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 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bam --METRICS_FILE 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:51:03.598 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Jun 08 07:51:03 GMT 2026] MarkDuplicates --INPUT 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bam --METRICS_FILE 1173_C31_T1_RNA_SLD_01_A23T55JLT4_1.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 07:51:03 GMT 2026] Executing as ?@nf-9dd9338f7dfa370cdbe9db25b61f5708-ced83-46kqp on Linux 6.12.88 amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0
INFO 2026-06-08 07:51:03 MarkDuplicates Start of doWork freeMemory: 105826728; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:51:03 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:51:03 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:51:10 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 4s. Last read position: chr1:8,358,209
INFO 2026-06-08 07:51:10 MarkDuplicates Tracking 2776 as yet unmatched pairs. 51 records in RAM.
INFO 2026-06-08 07:51:14 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 3s. Last read position: chr1:16,132,070
INFO 2026-06-08 07:51:14 MarkDuplicates Tracking 5487 as yet unmatched pairs. 29 records in RAM.
INFO 2026-06-08 07:51:17 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 3s. Last read position: chr1:21,848,896
INFO 2026-06-08 07:51:17 MarkDuplicates Tracking 8277 as yet unmatched pairs. 80 records in RAM.
INFO 2026-06-08 07:51:20 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: chr1:26,344,405
INFO 2026-06-08 07:51:20 MarkDuplicates Tracking 10886 as yet unmatched pairs. 32 records in RAM.
INFO 2026-06-08 07:51:24 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 3s. Last read position: chr1:32,222,428
INFO 2026-06-08 07:51:24 MarkDuplicates Tracking 13712 as yet unmatched pairs. 67 records in RAM.
INFO 2026-06-08 07:51:27 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 3s. Last read position: chr1:39,453,819
INFO 2026-06-08 07:51:27 MarkDuplicates Tracking 16405 as yet unmatched pairs. 80 records in RAM.
INFO 2026-06-08 07:51:31 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 3s. Last read position: chr1:46,131,893
INFO 2026-06-08 07:51:31 MarkDuplicates Tracking 19095 as yet unmatched pairs. 52 records in RAM.
INFO 2026-06-08 07:51:35 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 3s. Last read position: chr1:64,844,777
INFO 2026-06-08 07:51:35 MarkDuplicates Tracking 21630 as yet unmatched pairs. 43 records in RAM.
INFO 2026-06-08 07:51:38 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 3s. Last read position: chr1:100,027,099
INFO 2026-06-08 07:51:38 MarkDuplicates Tracking 24018 as yet unmatched pairs. 26 records in RAM.
INFO 2026-06-08 07:51:42 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 4s. Last read position: chr1:114,463,502
INFO 2026-06-08 07:51:42 MarkDuplicates Tracking 26771 as yet unmatched pairs. 255 records in RAM.
INFO 2026-06-08 07:51:46 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 3s. Last read position: chr1:145,623,086
INFO 2026-06-08 07:51:46 MarkDuplicates Tracking 28795 as yet unmatched pairs. 16 records in RAM.
INFO 2026-06-08 07:51:49 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chr1:150,294,328
INFO 2026-06-08 07:51:49 MarkDuplicates Tracking 30300 as yet unmatched pairs. 49 records in RAM.
INFO 2026-06-08 07:51:52 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 3s. Last read position: chr1:153,984,748
INFO 2026-06-08 07:51:52 MarkDuplicates Tracking 32865 as yet unmatched pairs. 38 records in RAM.
INFO 2026-06-08 07:51:55 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 3s. Last read position: chr1:155,679,444
INFO 2026-06-08 07:51:55 MarkDuplicates Tracking 35313 as yet unmatched pairs. 152 records in RAM.
INFO 2026-06-08 07:51:59 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 3s. Last read position: chr1:160,306,468
INFO 2026-06-08 07:51:59 MarkDuplicates Tracking 38029 as yet unmatched pairs. 62 records in RAM.
INFO 2026-06-08 07:52:03 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 3s. Last read position: chr1:169,130,016
INFO 2026-06-08 07:52:03 MarkDuplicates Tracking 42712 as yet unmatched pairs. 2181 records in RAM.
INFO 2026-06-08 07:52:06 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 3s. Last read position: chr1:183,546,180
INFO 2026-06-08 07:52:06 MarkDuplicates Tracking 43187 as yet unmatched pairs. 21 records in RAM.
INFO 2026-06-08 07:52:09 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 2s. Last read position: chr1:202,943,812
INFO 2026-06-08 07:52:09 MarkDuplicates Tracking 45636 as yet unmatched pairs. 56 records in RAM.
INFO 2026-06-08 07:52:12 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 3s. Last read position: chr1:206,933,064
INFO 2026-06-08 07:52:12 MarkDuplicates Tracking 49497 as yet unmatched pairs. 1441 records in RAM.
INFO 2026-06-08 07:52:15 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 2s. Last read position: chr1:212,787,598
INFO 2026-06-08 07:52:15 MarkDuplicates Tracking 50822 as yet unmatched pairs. 38 records in RAM.
INFO 2026-06-08 07:52:19 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 3s. Last read position: chr1:231,374,065
INFO 2026-06-08 07:52:19 MarkDuplicates Tracking 53295 as yet unmatched pairs. 10 records in RAM.
INFO 2026-06-08 07:52:23 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 4s. Last read position: chr2:10,572,066
INFO 2026-06-08 07:52:23 MarkDuplicates Tracking 56003 as yet unmatched pairs. 55476 records in RAM.
INFO 2026-06-08 07:52:26 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 3s. Last read position: chr2:27,440,825
INFO 2026-06-08 07:52:26 MarkDuplicates Tracking 58723 as yet unmatched pairs. 58165 records in RAM.
INFO 2026-06-08 07:52:30 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 3s. Last read position: chr2:32,916,264
INFO 2026-06-08 07:52:30 MarkDuplicates Tracking 245661 as yet unmatched pairs. 47723 records in RAM.
INFO 2026-06-08 07:52:33 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 3s. Last read position: chr2:32,916,415
INFO 2026-06-08 07:52:33 MarkDuplicates Tracking 483499 as yet unmatched pairs. 33432 records in RAM.
INFO 2026-06-08 07:52:36 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 3s. Last read position: chr2:47,369,556
INFO 2026-06-08 07:52:36 MarkDuplicates Tracking 499111 as yet unmatched pairs. 30271 records in RAM.
INFO 2026-06-08 07:52:40 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 3s. Last read position: chr2:65,265,156
INFO 2026-06-08 07:52:40 MarkDuplicates Tracking 496419 as yet unmatched pairs. 27561 records in RAM.
INFO 2026-06-08 07:52:44 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 3s. Last read position: chr2:85,327,105
INFO 2026-06-08 07:52:44 MarkDuplicates Tracking 493895 as yet unmatched pairs. 25002 records in RAM.
INFO 2026-06-08 07:52:46 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 2s. Last read position: chr2:100,820,398
INFO 2026-06-08 07:52:46 MarkDuplicates Tracking 491713 as yet unmatched pairs. 22797 records in RAM.
INFO 2026-06-08 07:52:50 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 3s. Last read position: chr2:110,562,637
INFO 2026-06-08 07:52:50 MarkDuplicates Tracking 490099 as yet unmatched pairs. 21162 records in RAM.
INFO 2026-06-08 07:52:53 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 3s. Last read position: chr2:135,135,868
INFO 2026-06-08 07:52:53 MarkDuplicates Tracking 487717 as yet unmatched pairs. 18752 records in RAM.
INFO 2026-06-08 07:52:56 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 3s. Last read position: chr2:172,474,061
INFO 2026-06-08 07:52:56 MarkDuplicates Tracking 485455 as yet unmatched pairs. 16445 records in RAM.
INFO 2026-06-08 07:53:00 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 3s. Last read position: chr2:189,002,956
INFO 2026-06-08 07:53:00 MarkDuplicates Tracking 483017 as yet unmatched pairs. 13973 records in RAM.
INFO 2026-06-08 07:53:04 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 3s. Last read position: chr2:203,132,024
INFO 2026-06-08 07:53:04 MarkDuplicates Tracking 480249 as yet unmatched pairs. 11181 records in RAM.
INFO 2026-06-08 07:53:07 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 3s. Last read position: chr2:215,391,723
INFO 2026-06-08 07:53:07 MarkDuplicates Tracking 477939 as yet unmatched pairs. 8856 records in RAM.
INFO 2026-06-08 07:53:10 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 3s. Last read position: chr2:218,281,939
INFO 2026-06-08 07:53:10 MarkDuplicates Tracking 475407 as yet unmatched pairs. 6310 records in RAM.
INFO 2026-06-08 07:53:15 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 4s. Last read position: chr2:231,455,151
INFO 2026-06-08 07:53:15 MarkDuplicates Tracking 472899 as yet unmatched pairs. 3750 records in RAM.
INFO 2026-06-08 07:53:18 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 3s. Last read position: chr2:240,630,111
INFO 2026-06-08 07:53:18 MarkDuplicates Tracking 470056 as yet unmatched pairs. 876 records in RAM.
INFO 2026-06-08 07:53:22 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 4s. Last read position: chr3:14,158,655
INFO 2026-06-08 07:53:22 MarkDuplicates Tracking 467369 as yet unmatched pairs. 25851 records in RAM.
INFO 2026-06-08 07:53:25 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 3s. Last read position: chr3:41,224,569
INFO 2026-06-08 07:53:25 MarkDuplicates Tracking 465400 as yet unmatched pairs. 23863 records in RAM.
INFO 2026-06-08 07:53:28 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 3s. Last read position: chr3:48,469,734
INFO 2026-06-08 07:53:28 MarkDuplicates Tracking 462448 as yet unmatched pairs. 20900 records in RAM.
INFO 2026-06-08 07:53:32 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 3s. Last read position: chr3:51,393,988
INFO 2026-06-08 07:53:32 MarkDuplicates Tracking 459558 as yet unmatched pairs. 17993 records in RAM.
INFO 2026-06-08 07:53:35 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 3s. Last read position: chr3:62,195,061
INFO 2026-06-08 07:53:35 MarkDuplicates Tracking 457022 as yet unmatched pairs. 15437 records in RAM.
INFO 2026-06-08 07:53:38 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 3s. Last read position: chr3:112,550,217
INFO 2026-06-08 07:53:38 MarkDuplicates Tracking 454738 as yet unmatched pairs. 13120 records in RAM.
INFO 2026-06-08 07:53:42 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 3s. Last read position: chr3:127,677,723
INFO 2026-06-08 07:53:42 MarkDuplicates Tracking 452206 as yet unmatched pairs. 10556 records in RAM.
INFO 2026-06-08 07:53:45 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 3s. Last read position: chr3:149,966,504
INFO 2026-06-08 07:53:45 MarkDuplicates Tracking 449670 as yet unmatched pairs. 7979 records in RAM.
INFO 2026-06-08 07:53:48 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 3s. Last read position: chr3:184,299,374
INFO 2026-06-08 07:53:48 MarkDuplicates Tracking 447384 as yet unmatched pairs. 5662 records in RAM.
INFO 2026-06-08 07:53:51 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 3s. Last read position: chr3:195,729,650
INFO 2026-06-08 07:53:51 MarkDuplicates Tracking 445023 as yet unmatched pairs. 3276 records in RAM.
INFO 2026-06-08 07:53:54 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 2s. Last read position: chr3:195,783,545
INFO 2026-06-08 07:53:54 MarkDuplicates Tracking 445384 as yet unmatched pairs. 3628 records in RAM.
INFO 2026-06-08 07:53:57 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 2s. Last read position: chr3:196,053,492
INFO 2026-06-08 07:53:57 MarkDuplicates Tracking 442499 as yet unmatched pairs. 737 records in RAM.
INFO 2026-06-08 07:54:00 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 3s. Last read position: chr4:6,862,084
INFO 2026-06-08 07:54:00 MarkDuplicates Tracking 439603 as yet unmatched pairs. 13565 records in RAM.
INFO 2026-06-08 07:54:04 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 3s. Last read position: chr4:47,512,581
INFO 2026-06-08 07:54:04 MarkDuplicates Tracking 437097 as yet unmatched pairs. 11010 records in RAM.
INFO 2026-06-08 07:54:07 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 3s. Last read position: chr4:76,739,489
INFO 2026-06-08 07:54:07 MarkDuplicates Tracking 434658 as yet unmatched pairs. 8545 records in RAM.
INFO 2026-06-08 07:54:11 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 3s. Last read position: chr4:105,275,517
INFO 2026-06-08 07:54:11 MarkDuplicates Tracking 432194 as yet unmatched pairs. 6050 records in RAM.
INFO 2026-06-08 07:54:13 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 2s. Last read position: chr4:143,546,898
INFO 2026-06-08 07:54:13 MarkDuplicates Tracking 429793 as yet unmatched pairs. 3603 records in RAM.
INFO 2026-06-08 07:54:17 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 3s. Last read position: chr4:185,657,577
INFO 2026-06-08 07:54:17 MarkDuplicates Tracking 427377 as yet unmatched pairs. 1160 records in RAM.
INFO 2026-06-08 07:54:20 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 3s. Last read position: chr5:14,405,868
INFO 2026-06-08 07:54:20 MarkDuplicates Tracking 424831 as yet unmatched pairs. 21931 records in RAM.
INFO 2026-06-08 07:54:23 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 3s. Last read position: chr5:55,976,240
INFO 2026-06-08 07:54:23 MarkDuplicates Tracking 422225 as yet unmatched pairs. 19297 records in RAM.
INFO 2026-06-08 07:54:27 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 3s. Last read position: chr5:81,080,678
INFO 2026-06-08 07:54:27 MarkDuplicates Tracking 419951 as yet unmatched pairs. 16995 records in RAM.
INFO 2026-06-08 07:54:30 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 2s. Last read position: chr5:124,648,743
INFO 2026-06-08 07:54:30 MarkDuplicates Tracking 417747 as yet unmatched pairs. 14763 records in RAM.
INFO 2026-06-08 07:54:33 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 2s. Last read position: chr5:138,556,053
INFO 2026-06-08 07:54:33 MarkDuplicates Tracking 415409 as yet unmatched pairs. 12412 records in RAM.
INFO 2026-06-08 07:54:36 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 3s. Last read position: chr5:146,128,978
INFO 2026-06-08 07:54:36 MarkDuplicates Tracking 412861 as yet unmatched pairs. 9753 records in RAM.
INFO 2026-06-08 07:54:39 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 2s. Last read position: chr5:150,407,252
INFO 2026-06-08 07:54:39 MarkDuplicates Tracking 411619 as yet unmatched pairs. 8494 records in RAM.
INFO 2026-06-08 07:54:42 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 2s. Last read position: chr5:171,390,059
INFO 2026-06-08 07:54:42 MarkDuplicates Tracking 408900 as yet unmatched pairs. 5742 records in RAM.
INFO 2026-06-08 07:54:45 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 3s. Last read position: chr5:179,616,913
INFO 2026-06-08 07:54:45 MarkDuplicates Tracking 405300 as yet unmatched pairs. 2125 records in RAM.
INFO 2026-06-08 07:54:48 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 2s. Last read position: chr6:4,892,157
INFO 2026-06-08 07:54:48 MarkDuplicates Tracking 402473 as yet unmatched pairs. 25472 records in RAM.
INFO 2026-06-08 07:54:50 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 2s. Last read position: chr6:26,094,318
INFO 2026-06-08 07:54:50 MarkDuplicates Tracking 399907 as yet unmatched pairs. 22862 records in RAM.
INFO 2026-06-08 07:54:52 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 2s. Last read position: chr6:30,743,949
INFO 2026-06-08 07:54:52 MarkDuplicates Tracking 397493 as yet unmatched pairs. 20437 records in RAM.
INFO 2026-06-08 07:54:55 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 3s. Last read position: chr6:31,943,712
INFO 2026-06-08 07:54:55 MarkDuplicates Tracking 394905 as yet unmatched pairs. 17841 records in RAM.
INFO 2026-06-08 07:54:59 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 3s. Last read position: chr6:33,670,439
INFO 2026-06-08 07:54:59 MarkDuplicates Tracking 392404 as yet unmatched pairs. 15323 records in RAM.
INFO 2026-06-08 07:55:02 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 3s. Last read position: chr6:43,560,993
INFO 2026-06-08 07:55:02 MarkDuplicates Tracking 389743 as yet unmatched pairs. 12631 records in RAM.
INFO 2026-06-08 07:55:06 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 3s. Last read position: chr6:75,284,429
INFO 2026-06-08 07:55:06 MarkDuplicates Tracking 387418 as yet unmatched pairs. 10268 records in RAM.
INFO 2026-06-08 07:55:09 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 2s. Last read position: chr6:110,893,569
INFO 2026-06-08 07:55:09 MarkDuplicates Tracking 384983 as yet unmatched pairs. 7809 records in RAM.
INFO 2026-06-08 07:55:12 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 3s. Last read position: chr6:137,871,291
INFO 2026-06-08 07:55:12 MarkDuplicates Tracking 382371 as yet unmatched pairs. 5172 records in RAM.
INFO 2026-06-08 07:55:15 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 3s. Last read position: chr6:158,429,763
INFO 2026-06-08 07:55:15 MarkDuplicates Tracking 379910 as yet unmatched pairs. 2682 records in RAM.
INFO 2026-06-08 07:55:18 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 3s. Last read position: chr7:518,954
INFO 2026-06-08 07:55:18 MarkDuplicates Tracking 377208 as yet unmatched pairs. 28861 records in RAM.
INFO 2026-06-08 07:55:21 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 2s. Last read position: chr7:5,529,284
INFO 2026-06-08 07:55:21 MarkDuplicates Tracking 376512 as yet unmatched pairs. 28144 records in RAM.
INFO 2026-06-08 07:55:24 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 3s. Last read position: chr7:32,495,751
INFO 2026-06-08 07:55:24 MarkDuplicates Tracking 371928 as yet unmatched pairs. 23541 records in RAM.
INFO 2026-06-08 07:55:28 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 3s. Last read position: chr7:55,202,609
INFO 2026-06-08 07:55:28 MarkDuplicates Tracking 369377 as yet unmatched pairs. 20972 records in RAM.
INFO 2026-06-08 07:55:31 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 3s. Last read position: chr7:75,187,249
INFO 2026-06-08 07:55:31 MarkDuplicates Tracking 367464 as yet unmatched pairs. 19044 records in RAM.
INFO 2026-06-08 07:55:34 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 2s. Last read position: chr7:92,086,290
INFO 2026-06-08 07:55:34 MarkDuplicates Tracking 365183 as yet unmatched pairs. 16756 records in RAM.
INFO 2026-06-08 07:55:37 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 3s. Last read position: chr7:99,674,536
INFO 2026-06-08 07:55:37 MarkDuplicates Tracking 362915 as yet unmatched pairs. 14472 records in RAM.
INFO 2026-06-08 07:55:40 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 2s. Last read position: chr7:100,994,634
INFO 2026-06-08 07:55:40 MarkDuplicates Tracking 360679 as yet unmatched pairs. 12233 records in RAM.
INFO 2026-06-08 07:55:42 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 2s. Last read position: chr7:100,999,954
INFO 2026-06-08 07:55:42 MarkDuplicates Tracking 359939 as yet unmatched pairs. 11491 records in RAM.
INFO 2026-06-08 07:55:44 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 1s. Last read position: chr7:101,036,595
INFO 2026-06-08 07:55:44 MarkDuplicates Tracking 358909 as yet unmatched pairs. 10457 records in RAM.
INFO 2026-06-08 07:55:47 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 2s. Last read position: chr7:103,327,701
INFO 2026-06-08 07:55:47 MarkDuplicates Tracking 356659 as yet unmatched pairs. 8200 records in RAM.
INFO 2026-06-08 07:55:50 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 3s. Last read position: chr7:128,580,024
INFO 2026-06-08 07:55:50 MarkDuplicates Tracking 354396 as yet unmatched pairs. 5913 records in RAM.
INFO 2026-06-08 07:55:53 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 3s. Last read position: chr7:142,171,394
INFO 2026-06-08 07:55:53 MarkDuplicates Tracking 351862 as yet unmatched pairs. 3364 records in RAM.
INFO 2026-06-08 07:55:56 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 2s. Last read position: chr7:151,374,108
INFO 2026-06-08 07:55:56 MarkDuplicates Tracking 349581 as yet unmatched pairs. 1074 records in RAM.
INFO 2026-06-08 07:55:58 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 2s. Last read position: chr8:19,823,965
INFO 2026-06-08 07:55:58 MarkDuplicates Tracking 346988 as yet unmatched pairs. 17180 records in RAM.
INFO 2026-06-08 07:56:00 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 2s. Last read position: chr8:37,697,920
INFO 2026-06-08 07:56:00 MarkDuplicates Tracking 344481 as yet unmatched pairs. 14658 records in RAM.
INFO 2026-06-08 07:56:04 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 3s. Last read position: chr8:56,073,141
INFO 2026-06-08 07:56:04 MarkDuplicates Tracking 343207 as yet unmatched pairs. 13368 records in RAM.
INFO 2026-06-08 07:56:06 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 2s. Last read position: chr8:94,159,971
INFO 2026-06-08 07:56:06 MarkDuplicates Tracking 339418 as yet unmatched pairs. 9556 records in RAM.
INFO 2026-06-08 07:56:09 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 3s. Last read position: chr8:120,270,043
INFO 2026-06-08 07:56:09 MarkDuplicates Tracking 336986 as yet unmatched pairs. 7113 records in RAM.
INFO 2026-06-08 07:56:13 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 3s. Last read position: chr8:143,858,086
INFO 2026-06-08 07:56:13 MarkDuplicates Tracking 334309 as yet unmatched pairs. 4407 records in RAM.
INFO 2026-06-08 07:56:15 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 2s. Last read position: chr8:143,866,434
INFO 2026-06-08 07:56:15 MarkDuplicates Tracking 333423 as yet unmatched pairs. 3519 records in RAM.
INFO 2026-06-08 07:56:18 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 2s. Last read position: chr8:144,790,420
INFO 2026-06-08 07:56:18 MarkDuplicates Tracking 330310 as yet unmatched pairs. 386 records in RAM.
INFO 2026-06-08 07:56:20 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 2s. Last read position: chr9:33,917,165
INFO 2026-06-08 07:56:20 MarkDuplicates Tracking 327703 as yet unmatched pairs. 16909 records in RAM.
INFO 2026-06-08 07:56:23 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 2s. Last read position: chr9:71,732,394
INFO 2026-06-08 07:56:23 MarkDuplicates Tracking 325489 as yet unmatched pairs. 14648 records in RAM.
INFO 2026-06-08 07:56:26 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 3s. Last read position: chr9:95,468,827
INFO 2026-06-08 07:56:26 MarkDuplicates Tracking 322853 as yet unmatched pairs. 11972 records in RAM.
INFO 2026-06-08 07:56:29 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 2s. Last read position: chr9:114,426,381
INFO 2026-06-08 07:56:29 MarkDuplicates Tracking 320298 as yet unmatched pairs. 9401 records in RAM.
INFO 2026-06-08 07:56:32 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 3s. Last read position: chr9:128,152,182
INFO 2026-06-08 07:56:32 MarkDuplicates Tracking 318380 as yet unmatched pairs. 7454 records in RAM.
INFO 2026-06-08 07:56:34 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 2s. Last read position: chr9:131,582,641
INFO 2026-06-08 07:56:34 MarkDuplicates Tracking 314979 as yet unmatched pairs. 4035 records in RAM.
INFO 2026-06-08 07:56:37 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 2s. Last read position: chr9:136,863,315
INFO 2026-06-08 07:56:37 MarkDuplicates Tracking 312474 as yet unmatched pairs. 1511 records in RAM.
INFO 2026-06-08 07:56:40 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 3s. Last read position: chr10:13,526,163
INFO 2026-06-08 07:56:40 MarkDuplicates Tracking 309569 as yet unmatched pairs. 19593 records in RAM.
INFO 2026-06-08 07:56:42 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 2s. Last read position: chr10:32,032,763
INFO 2026-06-08 07:56:42 MarkDuplicates Tracking 307505 as yet unmatched pairs. 17511 records in RAM.
INFO 2026-06-08 07:56:45 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 2s. Last read position: chr10:58,237,766
INFO 2026-06-08 07:56:45 MarkDuplicates Tracking 305242 as yet unmatched pairs. 15229 records in RAM.
INFO 2026-06-08 07:56:48 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 2s. Last read position: chr10:73,799,171
INFO 2026-06-08 07:56:48 MarkDuplicates Tracking 302802 as yet unmatched pairs. 12764 records in RAM.
INFO 2026-06-08 07:56:51 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 2s. Last read position: chr10:93,341,656
INFO 2026-06-08 07:56:51 MarkDuplicates Tracking 300402 as yet unmatched pairs. 10351 records in RAM.
INFO 2026-06-08 07:56:53 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 2s. Last read position: chr10:102,141,497
INFO 2026-06-08 07:56:53 MarkDuplicates Tracking 297825 as yet unmatched pairs. 7757 records in RAM.
INFO 2026-06-08 07:56:57 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 3s. Last read position: chr10:114,253,654
INFO 2026-06-08 07:56:57 MarkDuplicates Tracking 295217 as yet unmatched pairs. 5140 records in RAM.
INFO 2026-06-08 07:57:00 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 2s. Last read position: chr10:122,588,963
INFO 2026-06-08 07:57:00 MarkDuplicates Tracking 293245 as yet unmatched pairs. 3159 records in RAM.
INFO 2026-06-08 07:57:02 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 2s. Last read position: chr10:124,400,889
INFO 2026-06-08 07:57:02 MarkDuplicates Tracking 291198 as yet unmatched pairs. 1103 records in RAM.
INFO 2026-06-08 07:57:06 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 3s. Last read position: chr11:621,206
INFO 2026-06-08 07:57:06 MarkDuplicates Tracking 288496 as yet unmatched pairs. 32279 records in RAM.
INFO 2026-06-08 07:57:10 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 3s. Last read position: chr11:1,247,338
INFO 2026-06-08 07:57:10 MarkDuplicates Tracking 285903 as yet unmatched pairs. 29668 records in RAM.
INFO 2026-06-08 07:57:13 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 3s. Last read position: chr11:9,606,158
INFO 2026-06-08 07:57:13 MarkDuplicates Tracking 283105 as yet unmatched pairs. 26854 records in RAM.
INFO 2026-06-08 07:57:17 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 3s. Last read position: chr11:34,449,297
INFO 2026-06-08 07:57:17 MarkDuplicates Tracking 280644 as yet unmatched pairs. 24371 records in RAM.
INFO 2026-06-08 07:57:19 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 2s. Last read position: chr11:57,302,161
INFO 2026-06-08 07:57:19 MarkDuplicates Tracking 277929 as yet unmatched pairs. 21641 records in RAM.
INFO 2026-06-08 07:57:23 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:06:16s. Time for last 1,000,000: 3s. Last read position: chr11:62,519,581
INFO 2026-06-08 07:57:23 MarkDuplicates Tracking 275915 as yet unmatched pairs. 19602 records in RAM.
INFO 2026-06-08 07:57:26 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 3s. Last read position: chr11:63,753,072
INFO 2026-06-08 07:57:26 MarkDuplicates Tracking 273313 as yet unmatched pairs. 16993 records in RAM.
INFO 2026-06-08 07:57:29 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 3s. Last read position: chr11:65,655,688
INFO 2026-06-08 07:57:29 MarkDuplicates Tracking 270461 as yet unmatched pairs. 14111 records in RAM.
INFO 2026-06-08 07:57:32 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 3s. Last read position: chr11:68,389,892
INFO 2026-06-08 07:57:32 MarkDuplicates Tracking 267279 as yet unmatched pairs. 10915 records in RAM.
INFO 2026-06-08 07:57:35 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 3s. Last read position: chr11:75,402,436
INFO 2026-06-08 07:57:35 MarkDuplicates Tracking 264710 as yet unmatched pairs. 8333 records in RAM.
INFO 2026-06-08 07:57:39 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:06:33s. Time for last 1,000,000: 3s. Last read position: chr11:103,120,522
INFO 2026-06-08 07:57:39 MarkDuplicates Tracking 261997 as yet unmatched pairs. 5609 records in RAM.
INFO 2026-06-08 07:57:42 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 3s. Last read position: chr11:119,017,961
INFO 2026-06-08 07:57:42 MarkDuplicates Tracking 259440 as yet unmatched pairs. 3028 records in RAM.
INFO 2026-06-08 07:57:45 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 2s. Last read position: chr11:130,189,874
INFO 2026-06-08 07:57:45 MarkDuplicates Tracking 256918 as yet unmatched pairs. 482 records in RAM.
INFO 2026-06-08 07:57:48 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 3s. Last read position: chr12:6,769,932
INFO 2026-06-08 07:57:48 MarkDuplicates Tracking 254489 as yet unmatched pairs. 27180 records in RAM.
INFO 2026-06-08 07:57:52 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:06:46s. Time for last 1,000,000: 3s. Last read position: chr12:13,552,225
INFO 2026-06-08 07:57:52 MarkDuplicates Tracking 251809 as yet unmatched pairs. 24495 records in RAM.
INFO 2026-06-08 07:57:55 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 3s. Last read position: chr12:47,964,233
INFO 2026-06-08 07:57:55 MarkDuplicates Tracking 249443 as yet unmatched pairs. 22103 records in RAM.
INFO 2026-06-08 07:57:58 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 3s. Last read position: chr12:51,240,934
INFO 2026-06-08 07:57:58 MarkDuplicates Tracking 247031 as yet unmatched pairs. 19688 records in RAM.
INFO 2026-06-08 07:58:01 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 2s. Last read position: chr12:54,282,829
INFO 2026-06-08 07:58:01 MarkDuplicates Tracking 245077 as yet unmatched pairs. 17731 records in RAM.
INFO 2026-06-08 07:58:04 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 3s. Last read position: chr12:56,713,598
INFO 2026-06-08 07:58:04 MarkDuplicates Tracking 242283 as yet unmatched pairs. 14929 records in RAM.
INFO 2026-06-08 07:58:08 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 3s. Last read position: chr12:57,528,988
INFO 2026-06-08 07:58:08 MarkDuplicates Tracking 239384 as yet unmatched pairs. 12021 records in RAM.
INFO 2026-06-08 07:58:11 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 3s. Last read position: chr12:81,754,046
INFO 2026-06-08 07:58:11 MarkDuplicates Tracking 236869 as yet unmatched pairs. 9491 records in RAM.
INFO 2026-06-08 07:58:14 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 3s. Last read position: chr12:108,624,134
INFO 2026-06-08 07:58:14 MarkDuplicates Tracking 234553 as yet unmatched pairs. 7158 records in RAM.
INFO 2026-06-08 07:58:17 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:07:11s. Time for last 1,000,000: 3s. Last read position: chr12:119,522,940
INFO 2026-06-08 07:58:17 MarkDuplicates Tracking 231931 as yet unmatched pairs. 4524 records in RAM.
INFO 2026-06-08 07:58:20 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:07:14s. Time for last 1,000,000: 3s. Last read position: chr12:124,336,826
INFO 2026-06-08 07:58:20 MarkDuplicates Tracking 229303 as yet unmatched pairs. 1886 records in RAM.
INFO 2026-06-08 07:58:23 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:07:17s. Time for last 1,000,000: 3s. Last read position: chr13:24,452,434
INFO 2026-06-08 07:58:23 MarkDuplicates Tracking 226709 as yet unmatched pairs. 6823 records in RAM.
INFO 2026-06-08 07:58:27 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:07:21s. Time for last 1,000,000: 3s. Last read position: chr13:48,376,966
INFO 2026-06-08 07:58:27 MarkDuplicates Tracking 224285 as yet unmatched pairs. 4382 records in RAM.
INFO 2026-06-08 07:58:30 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:07:24s. Time for last 1,000,000: 3s. Last read position: chr13:99,540,748
INFO 2026-06-08 07:58:30 MarkDuplicates Tracking 221947 as yet unmatched pairs. 2035 records in RAM.
INFO 2026-06-08 07:58:34 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 3s. Last read position: chr14:21,230,343
INFO 2026-06-08 07:58:34 MarkDuplicates Tracking 220028 as yet unmatched pairs. 17974 records in RAM.
INFO 2026-06-08 07:58:37 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:07:30s. Time for last 1,000,000: 3s. Last read position: chr14:32,092,226
INFO 2026-06-08 07:58:37 MarkDuplicates Tracking 216571 as yet unmatched pairs. 14503 records in RAM.
INFO 2026-06-08 07:58:40 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:07:33s. Time for last 1,000,000: 3s. Last read position: chr14:59,483,762
INFO 2026-06-08 07:58:40 MarkDuplicates Tracking 214260 as yet unmatched pairs. 12177 records in RAM.
INFO 2026-06-08 07:58:43 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:07:37s. Time for last 1,000,000: 3s. Last read position: chr14:73,284,154
INFO 2026-06-08 07:58:43 MarkDuplicates Tracking 211797 as yet unmatched pairs. 9704 records in RAM.
INFO 2026-06-08 07:58:46 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:07:40s. Time for last 1,000,000: 3s. Last read position: chr14:92,839,382
INFO 2026-06-08 07:58:46 MarkDuplicates Tracking 209122 as yet unmatched pairs. 7009 records in RAM.
INFO 2026-06-08 07:58:49 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:07:43s. Time for last 1,000,000: 2s. Last read position: chr14:104,703,136
INFO 2026-06-08 07:58:49 MarkDuplicates Tracking 206503 as yet unmatched pairs. 4362 records in RAM.
INFO 2026-06-08 07:58:52 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:07:46s. Time for last 1,000,000: 2s. Last read position: chr14:105,588,236
INFO 2026-06-08 07:58:52 MarkDuplicates Tracking 206374 as yet unmatched pairs. 4226 records in RAM.
INFO 2026-06-08 07:58:55 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:07:49s. Time for last 1,000,000: 2s. Last read position: chr15:25,375,422
INFO 2026-06-08 07:58:55 MarkDuplicates Tracking 201874 as yet unmatched pairs. 16307 records in RAM.
INFO 2026-06-08 07:58:58 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:07:52s. Time for last 1,000,000: 2s. Last read position: chr15:40,662,093
INFO 2026-06-08 07:58:58 MarkDuplicates Tracking 199583 as yet unmatched pairs. 14003 records in RAM.
INFO 2026-06-08 07:59:01 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:07:55s. Time for last 1,000,000: 2s. Last read position: chr15:45,073,378
INFO 2026-06-08 07:59:01 MarkDuplicates Tracking 197199 as yet unmatched pairs. 11613 records in RAM.
INFO 2026-06-08 07:59:04 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:07:58s. Time for last 1,000,000: 3s. Last read position: chr15:59,768,828
INFO 2026-06-08 07:59:04 MarkDuplicates Tracking 194688 as yet unmatched pairs. 9085 records in RAM.
INFO 2026-06-08 07:59:08 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:08:02s. Time for last 1,000,000: 3s. Last read position: chr15:69,455,260
INFO 2026-06-08 07:59:08 MarkDuplicates Tracking 192181 as yet unmatched pairs. 6558 records in RAM.
INFO 2026-06-08 07:59:10 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:08:04s. Time for last 1,000,000: 2s. Last read position: chr15:77,180,420
INFO 2026-06-08 07:59:10 MarkDuplicates Tracking 189504 as yet unmatched pairs. 3878 records in RAM.
INFO 2026-06-08 07:59:13 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:08:07s. Time for last 1,000,000: 2s. Last read position: chr15:90,230,476
INFO 2026-06-08 07:59:13 MarkDuplicates Tracking 187385 as yet unmatched pairs. 1754 records in RAM.
INFO 2026-06-08 07:59:16 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:08:10s. Time for last 1,000,000: 3s. Last read position: chr16:1,314,050
INFO 2026-06-08 07:59:16 MarkDuplicates Tracking 184656 as yet unmatched pairs. 25726 records in RAM.
INFO 2026-06-08 07:59:19 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:08:13s. Time for last 1,000,000: 2s. Last read position: chr16:2,771,982
INFO 2026-06-08 07:59:19 MarkDuplicates Tracking 181662 as yet unmatched pairs. 22726 records in RAM.
INFO 2026-06-08 07:59:23 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 3s. Last read position: chr16:14,667,665
INFO 2026-06-08 07:59:23 MarkDuplicates Tracking 178944 as yet unmatched pairs. 20004 records in RAM.
INFO 2026-06-08 07:59:26 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 3s. Last read position: chr16:16,393,806
INFO 2026-06-08 07:59:26 MarkDuplicates Tracking 177351 as yet unmatched pairs. 18410 records in RAM.
INFO 2026-06-08 07:59:28 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:08:22s. Time for last 1,000,000: 2s. Last read position: chr16:21,519,952
INFO 2026-06-08 07:59:28 MarkDuplicates Tracking 176167 as yet unmatched pairs. 17223 records in RAM.
INFO 2026-06-08 07:59:31 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 2s. Last read position: chr16:24,931,092
INFO 2026-06-08 07:59:31 MarkDuplicates Tracking 174784 as yet unmatched pairs. 15835 records in RAM.
INFO 2026-06-08 07:59:33 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:08:27s. Time for last 1,000,000: 2s. Last read position: chr16:29,485,528
INFO 2026-06-08 07:59:33 MarkDuplicates Tracking 173282 as yet unmatched pairs. 14332 records in RAM.
INFO 2026-06-08 07:59:35 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 2s. Last read position: chr16:30,665,336
INFO 2026-06-08 07:59:35 MarkDuplicates Tracking 171132 as yet unmatched pairs. 12177 records in RAM.
INFO 2026-06-08 07:59:38 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 3s. Last read position: chr16:53,324,435
INFO 2026-06-08 07:59:38 MarkDuplicates Tracking 168595 as yet unmatched pairs. 9623 records in RAM.
INFO 2026-06-08 07:59:41 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 2s. Last read position: chr16:67,829,473
INFO 2026-06-08 07:59:41 MarkDuplicates Tracking 165800 as yet unmatched pairs. 6814 records in RAM.
INFO 2026-06-08 07:59:43 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 2s. Last read position: chr16:74,348,945
INFO 2026-06-08 07:59:43 MarkDuplicates Tracking 163163 as yet unmatched pairs. 4165 records in RAM.
INFO 2026-06-08 07:59:47 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:08:41s. Time for last 1,000,000: 4s. Last read position: chr16:88,658,678
INFO 2026-06-08 07:59:47 MarkDuplicates Tracking 160490 as yet unmatched pairs. 1474 records in RAM.
INFO 2026-06-08 07:59:51 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:08:45s. Time for last 1,000,000: 3s. Last read position: chr17:1,727,376
INFO 2026-06-08 07:59:51 MarkDuplicates Tracking 157715 as yet unmatched pairs. 46416 records in RAM.
INFO 2026-06-08 07:59:54 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 3s. Last read position: chr17:7,220,032
INFO 2026-06-08 07:59:54 MarkDuplicates Tracking 154885 as yet unmatched pairs. 43583 records in RAM.
INFO 2026-06-08 07:59:58 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:08:52s. Time for last 1,000,000: 3s. Last read position: chr17:8,234,558
INFO 2026-06-08 07:59:58 MarkDuplicates Tracking 152217 as yet unmatched pairs. 40914 records in RAM.
INFO 2026-06-08 08:00:01 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 2s. Last read position: chr17:20,455,303
INFO 2026-06-08 08:00:01 MarkDuplicates Tracking 149658 as yet unmatched pairs. 38345 records in RAM.
INFO 2026-06-08 08:00:03 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:08:56s. Time for last 1,000,000: 2s. Last read position: chr17:32,201,038
INFO 2026-06-08 08:00:03 MarkDuplicates Tracking 147267 as yet unmatched pairs. 35946 records in RAM.
INFO 2026-06-08 08:00:06 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:09:00s. Time for last 1,000,000: 3s. Last read position: chr17:39,202,413
INFO 2026-06-08 08:00:06 MarkDuplicates Tracking 145158 as yet unmatched pairs. 33831 records in RAM.
INFO 2026-06-08 08:00:10 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:09:04s. Time for last 1,000,000: 4s. Last read position: chr17:41,524,851
INFO 2026-06-08 08:00:10 MarkDuplicates Tracking 142858 as yet unmatched pairs. 31526 records in RAM.
INFO 2026-06-08 08:00:13 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:09:07s. Time for last 1,000,000: 2s. Last read position: chr17:44,399,096
INFO 2026-06-08 08:00:13 MarkDuplicates Tracking 139563 as yet unmatched pairs. 28230 records in RAM.
INFO 2026-06-08 08:00:15 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:09:09s. Time for last 1,000,000: 1s. Last read position: chr17:50,185,500
INFO 2026-06-08 08:00:15 MarkDuplicates Tracking 139140 as yet unmatched pairs. 27802 records in RAM.
INFO 2026-06-08 08:00:17 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:09:11s. Time for last 1,000,000: 2s. Last read position: chr17:50,188,775
INFO 2026-06-08 08:00:17 MarkDuplicates Tracking 138635 as yet unmatched pairs. 27295 records in RAM.
INFO 2026-06-08 08:00:19 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:09:13s. Time for last 1,000,000: 2s. Last read position: chr17:50,192,835
INFO 2026-06-08 08:00:19 MarkDuplicates Tracking 135024 as yet unmatched pairs. 23680 records in RAM.
INFO 2026-06-08 08:00:23 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 3s. Last read position: chr17:50,196,330
INFO 2026-06-08 08:00:23 MarkDuplicates Tracking 134333 as yet unmatched pairs. 22982 records in RAM.
INFO 2026-06-08 08:00:26 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 3s. Last read position: chr17:50,353,756
INFO 2026-06-08 08:00:26 MarkDuplicates Tracking 125228 as yet unmatched pairs. 13876 records in RAM.
INFO 2026-06-08 08:00:28 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 2s. Last read position: chr17:59,839,775
INFO 2026-06-08 08:00:28 MarkDuplicates Tracking 122488 as yet unmatched pairs. 11135 records in RAM.
INFO 2026-06-08 08:00:32 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 3s. Last read position: chr17:69,517,542
INFO 2026-06-08 08:00:32 MarkDuplicates Tracking 119968 as yet unmatched pairs. 8608 records in RAM.
INFO 2026-06-08 08:00:35 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:09:29s. Time for last 1,000,000: 3s. Last read position: chr17:75,847,559
INFO 2026-06-08 08:00:35 MarkDuplicates Tracking 117115 as yet unmatched pairs. 5749 records in RAM.
INFO 2026-06-08 08:00:38 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:09:31s. Time for last 1,000,000: 2s. Last read position: chr17:80,346,849
INFO 2026-06-08 08:00:38 MarkDuplicates Tracking 114229 as yet unmatched pairs. 2855 records in RAM.
INFO 2026-06-08 08:00:41 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:09:34s. Time for last 1,000,000: 2s. Last read position: chr18:3,253,232
INFO 2026-06-08 08:00:41 MarkDuplicates Tracking 111212 as yet unmatched pairs. 4145 records in RAM.
INFO 2026-06-08 08:00:44 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:09:38s. Time for last 1,000,000: 3s. Last read position: chr18:49,836,719
INFO 2026-06-08 08:00:44 MarkDuplicates Tracking 108739 as yet unmatched pairs. 1666 records in RAM.
INFO 2026-06-08 08:00:48 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:09:42s. Time for last 1,000,000: 3s. Last read position: chr19:1,013,258
INFO 2026-06-08 08:00:48 MarkDuplicates Tracking 105941 as yet unmatched pairs. 57455 records in RAM.
INFO 2026-06-08 08:00:51 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:09:45s. Time for last 1,000,000: 3s. Last read position: chr19:3,544,586
INFO 2026-06-08 08:00:51 MarkDuplicates Tracking 102675 as yet unmatched pairs. 54188 records in RAM.
INFO 2026-06-08 08:00:54 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:09:48s. Time for last 1,000,000: 3s. Last read position: chr19:6,454,636
INFO 2026-06-08 08:00:54 MarkDuplicates Tracking 99760 as yet unmatched pairs. 51271 records in RAM.
INFO 2026-06-08 08:00:57 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:09:51s. Time for last 1,000,000: 3s. Last read position: chr19:10,117,136
INFO 2026-06-08 08:00:57 MarkDuplicates Tracking 97059 as yet unmatched pairs. 48569 records in RAM.
INFO 2026-06-08 08:01:00 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:09:54s. Time for last 1,000,000: 3s. Last read position: chr19:11,507,746
INFO 2026-06-08 08:01:00 MarkDuplicates Tracking 94103 as yet unmatched pairs. 45612 records in RAM.
INFO 2026-06-08 08:01:04 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:09:58s. Time for last 1,000,000: 3s. Last read position: chr19:14,516,586
INFO 2026-06-08 08:01:04 MarkDuplicates Tracking 91740 as yet unmatched pairs. 43248 records in RAM.
INFO 2026-06-08 08:01:07 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:10:01s. Time for last 1,000,000: 2s. Last read position: chr19:16,862,490
INFO 2026-06-08 08:01:07 MarkDuplicates Tracking 88514 as yet unmatched pairs. 40021 records in RAM.
INFO 2026-06-08 08:01:10 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:10:04s. Time for last 1,000,000: 3s. Last read position: chr19:18,864,189
INFO 2026-06-08 08:01:10 MarkDuplicates Tracking 85531 as yet unmatched pairs. 37029 records in RAM.
INFO 2026-06-08 08:01:13 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:10:07s. Time for last 1,000,000: 3s. Last read position: chr19:35,267,319
INFO 2026-06-08 08:01:13 MarkDuplicates Tracking 82845 as yet unmatched pairs. 34342 records in RAM.
INFO 2026-06-08 08:01:16 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:10:10s. Time for last 1,000,000: 3s. Last read position: chr19:38,802,374
INFO 2026-06-08 08:01:16 MarkDuplicates Tracking 80251 as yet unmatched pairs. 31742 records in RAM.
INFO 2026-06-08 08:01:19 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:10:13s. Time for last 1,000,000: 2s. Last read position: chr19:39,873,668
INFO 2026-06-08 08:01:19 MarkDuplicates Tracking 77252 as yet unmatched pairs. 28742 records in RAM.
INFO 2026-06-08 08:01:22 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:10:16s. Time for last 1,000,000: 2s. Last read position: chr19:39,883,410
INFO 2026-06-08 08:01:22 MarkDuplicates Tracking 76963 as yet unmatched pairs. 28452 records in RAM.
INFO 2026-06-08 08:01:26 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:10:19s. Time for last 1,000,000: 3s. Last read position: chr19:39,892,070
INFO 2026-06-08 08:01:26 MarkDuplicates Tracking 74951 as yet unmatched pairs. 26440 records in RAM.
INFO 2026-06-08 08:01:29 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:10:23s. Time for last 1,000,000: 3s. Last read position: chr19:39,905,751
INFO 2026-06-08 08:01:29 MarkDuplicates Tracking 71691 as yet unmatched pairs. 23180 records in RAM.
INFO 2026-06-08 08:01:32 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 3s. Last read position: chr19:40,591,000
INFO 2026-06-08 08:01:32 MarkDuplicates Tracking 67972 as yet unmatched pairs. 19457 records in RAM.
INFO 2026-06-08 08:01:35 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:10:29s. Time for last 1,000,000: 3s. Last read position: chr19:41,715,148
INFO 2026-06-08 08:01:35 MarkDuplicates Tracking 67941 as yet unmatched pairs. 19425 records in RAM.
INFO 2026-06-08 08:01:38 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:10:32s. Time for last 1,000,000: 3s. Last read position: chr19:41,756,771
INFO 2026-06-08 08:01:38 MarkDuplicates Tracking 63932 as yet unmatched pairs. 15415 records in RAM.
INFO 2026-06-08 08:01:41 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:10:35s. Time for last 1,000,000: 3s. Last read position: chr19:42,589,562
INFO 2026-06-08 08:01:41 MarkDuplicates Tracking 60014 as yet unmatched pairs. 11490 records in RAM.
INFO 2026-06-08 08:01:45 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:10:39s. Time for last 1,000,000: 3s. Last read position: chr19:47,355,163
INFO 2026-06-08 08:01:45 MarkDuplicates Tracking 56937 as yet unmatched pairs. 8411 records in RAM.
INFO 2026-06-08 08:01:47 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:10:41s. Time for last 1,000,000: 2s. Last read position: chr19:49,662,212
INFO 2026-06-08 08:01:47 MarkDuplicates Tracking 54107 as yet unmatched pairs. 5577 records in RAM.
INFO 2026-06-08 08:01:50 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:10:44s. Time for last 1,000,000: 2s. Last read position: chr19:54,458,531
INFO 2026-06-08 08:01:50 MarkDuplicates Tracking 51306 as yet unmatched pairs. 2772 records in RAM.
INFO 2026-06-08 08:01:52 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 2s. Last read position: chr20:487,530
INFO 2026-06-08 08:01:52 MarkDuplicates Tracking 48438 as yet unmatched pairs. 12063 records in RAM.
INFO 2026-06-08 08:01:55 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:10:49s. Time for last 1,000,000: 2s. Last read position: chr20:20,503,375
INFO 2026-06-08 08:01:55 MarkDuplicates Tracking 45715 as yet unmatched pairs. 9339 records in RAM.
INFO 2026-06-08 08:01:57 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:10:51s. Time for last 1,000,000: 1s. Last read position: chr20:36,214,388
INFO 2026-06-08 08:01:57 MarkDuplicates Tracking 43137 as yet unmatched pairs. 6758 records in RAM.
INFO 2026-06-08 08:01:59 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:10:53s. Time for last 1,000,000: 2s. Last read position: chr20:47,652,448
INFO 2026-06-08 08:01:59 MarkDuplicates Tracking 40466 as yet unmatched pairs. 4086 records in RAM.
INFO 2026-06-08 08:02:01 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:10:55s. Time for last 1,000,000: 2s. Last read position: chr20:62,387,378
INFO 2026-06-08 08:02:01 MarkDuplicates Tracking 37855 as yet unmatched pairs. 1473 records in RAM.
INFO 2026-06-08 08:02:04 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 2s. Last read position: chr21:8,260,331
INFO 2026-06-08 08:02:04 MarkDuplicates Tracking 35848 as yet unmatched pairs. 7098 records in RAM.
INFO 2026-06-08 08:02:07 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:11:01s. Time for last 1,000,000: 2s. Last read position: chr21:29,342,637
INFO 2026-06-08 08:02:07 MarkDuplicates Tracking 34521 as yet unmatched pairs. 5764 records in RAM.
INFO 2026-06-08 08:02:10 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:11:04s. Time for last 1,000,000: 3s. Last read position: chr21:42,219,246
INFO 2026-06-08 08:02:10 MarkDuplicates Tracking 31707 as yet unmatched pairs. 2945 records in RAM.
INFO 2026-06-08 08:02:13 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:11:07s. Time for last 1,000,000: 3s. Last read position: chr21:46,636,964
INFO 2026-06-08 08:02:13 MarkDuplicates Tracking 28846 as yet unmatched pairs. 81 records in RAM.
INFO 2026-06-08 08:02:16 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:11:10s. Time for last 1,000,000: 3s. Last read position: chr22:24,226,631
INFO 2026-06-08 08:02:16 MarkDuplicates Tracking 25771 as yet unmatched pairs. 10707 records in RAM.
INFO 2026-06-08 08:02:18 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:11:12s. Time for last 1,000,000: 2s. Last read position: chr22:31,715,246
INFO 2026-06-08 08:02:18 MarkDuplicates Tracking 23029 as yet unmatched pairs. 7965 records in RAM.
INFO 2026-06-08 08:02:21 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:11:14s. Time for last 1,000,000: 2s. Last read position: chr22:38,298,783
INFO 2026-06-08 08:02:21 MarkDuplicates Tracking 20288 as yet unmatched pairs. 5221 records in RAM.
INFO 2026-06-08 08:02:23 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:11:17s. Time for last 1,000,000: 2s. Last read position: chr22:43,162,802
INFO 2026-06-08 08:02:23 MarkDuplicates Tracking 17616 as yet unmatched pairs. 2546 records in RAM.
INFO 2026-06-08 08:02:25 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:11:19s. Time for last 1,000,000: 2s. Last read position: chrX:2,920,648
INFO 2026-06-08 08:02:25 MarkDuplicates Tracking 14620 as yet unmatched pairs. 12413 records in RAM.
INFO 2026-06-08 08:02:28 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:11:22s. Time for last 1,000,000: 2s. Last read position: chrX:41,675,906
INFO 2026-06-08 08:02:28 MarkDuplicates Tracking 12337 as yet unmatched pairs. 10100 records in RAM.
INFO 2026-06-08 08:02:31 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:11:25s. Time for last 1,000,000: 2s. Last read position: chrX:53,993,654
INFO 2026-06-08 08:02:31 MarkDuplicates Tracking 9697 as yet unmatched pairs. 7460 records in RAM.
INFO 2026-06-08 08:02:34 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:11:28s. Time for last 1,000,000: 2s. Last read position: chrX:85,379,348
INFO 2026-06-08 08:02:34 MarkDuplicates Tracking 7333 as yet unmatched pairs. 5096 records in RAM.
INFO 2026-06-08 08:02:36 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:11:30s. Time for last 1,000,000: 1s. Last read position: chrX:136,879,056
INFO 2026-06-08 08:02:36 MarkDuplicates Tracking 5002 as yet unmatched pairs. 2764 records in RAM.
INFO 2026-06-08 08:02:38 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:11:32s. Time for last 1,000,000: 2s. Last read position: chrY:2,844,232
INFO 2026-06-08 08:02:38 MarkDuplicates Tracking 2370 as yet unmatched pairs. 434 records in RAM.
INFO 2026-06-08 08:02:40 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:11:34s. Time for last 1,000,000: 1s. Last read position: KI270733.1:130,996
INFO 2026-06-08 08:02:40 MarkDuplicates Tracking 890 as yet unmatched pairs. 884 records in RAM.
INFO 2026-06-08 08:02:41 MarkDuplicates Read 226557830 records. 0 pairs never matched.
INFO 2026-06-08 08:02:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 36156488344; totalMemory: 61975035904; maxMemory: 63585648640
INFO 2026-06-08 08:02:56 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:03:04 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:03:19 OpticalDuplicateFinder Large duplicate set. size = 1149
INFO 2026-06-08 08:03:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:25,238
INFO 2026-06-08 08:03:23 OpticalDuplicateFinder Large duplicate set. size = 1118
INFO 2026-06-08 08:03:23 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:23,458
INFO 2026-06-08 08:03:32 OpticalDuplicateFinder Large duplicate set. size = 1004
INFO 2026-06-08 08:03:32 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,499
INFO 2026-06-08 08:03:36 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 08:04:01 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:04:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300819768; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-08 08:04:05 MarkDuplicates Marking 69260793 records as duplicates.
INFO 2026-06-08 08:04:05 MarkDuplicates Found 2087909 optical duplicate clusters.
INFO 2026-06-08 08:04:05 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 08:04:32 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:27s. Time for last 10,000,000: 27s. Last read position: chr1:114,463,502
INFO 2026-06-08 08:04:59 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:54s. Time for last 10,000,000: 27s. Last read position: chr1:212,787,598
INFO 2026-06-08 08:05:27 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:22s. Time for last 10,000,000: 27s. Last read position: chr2:110,562,637
INFO 2026-06-08 08:05:56 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:51s. Time for last 10,000,000: 28s. Last read position: chr3:41,224,569
INFO 2026-06-08 08:06:23 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:02:18s. Time for last 10,000,000: 27s. Last read position: chr3:196,053,492
INFO 2026-06-08 08:06:48 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:42s. Time for last 10,000,000: 24s. Last read position: chr5:124,648,743
INFO 2026-06-08 08:07:12 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:03:07s. Time for last 10,000,000: 24s. Last read position: chr6:33,670,439
INFO 2026-06-08 08:07:37 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:03:32s. Time for last 10,000,000: 24s. Last read position: chr7:75,187,249
INFO 2026-06-08 08:08:03 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:03:58s. Time for last 10,000,000: 26s. Last read position: chr8:19,823,965
INFO 2026-06-08 08:08:31 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:04:25s. Time for last 10,000,000: 27s. Last read position: chr9:95,468,827
INFO 2026-06-08 08:08:57 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:04:52s. Time for last 10,000,000: 26s. Last read position: chr10:102,141,497
INFO 2026-06-08 08:09:24 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:05:19s. Time for last 10,000,000: 26s. Last read position: chr11:63,753,072
INFO 2026-06-08 08:09:52 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:05:47s. Time for last 10,000,000: 28s. Last read position: chr12:51,240,934
INFO 2026-06-08 08:10:17 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:06:12s. Time for last 10,000,000: 25s. Last read position: chr13:99,540,748
INFO 2026-06-08 08:10:44 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:06:39s. Time for last 10,000,000: 26s. Last read position: chr15:45,073,378
INFO 2026-06-08 08:11:09 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:07:04s. Time for last 10,000,000: 25s. Last read position: chr16:24,931,092
INFO 2026-06-08 08:11:33 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:07:28s. Time for last 10,000,000: 24s. Last read position: chr17:20,455,303
INFO 2026-06-08 08:11:59 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:07:54s. Time for last 10,000,000: 25s. Last read position: chr17:59,839,775
INFO 2026-06-08 08:12:24 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:08:18s. Time for last 10,000,000: 24s. Last read position: chr19:11,507,746
INFO 2026-06-08 08:12:47 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:08:42s. Time for last 10,000,000: 23s. Last read position: chr19:40,591,000
INFO 2026-06-08 08:13:10 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:09:04s. Time for last 10,000,000: 22s. Last read position: chr20:47,652,448
INFO 2026-06-08 08:13:34 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:09:29s. Time for last 10,000,000: 24s. Last read position: chrX:2,920,648
INFO 2026-06-08 08:13:55 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:13:55 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:13:55 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:13:56 MarkDuplicates Before output close freeMemory: 202119288; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:13:56 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:13:56 MarkDuplicates After output close freeMemory: 104287904; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 08:13:56 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 22.88 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory