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/f3/767f2189dcd0605550272ba4218330/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/767f2189dcd0605550272ba4218330/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/fb89939eba61d5b706cbb1ad481589/aih-tih-sc-2a5468-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam
==> 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 aih-tih-sc-2a5468-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-2a5468-R1_B23WHYVLT4_1.md.bam --METRICS_FILE aih-tih-sc-2a5468-R1_B23WHYVLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
09:35:06.807 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 09:35:06 GMT 2026] MarkDuplicates --INPUT aih-tih-sc-2a5468-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-2a5468-R1_B23WHYVLT4_1.md.bam --METRICS_FILE aih-tih-sc-2a5468-R1_B23WHYVLT4_1.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 09:35:06 GMT 2026] Executing as ?@nf-f3767f2189dcd0605550272ba4218330-fe7a5-jftjm 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 09:35:06 MarkDuplicates Start of doWork freeMemory: 105828712; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 09:35:06 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 09:35:06 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 09:35:10 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:1,436,969
INFO 2026-06-08 09:35:10 MarkDuplicates Tracking 4412 as yet unmatched pairs. 221 records in RAM.
INFO 2026-06-08 09:35:13 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 2s. Last read position: chr1:3,628,442
INFO 2026-06-08 09:35:13 MarkDuplicates Tracking 8136 as yet unmatched pairs. 96 records in RAM.
INFO 2026-06-08 09:35:14 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: chr1:8,656,109
INFO 2026-06-08 09:35:14 MarkDuplicates Tracking 12113 as yet unmatched pairs. 121 records in RAM.
INFO 2026-06-08 09:35:17 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: chr1:11,013,763
INFO 2026-06-08 09:35:17 MarkDuplicates Tracking 16302 as yet unmatched pairs. 589 records in RAM.
INFO 2026-06-08 09:35:18 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: chr1:13,607,230
INFO 2026-06-08 09:35:18 MarkDuplicates Tracking 19699 as yet unmatched pairs. 204 records in RAM.
INFO 2026-06-08 09:35:20 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 2s. Last read position: chr1:16,455,836
INFO 2026-06-08 09:35:20 MarkDuplicates Tracking 23077 as yet unmatched pairs. 80 records in RAM.
INFO 2026-06-08 09:35:22 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: chr1:19,165,658
INFO 2026-06-08 09:35:22 MarkDuplicates Tracking 27478 as yet unmatched pairs. 985 records in RAM.
INFO 2026-06-08 09:35:24 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr1:20,981,124
INFO 2026-06-08 09:35:24 MarkDuplicates Tracking 30497 as yet unmatched pairs. 603 records in RAM.
INFO 2026-06-08 09:35:26 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: chr1:22,086,747
INFO 2026-06-08 09:35:26 MarkDuplicates Tracking 35899 as yet unmatched pairs. 2039 records in RAM.
INFO 2026-06-08 09:35:28 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: chr1:23,323,695
INFO 2026-06-08 09:35:28 MarkDuplicates Tracking 38395 as yet unmatched pairs. 826 records in RAM.
INFO 2026-06-08 09:35:30 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 2s. Last read position: chr1:25,485,647
INFO 2026-06-08 09:35:30 MarkDuplicates Tracking 40920 as yet unmatched pairs. 126 records in RAM.
INFO 2026-06-08 09:35:32 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: chr1:26,941,747
INFO 2026-06-08 09:35:32 MarkDuplicates Tracking 44519 as yet unmatched pairs. 197 records in RAM.
INFO 2026-06-08 09:35:34 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 2s. Last read position: chr1:29,160,380
INFO 2026-06-08 09:35:34 MarkDuplicates Tracking 48289 as yet unmatched pairs. 767 records in RAM.
INFO 2026-06-08 09:35:37 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 2s. Last read position: chr1:32,333,024
INFO 2026-06-08 09:35:37 MarkDuplicates Tracking 52148 as yet unmatched pairs. 911 records in RAM.
INFO 2026-06-08 09:35:39 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 1s. Last read position: chr1:35,191,483
INFO 2026-06-08 09:35:39 MarkDuplicates Tracking 55198 as yet unmatched pairs. 347 records in RAM.
INFO 2026-06-08 09:35:41 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 1s. Last read position: chr1:37,808,060
INFO 2026-06-08 09:35:41 MarkDuplicates Tracking 58518 as yet unmatched pairs. 140 records in RAM.
INFO 2026-06-08 09:35:43 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 2s. Last read position: chr1:39,571,141
INFO 2026-06-08 09:35:43 MarkDuplicates Tracking 62050 as yet unmatched pairs. 355 records in RAM.
INFO 2026-06-08 09:35:44 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 1s. Last read position: chr1:42,927,758
INFO 2026-06-08 09:35:44 MarkDuplicates Tracking 66687 as yet unmatched pairs. 1548 records in RAM.
INFO 2026-06-08 09:35:46 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 1s. Last read position: chr1:43,970,277
INFO 2026-06-08 09:35:46 MarkDuplicates Tracking 69594 as yet unmatched pairs. 203 records in RAM.
INFO 2026-06-08 09:35:48 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 2s. Last read position: chr1:46,033,932
INFO 2026-06-08 09:35:48 MarkDuplicates Tracking 73229 as yet unmatched pairs. 460 records in RAM.
INFO 2026-06-08 09:35:50 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 1s. Last read position: chr1:51,787,351
INFO 2026-06-08 09:35:50 MarkDuplicates Tracking 76484 as yet unmatched pairs. 183 records in RAM.
INFO 2026-06-08 09:35:52 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 1s. Last read position: chr1:54,653,713
INFO 2026-06-08 09:35:52 MarkDuplicates Tracking 80134 as yet unmatched pairs. 603 records in RAM.
INFO 2026-06-08 09:35:54 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 1s. Last read position: chr1:61,997,748
INFO 2026-06-08 09:35:54 MarkDuplicates Tracking 84089 as yet unmatched pairs. 1175 records in RAM.
INFO 2026-06-08 09:35:56 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 2s. Last read position: chr1:70,292,414
INFO 2026-06-08 09:35:56 MarkDuplicates Tracking 86503 as yet unmatched pairs. 444 records in RAM.
INFO 2026-06-08 09:35:57 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 1s. Last read position: chr1:86,494,206
INFO 2026-06-08 09:35:57 MarkDuplicates Tracking 90361 as yet unmatched pairs. 1348 records in RAM.
INFO 2026-06-08 09:35:59 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 1s. Last read position: chr1:93,193,731
INFO 2026-06-08 09:35:59 MarkDuplicates Tracking 92414 as yet unmatched pairs. 185 records in RAM.
INFO 2026-06-08 09:36:01 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 1s. Last read position: chr1:108,161,265
INFO 2026-06-08 09:36:01 MarkDuplicates Tracking 95700 as yet unmatched pairs. 497 records in RAM.
INFO 2026-06-08 09:36:02 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 1s. Last read position: chr1:111,199,756
INFO 2026-06-08 09:36:02 MarkDuplicates Tracking 98856 as yet unmatched pairs. 239 records in RAM.
INFO 2026-06-08 09:36:04 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 1s. Last read position: chr1:114,720,622
INFO 2026-06-08 09:36:04 MarkDuplicates Tracking 102749 as yet unmatched pairs. 932 records in RAM.
INFO 2026-06-08 09:36:06 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 1s. Last read position: chr1:116,398,989
INFO 2026-06-08 09:36:06 MarkDuplicates Tracking 109334 as yet unmatched pairs. 4307 records in RAM.
INFO 2026-06-08 09:36:08 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 1s. Last read position: chr1:119,935,545
INFO 2026-06-08 09:36:08 MarkDuplicates Tracking 109731 as yet unmatched pairs. 1488 records in RAM.
INFO 2026-06-08 09:36:09 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 1s. Last read position: chr1:145,960,878
INFO 2026-06-08 09:36:09 MarkDuplicates Tracking 110514 as yet unmatched pairs. 116 records in RAM.
INFO 2026-06-08 09:36:11 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 1s. Last read position: chr1:148,536,231
INFO 2026-06-08 09:36:11 MarkDuplicates Tracking 112763 as yet unmatched pairs. 640 records in RAM.
INFO 2026-06-08 09:36:13 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 1s. Last read position: chr1:149,842,359
INFO 2026-06-08 09:36:13 MarkDuplicates Tracking 115676 as yet unmatched pairs. 1506 records in RAM.
INFO 2026-06-08 09:36:14 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 1s. Last read position: chr1:150,577,343
INFO 2026-06-08 09:36:14 MarkDuplicates Tracking 118990 as yet unmatched pairs. 2206 records in RAM.
INFO 2026-06-08 09:36:17 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 2s. Last read position: chr1:151,428,403
INFO 2026-06-08 09:36:17 MarkDuplicates Tracking 120348 as yet unmatched pairs. 330 records in RAM.
INFO 2026-06-08 09:36:18 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 1s. Last read position: chr1:153,995,093
INFO 2026-06-08 09:36:18 MarkDuplicates Tracking 123404 as yet unmatched pairs. 104 records in RAM.
INFO 2026-06-08 09:36:20 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 1s. Last read position: chr1:154,268,765
INFO 2026-06-08 09:36:20 MarkDuplicates Tracking 126527 as yet unmatched pairs. 212 records in RAM.
INFO 2026-06-08 09:36:22 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 1s. Last read position: chr1:155,192,139
INFO 2026-06-08 09:36:22 MarkDuplicates Tracking 130714 as yet unmatched pairs. 973 records in RAM.
INFO 2026-06-08 09:36:23 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 1s. Last read position: chr1:155,963,056
INFO 2026-06-08 09:36:23 MarkDuplicates Tracking 133317 as yet unmatched pairs. 465 records in RAM.
INFO 2026-06-08 09:36:25 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 1s. Last read position: chr1:156,530,287
INFO 2026-06-08 09:36:25 MarkDuplicates Tracking 137717 as yet unmatched pairs. 549 records in RAM.
INFO 2026-06-08 09:36:27 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 1s. Last read position: chr1:160,335,267
INFO 2026-06-08 09:36:27 MarkDuplicates Tracking 141884 as yet unmatched pairs. 1057 records in RAM.
INFO 2026-06-08 09:36:28 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 1s. Last read position: chr1:165,743,284
INFO 2026-06-08 09:36:28 MarkDuplicates Tracking 145471 as yet unmatched pairs. 1486 records in RAM.
INFO 2026-06-08 09:36:30 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 1s. Last read position: chr1:169,131,433
INFO 2026-06-08 09:36:30 MarkDuplicates Tracking 153166 as yet unmatched pairs. 5639 records in RAM.
INFO 2026-06-08 09:36:32 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 1s. Last read position: chr1:173,947,563
INFO 2026-06-08 09:36:32 MarkDuplicates Tracking 151039 as yet unmatched pairs. 476 records in RAM.
INFO 2026-06-08 09:36:33 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 1s. Last read position: chr1:182,858,783
INFO 2026-06-08 09:36:33 MarkDuplicates Tracking 154664 as yet unmatched pairs. 872 records in RAM.
INFO 2026-06-08 09:36:35 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 1s. Last read position: chr1:186,326,139
INFO 2026-06-08 09:36:35 MarkDuplicates Tracking 157915 as yet unmatched pairs. 886 records in RAM.
INFO 2026-06-08 09:36:37 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 1s. Last read position: chr1:186,362,845
INFO 2026-06-08 09:36:37 MarkDuplicates Tracking 164082 as yet unmatched pairs. 4281 records in RAM.
INFO 2026-06-08 09:36:38 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 1s. Last read position: chr1:201,363,313
INFO 2026-06-08 09:36:38 MarkDuplicates Tracking 163133 as yet unmatched pairs. 97 records in RAM.
INFO 2026-06-08 09:36:40 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 1s. Last read position: chr1:203,712,001
INFO 2026-06-08 09:36:40 MarkDuplicates Tracking 166835 as yet unmatched pairs. 153 records in RAM.
INFO 2026-06-08 09:36:42 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 1s. Last read position: chr1:205,720,527
INFO 2026-06-08 09:36:42 MarkDuplicates Tracking 170426 as yet unmatched pairs. 640 records in RAM.
INFO 2026-06-08 09:36:43 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 1s. Last read position: chr1:206,937,437
INFO 2026-06-08 09:36:43 MarkDuplicates Tracking 178199 as yet unmatched pairs. 4941 records in RAM.
INFO 2026-06-08 09:36:45 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 1s. Last read position: chr1:209,623,514
INFO 2026-06-08 09:36:45 MarkDuplicates Tracking 177318 as yet unmatched pairs. 514 records in RAM.
INFO 2026-06-08 09:36:47 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 1s. Last read position: chr1:219,610,253
INFO 2026-06-08 09:36:47 MarkDuplicates Tracking 180147 as yet unmatched pairs. 48 records in RAM.
INFO 2026-06-08 09:36:48 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 1s. Last read position: chr1:224,433,803
INFO 2026-06-08 09:36:48 MarkDuplicates Tracking 183271 as yet unmatched pairs. 96 records in RAM.
INFO 2026-06-08 09:36:50 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 1s. Last read position: chr1:227,119,809
INFO 2026-06-08 09:36:50 MarkDuplicates Tracking 186835 as yet unmatched pairs. 429 records in RAM.
INFO 2026-06-08 09:36:52 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 1s. Last read position: chr1:233,252,327
INFO 2026-06-08 09:36:52 MarkDuplicates Tracking 190587 as yet unmatched pairs. 345 records in RAM.
INFO 2026-06-08 09:36:53 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 1s. Last read position: chr1:240,142,731
INFO 2026-06-08 09:36:53 MarkDuplicates Tracking 193678 as yet unmatched pairs. 8 records in RAM.
INFO 2026-06-08 09:36:55 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 2s. Last read position: chr1:246,895,921
INFO 2026-06-08 09:36:55 MarkDuplicates Tracking 197412 as yet unmatched pairs. 482 records in RAM.
INFO 2026-06-08 09:36:59 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 3s. Last read position: chr2:9,630,345
INFO 2026-06-08 09:36:59 MarkDuplicates Tracking 200838 as yet unmatched pairs. 198372 records in RAM.
INFO 2026-06-08 09:37:01 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 2s. Last read position: chr2:20,032,954
INFO 2026-06-08 09:37:01 MarkDuplicates Tracking 203816 as yet unmatched pairs. 201288 records in RAM.
INFO 2026-06-08 09:37:04 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 2s. Last read position: chr2:24,310,538
INFO 2026-06-08 09:37:04 MarkDuplicates Tracking 207636 as yet unmatched pairs. 205056 records in RAM.
INFO 2026-06-08 09:37:06 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 2s. Last read position: chr2:27,201,698
INFO 2026-06-08 09:37:06 MarkDuplicates Tracking 211671 as yet unmatched pairs. 209060 records in RAM.
INFO 2026-06-08 09:37:08 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 1s. Last read position: chr2:28,926,486
INFO 2026-06-08 09:37:08 MarkDuplicates Tracking 214441 as yet unmatched pairs. 211793 records in RAM.
INFO 2026-06-08 09:37:09 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,255
INFO 2026-06-08 09:37:09 MarkDuplicates Tracking 307095 as yet unmatched pairs. 207807 records in RAM.
INFO 2026-06-08 09:37:11 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,263
INFO 2026-06-08 09:37:11 MarkDuplicates Tracking 327456 as yet unmatched pairs. 206693 records in RAM.
INFO 2026-06-08 09:37:13 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,264
INFO 2026-06-08 09:37:13 MarkDuplicates Tracking 974434 as yet unmatched pairs. 170787 records in RAM.
INFO 2026-06-08 09:37:15 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,265
INFO 2026-06-08 09:37:15 MarkDuplicates Tracking 1607447 as yet unmatched pairs. 137348 records in RAM.
INFO 2026-06-08 09:37:17 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,406
INFO 2026-06-08 09:37:17 MarkDuplicates Tracking 1745781 as yet unmatched pairs. 129480 records in RAM.
INFO 2026-06-08 09:37:18 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,406
INFO 2026-06-08 09:37:18 MarkDuplicates Tracking 1748882 as yet unmatched pairs. 129326 records in RAM.
INFO 2026-06-08 09:37:20 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 1s. Last read position: chr2:33,588,492
INFO 2026-06-08 09:37:20 MarkDuplicates Tracking 1863962 as yet unmatched pairs. 122652 records in RAM.
INFO 2026-06-08 09:37:21 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 1s. Last read position: chr2:42,245,606
INFO 2026-06-08 09:37:21 MarkDuplicates Tracking 1864515 as yet unmatched pairs. 123163 records in RAM.
INFO 2026-06-08 09:37:24 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 2s. Last read position: chr2:43,581,804
INFO 2026-06-08 09:37:24 MarkDuplicates Tracking 1858973 as yet unmatched pairs. 117566 records in RAM.
INFO 2026-06-08 09:37:26 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 2s. Last read position: chr2:47,373,921
INFO 2026-06-08 09:37:26 MarkDuplicates Tracking 1858516 as yet unmatched pairs. 117053 records in RAM.
INFO 2026-06-08 09:37:29 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 2s. Last read position: chr2:54,629,599
INFO 2026-06-08 09:37:29 MarkDuplicates Tracking 1852188 as yet unmatched pairs. 110687 records in RAM.
INFO 2026-06-08 09:37:30 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr2:55,599,025
INFO 2026-06-08 09:37:30 MarkDuplicates Tracking 1848002 as yet unmatched pairs. 106469 records in RAM.
INFO 2026-06-08 09:37:32 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 1s. Last read position: chr2:63,622,241
INFO 2026-06-08 09:37:32 MarkDuplicates Tracking 1844395 as yet unmatched pairs. 102798 records in RAM.
INFO 2026-06-08 09:37:34 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 1s. Last read position: chr2:69,806,402
INFO 2026-06-08 09:37:34 MarkDuplicates Tracking 1842392 as yet unmatched pairs. 100743 records in RAM.
INFO 2026-06-08 09:37:36 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 1s. Last read position: chr2:73,862,194
INFO 2026-06-08 09:37:36 MarkDuplicates Tracking 1838103 as yet unmatched pairs. 96397 records in RAM.
INFO 2026-06-08 09:37:38 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 1s. Last read position: chr2:79,157,124
INFO 2026-06-08 09:37:38 MarkDuplicates Tracking 1840990 as yet unmatched pairs. 99229 records in RAM.
INFO 2026-06-08 09:37:40 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 1s. Last read position: chr2:86,108,384
INFO 2026-06-08 09:37:40 MarkDuplicates Tracking 1832529 as yet unmatched pairs. 90746 records in RAM.
INFO 2026-06-08 09:37:41 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 1s. Last read position: chr2:95,792,518
INFO 2026-06-08 09:37:41 MarkDuplicates Tracking 1828324 as yet unmatched pairs. 86494 records in RAM.
INFO 2026-06-08 09:37:43 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 1s. Last read position: chr2:97,766,203
INFO 2026-06-08 09:37:43 MarkDuplicates Tracking 1825371 as yet unmatched pairs. 83493 records in RAM.
INFO 2026-06-08 09:37:46 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 2s. Last read position: chr2:106,423,451
INFO 2026-06-08 09:37:46 MarkDuplicates Tracking 1821967 as yet unmatched pairs. 80052 records in RAM.
INFO 2026-06-08 09:37:48 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 1s. Last read position: chr2:108,764,252
INFO 2026-06-08 09:37:48 MarkDuplicates Tracking 1822729 as yet unmatched pairs. 80794 records in RAM.
INFO 2026-06-08 09:37:50 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 1s. Last read position: chr2:109,826,830
INFO 2026-06-08 09:37:50 MarkDuplicates Tracking 1818517 as yet unmatched pairs. 76538 records in RAM.
INFO 2026-06-08 09:37:51 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 1s. Last read position: chr2:112,091,711
INFO 2026-06-08 09:37:51 MarkDuplicates Tracking 1816482 as yet unmatched pairs. 74485 records in RAM.
INFO 2026-06-08 09:37:53 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 1s. Last read position: chr2:117,946,728
INFO 2026-06-08 09:37:53 MarkDuplicates Tracking 1814152 as yet unmatched pairs. 72108 records in RAM.
INFO 2026-06-08 09:37:54 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 1s. Last read position: chr2:128,138,843
INFO 2026-06-08 09:37:54 MarkDuplicates Tracking 1811039 as yet unmatched pairs. 68952 records in RAM.
INFO 2026-06-08 09:37:56 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 1s. Last read position: chr2:144,398,653
INFO 2026-06-08 09:37:56 MarkDuplicates Tracking 1807228 as yet unmatched pairs. 65054 records in RAM.
INFO 2026-06-08 09:37:58 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 1s. Last read position: chr2:159,225,670
INFO 2026-06-08 09:37:58 MarkDuplicates Tracking 1804331 as yet unmatched pairs. 62090 records in RAM.
INFO 2026-06-08 09:38:00 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 1s. Last read position: chr2:169,606,094
INFO 2026-06-08 09:38:00 MarkDuplicates Tracking 1801681 as yet unmatched pairs. 59372 records in RAM.
INFO 2026-06-08 09:38:02 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 2s. Last read position: chr2:172,564,675
INFO 2026-06-08 09:38:02 MarkDuplicates Tracking 1798728 as yet unmatched pairs. 56365 records in RAM.
INFO 2026-06-08 09:38:04 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 1s. Last read position: chr2:178,545,858
INFO 2026-06-08 09:38:04 MarkDuplicates Tracking 1795443 as yet unmatched pairs. 53008 records in RAM.
INFO 2026-06-08 09:38:06 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 1s. Last read position: chr2:186,638,278
INFO 2026-06-08 09:38:06 MarkDuplicates Tracking 1792733 as yet unmatched pairs. 50231 records in RAM.
INFO 2026-06-08 09:38:07 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 1s. Last read position: chr2:189,565,390
INFO 2026-06-08 09:38:07 MarkDuplicates Tracking 1790609 as yet unmatched pairs. 48074 records in RAM.
INFO 2026-06-08 09:38:09 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 1s. Last read position: chr2:197,400,829
INFO 2026-06-08 09:38:09 MarkDuplicates Tracking 1786793 as yet unmatched pairs. 44194 records in RAM.
INFO 2026-06-08 09:38:11 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 1s. Last read position: chr2:201,228,931
INFO 2026-06-08 09:38:11 MarkDuplicates Tracking 1782674 as yet unmatched pairs. 40030 records in RAM.
INFO 2026-06-08 09:38:13 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 2s. Last read position: chr2:206,159,952
INFO 2026-06-08 09:38:13 MarkDuplicates Tracking 1783170 as yet unmatched pairs. 40467 records in RAM.
INFO 2026-06-08 09:38:15 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 1s. Last read position: chr2:215,364,885
INFO 2026-06-08 09:38:15 MarkDuplicates Tracking 1785025 as yet unmatched pairs. 42284 records in RAM.
INFO 2026-06-08 09:38:17 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 2s. Last read position: chr2:215,379,237
INFO 2026-06-08 09:38:17 MarkDuplicates Tracking 1778958 as yet unmatched pairs. 36197 records in RAM.
INFO 2026-06-08 09:38:19 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 2s. Last read position: chr2:215,404,586
INFO 2026-06-08 09:38:19 MarkDuplicates Tracking 1776790 as yet unmatched pairs. 34020 records in RAM.
INFO 2026-06-08 09:38:21 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 2s. Last read position: chr2:215,430,734
INFO 2026-06-08 09:38:21 MarkDuplicates Tracking 1772681 as yet unmatched pairs. 29878 records in RAM.
INFO 2026-06-08 09:38:23 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 1s. Last read position: chr2:218,279,046
INFO 2026-06-08 09:38:23 MarkDuplicates Tracking 1766404 as yet unmatched pairs. 23554 records in RAM.
INFO 2026-06-08 09:38:25 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 1s. Last read position: chr2:219,492,164
INFO 2026-06-08 09:38:25 MarkDuplicates Tracking 1760076 as yet unmatched pairs. 17185 records in RAM.
INFO 2026-06-08 09:38:27 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 1s. Last read position: chr2:230,461,367
INFO 2026-06-08 09:38:27 MarkDuplicates Tracking 1757135 as yet unmatched pairs. 14189 records in RAM.
INFO 2026-06-08 09:38:29 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 1s. Last read position: chr2:231,712,462
INFO 2026-06-08 09:38:29 MarkDuplicates Tracking 1755340 as yet unmatched pairs. 12364 records in RAM.
INFO 2026-06-08 09:38:30 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: chr2:237,344,347
INFO 2026-06-08 09:38:30 MarkDuplicates Tracking 1750688 as yet unmatched pairs. 7645 records in RAM.
INFO 2026-06-08 09:38:32 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 1s. Last read position: chr2:240,616,446
INFO 2026-06-08 09:38:32 MarkDuplicates Tracking 1746753 as yet unmatched pairs. 3640 records in RAM.
INFO 2026-06-08 09:38:35 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 2s. Last read position: chr3:5,172,533
INFO 2026-06-08 09:38:35 MarkDuplicates Tracking 1742695 as yet unmatched pairs. 87874 records in RAM.
INFO 2026-06-08 09:38:37 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 1s. Last read position: chr3:12,416,831
INFO 2026-06-08 09:38:37 MarkDuplicates Tracking 1739180 as yet unmatched pairs. 84310 records in RAM.
INFO 2026-06-08 09:38:38 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 1s. Last read position: chr3:15,686,088
INFO 2026-06-08 09:38:38 MarkDuplicates Tracking 1735752 as yet unmatched pairs. 80855 records in RAM.
INFO 2026-06-08 09:38:40 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 1s. Last read position: chr3:32,238,946
INFO 2026-06-08 09:38:40 MarkDuplicates Tracking 1732763 as yet unmatched pairs. 77780 records in RAM.
INFO 2026-06-08 09:38:42 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 1s. Last read position: chr3:37,862,255
INFO 2026-06-08 09:38:42 MarkDuplicates Tracking 1729568 as yet unmatched pairs. 74529 records in RAM.
INFO 2026-06-08 09:38:44 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 1s. Last read position: chr3:41,224,573
INFO 2026-06-08 09:38:44 MarkDuplicates Tracking 1737135 as yet unmatched pairs. 82056 records in RAM.
INFO 2026-06-08 09:38:45 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 1s. Last read position: chr3:45,828,582
INFO 2026-06-08 09:38:45 MarkDuplicates Tracking 1722986 as yet unmatched pairs. 67864 records in RAM.
INFO 2026-06-08 09:38:47 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 1s. Last read position: chr3:48,466,780
INFO 2026-06-08 09:38:47 MarkDuplicates Tracking 1719709 as yet unmatched pairs. 64541 records in RAM.
INFO 2026-06-08 09:38:50 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 2s. Last read position: chr3:49,358,064
INFO 2026-06-08 09:38:50 MarkDuplicates Tracking 1715968 as yet unmatched pairs. 60754 records in RAM.
INFO 2026-06-08 09:38:52 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 1s. Last read position: chr3:51,987,317
INFO 2026-06-08 09:38:52 MarkDuplicates Tracking 1712032 as yet unmatched pairs. 56778 records in RAM.
INFO 2026-06-08 09:38:54 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 2s. Last read position: chr3:56,633,227
INFO 2026-06-08 09:38:54 MarkDuplicates Tracking 1708879 as yet unmatched pairs. 53584 records in RAM.
INFO 2026-06-08 09:38:56 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 2s. Last read position: chr3:67,375,822
INFO 2026-06-08 09:38:56 MarkDuplicates Tracking 1705631 as yet unmatched pairs. 50281 records in RAM.
INFO 2026-06-08 09:38:58 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 2s. Last read position: chr3:99,848,760
INFO 2026-06-08 09:38:58 MarkDuplicates Tracking 1703221 as yet unmatched pairs. 47788 records in RAM.
INFO 2026-06-08 09:39:00 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 1s. Last read position: chr3:108,058,381
INFO 2026-06-08 09:39:00 MarkDuplicates Tracking 1700784 as yet unmatched pairs. 45282 records in RAM.
INFO 2026-06-08 09:39:02 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 1s. Last read position: chr3:120,411,903
INFO 2026-06-08 09:39:02 MarkDuplicates Tracking 1697004 as yet unmatched pairs. 41456 records in RAM.
INFO 2026-06-08 09:39:04 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 1s. Last read position: chr3:123,931,487
INFO 2026-06-08 09:39:04 MarkDuplicates Tracking 1694077 as yet unmatched pairs. 38489 records in RAM.
INFO 2026-06-08 09:39:06 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 1s. Last read position: chr3:128,052,487
INFO 2026-06-08 09:39:06 MarkDuplicates Tracking 1691212 as yet unmatched pairs. 35593 records in RAM.
INFO 2026-06-08 09:39:08 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 1s. Last read position: chr3:130,992,989
INFO 2026-06-08 09:39:08 MarkDuplicates Tracking 1686521 as yet unmatched pairs. 30852 records in RAM.
INFO 2026-06-08 09:39:09 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 1s. Last read position: chr3:139,378,127
INFO 2026-06-08 09:39:09 MarkDuplicates Tracking 1684308 as yet unmatched pairs. 28600 records in RAM.
INFO 2026-06-08 09:39:11 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 1s. Last read position: chr3:149,160,046
INFO 2026-06-08 09:39:11 MarkDuplicates Tracking 1680256 as yet unmatched pairs. 24485 records in RAM.
INFO 2026-06-08 09:39:13 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 1s. Last read position: chr3:160,419,448
INFO 2026-06-08 09:39:13 MarkDuplicates Tracking 1677025 as yet unmatched pairs. 21196 records in RAM.
INFO 2026-06-08 09:39:15 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 1s. Last read position: chr3:170,360,687
INFO 2026-06-08 09:39:15 MarkDuplicates Tracking 1675628 as yet unmatched pairs. 19740 records in RAM.
INFO 2026-06-08 09:39:17 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 1s. Last read position: chr3:182,837,078
INFO 2026-06-08 09:39:17 MarkDuplicates Tracking 1671916 as yet unmatched pairs. 15960 records in RAM.
INFO 2026-06-08 09:39:18 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 1s. Last read position: chr3:184,325,103
INFO 2026-06-08 09:39:18 MarkDuplicates Tracking 1668147 as yet unmatched pairs. 12144 records in RAM.
INFO 2026-06-08 09:39:20 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 1s. Last read position: chr3:188,609,286
INFO 2026-06-08 09:39:20 MarkDuplicates Tracking 1666357 as yet unmatched pairs. 10303 records in RAM.
INFO 2026-06-08 09:39:22 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 1s. Last read position: chr3:195,619,219
INFO 2026-06-08 09:39:22 MarkDuplicates Tracking 1662329 as yet unmatched pairs. 6256 records in RAM.
INFO 2026-06-08 09:39:23 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 1s. Last read position: chr3:195,781,314
INFO 2026-06-08 09:39:23 MarkDuplicates Tracking 1662873 as yet unmatched pairs. 6784 records in RAM.
INFO 2026-06-08 09:39:24 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 1s. Last read position: chr3:196,052,096
INFO 2026-06-08 09:39:24 MarkDuplicates Tracking 1663517 as yet unmatched pairs. 7412 records in RAM.
INFO 2026-06-08 09:39:27 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 2s. Last read position: chr4:499,370
INFO 2026-06-08 09:39:27 MarkDuplicates Tracking 1656543 as yet unmatched pairs. 64117 records in RAM.
INFO 2026-06-08 09:39:30 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 2s. Last read position: chr4:1,737,680
INFO 2026-06-08 09:39:30 MarkDuplicates Tracking 1654244 as yet unmatched pairs. 61792 records in RAM.
INFO 2026-06-08 09:39:32 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 2s. Last read position: chr4:3,214,028
INFO 2026-06-08 09:39:32 MarkDuplicates Tracking 1648318 as yet unmatched pairs. 55805 records in RAM.
INFO 2026-06-08 09:39:34 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 2s. Last read position: chr4:10,077,311
INFO 2026-06-08 09:39:34 MarkDuplicates Tracking 1645251 as yet unmatched pairs. 52703 records in RAM.
INFO 2026-06-08 09:39:36 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 2s. Last read position: chr4:25,263,718
INFO 2026-06-08 09:39:36 MarkDuplicates Tracking 1641496 as yet unmatched pairs. 48909 records in RAM.
INFO 2026-06-08 09:39:38 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 1s. Last read position: chr4:39,838,145
INFO 2026-06-08 09:39:38 MarkDuplicates Tracking 1638654 as yet unmatched pairs. 46019 records in RAM.
INFO 2026-06-08 09:39:40 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 1s. Last read position: chr4:48,851,933
INFO 2026-06-08 09:39:40 MarkDuplicates Tracking 1636168 as yet unmatched pairs. 43497 records in RAM.
INFO 2026-06-08 09:39:42 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 1s. Last read position: chr4:56,994,862
INFO 2026-06-08 09:39:42 MarkDuplicates Tracking 1632497 as yet unmatched pairs. 39777 records in RAM.
INFO 2026-06-08 09:39:43 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 1s. Last read position: chr4:73,102,381
INFO 2026-06-08 09:39:43 MarkDuplicates Tracking 1628966 as yet unmatched pairs. 36199 records in RAM.
INFO 2026-06-08 09:39:45 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 1s. Last read position: chr4:76,996,445
INFO 2026-06-08 09:39:45 MarkDuplicates Tracking 1627453 as yet unmatched pairs. 34626 records in RAM.
INFO 2026-06-08 09:39:47 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 1s. Last read position: chr4:83,462,834
INFO 2026-06-08 09:39:47 MarkDuplicates Tracking 1622644 as yet unmatched pairs. 29754 records in RAM.
INFO 2026-06-08 09:39:49 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 1s. Last read position: chr4:98,420,086
INFO 2026-06-08 09:39:49 MarkDuplicates Tracking 1619865 as yet unmatched pairs. 26906 records in RAM.
INFO 2026-06-08 09:39:51 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 2s. Last read position: chr4:108,079,579
INFO 2026-06-08 09:39:51 MarkDuplicates Tracking 1617073 as yet unmatched pairs. 24075 records in RAM.
INFO 2026-06-08 09:39:54 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 2s. Last read position: chr4:122,239,691
INFO 2026-06-08 09:39:54 MarkDuplicates Tracking 1614175 as yet unmatched pairs. 21125 records in RAM.
INFO 2026-06-08 09:39:55 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 1s. Last read position: chr4:140,677,039
INFO 2026-06-08 09:39:55 MarkDuplicates Tracking 1610734 as yet unmatched pairs. 17633 records in RAM.
INFO 2026-06-08 09:39:57 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 1s. Last read position: chr4:150,928,852
INFO 2026-06-08 09:39:57 MarkDuplicates Tracking 1608424 as yet unmatched pairs. 15270 records in RAM.
INFO 2026-06-08 09:39:59 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 1s. Last read position: chr4:159,104,214
INFO 2026-06-08 09:39:59 MarkDuplicates Tracking 1604641 as yet unmatched pairs. 11418 records in RAM.
INFO 2026-06-08 09:40:01 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 1s. Last read position: chr4:183,685,093
INFO 2026-06-08 09:40:01 MarkDuplicates Tracking 1602150 as yet unmatched pairs. 8865 records in RAM.
INFO 2026-06-08 09:40:03 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 2s. Last read position: chr4:186,613,327
INFO 2026-06-08 09:40:03 MarkDuplicates Tracking 1601318 as yet unmatched pairs. 7999 records in RAM.
INFO 2026-06-08 09:40:05 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 2s. Last read position: chr4:186,706,660
INFO 2026-06-08 09:40:05 MarkDuplicates Tracking 1598593 as yet unmatched pairs. 5252 records in RAM.
INFO 2026-06-08 09:40:08 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 2s. Last read position: chr5:612,398
INFO 2026-06-08 09:40:08 MarkDuplicates Tracking 1592273 as yet unmatched pairs. 94150 records in RAM.
INFO 2026-06-08 09:40:09 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 1s. Last read position: chr5:10,397,335
INFO 2026-06-08 09:40:09 MarkDuplicates Tracking 1589661 as yet unmatched pairs. 91497 records in RAM.
INFO 2026-06-08 09:40:11 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 1s. Last read position: chr5:14,472,640
INFO 2026-06-08 09:40:11 MarkDuplicates Tracking 1587011 as yet unmatched pairs. 88821 records in RAM.
INFO 2026-06-08 09:40:13 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 1s. Last read position: chr5:32,588,562
INFO 2026-06-08 09:40:13 MarkDuplicates Tracking 1583529 as yet unmatched pairs. 85306 records in RAM.
INFO 2026-06-08 09:40:15 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 1s. Last read position: chr5:40,832,486
INFO 2026-06-08 09:40:15 MarkDuplicates Tracking 1578898 as yet unmatched pairs. 80628 records in RAM.
INFO 2026-06-08 09:40:16 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 1s. Last read position: chr5:55,358,604
INFO 2026-06-08 09:40:16 MarkDuplicates Tracking 1576157 as yet unmatched pairs. 77836 records in RAM.
INFO 2026-06-08 09:40:20 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 3s. Last read position: chr5:66,170,813
INFO 2026-06-08 09:40:20 MarkDuplicates Tracking 1572919 as yet unmatched pairs. 74555 records in RAM.
INFO 2026-06-08 09:40:21 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 1s. Last read position: chr5:72,199,887
INFO 2026-06-08 09:40:21 MarkDuplicates Tracking 1570600 as yet unmatched pairs. 72229 records in RAM.
INFO 2026-06-08 09:40:23 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 1s. Last read position: chr5:77,583,126
INFO 2026-06-08 09:40:23 MarkDuplicates Tracking 1567502 as yet unmatched pairs. 69097 records in RAM.
INFO 2026-06-08 09:40:25 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 1s. Last read position: chr5:83,537,032
INFO 2026-06-08 09:40:25 MarkDuplicates Tracking 1565194 as yet unmatched pairs. 66732 records in RAM.
INFO 2026-06-08 09:40:27 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 1s. Last read position: chr5:96,742,653
INFO 2026-06-08 09:40:27 MarkDuplicates Tracking 1563434 as yet unmatched pairs. 64917 records in RAM.
INFO 2026-06-08 09:40:29 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:05:20s. Time for last 1,000,000: 1s. Last read position: chr5:112,864,669
INFO 2026-06-08 09:40:29 MarkDuplicates Tracking 1558864 as yet unmatched pairs. 60301 records in RAM.
INFO 2026-06-08 09:40:31 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 1s. Last read position: chr5:128,084,061
INFO 2026-06-08 09:40:31 MarkDuplicates Tracking 1556482 as yet unmatched pairs. 57848 records in RAM.
INFO 2026-06-08 09:40:34 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 2s. Last read position: chr5:131,672,688
INFO 2026-06-08 09:40:34 MarkDuplicates Tracking 1553111 as yet unmatched pairs. 54443 records in RAM.
INFO 2026-06-08 09:40:35 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 1s. Last read position: chr5:134,564,609
INFO 2026-06-08 09:40:35 MarkDuplicates Tracking 1549383 as yet unmatched pairs. 50700 records in RAM.
INFO 2026-06-08 09:40:37 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 1s. Last read position: chr5:138,171,058
INFO 2026-06-08 09:40:37 MarkDuplicates Tracking 1546482 as yet unmatched pairs. 47756 records in RAM.
INFO 2026-06-08 09:40:39 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 1s. Last read position: chr5:139,478,476
INFO 2026-06-08 09:40:39 MarkDuplicates Tracking 1543076 as yet unmatched pairs. 44323 records in RAM.
INFO 2026-06-08 09:40:40 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 1s. Last read position: chr5:141,357,482
INFO 2026-06-08 09:40:40 MarkDuplicates Tracking 1539403 as yet unmatched pairs. 40602 records in RAM.
INFO 2026-06-08 09:40:42 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 1s. Last read position: chr5:141,983,413
INFO 2026-06-08 09:40:42 MarkDuplicates Tracking 1536098 as yet unmatched pairs. 37276 records in RAM.
INFO 2026-06-08 09:40:44 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 2s. Last read position: chr5:150,001,114
INFO 2026-06-08 09:40:44 MarkDuplicates Tracking 1532944 as yet unmatched pairs. 34073 records in RAM.
INFO 2026-06-08 09:40:46 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 1s. Last read position: chr5:150,402,611
INFO 2026-06-08 09:40:46 MarkDuplicates Tracking 1539776 as yet unmatched pairs. 40896 records in RAM.
INFO 2026-06-08 09:40:48 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 1s. Last read position: chr5:150,695,573
INFO 2026-06-08 09:40:48 MarkDuplicates Tracking 1524985 as yet unmatched pairs. 26086 records in RAM.
INFO 2026-06-08 09:40:50 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 1s. Last read position: chr5:156,850,988
INFO 2026-06-08 09:40:50 MarkDuplicates Tracking 1521577 as yet unmatched pairs. 22643 records in RAM.
INFO 2026-06-08 09:40:53 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 2s. Last read position: chr5:171,183,204
INFO 2026-06-08 09:40:53 MarkDuplicates Tracking 1518487 as yet unmatched pairs. 19509 records in RAM.
INFO 2026-06-08 09:40:54 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 1s. Last read position: chr5:171,392,742
INFO 2026-06-08 09:40:54 MarkDuplicates Tracking 1543970 as yet unmatched pairs. 44956 records in RAM.
INFO 2026-06-08 09:40:56 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 1s. Last read position: chr5:172,656,462
INFO 2026-06-08 09:40:56 MarkDuplicates Tracking 1513223 as yet unmatched pairs. 14191 records in RAM.
INFO 2026-06-08 09:40:58 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 1s. Last read position: chr5:177,269,620
INFO 2026-06-08 09:40:58 MarkDuplicates Tracking 1510295 as yet unmatched pairs. 11226 records in RAM.
INFO 2026-06-08 09:40:59 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 1s. Last read position: chr5:179,618,144
INFO 2026-06-08 09:40:59 MarkDuplicates Tracking 1506848 as yet unmatched pairs. 7759 records in RAM.
INFO 2026-06-08 09:41:01 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 1s. Last read position: chr5:179,824,244
INFO 2026-06-08 09:41:01 MarkDuplicates Tracking 1506617 as yet unmatched pairs. 7507 records in RAM.
INFO 2026-06-08 09:41:03 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 1s. Last read position: chr5:181,239,539
INFO 2026-06-08 09:41:03 MarkDuplicates Tracking 1505614 as yet unmatched pairs. 6485 records in RAM.
INFO 2026-06-08 09:41:05 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 2s. Last read position: chr6:6,250,884
INFO 2026-06-08 09:41:05 MarkDuplicates Tracking 1496526 as yet unmatched pairs. 110221 records in RAM.
INFO 2026-06-08 09:41:07 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 2s. Last read position: chr6:7,585,219
INFO 2026-06-08 09:41:07 MarkDuplicates Tracking 1493246 as yet unmatched pairs. 106918 records in RAM.
INFO 2026-06-08 09:41:10 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 2s. Last read position: chr6:17,817,193
INFO 2026-06-08 09:41:10 MarkDuplicates Tracking 1489679 as yet unmatched pairs. 103332 records in RAM.
INFO 2026-06-08 09:41:11 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 1s. Last read position: chr6:26,124,311
INFO 2026-06-08 09:41:11 MarkDuplicates Tracking 1489912 as yet unmatched pairs. 103519 records in RAM.
INFO 2026-06-08 09:41:13 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 1s. Last read position: chr6:27,146,699
INFO 2026-06-08 09:41:13 MarkDuplicates Tracking 1482551 as yet unmatched pairs. 96146 records in RAM.
INFO 2026-06-08 09:41:14 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 1s. Last read position: chr6:29,942,561
INFO 2026-06-08 09:41:14 MarkDuplicates Tracking 1485661 as yet unmatched pairs. 99247 records in RAM.
INFO 2026-06-08 09:41:16 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 1s. Last read position: chr6:30,885,170
INFO 2026-06-08 09:41:16 MarkDuplicates Tracking 1475829 as yet unmatched pairs. 89383 records in RAM.
INFO 2026-06-08 09:41:18 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:06:09s. Time for last 1,000,000: 2s. Last read position: chr6:31,632,814
INFO 2026-06-08 09:41:18 MarkDuplicates Tracking 1472485 as yet unmatched pairs. 86019 records in RAM.
INFO 2026-06-08 09:41:20 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 1s. Last read position: chr6:31,829,082
INFO 2026-06-08 09:41:20 MarkDuplicates Tracking 1470136 as yet unmatched pairs. 83637 records in RAM.
INFO 2026-06-08 09:41:22 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 1s. Last read position: chr6:32,150,837
INFO 2026-06-08 09:41:22 MarkDuplicates Tracking 1465879 as yet unmatched pairs. 79352 records in RAM.
INFO 2026-06-08 09:41:23 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 1s. Last read position: chr6:33,280,784
INFO 2026-06-08 09:41:23 MarkDuplicates Tracking 1462736 as yet unmatched pairs. 76176 records in RAM.
INFO 2026-06-08 09:41:25 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 2s. Last read position: chr6:34,243,481
INFO 2026-06-08 09:41:25 MarkDuplicates Tracking 1460734 as yet unmatched pairs. 74146 records in RAM.
INFO 2026-06-08 09:41:28 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 2s. Last read position: chr6:36,495,870
INFO 2026-06-08 09:41:28 MarkDuplicates Tracking 1456038 as yet unmatched pairs. 69386 records in RAM.
INFO 2026-06-08 09:41:30 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 1s. Last read position: chr6:42,659,638
INFO 2026-06-08 09:41:30 MarkDuplicates Tracking 1451790 as yet unmatched pairs. 65089 records in RAM.
INFO 2026-06-08 09:41:32 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 1s. Last read position: chr6:43,778,393
INFO 2026-06-08 09:41:32 MarkDuplicates Tracking 1448707 as yet unmatched pairs. 61980 records in RAM.
INFO 2026-06-08 09:41:33 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 1s. Last read position: chr6:47,596,011
INFO 2026-06-08 09:41:33 MarkDuplicates Tracking 1445038 as yet unmatched pairs. 58285 records in RAM.
INFO 2026-06-08 09:41:35 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 1s. Last read position: chr6:56,632,912
INFO 2026-06-08 09:41:35 MarkDuplicates Tracking 1442399 as yet unmatched pairs. 55569 records in RAM.
INFO 2026-06-08 09:41:37 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 1s. Last read position: chr6:75,117,467
INFO 2026-06-08 09:41:37 MarkDuplicates Tracking 1439239 as yet unmatched pairs. 52347 records in RAM.