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 RGB_RLP_lowDV_1ststrand_27C_4.Aligned.sortedByCoord.out.bam --OUTPUT RGB_RLP_lowDV_1ststrand_27C_4.md.bam --METRICS_FILE RGB_RLP_lowDV_1ststrand_27C_4.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:05:01.998 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Thu Jun 04 07:05:02 GMT 2026] MarkDuplicates --INPUT RGB_RLP_lowDV_1ststrand_27C_4.Aligned.sortedByCoord.out.bam --OUTPUT RGB_RLP_lowDV_1ststrand_27C_4.md.bam --METRICS_FILE RGB_RLP_lowDV_1ststrand_27C_4.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Jun 04 07:05:02 GMT 2026] Executing as ?@nf-d295b797683399dfd235169d0b12d4c8-bd9f1-jhmjw 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 2026-06-04 07:05:02 MarkDuplicates Start of doWork freeMemory: 105495160; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-04 07:05:02 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-04 07:05:02 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-04 07:05:05 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:2,563,051
INFO 2026-06-04 07:05:05 MarkDuplicates Tracking 749 as yet unmatched pairs. 40 records in RAM.
INFO 2026-06-04 07:05:08 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 2s. Last read position: chr1:11,957,892
INFO 2026-06-04 07:05:08 MarkDuplicates Tracking 1658 as yet unmatched pairs. 208 records in RAM.
INFO 2026-06-04 07:05:09 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: chr1:19,626,389
INFO 2026-06-04 07:05:09 MarkDuplicates Tracking 2064 as yet unmatched pairs. 41 records in RAM.
INFO 2026-06-04 07:05:11 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: chr1:23,796,184
INFO 2026-06-04 07:05:11 MarkDuplicates Tracking 2618 as yet unmatched pairs. 4 records in RAM.
INFO 2026-06-04 07:05:13 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 2s. Last read position: chr1:30,876,651
INFO 2026-06-04 07:05:13 MarkDuplicates Tracking 3381 as yet unmatched pairs. 155 records in RAM.
INFO 2026-06-04 07:05:14 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: chr1:36,176,760
INFO 2026-06-04 07:05:14 MarkDuplicates Tracking 4035 as yet unmatched pairs. 166 records in RAM.
INFO 2026-06-04 07:05:17 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 2s. Last read position: chr1:43,446,177
INFO 2026-06-04 07:05:17 MarkDuplicates Tracking 4542 as yet unmatched pairs. 42 records in RAM.
INFO 2026-06-04 07:05:18 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: chr1:54,032,190
INFO 2026-06-04 07:05:18 MarkDuplicates Tracking 5427 as yet unmatched pairs. 232 records in RAM.
INFO 2026-06-04 07:05:20 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: chr1:90,938,581
INFO 2026-06-04 07:05:20 MarkDuplicates Tracking 5795 as yet unmatched pairs. 41 records in RAM.
INFO 2026-06-04 07:05:21 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: chr1:113,622,825
INFO 2026-06-04 07:05:21 MarkDuplicates Tracking 6402 as yet unmatched pairs. 61 records in RAM.
INFO 2026-06-04 07:05:24 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 3s. Last read position: chr1:120,548,655
INFO 2026-06-04 07:05:24 MarkDuplicates Tracking 6955 as yet unmatched pairs. 24 records in RAM.
INFO 2026-06-04 07:05:26 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 1s. Last read position: chr1:148,563,162
INFO 2026-06-04 07:05:26 MarkDuplicates Tracking 7362 as yet unmatched pairs. 140 records in RAM.
INFO 2026-06-04 07:05:28 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: chr1:150,627,540
INFO 2026-06-04 07:05:28 MarkDuplicates Tracking 8340 as yet unmatched pairs. 735 records in RAM.
INFO 2026-06-04 07:05:29 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 1s. Last read position: chr1:153,390,416
INFO 2026-06-04 07:05:29 MarkDuplicates Tracking 8183 as yet unmatched pairs. 67 records in RAM.
INFO 2026-06-04 07:05:30 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 1s. Last read position: chr1:154,946,430
INFO 2026-06-04 07:05:30 MarkDuplicates Tracking 8732 as yet unmatched pairs. 62 records in RAM.
INFO 2026-06-04 07:05:33 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 2s. Last read position: chr1:155,766,508
INFO 2026-06-04 07:05:33 MarkDuplicates Tracking 9289 as yet unmatched pairs. 97 records in RAM.
INFO 2026-06-04 07:05:34 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 1s. Last read position: chr1:159,016,560
INFO 2026-06-04 07:05:34 MarkDuplicates Tracking 9965 as yet unmatched pairs. 109 records in RAM.
INFO 2026-06-04 07:05:36 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 1s. Last read position: chr1:169,131,438
INFO 2026-06-04 07:05:36 MarkDuplicates Tracking 10869 as yet unmatched pairs. 412 records in RAM.
INFO 2026-06-04 07:05:39 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 2s. Last read position: chr1:185,994,862
INFO 2026-06-04 07:05:39 MarkDuplicates Tracking 10997 as yet unmatched pairs. 20 records in RAM.
INFO 2026-06-04 07:05:41 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 1s. Last read position: chr1:203,713,221
INFO 2026-06-04 07:05:41 MarkDuplicates Tracking 11725 as yet unmatched pairs. 191 records in RAM.
INFO 2026-06-04 07:05:42 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 1s. Last read position: chr1:220,100,521
INFO 2026-06-04 07:05:42 MarkDuplicates Tracking 12167 as yet unmatched pairs. 74 records in RAM.
INFO 2026-06-04 07:05:44 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 1s. Last read position: chr1:228,349,963
INFO 2026-06-04 07:05:44 MarkDuplicates Tracking 12782 as yet unmatched pairs. 72 records in RAM.
INFO 2026-06-04 07:05:46 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 1s. Last read position: chr1:246,840,947
INFO 2026-06-04 07:05:46 MarkDuplicates Tracking 13450 as yet unmatched pairs. 62 records in RAM.
INFO 2026-06-04 07:05:47 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 1s. Last read position: chr2:24,741,923
INFO 2026-06-04 07:05:47 MarkDuplicates Tracking 14063 as yet unmatched pairs. 13976 records in RAM.
INFO 2026-06-04 07:05:49 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,264
INFO 2026-06-04 07:05:49 MarkDuplicates Tracking 73622 as yet unmatched pairs. 10254 records in RAM.
INFO 2026-06-04 07:05:51 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 1s. Last read position: chr2:47,804,941
INFO 2026-06-04 07:05:51 MarkDuplicates Tracking 113021 as yet unmatched pairs. 7450 records in RAM.
INFO 2026-06-04 07:05:52 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 1s. Last read position: chr2:71,393,541
INFO 2026-06-04 07:05:52 MarkDuplicates Tracking 112489 as yet unmatched pairs. 6912 records in RAM.
INFO 2026-06-04 07:05:54 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 1s. Last read position: chr2:95,101,676
INFO 2026-06-04 07:05:54 MarkDuplicates Tracking 111965 as yet unmatched pairs. 6372 records in RAM.
INFO 2026-06-04 07:05:55 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 1s. Last read position: chr2:108,764,358
INFO 2026-06-04 07:05:55 MarkDuplicates Tracking 111640 as yet unmatched pairs. 6043 records in RAM.
INFO 2026-06-04 07:05:57 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 1s. Last read position: chr2:128,193,473
INFO 2026-06-04 07:05:57 MarkDuplicates Tracking 111020 as yet unmatched pairs. 5420 records in RAM.
INFO 2026-06-04 07:05:58 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 1s. Last read position: chr2:170,007,126
INFO 2026-06-04 07:05:58 MarkDuplicates Tracking 110516 as yet unmatched pairs. 4905 records in RAM.
INFO 2026-06-04 07:06:00 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 1s. Last read position: chr2:188,997,201
INFO 2026-06-04 07:06:00 MarkDuplicates Tracking 110523 as yet unmatched pairs. 4908 records in RAM.
INFO 2026-06-04 07:06:01 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 1s. Last read position: chr2:201,160,858
INFO 2026-06-04 07:06:01 MarkDuplicates Tracking 109376 as yet unmatched pairs. 3760 records in RAM.
INFO 2026-06-04 07:06:03 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 1s. Last read position: chr2:215,372,000
INFO 2026-06-04 07:06:03 MarkDuplicates Tracking 113910 as yet unmatched pairs. 8288 records in RAM.
INFO 2026-06-04 07:06:05 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 2s. Last read position: chr2:215,384,861
INFO 2026-06-04 07:06:05 MarkDuplicates Tracking 110847 as yet unmatched pairs. 5223 records in RAM.
INFO 2026-06-04 07:06:08 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 2s. Last read position: chr2:215,409,936
INFO 2026-06-04 07:06:08 MarkDuplicates Tracking 110516 as yet unmatched pairs. 4888 records in RAM.
INFO 2026-06-04 07:06:10 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 2s. Last read position: chr2:216,499,379
INFO 2026-06-04 07:06:10 MarkDuplicates Tracking 108573 as yet unmatched pairs. 2945 records in RAM.
INFO 2026-06-04 07:06:12 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 1s. Last read position: chr2:226,797,837
INFO 2026-06-04 07:06:12 MarkDuplicates Tracking 106836 as yet unmatched pairs. 1200 records in RAM.
INFO 2026-06-04 07:06:13 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 1s. Last read position: chr2:237,525,698
INFO 2026-06-04 07:06:13 MarkDuplicates Tracking 106273 as yet unmatched pairs. 634 records in RAM.
INFO 2026-06-04 07:06:15 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 1s. Last read position: chr3:10,249,213
INFO 2026-06-04 07:06:15 MarkDuplicates Tracking 105673 as yet unmatched pairs. 5302 records in RAM.
INFO 2026-06-04 07:06:17 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 1s. Last read position: chr3:37,327,130
INFO 2026-06-04 07:06:17 MarkDuplicates Tracking 104946 as yet unmatched pairs. 4574 records in RAM.
INFO 2026-06-04 07:06:18 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 1s. Last read position: chr3:48,251,909
INFO 2026-06-04 07:06:18 MarkDuplicates Tracking 104375 as yet unmatched pairs. 4003 records in RAM.
INFO 2026-06-04 07:06:20 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 1s. Last read position: chr3:51,663,174
INFO 2026-06-04 07:06:20 MarkDuplicates Tracking 103751 as yet unmatched pairs. 3373 records in RAM.
INFO 2026-06-04 07:06:22 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 2s. Last read position: chr3:87,253,731
INFO 2026-06-04 07:06:22 MarkDuplicates Tracking 103185 as yet unmatched pairs. 2799 records in RAM.
INFO 2026-06-04 07:06:23 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 1s. Last read position: chr3:122,325,323
INFO 2026-06-04 07:06:23 MarkDuplicates Tracking 102741 as yet unmatched pairs. 2353 records in RAM.
INFO 2026-06-04 07:06:25 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 1s. Last read position: chr3:131,489,983
INFO 2026-06-04 07:06:25 MarkDuplicates Tracking 102135 as yet unmatched pairs. 1746 records in RAM.
INFO 2026-06-04 07:06:27 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 1s. Last read position: chr3:158,710,839
INFO 2026-06-04 07:06:27 MarkDuplicates Tracking 101591 as yet unmatched pairs. 1197 records in RAM.
INFO 2026-06-04 07:06:28 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 1s. Last read position: chr3:185,248,508
INFO 2026-06-04 07:06:28 MarkDuplicates Tracking 100922 as yet unmatched pairs. 524 records in RAM.
INFO 2026-06-04 07:06:30 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 1s. Last read position: chr3:196,807,823
INFO 2026-06-04 07:06:30 MarkDuplicates Tracking 100556 as yet unmatched pairs. 154 records in RAM.
INFO 2026-06-04 07:06:31 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 1s. Last read position: chr4:6,641,172
INFO 2026-06-04 07:06:31 MarkDuplicates Tracking 99906 as yet unmatched pairs. 2397 records in RAM.
INFO 2026-06-04 07:06:33 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 1s. Last read position: chr4:53,573,720
INFO 2026-06-04 07:06:33 MarkDuplicates Tracking 99271 as yet unmatched pairs. 1760 records in RAM.
INFO 2026-06-04 07:06:34 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 1s. Last read position: chr4:84,796,543
INFO 2026-06-04 07:06:34 MarkDuplicates Tracking 98732 as yet unmatched pairs. 1212 records in RAM.
INFO 2026-06-04 07:06:36 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 1s. Last read position: chr4:125,415,520
INFO 2026-06-04 07:06:36 MarkDuplicates Tracking 98187 as yet unmatched pairs. 665 records in RAM.
INFO 2026-06-04 07:06:38 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 2s. Last read position: chr4:183,446,299
INFO 2026-06-04 07:06:38 MarkDuplicates Tracking 97655 as yet unmatched pairs. 125 records in RAM.
INFO 2026-06-04 07:06:40 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 1s. Last read position: chr5:14,498,591
INFO 2026-06-04 07:06:40 MarkDuplicates Tracking 97297 as yet unmatched pairs. 4496 records in RAM.
INFO 2026-06-04 07:06:41 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 1s. Last read position: chr5:62,390,907
INFO 2026-06-04 07:06:41 MarkDuplicates Tracking 96444 as yet unmatched pairs. 3641 records in RAM.
INFO 2026-06-04 07:06:43 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 1s. Last read position: chr5:93,683,676
INFO 2026-06-04 07:06:43 MarkDuplicates Tracking 95960 as yet unmatched pairs. 3149 records in RAM.
INFO 2026-06-04 07:06:45 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 1s. Last read position: chr5:136,054,070
INFO 2026-06-04 07:06:45 MarkDuplicates Tracking 95456 as yet unmatched pairs. 2642 records in RAM.
INFO 2026-06-04 07:06:46 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 1s. Last read position: chr5:141,574,170
INFO 2026-06-04 07:06:46 MarkDuplicates Tracking 94875 as yet unmatched pairs. 2042 records in RAM.
INFO 2026-06-04 07:06:48 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 1s. Last read position: chr5:150,405,120
INFO 2026-06-04 07:06:48 MarkDuplicates Tracking 99518 as yet unmatched pairs. 6684 records in RAM.
INFO 2026-06-04 07:06:50 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 1s. Last read position: chr5:170,270,740
INFO 2026-06-04 07:06:50 MarkDuplicates Tracking 93802 as yet unmatched pairs. 968 records in RAM.
INFO 2026-06-04 07:06:51 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 1s. Last read position: chr5:179,699,079
INFO 2026-06-04 07:06:51 MarkDuplicates Tracking 93277 as yet unmatched pairs. 436 records in RAM.
INFO 2026-06-04 07:06:53 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 1s. Last read position: chr6:7,231,764
INFO 2026-06-04 07:06:53 MarkDuplicates Tracking 92924 as yet unmatched pairs. 6205 records in RAM.
INFO 2026-06-04 07:06:55 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 2s. Last read position: chr6:27,831,263
INFO 2026-06-04 07:06:55 MarkDuplicates Tracking 92187 as yet unmatched pairs. 5468 records in RAM.
INFO 2026-06-04 07:06:57 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 1s. Last read position: chr6:31,356,332
INFO 2026-06-04 07:06:57 MarkDuplicates Tracking 91521 as yet unmatched pairs. 4791 records in RAM.
INFO 2026-06-04 07:06:59 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 2s. Last read position: chr6:31,994,626
INFO 2026-06-04 07:06:59 MarkDuplicates Tracking 91596 as yet unmatched pairs. 4864 records in RAM.
INFO 2026-06-04 07:07:01 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 1s. Last read position: chr6:33,296,766
INFO 2026-06-04 07:07:01 MarkDuplicates Tracking 90481 as yet unmatched pairs. 3749 records in RAM.
INFO 2026-06-04 07:07:02 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 1s. Last read position: chr6:42,066,394
INFO 2026-06-04 07:07:02 MarkDuplicates Tracking 89788 as yet unmatched pairs. 3053 records in RAM.
INFO 2026-06-04 07:07:04 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 1s. Last read position: chr6:56,141,814
INFO 2026-06-04 07:07:04 MarkDuplicates Tracking 89115 as yet unmatched pairs. 2379 records in RAM.
INFO 2026-06-04 07:07:05 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 1s. Last read position: chr6:101,924,626
INFO 2026-06-04 07:07:05 MarkDuplicates Tracking 88464 as yet unmatched pairs. 1716 records in RAM.
INFO 2026-06-04 07:07:07 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 1s. Last read position: chr6:136,356,721
INFO 2026-06-04 07:07:07 MarkDuplicates Tracking 87864 as yet unmatched pairs. 1115 records in RAM.
INFO 2026-06-04 07:07:08 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 1s. Last read position: chr6:157,653,424
INFO 2026-06-04 07:07:08 MarkDuplicates Tracking 87261 as yet unmatched pairs. 503 records in RAM.
INFO 2026-06-04 07:07:10 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 1s. Last read position: chr7:1,475,992
INFO 2026-06-04 07:07:10 MarkDuplicates Tracking 86723 as yet unmatched pairs. 5624 records in RAM.
INFO 2026-06-04 07:07:11 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 1s. Last read position: chr7:6,642,676
INFO 2026-06-04 07:07:11 MarkDuplicates Tracking 85996 as yet unmatched pairs. 4895 records in RAM.
INFO 2026-06-04 07:07:13 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 1s. Last read position: chr7:44,110,211
INFO 2026-06-04 07:07:13 MarkDuplicates Tracking 85475 as yet unmatched pairs. 4370 records in RAM.
INFO 2026-06-04 07:07:14 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 1s. Last read position: chr7:70,790,129
INFO 2026-06-04 07:07:14 MarkDuplicates Tracking 84921 as yet unmatched pairs. 3816 records in RAM.
INFO 2026-06-04 07:07:17 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 2s. Last read position: chr7:75,695,589
INFO 2026-06-04 07:07:17 MarkDuplicates Tracking 84443 as yet unmatched pairs. 3338 records in RAM.
INFO 2026-06-04 07:07:19 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 1s. Last read position: chr7:94,412,662
INFO 2026-06-04 07:07:19 MarkDuplicates Tracking 84975 as yet unmatched pairs. 3865 records in RAM.
INFO 2026-06-04 07:07:20 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 1s. Last read position: chr7:100,352,887
INFO 2026-06-04 07:07:20 MarkDuplicates Tracking 83472 as yet unmatched pairs. 2360 records in RAM.
INFO 2026-06-04 07:07:22 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 1s. Last read position: chr7:101,000,998
INFO 2026-06-04 07:07:22 MarkDuplicates Tracking 83153 as yet unmatched pairs. 2040 records in RAM.
INFO 2026-06-04 07:07:23 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 1s. Last read position: chr7:112,296,308
INFO 2026-06-04 07:07:23 MarkDuplicates Tracking 82599 as yet unmatched pairs. 1486 records in RAM.
INFO 2026-06-04 07:07:25 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 1s. Last read position: chr7:138,861,151
INFO 2026-06-04 07:07:25 MarkDuplicates Tracking 82193 as yet unmatched pairs. 1079 records in RAM.
INFO 2026-06-04 07:07:26 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr7:150,996,847
INFO 2026-06-04 07:07:26 MarkDuplicates Tracking 81469 as yet unmatched pairs. 352 records in RAM.
INFO 2026-06-04 07:07:28 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 1s. Last read position: chr8:19,817,585
INFO 2026-06-04 07:07:28 MarkDuplicates Tracking 80900 as yet unmatched pairs. 5555 records in RAM.
INFO 2026-06-04 07:07:29 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 1s. Last read position: chr8:37,877,256
INFO 2026-06-04 07:07:29 MarkDuplicates Tracking 80316 as yet unmatched pairs. 4967 records in RAM.
INFO 2026-06-04 07:07:31 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 1s. Last read position: chr8:47,511,937
INFO 2026-06-04 07:07:31 MarkDuplicates Tracking 79688 as yet unmatched pairs. 4332 records in RAM.
INFO 2026-06-04 07:07:32 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 1s. Last read position: chr8:70,141,289
INFO 2026-06-04 07:07:32 MarkDuplicates Tracking 79638 as yet unmatched pairs. 4281 records in RAM.
INFO 2026-06-04 07:07:33 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 1s. Last read position: chr8:102,272,539
INFO 2026-06-04 07:07:33 MarkDuplicates Tracking 78808 as yet unmatched pairs. 3451 records in RAM.
INFO 2026-06-04 07:07:35 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 1s. Last read position: chr8:125,076,426
INFO 2026-06-04 07:07:35 MarkDuplicates Tracking 78114 as yet unmatched pairs. 2745 records in RAM.
INFO 2026-06-04 07:07:37 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 1s. Last read position: chr8:143,858,145
INFO 2026-06-04 07:07:37 MarkDuplicates Tracking 77926 as yet unmatched pairs. 2553 records in RAM.
INFO 2026-06-04 07:07:38 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 1s. Last read position: chr8:143,860,742
INFO 2026-06-04 07:07:38 MarkDuplicates Tracking 78368 as yet unmatched pairs. 2995 records in RAM.
INFO 2026-06-04 07:07:39 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 1s. Last read position: chr8:143,863,094
INFO 2026-06-04 07:07:39 MarkDuplicates Tracking 78420 as yet unmatched pairs. 3042 records in RAM.
INFO 2026-06-04 07:07:41 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 1s. Last read position: chr8:143,865,560
INFO 2026-06-04 07:07:41 MarkDuplicates Tracking 76566 as yet unmatched pairs. 1188 records in RAM.
INFO 2026-06-04 07:07:43 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 1s. Last read position: chr8:143,929,699
INFO 2026-06-04 07:07:43 MarkDuplicates Tracking 76338 as yet unmatched pairs. 959 records in RAM.
INFO 2026-06-04 07:07:44 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 1s. Last read position: chr9:6,413,622
INFO 2026-06-04 07:07:44 MarkDuplicates Tracking 75280 as yet unmatched pairs. 4325 records in RAM.
INFO 2026-06-04 07:07:46 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 1s. Last read position: chr9:35,740,263
INFO 2026-06-04 07:07:46 MarkDuplicates Tracking 74676 as yet unmatched pairs. 3717 records in RAM.
INFO 2026-06-04 07:07:48 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 1s. Last read position: chr9:93,308,423
INFO 2026-06-04 07:07:48 MarkDuplicates Tracking 74082 as yet unmatched pairs. 3120 records in RAM.
INFO 2026-06-04 07:07:49 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 1s. Last read position: chr9:114,341,588
INFO 2026-06-04 07:07:49 MarkDuplicates Tracking 73421 as yet unmatched pairs. 2458 records in RAM.
INFO 2026-06-04 07:07:51 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 1s. Last read position: chr9:128,166,326
INFO 2026-06-04 07:07:51 MarkDuplicates Tracking 72879 as yet unmatched pairs. 1916 records in RAM.
INFO 2026-06-04 07:07:53 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 1s. Last read position: chr9:131,900,947
INFO 2026-06-04 07:07:53 MarkDuplicates Tracking 72168 as yet unmatched pairs. 1204 records in RAM.
INFO 2026-06-04 07:07:55 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 1s. Last read position: chr9:136,808,235
INFO 2026-06-04 07:07:55 MarkDuplicates Tracking 71565 as yet unmatched pairs. 600 records in RAM.
INFO 2026-06-04 07:07:56 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 1s. Last read position: chr10:8,058,604
INFO 2026-06-04 07:07:56 MarkDuplicates Tracking 71127 as yet unmatched pairs. 3963 records in RAM.
INFO 2026-06-04 07:07:58 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 1s. Last read position: chr10:32,901,551
INFO 2026-06-04 07:07:58 MarkDuplicates Tracking 70442 as yet unmatched pairs. 3277 records in RAM.
INFO 2026-06-04 07:07:59 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 1s. Last read position: chr10:50,129,618
INFO 2026-06-04 07:07:59 MarkDuplicates Tracking 69769 as yet unmatched pairs. 2604 records in RAM.
INFO 2026-06-04 07:08:00 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 1s. Last read position: chr10:74,899,500
INFO 2026-06-04 07:08:00 MarkDuplicates Tracking 69200 as yet unmatched pairs. 2035 records in RAM.
INFO 2026-06-04 07:08:02 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 1s. Last read position: chr10:93,587,246
INFO 2026-06-04 07:08:02 MarkDuplicates Tracking 68606 as yet unmatched pairs. 1439 records in RAM.
INFO 2026-06-04 07:08:03 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 1s. Last read position: chr10:103,617,247
INFO 2026-06-04 07:08:03 MarkDuplicates Tracking 68043 as yet unmatched pairs. 869 records in RAM.
INFO 2026-06-04 07:08:06 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 2s. Last read position: chr10:126,064,956
INFO 2026-06-04 07:08:06 MarkDuplicates Tracking 67413 as yet unmatched pairs. 236 records in RAM.
INFO 2026-06-04 07:08:07 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 1s. Last read position: chr11:724,804
INFO 2026-06-04 07:08:07 MarkDuplicates Tracking 66751 as yet unmatched pairs. 6512 records in RAM.
INFO 2026-06-04 07:08:09 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 1s. Last read position: chr11:2,884,657
INFO 2026-06-04 07:08:09 MarkDuplicates Tracking 66279 as yet unmatched pairs. 6035 records in RAM.
INFO 2026-06-04 07:08:10 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 1s. Last read position: chr11:16,974,710
INFO 2026-06-04 07:08:10 MarkDuplicates Tracking 65751 as yet unmatched pairs. 5504 records in RAM.
INFO 2026-06-04 07:08:12 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 1s. Last read position: chr11:46,429,030
INFO 2026-06-04 07:08:12 MarkDuplicates Tracking 65183 as yet unmatched pairs. 4931 records in RAM.
INFO 2026-06-04 07:08:13 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 1s. Last read position: chr11:61,368,021
INFO 2026-06-04 07:08:13 MarkDuplicates Tracking 64645 as yet unmatched pairs. 4391 records in RAM.
INFO 2026-06-04 07:08:15 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 1s. Last read position: chr11:62,801,580
INFO 2026-06-04 07:08:15 MarkDuplicates Tracking 64051 as yet unmatched pairs. 3795 records in RAM.
INFO 2026-06-04 07:08:16 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 1s. Last read position: chr11:65,546,442
INFO 2026-06-04 07:08:16 MarkDuplicates Tracking 63725 as yet unmatched pairs. 3467 records in RAM.
INFO 2026-06-04 07:08:18 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 1s. Last read position: chr11:66,692,981
INFO 2026-06-04 07:08:18 MarkDuplicates Tracking 62718 as yet unmatched pairs. 2460 records in RAM.
INFO 2026-06-04 07:08:19 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 1s. Last read position: chr11:71,439,003
INFO 2026-06-04 07:08:19 MarkDuplicates Tracking 62087 as yet unmatched pairs. 1829 records in RAM.
INFO 2026-06-04 07:08:21 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 1s. Last read position: chr11:77,701,117
INFO 2026-06-04 07:08:21 MarkDuplicates Tracking 61512 as yet unmatched pairs. 1253 records in RAM.
INFO 2026-06-04 07:08:22 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 1s. Last read position: chr11:117,838,252
INFO 2026-06-04 07:08:22 MarkDuplicates Tracking 60943 as yet unmatched pairs. 681 records in RAM.
INFO 2026-06-04 07:08:24 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 1s. Last read position: chr11:131,911,484
INFO 2026-06-04 07:08:24 MarkDuplicates Tracking 60320 as yet unmatched pairs. 56 records in RAM.
INFO 2026-06-04 07:08:25 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: chr12:6,936,262
INFO 2026-06-04 07:08:25 MarkDuplicates Tracking 60026 as yet unmatched pairs. 5683 records in RAM.
INFO 2026-06-04 07:08:27 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 1s. Last read position: chr12:19,347,904
INFO 2026-06-04 07:08:27 MarkDuplicates Tracking 59149 as yet unmatched pairs. 4804 records in RAM.
INFO 2026-06-04 07:08:29 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 1s. Last read position: chr12:47,798,785
INFO 2026-06-04 07:08:29 MarkDuplicates Tracking 58805 as yet unmatched pairs. 4460 records in RAM.
INFO 2026-06-04 07:08:31 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 2s. Last read position: chr12:51,291,806
INFO 2026-06-04 07:08:31 MarkDuplicates Tracking 58004 as yet unmatched pairs. 3659 records in RAM.
INFO 2026-06-04 07:08:33 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 1s. Last read position: chr12:54,407,659
INFO 2026-06-04 07:08:33 MarkDuplicates Tracking 57490 as yet unmatched pairs. 3144 records in RAM.
INFO 2026-06-04 07:08:35 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 2s. Last read position: chr12:57,154,253
INFO 2026-06-04 07:08:35 MarkDuplicates Tracking 57083 as yet unmatched pairs. 2735 records in RAM.
INFO 2026-06-04 07:08:37 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 1s. Last read position: chr12:76,030,711
INFO 2026-06-04 07:08:37 MarkDuplicates Tracking 56457 as yet unmatched pairs. 2108 records in RAM.
INFO 2026-06-04 07:08:38 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 1s. Last read position: chr12:109,227,430
INFO 2026-06-04 07:08:38 MarkDuplicates Tracking 55809 as yet unmatched pairs. 1460 records in RAM.
INFO 2026-06-04 07:08:40 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 1s. Last read position: chr12:120,469,478
INFO 2026-06-04 07:08:40 MarkDuplicates Tracking 55203 as yet unmatched pairs. 853 records in RAM.
INFO 2026-06-04 07:08:41 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 1s. Last read position: chr12:131,982,350
INFO 2026-06-04 07:08:41 MarkDuplicates Tracking 54686 as yet unmatched pairs. 335 records in RAM.
INFO 2026-06-04 07:08:43 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 1s. Last read position: chr13:31,145,619
INFO 2026-06-04 07:08:43 MarkDuplicates Tracking 54069 as yet unmatched pairs. 1811 records in RAM.
INFO 2026-06-04 07:08:44 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 1s. Last read position: chr13:81,690,136
INFO 2026-06-04 07:08:44 MarkDuplicates Tracking 53415 as yet unmatched pairs. 1156 records in RAM.
INFO 2026-06-04 07:08:46 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 1s. Last read position: chr13:112,857,863
INFO 2026-06-04 07:08:46 MarkDuplicates Tracking 52792 as yet unmatched pairs. 532 records in RAM.
INFO 2026-06-04 07:08:47 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 1s. Last read position: chr14:21,492,544
INFO 2026-06-04 07:08:47 MarkDuplicates Tracking 52160 as yet unmatched pairs. 3474 records in RAM.
INFO 2026-06-04 07:08:49 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 1s. Last read position: chr14:35,313,004
INFO 2026-06-04 07:08:49 MarkDuplicates Tracking 51960 as yet unmatched pairs. 3274 records in RAM.
INFO 2026-06-04 07:08:50 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 1s. Last read position: chr14:61,740,923
INFO 2026-06-04 07:08:50 MarkDuplicates Tracking 50943 as yet unmatched pairs. 2253 records in RAM.
INFO 2026-06-04 07:08:52 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 1s. Last read position: chr14:74,941,844
INFO 2026-06-04 07:08:52 MarkDuplicates Tracking 50321 as yet unmatched pairs. 1630 records in RAM.
INFO 2026-06-04 07:08:53 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 1s. Last read position: chr14:99,510,611
INFO 2026-06-04 07:08:53 MarkDuplicates Tracking 49884 as yet unmatched pairs. 1190 records in RAM.
INFO 2026-06-04 07:08:55 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 1s. Last read position: chr14:104,943,543
INFO 2026-06-04 07:08:55 MarkDuplicates Tracking 49274 as yet unmatched pairs. 579 records in RAM.
INFO 2026-06-04 07:08:57 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 1s. Last read position: chr15:28,168,435
INFO 2026-06-04 07:08:57 MarkDuplicates Tracking 48616 as yet unmatched pairs. 2778 records in RAM.
INFO 2026-06-04 07:08:58 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 1s. Last read position: chr15:41,988,069
INFO 2026-06-04 07:08:58 MarkDuplicates Tracking 48087 as yet unmatched pairs. 2247 records in RAM.
INFO 2026-06-04 07:09:00 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 2s. Last read position: chr15:57,252,317
INFO 2026-06-04 07:09:00 MarkDuplicates Tracking 47778 as yet unmatched pairs. 1933 records in RAM.
INFO 2026-06-04 07:09:03 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 2s. Last read position: chr15:72,210,349
INFO 2026-06-04 07:09:03 MarkDuplicates Tracking 47100 as yet unmatched pairs. 1254 records in RAM.
INFO 2026-06-04 07:09:05 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 1s. Last read position: chr15:84,191,288
INFO 2026-06-04 07:09:05 MarkDuplicates Tracking 46359 as yet unmatched pairs. 513 records in RAM.
INFO 2026-06-04 07:09:06 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 1s. Last read position: chr15:101,973,248
INFO 2026-06-04 07:09:06 MarkDuplicates Tracking 45874 as yet unmatched pairs. 27 records in RAM.
INFO 2026-06-04 07:09:08 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 1s. Last read position: chr16:1,772,830
INFO 2026-06-04 07:09:08 MarkDuplicates Tracking 45147 as yet unmatched pairs. 6015 records in RAM.
INFO 2026-06-04 07:09:09 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 1s. Last read position: chr16:2,765,808
INFO 2026-06-04 07:09:09 MarkDuplicates Tracking 44588 as yet unmatched pairs. 5456 records in RAM.
INFO 2026-06-04 07:09:11 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 1s. Last read position: chr16:5,056,069
INFO 2026-06-04 07:09:11 MarkDuplicates Tracking 43752 as yet unmatched pairs. 4620 records in RAM.
INFO 2026-06-04 07:09:12 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 1s. Last read position: chr16:15,617,066
INFO 2026-06-04 07:09:12 MarkDuplicates Tracking 43366 as yet unmatched pairs. 4234 records in RAM.
INFO 2026-06-04 07:09:13 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 1s. Last read position: chr16:18,380,384
INFO 2026-06-04 07:09:13 MarkDuplicates Tracking 43350 as yet unmatched pairs. 4218 records in RAM.
INFO 2026-06-04 07:09:15 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 1s. Last read position: chr16:21,851,074
INFO 2026-06-04 07:09:15 MarkDuplicates Tracking 42988 as yet unmatched pairs. 3853 records in RAM.
INFO 2026-06-04 07:09:16 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 1s. Last read position: chr16:28,723,492
INFO 2026-06-04 07:09:16 MarkDuplicates Tracking 42486 as yet unmatched pairs. 3351 records in RAM.
INFO 2026-06-04 07:09:17 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 1s. Last read position: chr16:30,001,469
INFO 2026-06-04 07:09:17 MarkDuplicates Tracking 42118 as yet unmatched pairs. 2983 records in RAM.
INFO 2026-06-04 07:09:19 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 1s. Last read position: chr16:31,094,392
INFO 2026-06-04 07:09:19 MarkDuplicates Tracking 41503 as yet unmatched pairs. 2366 records in RAM.
INFO 2026-06-04 07:09:20 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 1s. Last read position: chr16:57,047,608
INFO 2026-06-04 07:09:20 MarkDuplicates Tracking 40929 as yet unmatched pairs. 1791 records in RAM.
INFO 2026-06-04 07:09:23 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 2s. Last read position: chr16:70,364,591
INFO 2026-06-04 07:09:23 MarkDuplicates Tracking 40249 as yet unmatched pairs. 1110 records in RAM.
INFO 2026-06-04 07:09:25 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 1s. Last read position: chr16:88,429,733
INFO 2026-06-04 07:09:25 MarkDuplicates Tracking 39633 as yet unmatched pairs. 493 records in RAM.
INFO 2026-06-04 07:09:27 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 1s. Last read position: chr17:1,683,597
INFO 2026-06-04 07:09:27 MarkDuplicates Tracking 38928 as yet unmatched pairs. 11713 records in RAM.
INFO 2026-06-04 07:09:28 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 1s. Last read position: chr17:7,240,887
INFO 2026-06-04 07:09:28 MarkDuplicates Tracking 38646 as yet unmatched pairs. 11431 records in RAM.
INFO 2026-06-04 07:09:30 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr17:13,002,536
INFO 2026-06-04 07:09:30 MarkDuplicates Tracking 37777 as yet unmatched pairs. 10562 records in RAM.
INFO 2026-06-04 07:09:31 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr17:28,695,527
INFO 2026-06-04 07:09:31 MarkDuplicates Tracking 37188 as yet unmatched pairs. 9973 records in RAM.
INFO 2026-06-04 07:09:33 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 1s. Last read position: chr17:36,430,584
INFO 2026-06-04 07:09:33 MarkDuplicates Tracking 36715 as yet unmatched pairs. 9500 records in RAM.
INFO 2026-06-04 07:09:34 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 1s. Last read position: chr17:40,088,415
INFO 2026-06-04 07:09:34 MarkDuplicates Tracking 36120 as yet unmatched pairs. 8904 records in RAM.
INFO 2026-06-04 07:09:36 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 1s. Last read position: chr17:42,856,412
INFO 2026-06-04 07:09:36 MarkDuplicates Tracking 35384 as yet unmatched pairs. 8167 records in RAM.
INFO 2026-06-04 07:09:38 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 1s. Last read position: chr17:48,058,327
INFO 2026-06-04 07:09:38 MarkDuplicates Tracking 34934 as yet unmatched pairs. 7717 records in RAM.
INFO 2026-06-04 07:09:39 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 1s. Last read position: chr17:50,187,036
INFO 2026-06-04 07:09:39 MarkDuplicates Tracking 44070 as yet unmatched pairs. 16853 records in RAM.
INFO 2026-06-04 07:09:41 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 1s. Last read position: chr17:50,189,167
INFO 2026-06-04 07:09:41 MarkDuplicates Tracking 42140 as yet unmatched pairs. 14923 records in RAM.
INFO 2026-06-04 07:09:43 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 1s. Last read position: chr17:50,190,546
INFO 2026-06-04 07:09:43 MarkDuplicates Tracking 41401 as yet unmatched pairs. 14184 records in RAM.
INFO 2026-06-04 07:09:44 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 1s. Last read position: chr17:50,193,951
INFO 2026-06-04 07:09:44 MarkDuplicates Tracking 43582 as yet unmatched pairs. 16365 records in RAM.
INFO 2026-06-04 07:09:47 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 2s. Last read position: chr17:50,195,454
INFO 2026-06-04 07:09:47 MarkDuplicates Tracking 37912 as yet unmatched pairs. 10695 records in RAM.
INFO 2026-06-04 07:09:49 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 2s. Last read position: chr17:50,197,026
INFO 2026-06-04 07:09:49 MarkDuplicates Tracking 47472 as yet unmatched pairs. 20255 records in RAM.
INFO 2026-06-04 07:09:51 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 1s. Last read position: chr17:50,201,411
INFO 2026-06-04 07:09:51 MarkDuplicates Tracking 33191 as yet unmatched pairs. 5974 records in RAM.
INFO 2026-06-04 07:09:52 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 1s. Last read position: chr17:63,099,203
INFO 2026-06-04 07:09:52 MarkDuplicates Tracking 29824 as yet unmatched pairs. 2607 records in RAM.
INFO 2026-06-04 07:09:54 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 1s. Last read position: chr17:75,501,501
INFO 2026-06-04 07:09:54 MarkDuplicates Tracking 29196 as yet unmatched pairs. 1978 records in RAM.
INFO 2026-06-04 07:09:55 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 1s. Last read position: chr17:79,947,728
INFO 2026-06-04 07:09:55 MarkDuplicates Tracking 28469 as yet unmatched pairs. 1251 records in RAM.
INFO 2026-06-04 07:09:57 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 1s. Last read position: chr17:81,824,325
INFO 2026-06-04 07:09:57 MarkDuplicates Tracking 27824 as yet unmatched pairs. 606 records in RAM.
INFO 2026-06-04 07:09:59 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 1s. Last read position: chr18:9,254,821
INFO 2026-06-04 07:09:59 MarkDuplicates Tracking 27072 as yet unmatched pairs. 1058 records in RAM.
INFO 2026-06-04 07:10:00 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 1s. Last read position: chr18:49,333,767
INFO 2026-06-04 07:10:00 MarkDuplicates Tracking 26635 as yet unmatched pairs. 621 records in RAM.
INFO 2026-06-04 07:10:02 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 1s. Last read position: chr19:757,330
INFO 2026-06-04 07:10:02 MarkDuplicates Tracking 25922 as yet unmatched pairs. 11198 records in RAM.
INFO 2026-06-04 07:10:03 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 1s. Last read position: chr19:2,164,249
INFO 2026-06-04 07:10:03 MarkDuplicates Tracking 25165 as yet unmatched pairs. 10440 records in RAM.
INFO 2026-06-04 07:10:05 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 1s. Last read position: chr19:5,215,569
INFO 2026-06-04 07:10:05 MarkDuplicates Tracking 24550 as yet unmatched pairs. 9825 records in RAM.
INFO 2026-06-04 07:10:07 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 1s. Last read position: chr19:7,870,902
INFO 2026-06-04 07:10:07 MarkDuplicates Tracking 23743 as yet unmatched pairs. 9017 records in RAM.
INFO 2026-06-04 07:10:08 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 1s. Last read position: chr19:10,829,117
INFO 2026-06-04 07:10:08 MarkDuplicates Tracking 23180 as yet unmatched pairs. 8454 records in RAM.
INFO 2026-06-04 07:10:11 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 2s. Last read position: chr19:13,153,611
INFO 2026-06-04 07:10:11 MarkDuplicates Tracking 22468 as yet unmatched pairs. 7742 records in RAM.
INFO 2026-06-04 07:10:12 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr19:15,257,139
INFO 2026-06-04 07:10:12 MarkDuplicates Tracking 22133 as yet unmatched pairs. 7407 records in RAM.
INFO 2026-06-04 07:10:14 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 1s. Last read position: chr19:18,141,950
INFO 2026-06-04 07:10:14 MarkDuplicates Tracking 21094 as yet unmatched pairs. 6362 records in RAM.
INFO 2026-06-04 07:10:16 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 1s. Last read position: chr19:31,277,572
INFO 2026-06-04 07:10:16 MarkDuplicates Tracking 20367 as yet unmatched pairs. 5635 records in RAM.
INFO 2026-06-04 07:10:17 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 1s. Last read position: chr19:38,081,640
INFO 2026-06-04 07:10:17 MarkDuplicates Tracking 19477 as yet unmatched pairs. 4743 records in RAM.
INFO 2026-06-04 07:10:19 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 1s. Last read position: chr19:39,889,885
INFO 2026-06-04 07:10:19 MarkDuplicates Tracking 19321 as yet unmatched pairs. 4587 records in RAM.
INFO 2026-06-04 07:10:20 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 1s. Last read position: chr19:41,869,144
INFO 2026-06-04 07:10:20 MarkDuplicates Tracking 18705 as yet unmatched pairs. 3971 records in RAM.
INFO 2026-06-04 07:10:22 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 1s. Last read position: chr19:44,213,139
INFO 2026-06-04 07:10:22 MarkDuplicates Tracking 17608 as yet unmatched pairs. 2872 records in RAM.
INFO 2026-06-04 07:10:23 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:05:20s. Time for last 1,000,000: 1s. Last read position: chr19:47,417,216
INFO 2026-06-04 07:10:23 MarkDuplicates Tracking 16941 as yet unmatched pairs. 2205 records in RAM.
INFO 2026-06-04 07:10:25 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 1s. Last read position: chr19:49,673,706
INFO 2026-06-04 07:10:25 MarkDuplicates Tracking 16236 as yet unmatched pairs. 1500 records in RAM.
INFO 2026-06-04 07:10:27 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 1s. Last read position: chr19:54,462,941
INFO 2026-06-04 07:10:27 MarkDuplicates Tracking 15566 as yet unmatched pairs. 829 records in RAM.
INFO 2026-06-04 07:10:29 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 2s. Last read position: chr19:58,138,310
INFO 2026-06-04 07:10:29 MarkDuplicates Tracking 14908 as yet unmatched pairs. 171 records in RAM.
INFO 2026-06-04 07:10:31 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 1s. Last read position: chr20:5,558,036
INFO 2026-06-04 07:10:31 MarkDuplicates Tracking 14287 as yet unmatched pairs. 3486 records in RAM.
INFO 2026-06-04 07:10:32 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 1s. Last read position: chr20:32,788,882
INFO 2026-06-04 07:10:32 MarkDuplicates Tracking 13626 as yet unmatched pairs. 2824 records in RAM.
INFO 2026-06-04 07:10:34 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 1s. Last read position: chr20:38,057,644
INFO 2026-06-04 07:10:34 MarkDuplicates Tracking 12991 as yet unmatched pairs. 2189 records in RAM.
INFO 2026-06-04 07:10:35 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 1s. Last read position: chr20:47,227,128
INFO 2026-06-04 07:10:35 MarkDuplicates Tracking 12426 as yet unmatched pairs. 1623 records in RAM.
INFO 2026-06-04 07:10:37 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 1s. Last read position: chr20:59,030,315
INFO 2026-06-04 07:10:37 MarkDuplicates Tracking 12207 as yet unmatched pairs. 1403 records in RAM.
INFO 2026-06-04 07:10:38 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 1s. Last read position: chr20:63,698,484
INFO 2026-06-04 07:10:38 MarkDuplicates Tracking 11044 as yet unmatched pairs. 240 records in RAM.
INFO 2026-06-04 07:10:40 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 1s. Last read position: chr21:8,397,750
INFO 2026-06-04 07:10:40 MarkDuplicates Tracking 10491 as yet unmatched pairs. 2019 records in RAM.
INFO 2026-06-04 07:10:41 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 1s. Last read position: chr21:28,935,140
INFO 2026-06-04 07:10:41 MarkDuplicates Tracking 9849 as yet unmatched pairs. 1375 records in RAM.
INFO 2026-06-04 07:10:43 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 1s. Last read position: chr21:43,719,308
INFO 2026-06-04 07:10:43 MarkDuplicates Tracking 9301 as yet unmatched pairs. 827 records in RAM.
INFO 2026-06-04 07:10:44 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 1s. Last read position: chr21:46,537,194
INFO 2026-06-04 07:10:44 MarkDuplicates Tracking 8509 as yet unmatched pairs. 35 records in RAM.
INFO 2026-06-04 07:10:46 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 1s. Last read position: chr22:24,042,922
INFO 2026-06-04 07:10:46 MarkDuplicates Tracking 7872 as yet unmatched pairs. 2661 records in RAM.
INFO 2026-06-04 07:10:48 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 1s. Last read position: chr22:30,936,568
INFO 2026-06-04 07:10:48 MarkDuplicates Tracking 7205 as yet unmatched pairs. 1994 records in RAM.
INFO 2026-06-04 07:10:49 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 1s. Last read position: chr22:38,221,621
INFO 2026-06-04 07:10:49 MarkDuplicates Tracking 6594 as yet unmatched pairs. 1382 records in RAM.
INFO 2026-06-04 07:10:51 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 2s. Last read position: chr22:45,533,065
INFO 2026-06-04 07:10:51 MarkDuplicates Tracking 6004 as yet unmatched pairs. 792 records in RAM.
INFO 2026-06-04 07:10:53 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 1s. Last read position: chrX:2,789,656
INFO 2026-06-04 07:10:53 MarkDuplicates Tracking 5106 as yet unmatched pairs. 3039 records in RAM.
INFO 2026-06-04 07:10:55 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 1s. Last read position: chrX:41,334,236
INFO 2026-06-04 07:10:55 MarkDuplicates Tracking 4848 as yet unmatched pairs. 2778 records in RAM.
INFO 2026-06-04 07:10:56 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 1s. Last read position: chrX:53,409,205
INFO 2026-06-04 07:10:56 MarkDuplicates Tracking 4077 as yet unmatched pairs. 2006 records in RAM.
INFO 2026-06-04 07:10:58 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 1s. Last read position: chrX:74,741,388
INFO 2026-06-04 07:10:58 MarkDuplicates Tracking 3507 as yet unmatched pairs. 1436 records in RAM.
INFO 2026-06-04 07:10:59 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 1s. Last read position: chrX:129,810,947
INFO 2026-06-04 07:10:59 MarkDuplicates Tracking 3066 as yet unmatched pairs. 995 records in RAM.
INFO 2026-06-04 07:11:01 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 1s. Last read position: chrX:154,352,774
INFO 2026-06-04 07:11:01 MarkDuplicates Tracking 2540 as yet unmatched pairs. 468 records in RAM.
INFO 2026-06-04 07:11:02 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 1s. Last read position: GL000220.1:116,705
INFO 2026-06-04 07:11:02 MarkDuplicates Tracking 1399 as yet unmatched pairs. 55 records in RAM.
INFO 2026-06-04 07:11:03 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 1s. Last read position: KI270733.1:133,667
INFO 2026-06-04 07:11:03 MarkDuplicates Tracking 100 as yet unmatched pairs. 98 records in RAM.
INFO 2026-06-04 07:11:04 MarkDuplicates Read 217463897 records. 0 pairs never matched.
INFO 2026-06-04 07:11:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 38560746320; totalMemory: 63552094208; maxMemory: 63585648640
INFO 2026-06-04 07:11:14 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-04 07:11:21 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-04 07:11:41 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-04 07:11:57 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-04 07:12:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300839128; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-04 07:12:00 MarkDuplicates Marking 82867679 records as duplicates.
INFO 2026-06-04 07:12:00 MarkDuplicates Found 7365407 optical duplicate clusters.
INFO 2026-06-04 07:12:00 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-04 07:12:19 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:19s. Time for last 10,000,000: 19s. Last read position: chr1:113,622,825
INFO 2026-06-04 07:12:36 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:35s. Time for last 10,000,000: 16s. Last read position: chr1:203,713,221
INFO 2026-06-04 07:12:55 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:54s. Time for last 10,000,000: 18s. Last read position: chr2:128,193,473
INFO 2026-06-04 07:13:13 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:12s. Time for last 10,000,000: 18s. Last read position: chr3:10,249,213
INFO 2026-06-04 07:13:30 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:30s. Time for last 10,000,000: 17s. Last read position: chr4:6,641,172
INFO 2026-06-04 07:13:49 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:48s. Time for last 10,000,000: 18s. Last read position: chr5:150,405,120
INFO 2026-06-04 07:14:09 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:08s. Time for last 10,000,000: 20s. Last read position: chr6:101,924,626
INFO 2026-06-04 07:14:30 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:29s. Time for last 10,000,000: 20s. Last read position: chr7:101,000,998
INFO 2026-06-04 07:14:47 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:46s. Time for last 10,000,000: 17s. Last read position: chr8:143,858,145
INFO 2026-06-04 07:15:04 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:03:03s. Time for last 10,000,000: 17s. Last read position: chr9:131,900,947
INFO 2026-06-04 07:15:21 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:03:20s. Time for last 10,000,000: 16s. Last read position: chr11:2,884,657
INFO 2026-06-04 07:15:37 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:36s. Time for last 10,000,000: 16s. Last read position: chr11:131,911,484
INFO 2026-06-04 07:15:54 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:53s. Time for last 10,000,000: 16s. Last read position: chr12:131,982,350
INFO 2026-06-04 07:16:12 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:04:11s. Time for last 10,000,000: 17s. Last read position: chr15:28,168,435
INFO 2026-06-04 07:16:30 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:04:29s. Time for last 10,000,000: 18s. Last read position: chr16:18,380,384
INFO 2026-06-04 07:16:47 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:46s. Time for last 10,000,000: 16s. Last read position: chr17:13,002,536
INFO 2026-06-04 07:17:04 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:05:03s. Time for last 10,000,000: 16s. Last read position: chr17:50,195,454
INFO 2026-06-04 07:17:21 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:05:20s. Time for last 10,000,000: 17s. Last read position: chr19:2,164,249
INFO 2026-06-04 07:17:39 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:05:38s. Time for last 10,000,000: 17s. Last read position: chr19:41,869,144
INFO 2026-06-04 07:17:56 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:05:55s. Time for last 10,000,000: 16s. Last read position: chr20:59,030,315
INFO 2026-06-04 07:18:12 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:06:12s. Time for last 10,000,000: 16s. Last read position: chrX:2,789,656
INFO 2026-06-04 07:18:28 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-04 07:18:28 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-04 07:18:28 MarkDuplicates Getting Memory Stats.
INFO 2026-06-04 07:18:29 MarkDuplicates Before output close freeMemory: 202176128; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-04 07:18:29 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-04 07:18:29 MarkDuplicates After output close freeMemory: 104311184; totalMemory: 134217728; maxMemory: 63585648640
[Thu Jun 04 07:18:29 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 13.45 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory