09:01s. Time for last 1,000,000: 1s. Last read position: chr16:4,382,083
INFO 2026-06-08 08:21:06 MarkDuplicates Tracking 203519 as yet unmatched pairs. 27772 records in RAM.
INFO 2026-06-08 08:21:08 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:09:02s. Time for last 1,000,000: 1s. Last read position: chr16:11,350,690
INFO 2026-06-08 08:21:08 MarkDuplicates Tracking 201359 as yet unmatched pairs. 25606 records in RAM.
INFO 2026-06-08 08:21:09 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:09:04s. Time for last 1,000,000: 1s. Last read position: chr16:14,975,135
INFO 2026-06-08 08:21:09 MarkDuplicates Tracking 200385 as yet unmatched pairs. 24632 records in RAM.
INFO 2026-06-08 08:21:11 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 1s. Last read position: chr16:16,310,510
INFO 2026-06-08 08:21:11 MarkDuplicates Tracking 198912 as yet unmatched pairs. 23159 records in RAM.
INFO 2026-06-08 08:21:12 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:09:06s. Time for last 1,000,000: 1s. Last read position: chr16:18,351,241
INFO 2026-06-08 08:21:12 MarkDuplicates Tracking 198906 as yet unmatched pairs. 23153 records in RAM.
INFO 2026-06-08 08:21:13 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:09:07s. Time for last 1,000,000: 1s. Last read position: chr16:21,258,796
INFO 2026-06-08 08:21:13 MarkDuplicates Tracking 197265 as yet unmatched pairs. 21512 records in RAM.
INFO 2026-06-08 08:21:14 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:09:09s. Time for last 1,000,000: 1s. Last read position: chr16:22,534,903
INFO 2026-06-08 08:21:14 MarkDuplicates Tracking 196591 as yet unmatched pairs. 20838 records in RAM.
INFO 2026-06-08 08:21:16 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:09:10s. Time for last 1,000,000: 1s. Last read position: chr16:28,715,426
INFO 2026-06-08 08:21:16 MarkDuplicates Tracking 195131 as yet unmatched pairs. 19378 records in RAM.
INFO 2026-06-08 08:21:17 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:09:12s. Time for last 1,000,000: 1s. Last read position: chr16:29,813,384
INFO 2026-06-08 08:21:17 MarkDuplicates Tracking 194058 as yet unmatched pairs. 18305 records in RAM.
INFO 2026-06-08 08:21:19 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:09:13s. Time for last 1,000,000: 1s. Last read position: chr16:30,364,915
INFO 2026-06-08 08:21:19 MarkDuplicates Tracking 192287 as yet unmatched pairs. 16534 records in RAM.
INFO 2026-06-08 08:21:20 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 1s. Last read position: chr16:31,183,991
INFO 2026-06-08 08:21:20 MarkDuplicates Tracking 191141 as yet unmatched pairs. 15388 records in RAM.
INFO 2026-06-08 08:21:21 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 1s. Last read position: chr16:53,470,071
INFO 2026-06-08 08:21:21 MarkDuplicates Tracking 188965 as yet unmatched pairs. 13204 records in RAM.
INFO 2026-06-08 08:21:23 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:09:17s. Time for last 1,000,000: 1s. Last read position: chr16:57,248,631
INFO 2026-06-08 08:21:23 MarkDuplicates Tracking 187074 as yet unmatched pairs. 11313 records in RAM.
INFO 2026-06-08 08:21:24 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:09:19s. Time for last 1,000,000: 1s. Last read position: chr16:67,163,769
INFO 2026-06-08 08:21:24 MarkDuplicates Tracking 185208 as yet unmatched pairs. 9446 records in RAM.
INFO 2026-06-08 08:21:26 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 1s. Last read position: chr16:68,829,660
INFO 2026-06-08 08:21:26 MarkDuplicates Tracking 183634 as yet unmatched pairs. 7872 records in RAM.
INFO 2026-06-08 08:21:27 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 1s. Last read position: chr16:71,859,982
INFO 2026-06-08 08:21:27 MarkDuplicates Tracking 181208 as yet unmatched pairs. 5446 records in RAM.
INFO 2026-06-08 08:21:29 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:09:24s. Time for last 1,000,000: 1s. Last read position: chr16:84,170,133
INFO 2026-06-08 08:21:29 MarkDuplicates Tracking 179448 as yet unmatched pairs. 3686 records in RAM.
INFO 2026-06-08 08:21:31 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:09:26s. Time for last 1,000,000: 1s. Last read position: chr16:88,749,395
INFO 2026-06-08 08:21:31 MarkDuplicates Tracking 177550 as yet unmatched pairs. 1786 records in RAM.
INFO 2026-06-08 08:21:35 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:09:29s. Time for last 1,000,000: 3s. Last read position: chr17:1,361,262
INFO 2026-06-08 08:21:35 MarkDuplicates Tracking 177096 as yet unmatched pairs. 48558 records in RAM.
INFO 2026-06-08 08:21:36 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:09:31s. Time for last 1,000,000: 1s. Last read position: chr17:2,667,032
INFO 2026-06-08 08:21:36 MarkDuplicates Tracking 173381 as yet unmatched pairs. 44843 records in RAM.
INFO 2026-06-08 08:21:38 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:09:32s. Time for last 1,000,000: 1s. Last read position: chr17:5,022,358
INFO 2026-06-08 08:21:38 MarkDuplicates Tracking 171836 as yet unmatched pairs. 43298 records in RAM.
INFO 2026-06-08 08:21:40 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:09:34s. Time for last 1,000,000: 1s. Last read position: chr17:7,500,647
INFO 2026-06-08 08:21:40 MarkDuplicates Tracking 169829 as yet unmatched pairs. 41291 records in RAM.
INFO 2026-06-08 08:21:41 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:09:36s. Time for last 1,000,000: 1s. Last read position: chr17:8,046,715
INFO 2026-06-08 08:21:41 MarkDuplicates Tracking 168729 as yet unmatched pairs. 40191 records in RAM.
INFO 2026-06-08 08:21:43 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 1s. Last read position: chr17:11,886,953
INFO 2026-06-08 08:21:43 MarkDuplicates Tracking 166120 as yet unmatched pairs. 37582 records in RAM.
INFO 2026-06-08 08:21:44 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:09:39s. Time for last 1,000,000: 1s. Last read position: chr17:17,820,205
INFO 2026-06-08 08:21:44 MarkDuplicates Tracking 164234 as yet unmatched pairs. 35696 records in RAM.
INFO 2026-06-08 08:21:46 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:09:40s. Time for last 1,000,000: 1s. Last read position: chr17:28,354,489
INFO 2026-06-08 08:21:46 MarkDuplicates Tracking 162690 as yet unmatched pairs. 34152 records in RAM.
INFO 2026-06-08 08:21:48 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:09:43s. Time for last 1,000,000: 2s. Last read position: chr17:31,227,267
INFO 2026-06-08 08:21:48 MarkDuplicates Tracking 160827 as yet unmatched pairs. 32289 records in RAM.
INFO 2026-06-08 08:21:50 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 1s. Last read position: chr17:37,542,310
INFO 2026-06-08 08:21:50 MarkDuplicates Tracking 159316 as yet unmatched pairs. 30777 records in RAM.
INFO 2026-06-08 08:21:51 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:09:46s. Time for last 1,000,000: 1s. Last read position: chr17:39,707,060
INFO 2026-06-08 08:21:51 MarkDuplicates Tracking 158540 as yet unmatched pairs. 29992 records in RAM.
INFO 2026-06-08 08:21:53 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:09:47s. Time for last 1,000,000: 1s. Last read position: chr17:41,819,315
INFO 2026-06-08 08:21:53 MarkDuplicates Tracking 155435 as yet unmatched pairs. 26887 records in RAM.
INFO 2026-06-08 08:21:54 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:09:49s. Time for last 1,000,000: 1s. Last read position: chr17:42,854,614
INFO 2026-06-08 08:21:54 MarkDuplicates Tracking 154380 as yet unmatched pairs. 25832 records in RAM.
INFO 2026-06-08 08:21:56 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:09:50s. Time for last 1,000,000: 1s. Last read position: chr17:45,245,671
INFO 2026-06-08 08:21:56 MarkDuplicates Tracking 151866 as yet unmatched pairs. 23318 records in RAM.
INFO 2026-06-08 08:21:57 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:09:52s. Time for last 1,000,000: 1s. Last read position: chr17:48,059,157
INFO 2026-06-08 08:21:57 MarkDuplicates Tracking 150722 as yet unmatched pairs. 22174 records in RAM.
INFO 2026-06-08 08:21:59 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:09:54s. Time for last 1,000,000: 1s. Last read position: chr17:50,189,187
INFO 2026-06-08 08:21:59 MarkDuplicates Tracking 152593 as yet unmatched pairs. 24045 records in RAM.
INFO 2026-06-08 08:22:01 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:09:56s. Time for last 1,000,000: 2s. Last read position: chr17:50,195,287
INFO 2026-06-08 08:22:01 MarkDuplicates Tracking 151652 as yet unmatched pairs. 23104 records in RAM.
INFO 2026-06-08 08:22:03 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:09:58s. Time for last 1,000,000: 1s. Last read position: chr17:50,750,818
INFO 2026-06-08 08:22:03 MarkDuplicates Tracking 144965 as yet unmatched pairs. 16417 records in RAM.
INFO 2026-06-08 08:22:05 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 1s. Last read position: chr17:59,683,141
INFO 2026-06-08 08:22:05 MarkDuplicates Tracking 143916 as yet unmatched pairs. 15368 records in RAM.
INFO 2026-06-08 08:22:06 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:10:00s. Time for last 1,000,000: 1s. Last read position: chr17:63,817,918
INFO 2026-06-08 08:22:06 MarkDuplicates Tracking 141522 as yet unmatched pairs. 12974 records in RAM.
INFO 2026-06-08 08:22:08 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:10:02s. Time for last 1,000,000: 1s. Last read position: chr17:67,975,864
INFO 2026-06-08 08:22:08 MarkDuplicates Tracking 139915 as yet unmatched pairs. 11367 records in RAM.
INFO 2026-06-08 08:22:09 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:10:04s. Time for last 1,000,000: 1s. Last read position: chr17:75,497,795
INFO 2026-06-08 08:22:09 MarkDuplicates Tracking 138389 as yet unmatched pairs. 9841 records in RAM.
INFO 2026-06-08 08:22:11 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:10:05s. Time for last 1,000,000: 1s. Last read position: chr17:76,396,167
INFO 2026-06-08 08:22:11 MarkDuplicates Tracking 136214 as yet unmatched pairs. 7666 records in RAM.
INFO 2026-06-08 08:22:13 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:10:07s. Time for last 1,000,000: 1s. Last read position: chr17:79,083,887
INFO 2026-06-08 08:22:13 MarkDuplicates Tracking 134168 as yet unmatched pairs. 5620 records in RAM.
INFO 2026-06-08 08:22:14 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 1s. Last read position: chr17:81,452,166
INFO 2026-06-08 08:22:14 MarkDuplicates Tracking 132215 as yet unmatched pairs. 3666 records in RAM.
INFO 2026-06-08 08:22:16 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:10:10s. Time for last 1,000,000: 1s. Last read position: chr17:82,081,634
INFO 2026-06-08 08:22:16 MarkDuplicates Tracking 130874 as yet unmatched pairs. 2325 records in RAM.
INFO 2026-06-08 08:22:17 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 1s. Last read position: chr18:2,656,188
INFO 2026-06-08 08:22:17 MarkDuplicates Tracking 128581 as yet unmatched pairs. 6209 records in RAM.
INFO 2026-06-08 08:22:19 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:10:13s. Time for last 1,000,000: 1s. Last read position: chr18:22,171,767
INFO 2026-06-08 08:22:19 MarkDuplicates Tracking 126747 as yet unmatched pairs. 4374 records in RAM.
INFO 2026-06-08 08:22:20 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:10:15s. Time for last 1,000,000: 1s. Last read position: chr18:47,108,760
INFO 2026-06-08 08:22:20 MarkDuplicates Tracking 125235 as yet unmatched pairs. 2862 records in RAM.
INFO 2026-06-08 08:22:22 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:10:16s. Time for last 1,000,000: 1s. Last read position: chr18:69,127,351
INFO 2026-06-08 08:22:22 MarkDuplicates Tracking 123383 as yet unmatched pairs. 1010 records in RAM.
INFO 2026-06-08 08:22:24 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:10:18s. Time for last 1,000,000: 1s. Last read position: chr19:863,120
INFO 2026-06-08 08:22:24 MarkDuplicates Tracking 122470 as yet unmatched pairs. 53833 records in RAM.
INFO 2026-06-08 08:22:25 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:10:20s. Time for last 1,000,000: 1s. Last read position: chr19:1,440,351
INFO 2026-06-08 08:22:25 MarkDuplicates Tracking 119003 as yet unmatched pairs. 50366 records in RAM.
INFO 2026-06-08 08:22:27 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:10:22s. Time for last 1,000,000: 1s. Last read position: chr19:3,053,886
INFO 2026-06-08 08:22:27 MarkDuplicates Tracking 117745 as yet unmatched pairs. 49108 records in RAM.
INFO 2026-06-08 08:22:29 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:10:23s. Time for last 1,000,000: 1s. Last read position: chr19:5,110,704
INFO 2026-06-08 08:22:29 MarkDuplicates Tracking 114697 as yet unmatched pairs. 46059 records in RAM.
INFO 2026-06-08 08:22:30 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:10:25s. Time for last 1,000,000: 1s. Last read position: chr19:6,693,033
INFO 2026-06-08 08:22:30 MarkDuplicates Tracking 114602 as yet unmatched pairs. 45960 records in RAM.
INFO 2026-06-08 08:22:32 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:10:27s. Time for last 1,000,000: 2s. Last read position: chr19:7,642,217
INFO 2026-06-08 08:22:32 MarkDuplicates Tracking 111066 as yet unmatched pairs. 42424 records in RAM.
INFO 2026-06-08 08:22:35 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:10:29s. Time for last 1,000,000: 2s. Last read position: chr19:10,353,988
INFO 2026-06-08 08:22:35 MarkDuplicates Tracking 108879 as yet unmatched pairs. 40237 records in RAM.
INFO 2026-06-08 08:22:36 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:10:31s. Time for last 1,000,000: 1s. Last read position: chr19:11,345,524
INFO 2026-06-08 08:22:36 MarkDuplicates Tracking 107215 as yet unmatched pairs. 38572 records in RAM.
INFO 2026-06-08 08:22:38 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:10:32s. Time for last 1,000,000: 1s. Last read position: chr19:12,995,827
INFO 2026-06-08 08:22:38 MarkDuplicates Tracking 105701 as yet unmatched pairs. 37058 records in RAM.
INFO 2026-06-08 08:22:39 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:10:34s. Time for last 1,000,000: 1s. Last read position: chr19:15,109,061
INFO 2026-06-08 08:22:39 MarkDuplicates Tracking 102973 as yet unmatched pairs. 34326 records in RAM.
INFO 2026-06-08 08:22:41 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:10:35s. Time for last 1,000,000: 1s. Last read position: chr19:16,647,105
INFO 2026-06-08 08:22:41 MarkDuplicates Tracking 100636 as yet unmatched pairs. 31989 records in RAM.
INFO 2026-06-08 08:22:42 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:10:37s. Time for last 1,000,000: 1s. Last read position: chr19:18,220,463
INFO 2026-06-08 08:22:42 MarkDuplicates Tracking 98499 as yet unmatched pairs. 29851 records in RAM.
INFO 2026-06-08 08:22:44 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:10:38s. Time for last 1,000,000: 1s. Last read position: chr19:19,629,913
INFO 2026-06-08 08:22:44 MarkDuplicates Tracking 96390 as yet unmatched pairs. 27742 records in RAM.
INFO 2026-06-08 08:22:45 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:10:40s. Time for last 1,000,000: 1s. Last read position: chr19:35,269,100
INFO 2026-06-08 08:22:45 MarkDuplicates Tracking 94575 as yet unmatched pairs. 25927 records in RAM.
INFO 2026-06-08 08:22:47 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:10:41s. Time for last 1,000,000: 1s. Last read position: chr19:38,617,411
INFO 2026-06-08 08:22:47 MarkDuplicates Tracking 92024 as yet unmatched pairs. 23376 records in RAM.
INFO 2026-06-08 08:22:49 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:10:43s. Time for last 1,000,000: 1s. Last read position: chr19:39,459,200
INFO 2026-06-08 08:22:49 MarkDuplicates Tracking 90537 as yet unmatched pairs. 21889 records in RAM.
INFO 2026-06-08 08:22:50 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:10:44s. Time for last 1,000,000: 1s. Last read position: chr19:40,611,224
INFO 2026-06-08 08:22:50 MarkDuplicates Tracking 89551 as yet unmatched pairs. 20903 records in RAM.
INFO 2026-06-08 08:22:52 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 1s. Last read position: chr19:41,425,772
INFO 2026-06-08 08:22:52 MarkDuplicates Tracking 86639 as yet unmatched pairs. 17990 records in RAM.
INFO 2026-06-08 08:22:53 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:10:48s. Time for last 1,000,000: 1s. Last read position: chr19:42,293,224
INFO 2026-06-08 08:22:53 MarkDuplicates Tracking 84730 as yet unmatched pairs. 16081 records in RAM.
INFO 2026-06-08 08:22:55 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:10:49s. Time for last 1,000,000: 1s. Last read position: chr19:45,470,761
INFO 2026-06-08 08:22:55 MarkDuplicates Tracking 82952 as yet unmatched pairs. 14302 records in RAM.
INFO 2026-06-08 08:22:56 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:10:51s. Time for last 1,000,000: 1s. Last read position: chr19:47,274,976
INFO 2026-06-08 08:22:56 MarkDuplicates Tracking 80436 as yet unmatched pairs. 11786 records in RAM.
INFO 2026-06-08 08:22:58 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:10:52s. Time for last 1,000,000: 1s. Last read position: chr19:48,919,194
INFO 2026-06-08 08:22:58 MarkDuplicates Tracking 78552 as yet unmatched pairs. 9902 records in RAM.
INFO 2026-06-08 08:22:59 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:10:54s. Time for last 1,000,000: 1s. Last read position: chr19:49,652,281
INFO 2026-06-08 08:22:59 MarkDuplicates Tracking 76654 as yet unmatched pairs. 8004 records in RAM.
INFO 2026-06-08 08:23:02 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:10:56s. Time for last 1,000,000: 2s. Last read position: chr19:50,361,011
INFO 2026-06-08 08:23:02 MarkDuplicates Tracking 79148 as yet unmatched pairs. 10498 records in RAM.
INFO 2026-06-08 08:23:03 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 1s. Last read position: chr19:54,201,530
INFO 2026-06-08 08:23:03 MarkDuplicates Tracking 73661 as yet unmatched pairs. 5011 records in RAM.
INFO 2026-06-08 08:23:05 MarkDuplicates Read 368,000,000 records. Elapsed time: 00:10:59s. Time for last 1,000,000: 1s. Last read position: chr19:55,615,504
INFO 2026-06-08 08:23:05 MarkDuplicates Tracking 70771 as yet unmatched pairs. 2121 records in RAM.
INFO 2026-06-08 08:23:06 MarkDuplicates Read 369,000,000 records. Elapsed time: 00:11:01s. Time for last 1,000,000: 1s. Last read position: chr19:58,550,376
INFO 2026-06-08 08:23:06 MarkDuplicates Tracking 69080 as yet unmatched pairs. 430 records in RAM.
INFO 2026-06-08 08:23:08 MarkDuplicates Read 370,000,000 records. Elapsed time: 00:11:02s. Time for last 1,000,000: 1s. Last read position: chr20:5,119,585
INFO 2026-06-08 08:23:08 MarkDuplicates Tracking 66832 as yet unmatched pairs. 14312 records in RAM.
INFO 2026-06-08 08:23:09 MarkDuplicates Read 371,000,000 records. Elapsed time: 00:11:04s. Time for last 1,000,000: 1s. Last read position: chr20:23,048,223
INFO 2026-06-08 08:23:09 MarkDuplicates Tracking 65374 as yet unmatched pairs. 12854 records in RAM.
INFO 2026-06-08 08:23:11 MarkDuplicates Read 372,000,000 records. Elapsed time: 00:11:05s. Time for last 1,000,000: 1s. Last read position: chr20:34,295,408
INFO 2026-06-08 08:23:11 MarkDuplicates Tracking 63424 as yet unmatched pairs. 10903 records in RAM.
INFO 2026-06-08 08:23:12 MarkDuplicates Read 373,000,000 records. Elapsed time: 00:11:07s. Time for last 1,000,000: 1s. Last read position: chr20:37,384,281
INFO 2026-06-08 08:23:12 MarkDuplicates Tracking 61756 as yet unmatched pairs. 9235 records in RAM.
INFO 2026-06-08 08:23:14 MarkDuplicates Read 374,000,000 records. Elapsed time: 00:11:08s. Time for last 1,000,000: 1s. Last read position: chr20:45,253,655
INFO 2026-06-08 08:23:14 MarkDuplicates Tracking 61174 as yet unmatched pairs. 8652 records in RAM.
INFO 2026-06-08 08:23:15 MarkDuplicates Read 375,000,000 records. Elapsed time: 00:11:10s. Time for last 1,000,000: 1s. Last read position: chr20:49,253,734
INFO 2026-06-08 08:23:15 MarkDuplicates Tracking 58052 as yet unmatched pairs. 5530 records in RAM.
INFO 2026-06-08 08:23:17 MarkDuplicates Read 376,000,000 records. Elapsed time: 00:11:11s. Time for last 1,000,000: 1s. Last read position: chr20:59,030,342
INFO 2026-06-08 08:23:17 MarkDuplicates Tracking 56705 as yet unmatched pairs. 4183 records in RAM.
INFO 2026-06-08 08:23:18 MarkDuplicates Read 377,000,000 records. Elapsed time: 00:11:13s. Time for last 1,000,000: 1s. Last read position: chr20:63,565,722
INFO 2026-06-08 08:23:18 MarkDuplicates Tracking 53567 as yet unmatched pairs. 1045 records in RAM.
INFO 2026-06-08 08:23:20 MarkDuplicates Read 378,000,000 records. Elapsed time: 00:11:14s. Time for last 1,000,000: 1s. Last read position: chr21:8,217,312
INFO 2026-06-08 08:23:20 MarkDuplicates Tracking 51928 as yet unmatched pairs. 8261 records in RAM.
INFO 2026-06-08 08:23:21 MarkDuplicates Read 379,000,000 records. Elapsed time: 00:11:15s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,636
INFO 2026-06-08 08:23:21 MarkDuplicates Tracking 50441 as yet unmatched pairs. 6772 records in RAM.
INFO 2026-06-08 08:23:23 MarkDuplicates Read 380,000,000 records. Elapsed time: 00:11:17s. Time for last 1,000,000: 1s. Last read position: chr21:33,555,089
INFO 2026-06-08 08:23:23 MarkDuplicates Tracking 48838 as yet unmatched pairs. 5169 records in RAM.
INFO 2026-06-08 08:23:24 MarkDuplicates Read 381,000,000 records. Elapsed time: 00:11:19s. Time for last 1,000,000: 1s. Last read position: chr21:43,053,964
INFO 2026-06-08 08:23:24 MarkDuplicates Tracking 47026 as yet unmatched pairs. 3357 records in RAM.
INFO 2026-06-08 08:23:26 MarkDuplicates Read 382,000,000 records. Elapsed time: 00:11:20s. Time for last 1,000,000: 1s. Last read position: chr21:45,989,632
INFO 2026-06-08 08:23:26 MarkDuplicates Tracking 45159 as yet unmatched pairs. 1490 records in RAM.
INFO 2026-06-08 08:23:28 MarkDuplicates Read 383,000,000 records. Elapsed time: 00:11:22s. Time for last 1,000,000: 2s. Last read position: chr22:17,899,447
INFO 2026-06-08 08:23:28 MarkDuplicates Tracking 43351 as yet unmatched pairs. 22292 records in RAM.
INFO 2026-06-08 08:23:30 MarkDuplicates Read 384,000,000 records. Elapsed time: 00:11:24s. Time for last 1,000,000: 1s. Last read position: chr22:20,585,811
INFO 2026-06-08 08:23:30 MarkDuplicates Tracking 41406 as yet unmatched pairs. 20347 records in RAM.
INFO 2026-06-08 08:23:31 MarkDuplicates Read 385,000,000 records. Elapsed time: 00:11:26s. Time for last 1,000,000: 1s. Last read position: chr22:23,894,389
INFO 2026-06-08 08:23:31 MarkDuplicates Tracking 39284 as yet unmatched pairs. 18225 records in RAM.
INFO 2026-06-08 08:23:33 MarkDuplicates Read 386,000,000 records. Elapsed time: 00:11:27s. Time for last 1,000,000: 1s. Last read position: chr22:27,983,445
INFO 2026-06-08 08:23:33 MarkDuplicates Tracking 37525 as yet unmatched pairs. 16466 records in RAM.
INFO 2026-06-08 08:23:34 MarkDuplicates Read 387,000,000 records. Elapsed time: 00:11:29s. Time for last 1,000,000: 1s. Last read position: chr22:30,494,906
INFO 2026-06-08 08:23:34 MarkDuplicates Tracking 35928 as yet unmatched pairs. 14869 records in RAM.
INFO 2026-06-08 08:23:36 MarkDuplicates Read 388,000,000 records. Elapsed time: 00:11:30s. Time for last 1,000,000: 1s. Last read position: chr22:36,285,733
INFO 2026-06-08 08:23:36 MarkDuplicates Tracking 34853 as yet unmatched pairs. 13794 records in RAM.
INFO 2026-06-08 08:23:37 MarkDuplicates Read 389,000,000 records. Elapsed time: 00:11:32s. Time for last 1,000,000: 1s. Last read position: chr22:37,630,011
INFO 2026-06-08 08:23:37 MarkDuplicates Tracking 32050 as yet unmatched pairs. 10991 records in RAM.
INFO 2026-06-08 08:23:39 MarkDuplicates Read 390,000,000 records. Elapsed time: 00:11:33s. Time for last 1,000,000: 1s. Last read position: chr22:39,224,665
INFO 2026-06-08 08:23:39 MarkDuplicates Tracking 30303 as yet unmatched pairs. 9244 records in RAM.
INFO 2026-06-08 08:23:40 MarkDuplicates Read 391,000,000 records. Elapsed time: 00:11:35s. Time for last 1,000,000: 1s. Last read position: chr22:41,523,883
INFO 2026-06-08 08:23:40 MarkDuplicates Tracking 28539 as yet unmatched pairs. 7480 records in RAM.
INFO 2026-06-08 08:23:42 MarkDuplicates Read 392,000,000 records. Elapsed time: 00:11:36s. Time for last 1,000,000: 1s. Last read position: chr22:45,503,013
INFO 2026-06-08 08:23:42 MarkDuplicates Tracking 27368 as yet unmatched pairs. 6309 records in RAM.
INFO 2026-06-08 08:23:43 MarkDuplicates Read 393,000,000 records. Elapsed time: 00:11:38s. Time for last 1,000,000: 1s. Last read position: chr22:50,218,736
INFO 2026-06-08 08:23:43 MarkDuplicates Tracking 24209 as yet unmatched pairs. 3148 records in RAM.
INFO 2026-06-08 08:23:45 MarkDuplicates Read 394,000,000 records. Elapsed time: 00:11:39s. Time for last 1,000,000: 1s. Last read position: chr22:50,530,538
INFO 2026-06-08 08:23:45 MarkDuplicates Tracking 22295 as yet unmatched pairs. 1234 records in RAM.
INFO 2026-06-08 08:23:46 MarkDuplicates Read 395,000,000 records. Elapsed time: 00:11:41s. Time for last 1,000,000: 1s. Last read position: chrX:10,127,995
INFO 2026-06-08 08:23:46 MarkDuplicates Tracking 19980 as yet unmatched pairs. 17055 records in RAM.
INFO 2026-06-08 08:23:48 MarkDuplicates Read 396,000,000 records. Elapsed time: 00:11:42s. Time for last 1,000,000: 1s. Last read position: chrX:38,154,494
INFO 2026-06-08 08:23:48 MarkDuplicates Tracking 18169 as yet unmatched pairs. 15244 records in RAM.
INFO 2026-06-08 08:23:49 MarkDuplicates Read 397,000,000 records. Elapsed time: 00:11:44s. Time for last 1,000,000: 1s. Last read position: chrX:47,563,253
INFO 2026-06-08 08:23:49 MarkDuplicates Tracking 16503 as yet unmatched pairs. 13577 records in RAM.
INFO 2026-06-08 08:23:51 MarkDuplicates Read 398,000,000 records. Elapsed time: 00:11:45s. Time for last 1,000,000: 1s. Last read position: chrX:53,085,964
INFO 2026-06-08 08:23:51 MarkDuplicates Tracking 14644 as yet unmatched pairs. 11718 records in RAM.
INFO 2026-06-08 08:23:53 MarkDuplicates Read 399,000,000 records. Elapsed time: 00:11:47s. Time for last 1,000,000: 1s. Last read position: chrX:65,739,740
INFO 2026-06-08 08:23:53 MarkDuplicates Tracking 13243 as yet unmatched pairs. 10317 records in RAM.
INFO 2026-06-08 08:23:55 MarkDuplicates Read 400,000,000 records. Elapsed time: 00:11:49s. Time for last 1,000,000: 1s. Last read position: chrX:77,618,916
INFO 2026-06-08 08:23:55 MarkDuplicates Tracking 11157 as yet unmatched pairs. 8231 records in RAM.
INFO 2026-06-08 08:23:57 MarkDuplicates Read 401,000,000 records. Elapsed time: 00:11:52s. Time for last 1,000,000: 2s. Last read position: chrX:108,164,992
INFO 2026-06-08 08:23:57 MarkDuplicates Tracking 9396 as yet unmatched pairs. 6470 records in RAM.
INFO 2026-06-08 08:23:59 MarkDuplicates Read 402,000,000 records. Elapsed time: 00:11:53s. Time for last 1,000,000: 1s. Last read position: chrX:133,536,244
INFO 2026-06-08 08:23:59 MarkDuplicates Tracking 8164 as yet unmatched pairs. 5238 records in RAM.
INFO 2026-06-08 08:24:00 MarkDuplicates Read 403,000,000 records. Elapsed time: 00:11:55s. Time for last 1,000,000: 1s. Last read position: chrX:153,950,944
INFO 2026-06-08 08:24:00 MarkDuplicates Tracking 6511 as yet unmatched pairs. 3585 records in RAM.
INFO 2026-06-08 08:24:02 MarkDuplicates Read 404,000,000 records. Elapsed time: 00:11:56s. Time for last 1,000,000: 1s. Last read position: chrX:154,361,670
INFO 2026-06-08 08:24:02 MarkDuplicates Tracking 5318 as yet unmatched pairs. 2392 records in RAM.
INFO 2026-06-08 08:24:03 MarkDuplicates Read 405,000,000 records. Elapsed time: 00:11:58s. Time for last 1,000,000: 1s. Last read position: chrX:155,458,155
INFO 2026-06-08 08:24:03 MarkDuplicates Tracking 2964 as yet unmatched pairs. 38 records in RAM.
INFO 2026-06-08 08:24:04 MarkDuplicates Read 406,000,000 records. Elapsed time: 00:11:59s. Time for last 1,000,000: 1s. Last read position: KI270733.1:130,382
INFO 2026-06-08 08:24:04 MarkDuplicates Tracking 1626 as yet unmatched pairs. 1431 records in RAM.
INFO 2026-06-08 08:24:05 MarkDuplicates Read 406797040 records. 0 pairs never matched.
INFO 2026-06-08 08:24:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 36330004872; totalMemory: 51908706304; maxMemory: 63585648640
INFO 2026-06-08 08:24:45 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:24:50 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:25:06 OpticalDuplicateFinder Large duplicate set. size = 1428
INFO 2026-06-08 08:25:06 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,442
INFO 2026-06-08 08:25:13 OpticalDuplicateFinder Large duplicate set. size = 1092
INFO 2026-06-08 08:25:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,048
INFO 2026-06-08 08:25:13 OpticalDuplicateFinder Large duplicate set. size = 1822
INFO 2026-06-08 08:25:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,145
INFO 2026-06-08 08:25:13 OpticalDuplicateFinder Large duplicate set. size = 1134
INFO 2026-06-08 08:25:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,721
INFO 2026-06-08 08:25:13 OpticalDuplicateFinder Large duplicate set. size = 1052
INFO 2026-06-08 08:25:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,067
INFO 2026-06-08 08:25:13 OpticalDuplicateFinder Large duplicate set. size = 1037
INFO 2026-06-08 08:25:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,324
INFO 2026-06-08 08:25:13 OpticalDuplicateFinder Large duplicate set. size = 1218
INFO 2026-06-08 08:25:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:5,538
INFO 2026-06-08 08:25:18 OpticalDuplicateFinder Large duplicate set. size = 1365
INFO 2026-06-08 08:25:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-27,549
INFO 2026-06-08 08:25:54 MarkDuplicates Traversing fragment information and detecting duplicates.
WARNING 2026-06-08 08:25:54 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
INFO 2026-06-08 08:26:35 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:26:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 203987568; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:26:38 MarkDuplicates Marking 313863649 records as duplicates.
INFO 2026-06-08 08:26:38 MarkDuplicates Found 7509789 optical duplicate clusters.
INFO 2026-06-08 08:26:38 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 08:26:54 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:15s. Time for last 10,000,000: 15s. Last read position: chr1:32,964,293
INFO 2026-06-08 08:27:09 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:30s. Time for last 10,000,000: 15s. Last read position: chr1:117,623,984
INFO 2026-06-08 08:27:23 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:45s. Time for last 10,000,000: 14s. Last read position: chr1:156,767,821
INFO 2026-06-08 08:27:38 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:00s. Time for last 10,000,000: 14s. Last read position: chr1:228,406,380
INFO 2026-06-08 08:27:53 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:15s. Time for last 10,000,000: 14s. Last read position: chr2:55,233,361
INFO 2026-06-08 08:28:08 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:30s. Time for last 10,000,000: 15s. Last read position: chr2:152,673,641
INFO 2026-06-08 08:28:23 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:01:45s. Time for last 10,000,000: 15s. Last read position: chr2:217,818,568
INFO 2026-06-08 08:28:38 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:00s. Time for last 10,000,000: 15s. Last read position: chr3:49,098,386
INFO 2026-06-08 08:28:53 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:15s. Time for last 10,000,000: 15s. Last read position: chr3:170,384,569
INFO 2026-06-08 08:29:09 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:30s. Time for last 10,000,000: 15s. Last read position: chr4:82,851,591
INFO 2026-06-08 08:29:24 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:02:46s. Time for last 10,000,000: 15s. Last read position: chr5:67,145,337
INFO 2026-06-08 08:29:39 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:01s. Time for last 10,000,000: 15s. Last read position: chr5:150,405,112
INFO 2026-06-08 08:29:54 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:16s. Time for last 10,000,000: 15s. Last read position: chr6:24,843,292
INFO 2026-06-08 08:30:09 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:03:31s. Time for last 10,000,000: 15s. Last read position: chr6:41,740,576
INFO 2026-06-08 08:30:25 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:03:46s. Time for last 10,000,000: 15s. Last read position: chr6:168,598,876
INFO 2026-06-08 08:30:40 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:02s. Time for last 10,000,000: 15s. Last read position: chr7:94,408,362
INFO 2026-06-08 08:30:55 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:04:17s. Time for last 10,000,000: 15s. Last read position: chr8:22,162,573
INFO 2026-06-08 08:31:10 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:04:32s. Time for last 10,000,000: 15s. Last read position: chr8:141,128,785
INFO 2026-06-08 08:31:25 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:04:47s. Time for last 10,000,000: 14s. Last read position: chr9:99,984,991
INFO 2026-06-08 08:31:40 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:05:02s. Time for last 10,000,000: 14s. Last read position: chr10:17,229,680
INFO 2026-06-08 08:31:56 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:05:17s. Time for last 10,000,000: 15s. Last read position: chr10:114,044,858
INFO 2026-06-08 08:32:12 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:05:34s. Time for last 10,000,000: 16s. Last read position: chr11:61,965,035
INFO 2026-06-08 08:32:28 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:05:49s. Time for last 10,000,000: 15s. Last read position: chr11:102,186,054
INFO 2026-06-08 08:32:44 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:06:06s. Time for last 10,000,000: 16s. Last read position: chr12:12,908,618
INFO 2026-06-08 08:33:00 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:06:22s. Time for last 10,000,000: 16s. Last read position: chr12:76,347,098
INFO 2026-06-08 08:33:16 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:06:38s. Time for last 10,000,000: 16s. Last read position: chr13:98,888,636
INFO 2026-06-08 08:33:32 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:06:53s. Time for last 10,000,000: 15s. Last read position: chr14:75,103,915
INFO 2026-06-08 08:33:47 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:07:08s. Time for last 10,000,000: 15s. Last read position: chr15:44,668,329
INFO 2026-06-08 08:34:03 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:07:25s. Time for last 10,000,000: 16s. Last read position: chr16:79,441
INFO 2026-06-08 08:34:18 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:07:40s. Time for last 10,000,000: 15s. Last read position: chr16:21,258,796
INFO 2026-06-08 08:34:34 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:07:55s. Time for last 10,000,000: 15s. Last read position: chr16:71,859,982
INFO 2026-06-08 08:34:49 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:08:11s. Time for last 10,000,000: 15s. Last read position: chr17:28,354,489
INFO 2026-06-08 08:35:04 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:08:26s. Time for last 10,000,000: 15s. Last read position: chr17:50,750,818
INFO 2026-06-08 08:35:20 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:08:41s. Time for last 10,000,000: 15s. Last read position: chr18:22,171,767
INFO 2026-06-08 08:35:35 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:08:56s. Time for last 10,000,000: 15s. Last read position: chr19:11,345,524
INFO 2026-06-08 08:35:50 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:09:12s. Time for last 10,000,000: 15s. Last read position: chr19:41,425,772
INFO 2026-06-08 08:36:05 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:09:27s. Time for last 10,000,000: 15s. Last read position: chr20:5,119,585
INFO 2026-06-08 08:36:20 MarkDuplicates Written 380,000,000 records. Elapsed time: 00:09:42s. Time for last 10,000,000: 15s. Last read position: chr21:33,555,089
INFO 2026-06-08 08:36:35 MarkDuplicates Written 390,000,000 records. Elapsed time: 00:09:57s. Time for last 10,000,000: 15s. Last read position: chr22:39,224,665
INFO 2026-06-08 08:36:50 MarkDuplicates Written 400,000,000 records. Elapsed time: 00:10:12s. Time for last 10,000,000: 14s. Last read position: chrX:77,618,916
INFO 2026-06-08 08:37:05 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:37:05 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:37:05 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:37:05 MarkDuplicates Before output close freeMemory: 203981128; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:37:05 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:37:05 MarkDuplicates After output close freeMemory: 104207632; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 08:37:05 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 25.03 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory