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_40C_1.Aligned.sortedByCoord.out.bam --OUTPUT RGB_RLP_lowDV_1ststrand_40C_1.md.bam --METRICS_FILE RGB_RLP_lowDV_1ststrand_40C_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:04:58.234 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 07:04:58 GMT 2026] MarkDuplicates --INPUT RGB_RLP_lowDV_1ststrand_40C_1.Aligned.sortedByCoord.out.bam --OUTPUT RGB_RLP_lowDV_1ststrand_40C_1.md.bam --METRICS_FILE RGB_RLP_lowDV_1ststrand_40C_1.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Jun 04 07:04:58 GMT 2026] Executing as ?@nf-eeac6fe2f09ae47e075147b64e658c11-bf290-ckfhl 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 07:04:58 MarkDuplicates Start of doWork freeMemory: 105827344; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-04 07:04:58 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-04 07:04:58 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-04 07:05:03 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:2,306,606
INFO 2026-06-04 07:05:03 MarkDuplicates Tracking 758 as yet unmatched pairs. 85 records in RAM.
INFO 2026-06-04 07:05:05 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: chr1:11,795,268
INFO 2026-06-04 07:05:05 MarkDuplicates Tracking 1348 as yet unmatched pairs. 44 records in RAM.
INFO 2026-06-04 07:05:07 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 2s. Last read position: chr1:19,242,457
INFO 2026-06-04 07:05:07 MarkDuplicates Tracking 1878 as yet unmatched pairs. 34 records in RAM.
INFO 2026-06-04 07:05:09 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: chr1:23,559,311
INFO 2026-06-04 07:05:09 MarkDuplicates Tracking 2447 as yet unmatched pairs. 78 records in RAM.
INFO 2026-06-04 07:05:11 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 2s. Last read position: chr1:29,150,166
INFO 2026-06-04 07:05:11 MarkDuplicates Tracking 3001 as yet unmatched pairs. 59 records in RAM.
INFO 2026-06-04 07:05:13 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: chr1:35,641,377
INFO 2026-06-04 07:05:13 MarkDuplicates Tracking 3559 as yet unmatched pairs. 14 records in RAM.
INFO 2026-06-04 07:05:15 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: chr1:42,958,666
INFO 2026-06-04 07:05:15 MarkDuplicates Tracking 4190 as yet unmatched pairs. 109 records in RAM.
INFO 2026-06-04 07:05:17 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 2s. Last read position: chr1:52,779,855
INFO 2026-06-04 07:05:17 MarkDuplicates Tracking 4720 as yet unmatched pairs. 53 records in RAM.
INFO 2026-06-04 07:05:19 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: chr1:89,117,003
INFO 2026-06-04 07:05:19 MarkDuplicates Tracking 5249 as yet unmatched pairs. 68 records in RAM.
INFO 2026-06-04 07:05:20 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: chr1:113,585,520
INFO 2026-06-04 07:05:20 MarkDuplicates Tracking 5860 as yet unmatched pairs. 95 records in RAM.
INFO 2026-06-04 07:05:22 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: chr1:120,784,993
INFO 2026-06-04 07:05:22 MarkDuplicates Tracking 6373 as yet unmatched pairs. 41 records in RAM.
INFO 2026-06-04 07:05:24 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: chr1:148,591,451
INFO 2026-06-04 07:05:24 MarkDuplicates Tracking 6647 as yet unmatched pairs. 55 records in RAM.
INFO 2026-06-04 07:05:25 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 1s. Last read position: chr1:150,997,219
INFO 2026-06-04 07:05:25 MarkDuplicates Tracking 7157 as yet unmatched pairs. 134 records in RAM.
INFO 2026-06-04 07:05:27 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 1s. Last read position: chr1:153,762,780
INFO 2026-06-04 07:05:27 MarkDuplicates Tracking 7494 as yet unmatched pairs. 30 records in RAM.
INFO 2026-06-04 07:05:29 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 1s. Last read position: chr1:155,053,913
INFO 2026-06-04 07:05:29 MarkDuplicates Tracking 8115 as yet unmatched pairs. 158 records in RAM.
INFO 2026-06-04 07:05:31 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 1s. Last read position: chr1:156,115,022
INFO 2026-06-04 07:05:31 MarkDuplicates Tracking 9014 as yet unmatched pairs. 571 records in RAM.
INFO 2026-06-04 07:05:33 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 2s. Last read position: chr1:160,213,476
INFO 2026-06-04 07:05:33 MarkDuplicates Tracking 9126 as yet unmatched pairs. 11 records in RAM.
INFO 2026-06-04 07:05:35 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 1s. Last read position: chr1:171,557,624
INFO 2026-06-04 07:05:35 MarkDuplicates Tracking 10008 as yet unmatched pairs. 359 records in RAM.
INFO 2026-06-04 07:05:37 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 2s. Last read position: chr1:186,347,358
INFO 2026-06-04 07:05:37 MarkDuplicates Tracking 10422 as yet unmatched pairs. 240 records in RAM.
INFO 2026-06-04 07:05:39 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 1s. Last read position: chr1:204,549,304
INFO 2026-06-04 07:05:39 MarkDuplicates Tracking 11019 as yet unmatched pairs. 257 records in RAM.
INFO 2026-06-04 07:05:41 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 1s. Last read position: chr1:224,434,011
INFO 2026-06-04 07:05:41 MarkDuplicates Tracking 11369 as yet unmatched pairs. 119 records in RAM.
INFO 2026-06-04 07:05:43 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 1s. Last read position: chr1:232,514,904
INFO 2026-06-04 07:05:43 MarkDuplicates Tracking 11928 as yet unmatched pairs. 47 records in RAM.
INFO 2026-06-04 07:05:45 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: chr2:6,897,143
INFO 2026-06-04 07:05:45 MarkDuplicates Tracking 12717 as yet unmatched pairs. 12646 records in RAM.
INFO 2026-06-04 07:05:47 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 1s. Last read position: chr2:27,216,551
INFO 2026-06-04 07:05:47 MarkDuplicates Tracking 13207 as yet unmatched pairs. 13132 records in RAM.
INFO 2026-06-04 07:05:48 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 1s. Last read position: chr2:36,878,020
INFO 2026-06-04 07:05:48 MarkDuplicates Tracking 109289 as yet unmatched pairs. 7598 records in RAM.
INFO 2026-06-04 07:05:50 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 1s. Last read position: chr2:55,558,783
INFO 2026-06-04 07:05:50 MarkDuplicates Tracking 108736 as yet unmatched pairs. 7044 records in RAM.
INFO 2026-06-04 07:05:53 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 3s. Last read position: chr2:74,464,519
INFO 2026-06-04 07:05:53 MarkDuplicates Tracking 108163 as yet unmatched pairs. 6470 records in RAM.
INFO 2026-06-04 07:05:55 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 1s. Last read position: chr2:97,792,866
INFO 2026-06-04 07:05:55 MarkDuplicates Tracking 107588 as yet unmatched pairs. 5893 records in RAM.
INFO 2026-06-04 07:05:57 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 1s. Last read position: chr2:112,388,587
INFO 2026-06-04 07:05:57 MarkDuplicates Tracking 107170 as yet unmatched pairs. 5474 records in RAM.
INFO 2026-06-04 07:05:59 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 2s. Last read position: chr2:152,147,192
INFO 2026-06-04 07:05:59 MarkDuplicates Tracking 106685 as yet unmatched pairs. 4983 records in RAM.
INFO 2026-06-04 07:06:00 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 1s. Last read position: chr2:178,769,752
INFO 2026-06-04 07:06:00 MarkDuplicates Tracking 106160 as yet unmatched pairs. 4456 records in RAM.
INFO 2026-06-04 07:06:02 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 1s. Last read position: chr2:190,905,014
INFO 2026-06-04 07:06:02 MarkDuplicates Tracking 105503 as yet unmatched pairs. 3799 records in RAM.
INFO 2026-06-04 07:06:04 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 2s. Last read position: chr2:215,362,057
INFO 2026-06-04 07:06:04 MarkDuplicates Tracking 108599 as yet unmatched pairs. 6893 records in RAM.
INFO 2026-06-04 07:06:07 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 2s. Last read position: chr2:215,379,257
INFO 2026-06-04 07:06:07 MarkDuplicates Tracking 108496 as yet unmatched pairs. 6788 records in RAM.
INFO 2026-06-04 07:06:09 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 2s. Last read position: chr2:215,407,262
INFO 2026-06-04 07:06:09 MarkDuplicates Tracking 106546 as yet unmatched pairs. 4835 records in RAM.
INFO 2026-06-04 07:06:11 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 1s. Last read position: chr2:215,434,732
INFO 2026-06-04 07:06:11 MarkDuplicates Tracking 105381 as yet unmatched pairs. 3670 records in RAM.
INFO 2026-06-04 07:06:12 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 1s. Last read position: chr2:219,543,336
INFO 2026-06-04 07:06:12 MarkDuplicates Tracking 102937 as yet unmatched pairs. 1222 records in RAM.
INFO 2026-06-04 07:06:14 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 1s. Last read position: chr2:237,357,337
INFO 2026-06-04 07:06:14 MarkDuplicates Tracking 102305 as yet unmatched pairs. 580 records in RAM.
INFO 2026-06-04 07:06:16 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 1s. Last read position: chr3:9,470,690
INFO 2026-06-04 07:06:16 MarkDuplicates Tracking 101654 as yet unmatched pairs. 5148 records in RAM.
INFO 2026-06-04 07:06:18 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 2s. Last read position: chr3:33,114,357
INFO 2026-06-04 07:06:18 MarkDuplicates Tracking 101067 as yet unmatched pairs. 4558 records in RAM.
INFO 2026-06-04 07:06:20 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 1s. Last read position: chr3:47,414,325
INFO 2026-06-04 07:06:20 MarkDuplicates Tracking 100449 as yet unmatched pairs. 3940 records in RAM.
INFO 2026-06-04 07:06:22 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 1s. Last read position: chr3:50,185,445
INFO 2026-06-04 07:06:22 MarkDuplicates Tracking 99789 as yet unmatched pairs. 3277 records in RAM.
INFO 2026-06-04 07:06:24 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 1s. Last read position: chr3:66,417,151
INFO 2026-06-04 07:06:24 MarkDuplicates Tracking 99274 as yet unmatched pairs. 2756 records in RAM.
INFO 2026-06-04 07:06:25 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 1s. Last read position: chr3:120,596,382
INFO 2026-06-04 07:06:25 MarkDuplicates Tracking 98762 as yet unmatched pairs. 2229 records in RAM.
INFO 2026-06-04 07:06:27 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 1s. Last read position: chr3:129,575,540
INFO 2026-06-04 07:06:27 MarkDuplicates Tracking 98268 as yet unmatched pairs. 1732 records in RAM.
INFO 2026-06-04 07:06:28 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 1s. Last read position: chr3:155,898,005
INFO 2026-06-04 07:06:28 MarkDuplicates Tracking 97627 as yet unmatched pairs. 1081 records in RAM.
INFO 2026-06-04 07:06:31 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 2s. Last read position: chr3:184,572,513
INFO 2026-06-04 07:06:31 MarkDuplicates Tracking 97119 as yet unmatched pairs. 570 records in RAM.
INFO 2026-06-04 07:06:32 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 1s. Last read position: chr3:196,812,219
INFO 2026-06-04 07:06:32 MarkDuplicates Tracking 96684 as yet unmatched pairs. 130 records in RAM.
INFO 2026-06-04 07:06:34 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 1s. Last read position: chr4:6,619,997
INFO 2026-06-04 07:06:34 MarkDuplicates Tracking 96038 as yet unmatched pairs. 2148 records in RAM.
INFO 2026-06-04 07:06:35 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 1s. Last read position: chr4:54,267,309
INFO 2026-06-04 07:06:35 MarkDuplicates Tracking 95718 as yet unmatched pairs. 1820 records in RAM.
INFO 2026-06-04 07:06:37 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 1s. Last read position: chr4:87,046,181
INFO 2026-06-04 07:06:37 MarkDuplicates Tracking 95017 as yet unmatched pairs. 1119 records in RAM.
INFO 2026-06-04 07:06:38 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 1s. Last read position: chr4:139,351,226
INFO 2026-06-04 07:06:38 MarkDuplicates Tracking 94447 as yet unmatched pairs. 543 records in RAM.
INFO 2026-06-04 07:06:40 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 1s. Last read position: chr4:190,174,159
INFO 2026-06-04 07:06:40 MarkDuplicates Tracking 93941 as yet unmatched pairs. 33 records in RAM.
INFO 2026-06-04 07:06:42 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 1s. Last read position: chr5:31,421,269
INFO 2026-06-04 07:06:42 MarkDuplicates Tracking 93331 as yet unmatched pairs. 3922 records in RAM.
INFO 2026-06-04 07:06:43 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 1s. Last read position: chr5:70,108,317
INFO 2026-06-04 07:06:43 MarkDuplicates Tracking 92818 as yet unmatched pairs. 3409 records in RAM.
INFO 2026-06-04 07:06:45 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 2s. Last read position: chr5:112,838,748
INFO 2026-06-04 07:06:45 MarkDuplicates Tracking 92341 as yet unmatched pairs. 2930 records in RAM.
INFO 2026-06-04 07:06:47 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 1s. Last read position: chr5:139,363,836
INFO 2026-06-04 07:06:47 MarkDuplicates Tracking 91859 as yet unmatched pairs. 2447 records in RAM.
INFO 2026-06-04 07:06:48 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 1s. Last read position: chr5:149,511,810
INFO 2026-06-04 07:06:48 MarkDuplicates Tracking 91358 as yet unmatched pairs. 1932 records in RAM.
INFO 2026-06-04 07:06:50 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 1s. Last read position: chr5:150,446,820
INFO 2026-06-04 07:06:50 MarkDuplicates Tracking 90935 as yet unmatched pairs. 1509 records in RAM.
INFO 2026-06-04 07:06:52 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 1s. Last read position: chr5:172,769,036
INFO 2026-06-04 07:06:52 MarkDuplicates Tracking 90330 as yet unmatched pairs. 899 records in RAM.
INFO 2026-06-04 07:06:53 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 1s. Last read position: chr5:179,833,114
INFO 2026-06-04 07:06:53 MarkDuplicates Tracking 90377 as yet unmatched pairs. 944 records in RAM.
INFO 2026-06-04 07:06:55 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 1s. Last read position: chr6:8,751,887
INFO 2026-06-04 07:06:55 MarkDuplicates Tracking 89030 as yet unmatched pairs. 5447 records in RAM.
INFO 2026-06-04 07:06:56 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 1s. Last read position: chr6:30,009,330
INFO 2026-06-04 07:06:56 MarkDuplicates Tracking 88540 as yet unmatched pairs. 4955 records in RAM.
INFO 2026-06-04 07:06:57 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 1s. Last read position: chr6:31,647,597
INFO 2026-06-04 07:06:57 MarkDuplicates Tracking 88222 as yet unmatched pairs. 4637 records in RAM.
INFO 2026-06-04 07:06:59 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 1s. Last read position: chr6:32,061,660
INFO 2026-06-04 07:06:59 MarkDuplicates Tracking 87612 as yet unmatched pairs. 4027 records in RAM.
INFO 2026-06-04 07:07:01 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 1s. Last read position: chr6:33,685,496
INFO 2026-06-04 07:07:01 MarkDuplicates Tracking 86956 as yet unmatched pairs. 3371 records in RAM.
INFO 2026-06-04 07:07:02 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 1s. Last read position: chr6:43,176,562
INFO 2026-06-04 07:07:02 MarkDuplicates Tracking 86272 as yet unmatched pairs. 2684 records in RAM.
INFO 2026-06-04 07:07:05 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 2s. Last read position: chr6:75,117,471
INFO 2026-06-04 07:07:05 MarkDuplicates Tracking 85781 as yet unmatched pairs. 2186 records in RAM.
INFO 2026-06-04 07:07:07 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 2s. Last read position: chr6:113,859,707
INFO 2026-06-04 07:07:07 MarkDuplicates Tracking 85128 as yet unmatched pairs. 1531 records in RAM.
INFO 2026-06-04 07:07:08 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 1s. Last read position: chr6:148,959,920
INFO 2026-06-04 07:07:08 MarkDuplicates Tracking 84554 as yet unmatched pairs. 954 records in RAM.
INFO 2026-06-04 07:07:10 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 1s. Last read position: chr6:160,043,198
INFO 2026-06-04 07:07:10 MarkDuplicates Tracking 83944 as yet unmatched pairs. 344 records in RAM.
INFO 2026-06-04 07:07:12 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 1s. Last read position: chr7:5,370,674
INFO 2026-06-04 07:07:12 MarkDuplicates Tracking 83442 as yet unmatched pairs. 5245 records in RAM.
INFO 2026-06-04 07:07:13 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 1s. Last read position: chr7:26,371,824
INFO 2026-06-04 07:07:13 MarkDuplicates Tracking 82707 as yet unmatched pairs. 4508 records in RAM.
INFO 2026-06-04 07:07:15 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 1s. Last read position: chr7:50,447,129
INFO 2026-06-04 07:07:15 MarkDuplicates Tracking 82147 as yet unmatched pairs. 3940 records in RAM.
INFO 2026-06-04 07:07:16 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 1s. Last read position: chr7:73,682,990
INFO 2026-06-04 07:07:16 MarkDuplicates Tracking 81722 as yet unmatched pairs. 3509 records in RAM.
INFO 2026-06-04 07:07:17 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 1s. Last read position: chr7:88,206,443
INFO 2026-06-04 07:07:17 MarkDuplicates Tracking 81288 as yet unmatched pairs. 3067 records in RAM.
INFO 2026-06-04 07:07:19 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 1s. Last read position: chr7:97,024,309
INFO 2026-06-04 07:07:19 MarkDuplicates Tracking 80615 as yet unmatched pairs. 2394 records in RAM.
INFO 2026-06-04 07:07:20 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 1s. Last read position: chr7:100,992,195
INFO 2026-06-04 07:07:20 MarkDuplicates Tracking 80062 as yet unmatched pairs. 1840 records in RAM.
INFO 2026-06-04 07:07:21 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr7:102,541,534
INFO 2026-06-04 07:07:21 MarkDuplicates Tracking 79960 as yet unmatched pairs. 1738 records in RAM.
INFO 2026-06-04 07:07:23 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 1s. Last read position: chr7:128,395,175
INFO 2026-06-04 07:07:23 MarkDuplicates Tracking 79388 as yet unmatched pairs. 1164 records in RAM.
INFO 2026-06-04 07:07:25 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 1s. Last read position: chr7:143,644,025
INFO 2026-06-04 07:07:25 MarkDuplicates Tracking 78819 as yet unmatched pairs. 588 records in RAM.
INFO 2026-06-04 07:07:26 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 1s. Last read position: chr7:158,644,303
INFO 2026-06-04 07:07:26 MarkDuplicates Tracking 78299 as yet unmatched pairs. 66 records in RAM.
INFO 2026-06-04 07:07:29 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 2s. Last read position: chr8:27,605,030
INFO 2026-06-04 07:07:29 MarkDuplicates Tracking 77856 as yet unmatched pairs. 5343 records in RAM.
INFO 2026-06-04 07:07:31 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 1s. Last read position: chr8:38,428,346
INFO 2026-06-04 07:07:31 MarkDuplicates Tracking 77470 as yet unmatched pairs. 4956 records in RAM.
INFO 2026-06-04 07:07:32 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 1s. Last read position: chr8:61,555,965
INFO 2026-06-04 07:07:32 MarkDuplicates Tracking 76658 as yet unmatched pairs. 4143 records in RAM.
INFO 2026-06-04 07:07:34 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 1s. Last read position: chr8:97,722,953
INFO 2026-06-04 07:07:34 MarkDuplicates Tracking 76061 as yet unmatched pairs. 3544 records in RAM.
INFO 2026-06-04 07:07:35 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 1s. Last read position: chr8:119,208,507
INFO 2026-06-04 07:07:35 MarkDuplicates Tracking 75609 as yet unmatched pairs. 3086 records in RAM.
INFO 2026-06-04 07:07:37 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 1s. Last read position: chr8:143,574,996
INFO 2026-06-04 07:07:37 MarkDuplicates Tracking 74839 as yet unmatched pairs. 2310 records in RAM.
INFO 2026-06-04 07:07:38 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 1s. Last read position: chr8:143,859,685
INFO 2026-06-04 07:07:38 MarkDuplicates Tracking 74775 as yet unmatched pairs. 2246 records in RAM.
INFO 2026-06-04 07:07:39 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 1s. Last read position: chr8:143,861,738
INFO 2026-06-04 07:07:39 MarkDuplicates Tracking 75260 as yet unmatched pairs. 2731 records in RAM.
INFO 2026-06-04 07:07:40 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 1s. Last read position: chr8:143,863,801
INFO 2026-06-04 07:07:40 MarkDuplicates Tracking 73895 as yet unmatched pairs. 1362 records in RAM.
INFO 2026-06-04 07:07:41 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 1s. Last read position: chr8:143,866,123
INFO 2026-06-04 07:07:41 MarkDuplicates Tracking 73735 as yet unmatched pairs. 1202 records in RAM.
INFO 2026-06-04 07:07:42 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 1s. Last read position: chr8:143,983,282
INFO 2026-06-04 07:07:42 MarkDuplicates Tracking 73245 as yet unmatched pairs. 710 records in RAM.
INFO 2026-06-04 07:07:44 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 1s. Last read position: chr9:14,088,267
INFO 2026-06-04 07:07:44 MarkDuplicates Tracking 72855 as yet unmatched pairs. 4305 records in RAM.
INFO 2026-06-04 07:07:46 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 1s. Last read position: chr9:37,432,115
INFO 2026-06-04 07:07:46 MarkDuplicates Tracking 71853 as yet unmatched pairs. 3299 records in RAM.
INFO 2026-06-04 07:07:47 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 1s. Last read position: chr9:95,468,772
INFO 2026-06-04 07:07:47 MarkDuplicates Tracking 71274 as yet unmatched pairs. 2717 records in RAM.
INFO 2026-06-04 07:07:48 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 1s. Last read position: chr9:115,086,438
INFO 2026-06-04 07:07:48 MarkDuplicates Tracking 70922 as yet unmatched pairs. 2364 records in RAM.
INFO 2026-06-04 07:07:50 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 1s. Last read position: chr9:128,434,589
INFO 2026-06-04 07:07:50 MarkDuplicates Tracking 70224 as yet unmatched pairs. 1666 records in RAM.
INFO 2026-06-04 07:07:51 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 1s. Last read position: chr9:133,108,698
INFO 2026-06-04 07:07:51 MarkDuplicates Tracking 69621 as yet unmatched pairs. 1062 records in RAM.
INFO 2026-06-04 07:07:53 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 1s. Last read position: chr9:136,863,329
INFO 2026-06-04 07:07:53 MarkDuplicates Tracking 68928 as yet unmatched pairs. 369 records in RAM.
INFO 2026-06-04 07:07:54 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 1s. Last read position: chr10:12,035,258
INFO 2026-06-04 07:07:54 MarkDuplicates Tracking 68363 as yet unmatched pairs. 3299 records in RAM.
INFO 2026-06-04 07:07:56 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 1s. Last read position: chr10:35,178,892
INFO 2026-06-04 07:07:56 MarkDuplicates Tracking 67850 as yet unmatched pairs. 2786 records in RAM.
INFO 2026-06-04 07:07:57 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 1s. Last read position: chr10:59,906,185
INFO 2026-06-04 07:07:57 MarkDuplicates Tracking 67575 as yet unmatched pairs. 2510 records in RAM.
INFO 2026-06-04 07:07:59 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 1s. Last read position: chr10:78,026,056
INFO 2026-06-04 07:07:59 MarkDuplicates Tracking 66807 as yet unmatched pairs. 1742 records in RAM.
INFO 2026-06-04 07:08:00 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 1s. Last read position: chr10:96,983,223
INFO 2026-06-04 07:08:00 MarkDuplicates Tracking 66293 as yet unmatched pairs. 1228 records in RAM.
INFO 2026-06-04 07:08:02 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 1s. Last read position: chr10:113,879,622
INFO 2026-06-04 07:08:02 MarkDuplicates Tracking 65717 as yet unmatched pairs. 649 records in RAM.
INFO 2026-06-04 07:08:04 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 2s. Last read position: chr10:133,351,988
INFO 2026-06-04 07:08:04 MarkDuplicates Tracking 65129 as yet unmatched pairs. 60 records in RAM.
INFO 2026-06-04 07:08:06 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 1s. Last read position: chr11:1,017,244
INFO 2026-06-04 07:08:06 MarkDuplicates Tracking 64616 as yet unmatched pairs. 6514 records in RAM.
INFO 2026-06-04 07:08:07 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 1s. Last read position: chr11:6,451,287
INFO 2026-06-04 07:08:07 MarkDuplicates Tracking 63989 as yet unmatched pairs. 5886 records in RAM.
INFO 2026-06-04 07:08:09 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 1s. Last read position: chr11:31,432,465
INFO 2026-06-04 07:08:09 MarkDuplicates Tracking 63507 as yet unmatched pairs. 5397 records in RAM.
INFO 2026-06-04 07:08:10 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 1s. Last read position: chr11:47,797,776
INFO 2026-06-04 07:08:10 MarkDuplicates Tracking 62833 as yet unmatched pairs. 4722 records in RAM.
INFO 2026-06-04 07:08:12 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 1s. Last read position: chr11:62,518,587
INFO 2026-06-04 07:08:12 MarkDuplicates Tracking 62350 as yet unmatched pairs. 4236 records in RAM.
INFO 2026-06-04 07:08:13 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 1s. Last read position: chr11:64,245,236
INFO 2026-06-04 07:08:13 MarkDuplicates Tracking 61979 as yet unmatched pairs. 3865 records in RAM.
INFO 2026-06-04 07:08:15 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 1s. Last read position: chr11:65,635,745
INFO 2026-06-04 07:08:15 MarkDuplicates Tracking 61063 as yet unmatched pairs. 2946 records in RAM.
INFO 2026-06-04 07:08:16 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 1s. Last read position: chr11:67,365,186
INFO 2026-06-04 07:08:16 MarkDuplicates Tracking 60389 as yet unmatched pairs. 2268 records in RAM.
INFO 2026-06-04 07:08:18 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 1s. Last read position: chr11:72,016,466
INFO 2026-06-04 07:08:18 MarkDuplicates Tracking 59931 as yet unmatched pairs. 1809 records in RAM.
INFO 2026-06-04 07:08:19 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 1s. Last read position: chr11:85,976,655
INFO 2026-06-04 07:08:19 MarkDuplicates Tracking 59183 as yet unmatched pairs. 1060 records in RAM.
INFO 2026-06-04 07:08:21 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 1s. Last read position: chr11:118,897,086
INFO 2026-06-04 07:08:21 MarkDuplicates Tracking 58649 as yet unmatched pairs. 526 records in RAM.
INFO 2026-06-04 07:08:22 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: chr12:896,067
INFO 2026-06-04 07:08:22 MarkDuplicates Tracking 58130 as yet unmatched pairs. 5647 records in RAM.
INFO 2026-06-04 07:08:24 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 1s. Last read position: chr12:7,080,917
INFO 2026-06-04 07:08:24 MarkDuplicates Tracking 57595 as yet unmatched pairs. 5112 records in RAM.
INFO 2026-06-04 07:08:25 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 1s. Last read position: chr12:30,753,451
INFO 2026-06-04 07:08:25 MarkDuplicates Tracking 56925 as yet unmatched pairs. 4442 records in RAM.
INFO 2026-06-04 07:08:27 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 1s. Last read position: chr12:49,033,646
INFO 2026-06-04 07:08:27 MarkDuplicates Tracking 56402 as yet unmatched pairs. 3918 records in RAM.
INFO 2026-06-04 07:08:28 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 1s. Last read position: chr12:52,952,105
INFO 2026-06-04 07:08:28 MarkDuplicates Tracking 55852 as yet unmatched pairs. 3368 records in RAM.
INFO 2026-06-04 07:08:30 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 1s. Last read position: chr12:56,160,117
INFO 2026-06-04 07:08:30 MarkDuplicates Tracking 55667 as yet unmatched pairs. 3182 records in RAM.
INFO 2026-06-04 07:08:31 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 1s. Last read position: chr12:57,298,107
INFO 2026-06-04 07:08:31 MarkDuplicates Tracking 54838 as yet unmatched pairs. 2353 records in RAM.
INFO 2026-06-04 07:08:32 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 1s. Last read position: chr12:94,149,337
INFO 2026-06-04 07:08:32 MarkDuplicates Tracking 54248 as yet unmatched pairs. 1761 records in RAM.
INFO 2026-06-04 07:08:34 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 2s. Last read position: chr12:112,405,209
INFO 2026-06-04 07:08:34 MarkDuplicates Tracking 54252 as yet unmatched pairs. 1762 records in RAM.
INFO 2026-06-04 07:08:36 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 1s. Last read position: chr12:122,575,572
INFO 2026-06-04 07:08:36 MarkDuplicates Tracking 53137 as yet unmatched pairs. 646 records in RAM.
INFO 2026-06-04 07:08:37 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 1s. Last read position: chr12:132,869,714
INFO 2026-06-04 07:08:37 MarkDuplicates Tracking 52613 as yet unmatched pairs. 122 records in RAM.
INFO 2026-06-04 07:08:39 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 1s. Last read position: chr13:42,194,924
INFO 2026-06-04 07:08:39 MarkDuplicates Tracking 52048 as yet unmatched pairs. 1401 records in RAM.
INFO 2026-06-04 07:08:41 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 1s. Last read position: chr13:109,784,190
INFO 2026-06-04 07:08:41 MarkDuplicates Tracking 51849 as yet unmatched pairs. 1193 records in RAM.
INFO 2026-06-04 07:08:42 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 1s. Last read position: chr13:113,309,845
INFO 2026-06-04 07:08:42 MarkDuplicates Tracking 51977 as yet unmatched pairs. 1319 records in RAM.
INFO 2026-06-04 07:08:44 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 1s. Last read position: chr14:23,968,804
INFO 2026-06-04 07:08:44 MarkDuplicates Tracking 50225 as yet unmatched pairs. 2940 records in RAM.
INFO 2026-06-04 07:08:46 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 1s. Last read position: chr14:50,130,572
INFO 2026-06-04 07:08:46 MarkDuplicates Tracking 49640 as yet unmatched pairs. 2355 records in RAM.
INFO 2026-06-04 07:08:47 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 1s. Last read position: chr14:69,325,341
INFO 2026-06-04 07:08:47 MarkDuplicates Tracking 49134 as yet unmatched pairs. 1841 records in RAM.
INFO 2026-06-04 07:08:49 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 1s. Last read position: chr14:91,881,337
INFO 2026-06-04 07:08:49 MarkDuplicates Tracking 48666 as yet unmatched pairs. 1370 records in RAM.
INFO 2026-06-04 07:08:50 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 1s. Last read position: chr14:103,385,999
INFO 2026-06-04 07:08:50 MarkDuplicates Tracking 48089 as yet unmatched pairs. 790 records in RAM.
INFO 2026-06-04 07:08:52 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 1s. Last read position: chr14:105,643,419
INFO 2026-06-04 07:08:52 MarkDuplicates Tracking 47526 as yet unmatched pairs. 226 records in RAM.
INFO 2026-06-04 07:08:53 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 1s. Last read position: chr15:39,617,963
INFO 2026-06-04 07:08:53 MarkDuplicates Tracking 46940 as yet unmatched pairs. 2498 records in RAM.
INFO 2026-06-04 07:08:54 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 1s. Last read position: chr15:48,468,430
INFO 2026-06-04 07:08:54 MarkDuplicates Tracking 46416 as yet unmatched pairs. 1974 records in RAM.
INFO 2026-06-04 07:08:56 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 1s. Last read position: chr15:66,333,163
INFO 2026-06-04 07:08:56 MarkDuplicates Tracking 45738 as yet unmatched pairs. 1296 records in RAM.
INFO 2026-06-04 07:08:57 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 1s. Last read position: chr15:76,225,880
INFO 2026-06-04 07:08:57 MarkDuplicates Tracking 45173 as yet unmatched pairs. 730 records in RAM.
INFO 2026-06-04 07:08:59 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 1s. Last read position: chr15:90,878,231
INFO 2026-06-04 07:08:59 MarkDuplicates Tracking 44688 as yet unmatched pairs. 245 records in RAM.
INFO 2026-06-04 07:09:00 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 1s. Last read position: chr16:795,196
INFO 2026-06-04 07:09:00 MarkDuplicates Tracking 44156 as yet unmatched pairs. 6181 records in RAM.
INFO 2026-06-04 07:09:02 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 1s. Last read position: chr16:2,239,972
INFO 2026-06-04 07:09:02 MarkDuplicates Tracking 43345 as yet unmatched pairs. 5365 records in RAM.
INFO 2026-06-04 07:09:03 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 1s. Last read position: chr16:3,729,316
INFO 2026-06-04 07:09:03 MarkDuplicates Tracking 42881 as yet unmatched pairs. 4901 records in RAM.
INFO 2026-06-04 07:09:05 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 1s. Last read position: chr16:14,889,111
INFO 2026-06-04 07:09:05 MarkDuplicates Tracking 42225 as yet unmatched pairs. 4245 records in RAM.
INFO 2026-06-04 07:09:06 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 1s. Last read position: chr16:16,357,263
INFO 2026-06-04 07:09:06 MarkDuplicates Tracking 42078 as yet unmatched pairs. 4097 records in RAM.
INFO 2026-06-04 07:09:07 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 1s. Last read position: chr16:21,402,901
INFO 2026-06-04 07:09:07 MarkDuplicates Tracking 41554 as yet unmatched pairs. 3573 records in RAM.
INFO 2026-06-04 07:09:08 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 1s. Last read position: chr16:24,572,055
INFO 2026-06-04 07:09:08 MarkDuplicates Tracking 41350 as yet unmatched pairs. 3368 records in RAM.
INFO 2026-06-04 07:09:10 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 1s. Last read position: chr16:29,495,505
INFO 2026-06-04 07:09:10 MarkDuplicates Tracking 41097 as yet unmatched pairs. 3115 records in RAM.
INFO 2026-06-04 07:09:12 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 1s. Last read position: chr16:30,669,381
INFO 2026-06-04 07:09:12 MarkDuplicates Tracking 40478 as yet unmatched pairs. 2496 records in RAM.
INFO 2026-06-04 07:09:13 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 1s. Last read position: chr16:50,315,565
INFO 2026-06-04 07:09:13 MarkDuplicates Tracking 39821 as yet unmatched pairs. 1838 records in RAM.
INFO 2026-06-04 07:09:15 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 1s. Last read position: chr16:67,868,353
INFO 2026-06-04 07:09:15 MarkDuplicates Tracking 39432 as yet unmatched pairs. 1449 records in RAM.
INFO 2026-06-04 07:09:16 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 1s. Last read position: chr16:81,044,250
INFO 2026-06-04 07:09:16 MarkDuplicates Tracking 38733 as yet unmatched pairs. 750 records in RAM.
INFO 2026-06-04 07:09:18 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 1s. Last read position: chr16:89,889,179
INFO 2026-06-04 07:09:18 MarkDuplicates Tracking 38089 as yet unmatched pairs. 106 records in RAM.
INFO 2026-06-04 07:09:20 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 1s. Last read position: chr17:4,894,109
INFO 2026-06-04 07:09:20 MarkDuplicates Tracking 37522 as yet unmatched pairs. 11387 records in RAM.
INFO 2026-06-04 07:09:22 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 1s. Last read position: chr17:7,676,102
INFO 2026-06-04 07:09:22 MarkDuplicates Tracking 37228 as yet unmatched pairs. 11093 records in RAM.
INFO 2026-06-04 07:09:23 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 1s. Last read position: chr17:18,839,613
INFO 2026-06-04 07:09:23 MarkDuplicates Tracking 36297 as yet unmatched pairs. 10159 records in RAM.
INFO 2026-06-04 07:09:25 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 1s. Last read position: chr17:31,528,699
INFO 2026-06-04 07:09:25 MarkDuplicates Tracking 35787 as yet unmatched pairs. 9647 records in RAM.
INFO 2026-06-04 07:09:27 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:04:27s. Time for last 1,000,000: 1s. Last read position: chr17:39,204,606
INFO 2026-06-04 07:09:27 MarkDuplicates Tracking 35303 as yet unmatched pairs. 9163 records in RAM.
INFO 2026-06-04 07:09:28 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr17:41,811,214
INFO 2026-06-04 07:09:28 MarkDuplicates Tracking 34682 as yet unmatched pairs. 8542 records in RAM.
INFO 2026-06-04 07:09:30 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 1s. Last read position: chr17:45,086,515
INFO 2026-06-04 07:09:30 MarkDuplicates Tracking 34167 as yet unmatched pairs. 8027 records in RAM.
INFO 2026-06-04 07:09:31 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 1s. Last read position: chr17:50,185,905
INFO 2026-06-04 07:09:31 MarkDuplicates Tracking 35618 as yet unmatched pairs. 9478 records in RAM.
INFO 2026-06-04 07:09:33 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 1s. Last read position: chr17:50,188,095
INFO 2026-06-04 07:09:33 MarkDuplicates Tracking 44461 as yet unmatched pairs. 18321 records in RAM.
INFO 2026-06-04 07:09:34 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 1s. Last read position: chr17:50,189,522
INFO 2026-06-04 07:09:34 MarkDuplicates Tracking 45363 as yet unmatched pairs. 19223 records in RAM.
INFO 2026-06-04 07:09:36 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 1s. Last read position: chr17:50,191,792
INFO 2026-06-04 07:09:36 MarkDuplicates Tracking 37884 as yet unmatched pairs. 11744 records in RAM.
INFO 2026-06-04 07:09:38 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 1s. Last read position: chr17:50,194,136
INFO 2026-06-04 07:09:38 MarkDuplicates Tracking 47283 as yet unmatched pairs. 21143 records in RAM.
INFO 2026-06-04 07:09:40 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 1s. Last read position: chr17:50,195,598
INFO 2026-06-04 07:09:40 MarkDuplicates Tracking 41989 as yet unmatched pairs. 15849 records in RAM.
INFO 2026-06-04 07:09:41 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 1s. Last read position: chr17:50,197,189
INFO 2026-06-04 07:09:41 MarkDuplicates Tracking 43047 as yet unmatched pairs. 16907 records in RAM.
INFO 2026-06-04 07:09:43 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 1s. Last read position: chr17:50,201,411
INFO 2026-06-04 07:09:43 MarkDuplicates Tracking 32283 as yet unmatched pairs. 6143 records in RAM.
INFO 2026-06-04 07:09:44 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 1s. Last read position: chr17:63,435,141
INFO 2026-06-04 07:09:44 MarkDuplicates Tracking 28638 as yet unmatched pairs. 2497 records in RAM.
INFO 2026-06-04 07:09:46 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 1s. Last read position: chr17:75,543,470
INFO 2026-06-04 07:09:46 MarkDuplicates Tracking 28036 as yet unmatched pairs. 1895 records in RAM.
INFO 2026-06-04 07:09:47 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 1s. Last read position: chr17:79,947,717
INFO 2026-06-04 07:09:47 MarkDuplicates Tracking 27343 as yet unmatched pairs. 1202 records in RAM.
INFO 2026-06-04 07:09:49 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 1s. Last read position: chr17:81,720,288
INFO 2026-06-04 07:09:49 MarkDuplicates Tracking 26781 as yet unmatched pairs. 640 records in RAM.
INFO 2026-06-04 07:09:51 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 1s. Last read position: chr18:8,378,369
INFO 2026-06-04 07:09:51 MarkDuplicates Tracking 26044 as yet unmatched pairs. 984 records in RAM.
INFO 2026-06-04 07:09:52 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 1s. Last read position: chr18:48,950,335
INFO 2026-06-04 07:09:52 MarkDuplicates Tracking 25595 as yet unmatched pairs. 534 records in RAM.
INFO 2026-06-04 07:09:54 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 1s. Last read position: chr19:746,649
INFO 2026-06-04 07:09:54 MarkDuplicates Tracking 24975 as yet unmatched pairs. 11010 records in RAM.
INFO 2026-06-04 07:09:55 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 1s. Last read position: chr19:2,046,626
INFO 2026-06-04 07:09:55 MarkDuplicates Tracking 24350 as yet unmatched pairs. 10385 records in RAM.
INFO 2026-06-04 07:09:57 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 1s. Last read position: chr19:4,859,633
INFO 2026-06-04 07:09:57 MarkDuplicates Tracking 23565 as yet unmatched pairs. 9599 records in RAM.
INFO 2026-06-04 07:09:59 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 1s. Last read position: chr19:7,610,742
INFO 2026-06-04 07:09:59 MarkDuplicates Tracking 22990 as yet unmatched pairs. 9024 records in RAM.
INFO 2026-06-04 07:10:01 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 1s. Last read position: chr19:10,627,965
INFO 2026-06-04 07:10:01 MarkDuplicates Tracking 22226 as yet unmatched pairs. 8260 records in RAM.
INFO 2026-06-04 07:10:03 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 2s. Last read position: chr19:12,943,918
INFO 2026-06-04 07:10:03 MarkDuplicates Tracking 21923 as yet unmatched pairs. 7957 records in RAM.
INFO 2026-06-04 07:10:05 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 1s. Last read position: chr19:15,239,187
INFO 2026-06-04 07:10:05 MarkDuplicates Tracking 21633 as yet unmatched pairs. 7667 records in RAM.
INFO 2026-06-04 07:10:06 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 1s. Last read position: chr19:17,339,576
INFO 2026-06-04 07:10:06 MarkDuplicates Tracking 20427 as yet unmatched pairs. 6461 records in RAM.
INFO 2026-06-04 07:10:08 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 1s. Last read position: chr19:19,355,745
INFO 2026-06-04 07:10:08 MarkDuplicates Tracking 19754 as yet unmatched pairs. 5785 records in RAM.
INFO 2026-06-04 07:10:10 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 1s. Last read position: chr19:35,733,106
INFO 2026-06-04 07:10:10 MarkDuplicates Tracking 18848 as yet unmatched pairs. 4877 records in RAM.
INFO 2026-06-04 07:10:11 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 1s. Last read position: chr19:39,415,359
INFO 2026-06-04 07:10:11 MarkDuplicates Tracking 18356 as yet unmatched pairs. 4381 records in RAM.
INFO 2026-06-04 07:10:13 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 1s. Last read position: chr19:40,692,159
INFO 2026-06-04 07:10:13 MarkDuplicates Tracking 17728 as yet unmatched pairs. 3753 records in RAM.
INFO 2026-06-04 07:10:14 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 1s. Last read position: chr19:42,292,626
INFO 2026-06-04 07:10:14 MarkDuplicates Tracking 17648 as yet unmatched pairs. 3673 records in RAM.
INFO 2026-06-04 07:10:16 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 1s. Last read position: chr19:45,765,982
INFO 2026-06-04 07:10:16 MarkDuplicates Tracking 16505 as yet unmatched pairs. 2526 records in RAM.
INFO 2026-06-04 07:10:18 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 1s. Last read position: chr19:49,104,679
INFO 2026-06-04 07:10:18 MarkDuplicates Tracking 15909 as yet unmatched pairs. 1930 records in RAM.
INFO 2026-06-04 07:10:20 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:05:20s. Time for last 1,000,000: 1s. Last read position: chr19:51,891,134
INFO 2026-06-04 07:10:20 MarkDuplicates Tracking 15091 as yet unmatched pairs. 1112 records in RAM.
INFO 2026-06-04 07:10:22 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 2s. Last read position: chr19:55,643,692
INFO 2026-06-04 07:10:22 MarkDuplicates Tracking 14488 as yet unmatched pairs. 509 records in RAM.
INFO 2026-06-04 07:10:24 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 1s. Last read position: chr20:1,375,451
INFO 2026-06-04 07:10:24 MarkDuplicates Tracking 14322 as yet unmatched pairs. 3974 records in RAM.
INFO 2026-06-04 07:10:25 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 1s. Last read position: chr20:19,956,793
INFO 2026-06-04 07:10:25 MarkDuplicates Tracking 13261 as yet unmatched pairs. 2912 records in RAM.
INFO 2026-06-04 07:10:27 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 1s. Last read position: chr20:35,557,193
INFO 2026-06-04 07:10:27 MarkDuplicates Tracking 12811 as yet unmatched pairs. 2458 records in RAM.
INFO 2026-06-04 07:10:28 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 1s. Last read position: chr20:44,480,372
INFO 2026-06-04 07:10:28 MarkDuplicates Tracking 12117 as yet unmatched pairs. 1764 records in RAM.
INFO 2026-06-04 07:10:30 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 1s. Last read position: chr20:50,840,648
INFO 2026-06-04 07:10:30 MarkDuplicates Tracking 11564 as yet unmatched pairs. 1211 records in RAM.
INFO 2026-06-04 07:10:31 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 1s. Last read position: chr20:62,396,583
INFO 2026-06-04 07:10:31 MarkDuplicates Tracking 10952 as yet unmatched pairs. 596 records in RAM.
INFO 2026-06-04 07:10:33 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 1s. Last read position: chr21:8,211,846
INFO 2026-06-04 07:10:33 MarkDuplicates Tracking 10324 as yet unmatched pairs. 2284 records in RAM.
INFO 2026-06-04 07:10:34 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 0s. Last read position: chr21:8,444,608
INFO 2026-06-04 07:10:34 MarkDuplicates Tracking 9592 as yet unmatched pairs. 1549 records in RAM.
INFO 2026-06-04 07:10:36 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 1s. Last read position: chr21:39,276,173
INFO 2026-06-04 07:10:36 MarkDuplicates Tracking 9038 as yet unmatched pairs. 995 records in RAM.
INFO 2026-06-04 07:10:37 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 1s. Last read position: chr21:46,111,532
INFO 2026-06-04 07:10:37 MarkDuplicates Tracking 8544 as yet unmatched pairs. 500 records in RAM.
INFO 2026-06-04 07:10:39 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 1s. Last read position: chr22:21,805,906
INFO 2026-06-04 07:10:39 MarkDuplicates Tracking 7697 as yet unmatched pairs. 2826 records in RAM.
INFO 2026-06-04 07:10:40 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 1s. Last read position: chr22:29,298,744
INFO 2026-06-04 07:10:40 MarkDuplicates Tracking 7846 as yet unmatched pairs. 2975 records in RAM.
INFO 2026-06-04 07:10:42 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 1s. Last read position: chr22:36,322,434
INFO 2026-06-04 07:10:42 MarkDuplicates Tracking 6567 as yet unmatched pairs. 1696 records in RAM.
INFO 2026-06-04 07:10:43 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 1s. Last read position: chr22:41,527,983
INFO 2026-06-04 07:10:43 MarkDuplicates Tracking 5904 as yet unmatched pairs. 1032 records in RAM.
INFO 2026-06-04 07:10:46 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 2s. Last read position: chr22:50,461,557
INFO 2026-06-04 07:10:46 MarkDuplicates Tracking 5328 as yet unmatched pairs. 456 records in RAM.
INFO 2026-06-04 07:10:48 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 1s. Last read position: chrX:21,858,778
INFO 2026-06-04 07:10:48 MarkDuplicates Tracking 4512 as yet unmatched pairs. 2645 records in RAM.
INFO 2026-06-04 07:10:49 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 1s. Last read position: chrX:49,030,361
INFO 2026-06-04 07:10:49 MarkDuplicates Tracking 4140 as yet unmatched pairs. 2272 records in RAM.
INFO 2026-06-04 07:10:51 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 1s. Last read position: chrX:69,616,529
INFO 2026-06-04 07:10:51 MarkDuplicates Tracking 3399 as yet unmatched pairs. 1531 records in RAM.
INFO 2026-06-04 07:10:52 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 1s. Last read position: chrX:110,109,094
INFO 2026-06-04 07:10:52 MarkDuplicates Tracking 2974 as yet unmatched pairs. 1106 records in RAM.
INFO 2026-06-04 07:10:54 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 1s. Last read position: chrX:153,767,099
INFO 2026-06-04 07:10:54 MarkDuplicates Tracking 2420 as yet unmatched pairs. 551 records in RAM.
INFO 2026-06-04 07:10:55 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 1s. Last read position: GL000220.1:113,163
INFO 2026-06-04 07:10:55 MarkDuplicates Tracking 1835 as yet unmatched pairs. 812 records in RAM.
INFO 2026-06-04 07:10:56 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 1s. Last read position: KI270733.1:133,629
INFO 2026-06-04 07:10:56 MarkDuplicates Tracking 285 as yet unmatched pairs. 280 records in RAM.
INFO 2026-06-04 07:10:57 MarkDuplicates Read 216382575 records. 0 pairs never matched.
INFO 2026-06-04 07:11:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 38250046024; totalMemory: 63250104320; maxMemory: 63585648640
INFO 2026-06-04 07:11:07 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-04 07:11:16 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-04 07:11:36 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-04 07:11:50 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-04 07:11:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300831720; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-04 07:11:53 MarkDuplicates Marking 79448668 records as duplicates.
INFO 2026-06-04 07:11:53 MarkDuplicates Found 4498595 optical duplicate clusters.
INFO 2026-06-04 07:11:53 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-04 07:12:11 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:17s. Time for last 10,000,000: 17s. Last read position: chr1:113,585,520
INFO 2026-06-04 07:12:27 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:34s. Time for last 10,000,000: 16s. Last read position: chr1:204,549,304
INFO 2026-06-04 07:12:45 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:52s. Time for last 10,000,000: 17s. Last read position: chr2:152,147,192
INFO 2026-06-04 07:13:01 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:08s. Time for last 10,000,000: 16s. Last read position: chr3:33,114,357
INFO 2026-06-04 07:13:17 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:24s. Time for last 10,000,000: 15s. Last read position: chr4:54,267,309
INFO 2026-06-04 07:13:34 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:40s. Time for last 10,000,000: 16s. Last read position: chr5:172,769,036
INFO 2026-06-04 07:13:51 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:01:57s. Time for last 10,000,000: 16s. Last read position: chr6:148,959,920
INFO 2026-06-04 07:14:07 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:13s. Time for last 10,000,000: 16s. Last read position: chr7:128,395,175
INFO 2026-06-04 07:14:23 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:30s. Time for last 10,000,000: 16s. Last read position: chr8:143,861,738
INFO 2026-06-04 07:14:39 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:45s. Time for last 10,000,000: 15s. Last read position: chr9:136,863,329
INFO 2026-06-04 07:14:55 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:03:02s. Time for last 10,000,000: 16s. Last read position: chr11:31,432,465
INFO 2026-06-04 07:15:11 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:18s. Time for last 10,000,000: 16s. Last read position: chr12:7,080,917
INFO 2026-06-04 07:15:28 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:34s. Time for last 10,000,000: 16s. Last read position: chr13:42,194,924
INFO 2026-06-04 07:15:44 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:03:51s. Time for last 10,000,000: 16s. Last read position: chr15:48,468,430
INFO 2026-06-04 07:16:00 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:04:06s. Time for last 10,000,000: 15s. Last read position: chr16:24,572,055
INFO 2026-06-04 07:16:16 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:22s. Time for last 10,000,000: 16s. Last read position: chr17:31,528,699
INFO 2026-06-04 07:16:32 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:04:39s. Time for last 10,000,000: 16s. Last read position: chr17:50,197,189
INFO 2026-06-04 07:16:49 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:04:56s. Time for last 10,000,000: 16s. Last read position: chr19:4,859,633
INFO 2026-06-04 07:17:06 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:05:13s. Time for last 10,000,000: 16s. Last read position: chr19:42,292,626
INFO 2026-06-04 07:17:23 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:05:30s. Time for last 10,000,000: 16s. Last read position: chr20:62,396,583
INFO 2026-06-04 07:17:39 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:05:46s. Time for last 10,000,000: 16s. Last read position: chrX:21,858,778
INFO 2026-06-04 07:17:53 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-04 07:17:53 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-04 07:17:53 MarkDuplicates Getting Memory Stats.
INFO 2026-06-04 07:17:53 MarkDuplicates Before output close freeMemory: 202274344; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-04 07:17:53 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-04 07:17:53 MarkDuplicates After output close freeMemory: 104303192; totalMemory: 134217728; maxMemory: 63585648640
[Thu Jun 04 07:17:53 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 12.92 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory