Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/e0d1674fcabc8ec35caf1f141c25ba/dna_s756.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/4159ca84e8e107c813dbc2df3938e6/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/4159ca84e8e107c813dbc2df3938e6/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai
==> STAGING COMPLETE (5 inputs)
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 dna_s756.Aligned.sortedByCoord.out.bam --OUTPUT dna_s756.md.bam --METRICS_FILE dna_s756.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:58:55.322 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Jun 08 07:58:55 GMT 2026] MarkDuplicates --INPUT dna_s756.Aligned.sortedByCoord.out.bam --OUTPUT dna_s756.md.bam --METRICS_FILE dna_s756.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 07:58:55 GMT 2026] Executing as ?@nf-784159ca84e8e107c813dbc2df3938e6-7d557-pr8j4 on Linux 6.12.88 amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0
INFO 2026-06-08 07:58:55 MarkDuplicates Start of doWork freeMemory: 105827624; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:58:55 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:58:55 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:59:01 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 4s. Last read position: chr1:1,956,845
INFO 2026-06-08 07:59:01 MarkDuplicates Tracking 2427 as yet unmatched pairs. 208 records in RAM.
INFO 2026-06-08 07:59:05 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 4s. Last read position: chr1:8,014,852
INFO 2026-06-08 07:59:05 MarkDuplicates Tracking 8801 as yet unmatched pairs. 2656 records in RAM.
INFO 2026-06-08 07:59:09 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 4s. Last read position: chr1:11,681,769
INFO 2026-06-08 07:59:09 MarkDuplicates Tracking 12170 as yet unmatched pairs. 2543 records in RAM.
INFO 2026-06-08 07:59:13 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 4s. Last read position: chr1:15,463,414
INFO 2026-06-08 07:59:13 MarkDuplicates Tracking 13681 as yet unmatched pairs. 1061 records in RAM.
INFO 2026-06-08 07:59:17 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 3s. Last read position: chr1:16,647,849
INFO 2026-06-08 07:59:17 MarkDuplicates Tracking 19950 as yet unmatched pairs. 4591 records in RAM.
INFO 2026-06-08 07:59:20 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 3s. Last read position: chr1:18,875,404
INFO 2026-06-08 07:59:20 MarkDuplicates Tracking 19614 as yet unmatched pairs. 1317 records in RAM.
INFO 2026-06-08 07:59:24 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 4s. Last read position: chr1:23,561,122
INFO 2026-06-08 07:59:24 MarkDuplicates Tracking 23283 as yet unmatched pairs. 1459 records in RAM.
INFO 2026-06-08 07:59:27 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 3s. Last read position: chr1:27,360,294
INFO 2026-06-08 07:59:27 MarkDuplicates Tracking 26795 as yet unmatched pairs. 1664 records in RAM.
INFO 2026-06-08 07:59:31 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 3s. Last read position: chr1:33,295,228
INFO 2026-06-08 07:59:31 MarkDuplicates Tracking 30958 as yet unmatched pairs. 1944 records in RAM.
INFO 2026-06-08 07:59:35 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 4s. Last read position: chr1:38,361,772
INFO 2026-06-08 07:59:35 MarkDuplicates Tracking 34602 as yet unmatched pairs. 1846 records in RAM.
INFO 2026-06-08 07:59:38 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 3s. Last read position: chr1:43,338,244
INFO 2026-06-08 07:59:38 MarkDuplicates Tracking 38999 as yet unmatched pairs. 2576 records in RAM.
INFO 2026-06-08 07:59:41 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 3s. Last read position: chr1:46,065,901
INFO 2026-06-08 07:59:41 MarkDuplicates Tracking 42034 as yet unmatched pairs. 2487 records in RAM.
INFO 2026-06-08 07:59:45 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 3s. Last read position: chr1:52,877,669
INFO 2026-06-08 07:59:45 MarkDuplicates Tracking 46367 as yet unmatched pairs. 2578 records in RAM.
INFO 2026-06-08 07:59:48 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 3s. Last read position: chr1:62,539,688
INFO 2026-06-08 07:59:48 MarkDuplicates Tracking 51367 as yet unmatched pairs. 2681 records in RAM.
INFO 2026-06-08 07:59:51 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 3s. Last read position: chr1:71,405,782
INFO 2026-06-08 07:59:51 MarkDuplicates Tracking 57741 as yet unmatched pairs. 4130 records in RAM.
INFO 2026-06-08 07:59:54 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 2s. Last read position: chr1:85,677,179
INFO 2026-06-08 07:59:54 MarkDuplicates Tracking 62830 as yet unmatched pairs. 2821 records in RAM.
INFO 2026-06-08 07:59:57 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 3s. Last read position: chr1:96,806,850
INFO 2026-06-08 07:59:57 MarkDuplicates Tracking 68526 as yet unmatched pairs. 2971 records in RAM.
INFO 2026-06-08 08:00:00 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 2s. Last read position: chr1:103,757,234
INFO 2026-06-08 08:00:00 MarkDuplicates Tracking 72522 as yet unmatched pairs. 3095 records in RAM.
INFO 2026-06-08 08:00:02 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 2s. Last read position: chr1:111,195,817
INFO 2026-06-08 08:00:02 MarkDuplicates Tracking 76519 as yet unmatched pairs. 3030 records in RAM.
INFO 2026-06-08 08:00:05 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 3s. Last read position: chr1:117,624,211
INFO 2026-06-08 08:00:05 MarkDuplicates Tracking 82493 as yet unmatched pairs. 4757 records in RAM.
INFO 2026-06-08 08:00:07 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 2s. Last read position: chr1:121,012,693
INFO 2026-06-08 08:00:07 MarkDuplicates Tracking 84108 as yet unmatched pairs. 3115 records in RAM.
INFO 2026-06-08 08:00:10 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 2s. Last read position: chr1:145,634,542
INFO 2026-06-08 08:00:10 MarkDuplicates Tracking 88136 as yet unmatched pairs. 2853 records in RAM.
INFO 2026-06-08 08:00:13 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 2s. Last read position: chr1:149,200,961
INFO 2026-06-08 08:00:13 MarkDuplicates Tracking 90865 as yet unmatched pairs. 2989 records in RAM.
INFO 2026-06-08 08:00:16 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 3s. Last read position: chr1:151,291,120
INFO 2026-06-08 08:00:16 MarkDuplicates Tracking 93584 as yet unmatched pairs. 2983 records in RAM.
INFO 2026-06-08 08:00:19 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 3s. Last read position: chr1:153,982,500
INFO 2026-06-08 08:00:19 MarkDuplicates Tracking 96293 as yet unmatched pairs. 2942 records in RAM.
INFO 2026-06-08 08:00:22 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 3s. Last read position: chr1:156,346,901
INFO 2026-06-08 08:00:22 MarkDuplicates Tracking 99168 as yet unmatched pairs. 2828 records in RAM.
INFO 2026-06-08 08:00:26 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 3s. Last read position: chr1:158,622,893
INFO 2026-06-08 08:00:26 MarkDuplicates Tracking 102389 as yet unmatched pairs. 2913 records in RAM.
INFO 2026-06-08 08:00:28 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 2s. Last read position: chr1:162,411,728
INFO 2026-06-08 08:00:28 MarkDuplicates Tracking 105553 as yet unmatched pairs. 2628 records in RAM.
INFO 2026-06-08 08:00:31 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 2s. Last read position: chr1:171,239,256
INFO 2026-06-08 08:00:31 MarkDuplicates Tracking 110250 as yet unmatched pairs. 2481 records in RAM.
INFO 2026-06-08 08:00:35 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 3s. Last read position: chr1:179,108,563
INFO 2026-06-08 08:00:35 MarkDuplicates Tracking 116491 as yet unmatched pairs. 3996 records in RAM.
INFO 2026-06-08 08:00:38 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 3s. Last read position: chr1:186,676,239
INFO 2026-06-08 08:00:38 MarkDuplicates Tracking 119086 as yet unmatched pairs. 2213 records in RAM.
INFO 2026-06-08 08:00:41 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 3s. Last read position: chr1:201,385,584
INFO 2026-06-08 08:00:41 MarkDuplicates Tracking 125457 as yet unmatched pairs. 2044 records in RAM.
INFO 2026-06-08 08:00:44 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 2s. Last read position: chr1:204,551,386
INFO 2026-06-08 08:00:44 MarkDuplicates Tracking 130429 as yet unmatched pairs. 3539 records in RAM.
INFO 2026-06-08 08:00:46 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 2s. Last read position: chr1:206,342,857
INFO 2026-06-08 08:00:46 MarkDuplicates Tracking 132036 as yet unmatched pairs. 1984 records in RAM.
INFO 2026-06-08 08:00:49 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 2s. Last read position: chr1:213,242,091
INFO 2026-06-08 08:00:49 MarkDuplicates Tracking 135937 as yet unmatched pairs. 1695 records in RAM.
INFO 2026-06-08 08:00:53 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 3s. Last read position: chr1:225,859,119
INFO 2026-06-08 08:00:53 MarkDuplicates Tracking 141082 as yet unmatched pairs. 1149 records in RAM.
INFO 2026-06-08 08:00:56 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 2s. Last read position: chr1:229,286,540
INFO 2026-06-08 08:00:56 MarkDuplicates Tracking 144354 as yet unmatched pairs. 833 records in RAM.
INFO 2026-06-08 08:00:58 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 2s. Last read position: chr1:240,207,536
INFO 2026-06-08 08:00:58 MarkDuplicates Tracking 149518 as yet unmatched pairs. 629 records in RAM.
INFO 2026-06-08 08:01:02 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 3s. Last read position: chr1:247,965,784
INFO 2026-06-08 08:01:02 MarkDuplicates Tracking 153747 as yet unmatched pairs. 263 records in RAM.
INFO 2026-06-08 08:01:05 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 3s. Last read position: chr2:9,607,790
INFO 2026-06-08 08:01:05 MarkDuplicates Tracking 158277 as yet unmatched pairs. 39734 records in RAM.
INFO 2026-06-08 08:01:08 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 3s. Last read position: chr2:21,137,784
INFO 2026-06-08 08:01:08 MarkDuplicates Tracking 163562 as yet unmatched pairs. 40740 records in RAM.
INFO 2026-06-08 08:01:11 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 2s. Last read position: chr2:26,313,836
INFO 2026-06-08 08:01:11 MarkDuplicates Tracking 167033 as yet unmatched pairs. 41353 records in RAM.
INFO 2026-06-08 08:01:13 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 2s. Last read position: chr2:29,226,988
INFO 2026-06-08 08:01:13 MarkDuplicates Tracking 171154 as yet unmatched pairs. 43202 records in RAM.
INFO 2026-06-08 08:01:16 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 3s. Last read position: chr2:32,916,264
INFO 2026-06-08 08:01:16 MarkDuplicates Tracking 362957 as yet unmatched pairs. 33314 records in RAM.
INFO 2026-06-08 08:01:18 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 2s. Last read position: chr2:38,983,459
INFO 2026-06-08 08:01:18 MarkDuplicates Tracking 418272 as yet unmatched pairs. 32574 records in RAM.
INFO 2026-06-08 08:01:21 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 2s. Last read position: chr2:47,049,979
INFO 2026-06-08 08:01:21 MarkDuplicates Tracking 418801 as yet unmatched pairs. 29522 records in RAM.
INFO 2026-06-08 08:01:23 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 2s. Last read position: chr2:54,968,716
INFO 2026-06-08 08:01:23 MarkDuplicates Tracking 421364 as yet unmatched pairs. 28469 records in RAM.
INFO 2026-06-08 08:01:26 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 2s. Last read position: chr2:62,610,508
INFO 2026-06-08 08:01:26 MarkDuplicates Tracking 424047 as yet unmatched pairs. 27407 records in RAM.
INFO 2026-06-08 08:01:29 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 3s. Last read position: chr2:73,816,186
INFO 2026-06-08 08:01:29 MarkDuplicates Tracking 427516 as yet unmatched pairs. 26659 records in RAM.
INFO 2026-06-08 08:01:32 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 2s. Last read position: chr2:85,309,181
INFO 2026-06-08 08:01:32 MarkDuplicates Tracking 430684 as yet unmatched pairs. 25437 records in RAM.
INFO 2026-06-08 08:01:34 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 2s. Last read position: chr2:89,626,231
INFO 2026-06-08 08:01:34 MarkDuplicates Tracking 432468 as yet unmatched pairs. 25129 records in RAM.
INFO 2026-06-08 08:01:38 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 3s. Last read position: chr2:96,297,271
INFO 2026-06-08 08:01:38 MarkDuplicates Tracking 434066 as yet unmatched pairs. 23937 records in RAM.
INFO 2026-06-08 08:01:41 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 3s. Last read position: chr2:98,592,019
INFO 2026-06-08 08:01:41 MarkDuplicates Tracking 437049 as yet unmatched pairs. 24861 records in RAM.
INFO 2026-06-08 08:01:45 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 3s. Last read position: chr2:107,866,240
INFO 2026-06-08 08:01:45 MarkDuplicates Tracking 438242 as yet unmatched pairs. 22313 records in RAM.
INFO 2026-06-08 08:01:48 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 3s. Last read position: chr2:110,540,152
INFO 2026-06-08 08:01:48 MarkDuplicates Tracking 439124 as yet unmatched pairs. 21310 records in RAM.
INFO 2026-06-08 08:01:51 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 2s. Last read position: chr2:113,215,896
INFO 2026-06-08 08:01:51 MarkDuplicates Tracking 440947 as yet unmatched pairs. 21283 records in RAM.
INFO 2026-06-08 08:01:54 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 2s. Last read position: chr2:116,587,407
INFO 2026-06-08 08:01:54 MarkDuplicates Tracking 441798 as yet unmatched pairs. 19748 records in RAM.
INFO 2026-06-08 08:01:56 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 2s. Last read position: chr2:130,230,719
INFO 2026-06-08 08:01:56 MarkDuplicates Tracking 445702 as yet unmatched pairs. 18933 records in RAM.
INFO 2026-06-08 08:01:58 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 2s. Last read position: chr2:136,116,069
INFO 2026-06-08 08:01:58 MarkDuplicates Tracking 448310 as yet unmatched pairs. 18822 records in RAM.
INFO 2026-06-08 08:02:01 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 2s. Last read position: chr2:151,591,402
INFO 2026-06-08 08:02:01 MarkDuplicates Tracking 451368 as yet unmatched pairs. 16470 records in RAM.
INFO 2026-06-08 08:02:03 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 2s. Last read position: chr2:162,384,763
INFO 2026-06-08 08:02:03 MarkDuplicates Tracking 454474 as yet unmatched pairs. 15239 records in RAM.
INFO 2026-06-08 08:02:06 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 3s. Last read position: chr2:172,555,524
INFO 2026-06-08 08:02:06 MarkDuplicates Tracking 458812 as yet unmatched pairs. 15391 records in RAM.
INFO 2026-06-08 08:02:09 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 3s. Last read position: chr2:178,441,544
INFO 2026-06-08 08:02:09 MarkDuplicates Tracking 459389 as yet unmatched pairs. 12811 records in RAM.
INFO 2026-06-08 08:02:12 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 2s. Last read position: chr2:181,480,124
INFO 2026-06-08 08:02:12 MarkDuplicates Tracking 461275 as yet unmatched pairs. 12438 records in RAM.
INFO 2026-06-08 08:02:15 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 2s. Last read position: chr2:191,097,393
INFO 2026-06-08 08:02:15 MarkDuplicates Tracking 463116 as yet unmatched pairs. 10209 records in RAM.
INFO 2026-06-08 08:02:20 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 4s. Last read position: chr2:201,477,717
INFO 2026-06-08 08:02:20 MarkDuplicates Tracking 466577 as yet unmatched pairs. 9271 records in RAM.
INFO 2026-06-08 08:02:22 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 2s. Last read position: chr2:210,015,865
INFO 2026-06-08 08:02:22 MarkDuplicates Tracking 468572 as yet unmatched pairs. 7636 records in RAM.
INFO 2026-06-08 08:02:25 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 2s. Last read position: chr2:218,435,283
INFO 2026-06-08 08:02:25 MarkDuplicates Tracking 471170 as yet unmatched pairs. 6362 records in RAM.
INFO 2026-06-08 08:02:28 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 3s. Last read position: chr2:222,207,106
INFO 2026-06-08 08:02:28 MarkDuplicates Tracking 474022 as yet unmatched pairs. 6758 records in RAM.
INFO 2026-06-08 08:02:32 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 3s. Last read position: chr2:226,796,755
INFO 2026-06-08 08:02:32 MarkDuplicates Tracking 475672 as yet unmatched pairs. 5198 records in RAM.
INFO 2026-06-08 08:02:36 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 4s. Last read position: chr2:233,672,231
INFO 2026-06-08 08:02:36 MarkDuplicates Tracking 476052 as yet unmatched pairs. 2557 records in RAM.
INFO 2026-06-08 08:02:38 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 2s. Last read position: chr2:239,176,427
INFO 2026-06-08 08:02:38 MarkDuplicates Tracking 477983 as yet unmatched pairs. 1663 records in RAM.
INFO 2026-06-08 08:02:41 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 2s. Last read position: chr3:6,492,985
INFO 2026-06-08 08:02:41 MarkDuplicates Tracking 479519 as yet unmatched pairs. 36538 records in RAM.
INFO 2026-06-08 08:02:44 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 3s. Last read position: chr3:12,296,254
INFO 2026-06-08 08:02:44 MarkDuplicates Tracking 481638 as yet unmatched pairs. 35909 records in RAM.
INFO 2026-06-08 08:02:47 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 2s. Last read position: chr3:12,339,233
INFO 2026-06-08 08:02:47 MarkDuplicates Tracking 484331 as yet unmatched pairs. 36381 records in RAM.
INFO 2026-06-08 08:02:49 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 2s. Last read position: chr3:12,583,181
INFO 2026-06-08 08:02:49 MarkDuplicates Tracking 485578 as yet unmatched pairs. 35507 records in RAM.
INFO 2026-06-08 08:02:52 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 3s. Last read position: chr3:17,372,070
INFO 2026-06-08 08:02:52 MarkDuplicates Tracking 485072 as yet unmatched pairs. 32379 records in RAM.
INFO 2026-06-08 08:02:55 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 3s. Last read position: chr3:36,832,952
INFO 2026-06-08 08:02:55 MarkDuplicates Tracking 489112 as yet unmatched pairs. 30770 records in RAM.
INFO 2026-06-08 08:02:57 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 2s. Last read position: chr3:41,224,185
INFO 2026-06-08 08:02:57 MarkDuplicates Tracking 491788 as yet unmatched pairs. 30993 records in RAM.
INFO 2026-06-08 08:03:00 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 3s. Last read position: chr3:47,016,704
INFO 2026-06-08 08:03:00 MarkDuplicates Tracking 493649 as yet unmatched pairs. 30026 records in RAM.
INFO 2026-06-08 08:03:03 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 2s. Last read position: chr3:49,271,426
INFO 2026-06-08 08:03:03 MarkDuplicates Tracking 492455 as yet unmatched pairs. 27024 records in RAM.
INFO 2026-06-08 08:03:06 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 2s. Last read position: chr3:51,460,104
INFO 2026-06-08 08:03:06 MarkDuplicates Tracking 493076 as yet unmatched pairs. 25865 records in RAM.
INFO 2026-06-08 08:03:09 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 3s. Last read position: chr3:53,225,839
INFO 2026-06-08 08:03:09 MarkDuplicates Tracking 493808 as yet unmatched pairs. 24820 records in RAM.
INFO 2026-06-08 08:03:11 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 2s. Last read position: chr3:64,099,268
INFO 2026-06-08 08:03:11 MarkDuplicates Tracking 496155 as yet unmatched pairs. 23183 records in RAM.
INFO 2026-06-08 08:03:14 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 3s. Last read position: chr3:72,421,422
INFO 2026-06-08 08:03:14 MarkDuplicates Tracking 498304 as yet unmatched pairs. 21543 records in RAM.
INFO 2026-06-08 08:03:17 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 2s. Last read position: chr3:97,873,848
INFO 2026-06-08 08:03:17 MarkDuplicates Tracking 503319 as yet unmatched pairs. 19235 records in RAM.
INFO 2026-06-08 08:03:20 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 3s. Last read position: chr3:112,202,049
INFO 2026-06-08 08:03:20 MarkDuplicates Tracking 505938 as yet unmatched pairs. 17241 records in RAM.
INFO 2026-06-08 08:03:23 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 2s. Last read position: chr3:121,493,582
INFO 2026-06-08 08:03:23 MarkDuplicates Tracking 508832 as yet unmatched pairs. 16530 records in RAM.
INFO 2026-06-08 08:03:27 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 3s. Last read position: chr3:128,067,569
INFO 2026-06-08 08:03:27 MarkDuplicates Tracking 509307 as yet unmatched pairs. 14262 records in RAM.
INFO 2026-06-08 08:03:31 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 4s. Last read position: chr3:133,400,553
INFO 2026-06-08 08:03:31 MarkDuplicates Tracking 510575 as yet unmatched pairs. 12872 records in RAM.
INFO 2026-06-08 08:03:33 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 2s. Last read position: chr3:139,052,119
INFO 2026-06-08 08:03:33 MarkDuplicates Tracking 511843 as yet unmatched pairs. 11253 records in RAM.
INFO 2026-06-08 08:03:36 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 3s. Last read position: chr3:151,442,926
INFO 2026-06-08 08:03:36 MarkDuplicates Tracking 514314 as yet unmatched pairs. 9500 records in RAM.
INFO 2026-06-08 08:03:39 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 2s. Last read position: chr3:169,095,033
INFO 2026-06-08 08:03:39 MarkDuplicates Tracking 517548 as yet unmatched pairs. 7228 records in RAM.
INFO 2026-06-08 08:03:42 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 2s. Last read position: chr3:180,542,779
INFO 2026-06-08 08:03:42 MarkDuplicates Tracking 519841 as yet unmatched pairs. 5218 records in RAM.
INFO 2026-06-08 08:03:44 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 2s. Last read position: chr3:184,579,770
INFO 2026-06-08 08:03:44 MarkDuplicates Tracking 520918 as yet unmatched pairs. 3964 records in RAM.
INFO 2026-06-08 08:03:47 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 2s. Last read position: chr3:186,801,087
INFO 2026-06-08 08:03:47 MarkDuplicates Tracking 521749 as yet unmatched pairs. 2487 records in RAM.
INFO 2026-06-08 08:03:50 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 2s. Last read position: chr3:195,971,368
INFO 2026-06-08 08:03:50 MarkDuplicates Tracking 523794 as yet unmatched pairs. 1053 records in RAM.
INFO 2026-06-08 08:03:53 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 2s. Last read position: chr4:1,806,360
INFO 2026-06-08 08:03:53 MarkDuplicates Tracking 525572 as yet unmatched pairs. 32741 records in RAM.
INFO 2026-06-08 08:03:56 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 2s. Last read position: chr4:4,457,305
INFO 2026-06-08 08:03:56 MarkDuplicates Tracking 525102 as yet unmatched pairs. 30289 records in RAM.
INFO 2026-06-08 08:03:58 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 2s. Last read position: chr4:9,250,058
INFO 2026-06-08 08:03:58 MarkDuplicates Tracking 525753 as yet unmatched pairs. 28879 records in RAM.
INFO 2026-06-08 08:04:00 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 2s. Last read position: chr4:20,488,798
INFO 2026-06-08 08:04:00 MarkDuplicates Tracking 528364 as yet unmatched pairs. 28069 records in RAM.
INFO 2026-06-08 08:04:03 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 2s. Last read position: chr4:38,797,212
INFO 2026-06-08 08:04:03 MarkDuplicates Tracking 531112 as yet unmatched pairs. 25522 records in RAM.
INFO 2026-06-08 08:04:07 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 4s. Last read position: chr4:52,023,992
INFO 2026-06-08 08:04:07 MarkDuplicates Tracking 532814 as yet unmatched pairs. 23348 records in RAM.
INFO 2026-06-08 08:04:10 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 3s. Last read position: chr4:56,400,752
INFO 2026-06-08 08:04:10 MarkDuplicates Tracking 533758 as yet unmatched pairs. 21797 records in RAM.
INFO 2026-06-08 08:04:13 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 2s. Last read position: chr4:70,384,514
INFO 2026-06-08 08:04:13 MarkDuplicates Tracking 536140 as yet unmatched pairs. 19693 records in RAM.
INFO 2026-06-08 08:04:17 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 3s. Last read position: chr4:80,287,472
INFO 2026-06-08 08:04:17 MarkDuplicates Tracking 539548 as yet unmatched pairs. 19812 records in RAM.
INFO 2026-06-08 08:04:20 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 3s. Last read position: chr4:90,468,179
INFO 2026-06-08 08:04:20 MarkDuplicates Tracking 539186 as yet unmatched pairs. 15965 records in RAM.
INFO 2026-06-08 08:04:22 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 2s. Last read position: chr4:105,259,644
INFO 2026-06-08 08:04:22 MarkDuplicates Tracking 542984 as yet unmatched pairs. 15048 records in RAM.
INFO 2026-06-08 08:04:25 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 2s. Last read position: chr4:119,027,214
INFO 2026-06-08 08:04:25 MarkDuplicates Tracking 543917 as yet unmatched pairs. 11711 records in RAM.
INFO 2026-06-08 08:04:27 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 2s. Last read position: chr4:138,214,558
INFO 2026-06-08 08:04:27 MarkDuplicates Tracking 546547 as yet unmatched pairs. 8828 records in RAM.
INFO 2026-06-08 08:04:30 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 2s. Last read position: chr4:149,919,483
INFO 2026-06-08 08:04:30 MarkDuplicates Tracking 548363 as yet unmatched pairs. 6611 records in RAM.
INFO 2026-06-08 08:04:32 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 2s. Last read position: chr4:164,190,296
INFO 2026-06-08 08:04:32 MarkDuplicates Tracking 550394 as yet unmatched pairs. 4334 records in RAM.
INFO 2026-06-08 08:04:34 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 2s. Last read position: chr4:184,697,647
INFO 2026-06-08 08:04:34 MarkDuplicates Tracking 553191 as yet unmatched pairs. 1391 records in RAM.
INFO 2026-06-08 08:04:37 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 3s. Last read position: chr5:756,017
INFO 2026-06-08 08:04:37 MarkDuplicates Tracking 554395 as yet unmatched pairs. 37722 records in RAM.
INFO 2026-06-08 08:04:40 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 2s. Last read position: chr5:14,711,275
INFO 2026-06-08 08:04:40 MarkDuplicates Tracking 555892 as yet unmatched pairs. 35319 records in RAM.
INFO 2026-06-08 08:04:42 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 2s. Last read position: chr5:35,878,811
INFO 2026-06-08 08:04:42 MarkDuplicates Tracking 559654 as yet unmatched pairs. 33669 records in RAM.
INFO 2026-06-08 08:04:45 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 2s. Last read position: chr5:43,971,135
INFO 2026-06-08 08:04:45 MarkDuplicates Tracking 559449 as yet unmatched pairs. 30644 records in RAM.
INFO 2026-06-08 08:04:47 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 2s. Last read position: chr5:58,457,173
INFO 2026-06-08 08:04:47 MarkDuplicates Tracking 562366 as yet unmatched pairs. 29067 records in RAM.
INFO 2026-06-08 08:04:50 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 2s. Last read position: chr5:69,410,568
INFO 2026-06-08 08:04:50 MarkDuplicates Tracking 562827 as yet unmatched pairs. 26115 records in RAM.
INFO 2026-06-08 08:04:53 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 2s. Last read position: chr5:75,705,801
INFO 2026-06-08 08:04:53 MarkDuplicates Tracking 563505 as yet unmatched pairs. 24684 records in RAM.
INFO 2026-06-08 08:04:55 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 2s. Last read position: chr5:87,369,843
INFO 2026-06-08 08:04:55 MarkDuplicates Tracking 565282 as yet unmatched pairs. 22830 records in RAM.
INFO 2026-06-08 08:04:58 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 2s. Last read position: chr5:108,493,018
INFO 2026-06-08 08:04:58 MarkDuplicates Tracking 567326 as yet unmatched pairs. 19452 records in RAM.
INFO 2026-06-08 08:05:01 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 2s. Last read position: chr5:122,020,612
INFO 2026-06-08 08:05:01 MarkDuplicates Tracking 569061 as yet unmatched pairs. 17122 records in RAM.
INFO 2026-06-08 08:05:03 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 2s. Last read position: chr5:132,579,830
INFO 2026-06-08 08:05:03 MarkDuplicates Tracking 571065 as yet unmatched pairs. 15922 records in RAM.
INFO 2026-06-08 08:05:05 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 2s. Last read position: chr5:139,377,891
INFO 2026-06-08 08:05:05 MarkDuplicates Tracking 570791 as yet unmatched pairs. 13010 records in RAM.
INFO 2026-06-08 08:05:07 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 1s. Last read position: chr5:141,403,892
INFO 2026-06-08 08:05:07 MarkDuplicates Tracking 570717 as yet unmatched pairs. 11482 records in RAM.
INFO 2026-06-08 08:05:10 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 2s. Last read position: chr5:149,495,773
INFO 2026-06-08 08:05:10 MarkDuplicates Tracking 572347 as yet unmatched pairs. 10319 records in RAM.
INFO 2026-06-08 08:05:12 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 2s. Last read position: chr5:151,892,165
INFO 2026-06-08 08:05:12 MarkDuplicates Tracking 571237 as yet unmatched pairs. 7551 records in RAM.
INFO 2026-06-08 08:05:15 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 2s. Last read position: chr5:168,772,711
INFO 2026-06-08 08:05:15 MarkDuplicates Tracking 572939 as yet unmatched pairs. 4748 records in RAM.
INFO 2026-06-08 08:05:19 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 3s. Last read position: chr5:177,139,598
INFO 2026-06-08 08:05:19 MarkDuplicates Tracking 573670 as yet unmatched pairs. 2590 records in RAM.
INFO 2026-06-08 08:05:21 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 2s. Last read position: chr5:180,137,990
INFO 2026-06-08 08:05:21 MarkDuplicates Tracking 573454 as yet unmatched pairs. 772 records in RAM.
INFO 2026-06-08 08:05:25 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 3s. Last read position: chr6:6,649,581
INFO 2026-06-08 08:05:25 MarkDuplicates Tracking 573971 as yet unmatched pairs. 46335 records in RAM.
INFO 2026-06-08 08:05:29 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:06:31s. Time for last 1,000,000: 3s. Last read position: chr6:22,175,851
INFO 2026-06-08 08:05:29 MarkDuplicates Tracking 575147 as yet unmatched pairs. 43625 records in RAM.
INFO 2026-06-08 08:05:31 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 2s. Last read position: chr6:28,996,409
INFO 2026-06-08 08:05:31 MarkDuplicates Tracking 575754 as yet unmatched pairs. 41892 records in RAM.
INFO 2026-06-08 08:05:33 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 2s. Last read position: chr6:31,029,375
INFO 2026-06-08 08:05:33 MarkDuplicates Tracking 576082 as yet unmatched pairs. 40701 records in RAM.
INFO 2026-06-08 08:05:36 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 2s. Last read position: chr6:32,028,200
INFO 2026-06-08 08:05:36 MarkDuplicates Tracking 575578 as yet unmatched pairs. 39163 records in RAM.
INFO 2026-06-08 08:05:39 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 3s. Last read position: chr6:33,004,872
INFO 2026-06-08 08:05:39 MarkDuplicates Tracking 577297 as yet unmatched pairs. 39723 records in RAM.
INFO 2026-06-08 08:05:41 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:06:44s. Time for last 1,000,000: 2s. Last read position: chr6:35,795,676
INFO 2026-06-08 08:05:41 MarkDuplicates Tracking 575417 as yet unmatched pairs. 36193 records in RAM.
INFO 2026-06-08 08:05:44 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:06:46s. Time for last 1,000,000: 2s. Last read position: chr6:41,936,202
INFO 2026-06-08 08:05:44 MarkDuplicates Tracking 577594 as yet unmatched pairs. 36254 records in RAM.
INFO 2026-06-08 08:05:46 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 2s. Last read position: chr6:44,393,390
INFO 2026-06-08 08:05:46 MarkDuplicates Tracking 575427 as yet unmatched pairs. 32549 records in RAM.
INFO 2026-06-08 08:05:49 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:06:51s. Time for last 1,000,000: 2s. Last read position: chr6:56,619,206
INFO 2026-06-08 08:05:49 MarkDuplicates Tracking 576705 as yet unmatched pairs. 30478 records in RAM.
INFO 2026-06-08 08:05:51 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 1s. Last read position: chr6:75,623,900
INFO 2026-06-08 08:05:51 MarkDuplicates Tracking 577436 as yet unmatched pairs. 27010 records in RAM.
INFO 2026-06-08 08:05:53 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 2s. Last read position: chr6:87,563,694
INFO 2026-06-08 08:05:53 MarkDuplicates Tracking 578070 as yet unmatched pairs. 24383 records in RAM.
INFO 2026-06-08 08:05:55 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 2s. Last read position: chr6:103,496,571
INFO 2026-06-08 08:05:55 MarkDuplicates Tracking 579418 as yet unmatched pairs. 21480 records in RAM.
INFO 2026-06-08 08:05:57 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:07:00s. Time for last 1,000,000: 2s. Last read position: chr6:112,533,632
INFO 2026-06-08 08:05:57 MarkDuplicates Tracking 579861 as yet unmatched pairs. 19097 records in RAM.
INFO 2026-06-08 08:06:00 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:07:03s. Time for last 1,000,000: 2s. Last read position: chr6:117,339,090
INFO 2026-06-08 08:06:00 MarkDuplicates Tracking 582181 as yet unmatched pairs. 19150 records in RAM.
INFO 2026-06-08 08:06:02 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 2s. Last read position: chr6:127,138,057
INFO 2026-06-08 08:06:02 MarkDuplicates Tracking 581925 as yet unmatched pairs. 15877 records in RAM.
INFO 2026-06-08 08:06:05 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:07:07s. Time for last 1,000,000: 2s. Last read position: chr6:134,317,398
INFO 2026-06-08 08:06:05 MarkDuplicates Tracking 582097 as yet unmatched pairs. 13466 records in RAM.
INFO 2026-06-08 08:06:07 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 2s. Last read position: chr6:138,941,280
INFO 2026-06-08 08:06:07 MarkDuplicates Tracking 581122 as yet unmatched pairs. 10284 records in RAM.
INFO 2026-06-08 08:06:10 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:07:12s. Time for last 1,000,000: 2s. Last read position: chr6:149,969,085
INFO 2026-06-08 08:06:10 MarkDuplicates Tracking 581461 as yet unmatched pairs. 7600 records in RAM.
INFO 2026-06-08 08:06:13 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:07:16s. Time for last 1,000,000: 3s. Last read position: chr6:154,832,702
INFO 2026-06-08 08:06:13 MarkDuplicates Tracking 581367 as yet unmatched pairs. 5476 records in RAM.
INFO 2026-06-08 08:06:15 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:07:18s. Time for last 1,000,000: 2s. Last read position: chr6:160,224,692
INFO 2026-06-08 08:06:15 MarkDuplicates Tracking 581294 as yet unmatched pairs. 3299 records in RAM.
INFO 2026-06-08 08:06:18 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:07:21s. Time for last 1,000,000: 2s. Last read position: chr6:167,340,531
INFO 2026-06-08 08:06:18 MarkDuplicates Tracking 581390 as yet unmatched pairs. 992 records in RAM.
INFO 2026-06-08 08:06:21 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:07:24s. Time for last 1,000,000: 3s. Last read position: chr7:4,781,552
INFO 2026-06-08 08:06:21 MarkDuplicates Tracking 581488 as yet unmatched pairs. 50555 records in RAM.
INFO 2026-06-08 08:06:25 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:07:28s. Time for last 1,000,000: 3s. Last read position: chr7:8,235,675
INFO 2026-06-08 08:06:25 MarkDuplicates Tracking 580960 as yet unmatched pairs. 48605 records in RAM.
INFO 2026-06-08 08:06:28 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:07:31s. Time for last 1,000,000: 3s. Last read position: chr7:13,946,101
INFO 2026-06-08 08:06:28 MarkDuplicates Tracking 582551 as yet unmatched pairs. 47939 records in RAM.
INFO 2026-06-08 08:06:31 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:07:34s. Time for last 1,000,000: 2s. Last read position: chr7:17,801,242
INFO 2026-06-08 08:06:31 MarkDuplicates Tracking 580909 as yet unmatched pairs. 44280 records in RAM.
INFO 2026-06-08 08:06:33 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:07:36s. Time for last 1,000,000: 2s. Last read position: chr7:31,578,264
INFO 2026-06-08 08:06:33 MarkDuplicates Tracking 581600 as yet unmatched pairs. 41593 records in RAM.
INFO 2026-06-08 08:06:36 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:07:38s. Time for last 1,000,000: 2s. Last read position: chr7:44,065,052
INFO 2026-06-08 08:06:36 MarkDuplicates Tracking 581963 as yet unmatched pairs. 38962 records in RAM.