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/b9/565bcb7ba573b981b8532a0dcb9c7f/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/565bcb7ba573b981b8532a0dcb9c7f/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/5da4b0f0dc5b55b097fe818cf33f1e/aih-tih-sc-3924cb-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam 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 -Xmx121241M -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-3924cb-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-3924cb-R1_B23WHYVLT4_1.md.bam --METRICS_FILE aih-tih-sc-3924cb-R1_B23WHYVLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT 09:27:28.956 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 09:27:28 GMT 2026] MarkDuplicates --INPUT aih-tih-sc-3924cb-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-3924cb-R1_B23WHYVLT4_1.md.bam --METRICS_FILE aih-tih-sc-3924cb-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 --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 09:27:28 GMT 2026] Executing as ?@nf-b9565bcb7ba573b981b8532a0dcb9c7f-a5f2b-tln2b 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 09:27:29 MarkDuplicates Start of doWork freeMemory: 105133384; totalMemory: 134217728; maxMemory: 127137742848 INFO 2026-06-08 09:27:29 MarkDuplicates Reading input file and constructing read end information. INFO 2026-06-08 09:27:29 MarkDuplicates Will retain up to 460643995 data points before spilling to disk. INFO 2026-06-08 09:27:35 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:1,460,892 INFO 2026-06-08 09:27:35 MarkDuplicates Tracking 3289 as yet unmatched pairs. 93 records in RAM. INFO 2026-06-08 09:27:37 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: chr1:6,136,816 INFO 2026-06-08 09:27:37 MarkDuplicates Tracking 6283 as yet unmatched pairs. 22 records in RAM. INFO 2026-06-08 09:27:40 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: chr1:8,624,356 INFO 2026-06-08 09:27:40 MarkDuplicates Tracking 9762 as yet unmatched pairs. 537 records in RAM. INFO 2026-06-08 09:27:43 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 2s. Last read position: chr1:11,243,113 INFO 2026-06-08 09:27:43 MarkDuplicates Tracking 12195 as yet unmatched pairs. 121 records in RAM. INFO 2026-06-08 09:27:45 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 2s. Last read position: chr1:15,719,870 INFO 2026-06-08 09:27:45 MarkDuplicates Tracking 15227 as yet unmatched pairs. 368 records in RAM. INFO 2026-06-08 09:27:48 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr1:17,438,263 INFO 2026-06-08 09:27:48 MarkDuplicates Tracking 17471 as yet unmatched pairs. 61 records in RAM. INFO 2026-06-08 09:27:50 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 2s. Last read position: chr1:20,776,614 INFO 2026-06-08 09:27:50 MarkDuplicates Tracking 20642 as yet unmatched pairs. 302 records in RAM. INFO 2026-06-08 09:27:54 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 3s. Last read position: chr1:21,884,804 INFO 2026-06-08 09:27:54 MarkDuplicates Tracking 23972 as yet unmatched pairs. 562 records in RAM. INFO 2026-06-08 09:27:56 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 2s. Last read position: chr1:23,961,659 INFO 2026-06-08 09:27:56 MarkDuplicates Tracking 26285 as yet unmatched pairs. 158 records in RAM. INFO 2026-06-08 09:27:59 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 2s. Last read position: chr1:27,102,672 INFO 2026-06-08 09:27:59 MarkDuplicates Tracking 28953 as yet unmatched pairs. 159 records in RAM. INFO 2026-06-08 09:28:01 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 2s. Last read position: chr1:31,425,870 INFO 2026-06-08 09:28:01 MarkDuplicates Tracking 32326 as yet unmatched pairs. 792 records in RAM. INFO 2026-06-08 09:28:04 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 3s. Last read position: chr1:33,024,536 INFO 2026-06-08 09:28:04 MarkDuplicates Tracking 34726 as yet unmatched pairs. 210 records in RAM. INFO 2026-06-08 09:28:07 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 2s. Last read position: chr1:38,839,690 INFO 2026-06-08 09:28:07 MarkDuplicates Tracking 37571 as yet unmatched pairs. 166 records in RAM. INFO 2026-06-08 09:28:10 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 2s. Last read position: chr1:42,683,402 INFO 2026-06-08 09:28:10 MarkDuplicates Tracking 40805 as yet unmatched pairs. 698 records in RAM. INFO 2026-06-08 09:28:12 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 2s. Last read position: chr1:45,514,561 INFO 2026-06-08 09:28:12 MarkDuplicates Tracking 44684 as yet unmatched pairs. 1634 records in RAM. INFO 2026-06-08 09:28:15 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 2s. Last read position: chr1:47,219,256 INFO 2026-06-08 09:28:15 MarkDuplicates Tracking 45840 as yet unmatched pairs. 96 records in RAM. INFO 2026-06-08 09:28:18 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 3s. Last read position: chr1:53,828,022 INFO 2026-06-08 09:28:18 MarkDuplicates Tracking 48977 as yet unmatched pairs. 347 records in RAM. INFO 2026-06-08 09:28:21 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 2s. Last read position: chr1:62,114,188 INFO 2026-06-08 09:28:21 MarkDuplicates Tracking 51679 as yet unmatched pairs. 172 records in RAM. INFO 2026-06-08 09:28:23 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 2s. Last read position: chr1:77,154,512 INFO 2026-06-08 09:28:23 MarkDuplicates Tracking 54391 as yet unmatched pairs. 458 records in RAM. INFO 2026-06-08 09:28:26 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 3s. Last read position: chr1:86,432,377 INFO 2026-06-08 09:28:26 MarkDuplicates Tracking 57440 as yet unmatched pairs. 865 records in RAM. INFO 2026-06-08 09:28:28 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 2s. Last read position: chr1:93,156,407 INFO 2026-06-08 09:28:28 MarkDuplicates Tracking 60478 as yet unmatched pairs. 1461 records in RAM. INFO 2026-06-08 09:28:31 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 2s. Last read position: chr1:100,992,613 INFO 2026-06-08 09:28:31 MarkDuplicates Tracking 61738 as yet unmatched pairs. 168 records in RAM. INFO 2026-06-08 09:28:33 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 2s. Last read position: chr1:109,191,791 INFO 2026-06-08 09:28:33 MarkDuplicates Tracking 65669 as yet unmatched pairs. 1466 records in RAM. INFO 2026-06-08 09:28:35 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 2s. Last read position: chr1:110,346,298 INFO 2026-06-08 09:28:35 MarkDuplicates Tracking 67486 as yet unmatched pairs. 472 records in RAM. INFO 2026-06-08 09:28:37 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 2s. Last read position: chr1:113,642,340 INFO 2026-06-08 09:28:37 MarkDuplicates Tracking 72102 as yet unmatched pairs. 2517 records in RAM. INFO 2026-06-08 09:28:41 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 3s. Last read position: chr1:114,510,555 INFO 2026-06-08 09:28:41 MarkDuplicates Tracking 73257 as yet unmatched pairs. 1174 records in RAM. INFO 2026-06-08 09:28:44 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 3s. Last read position: chr1:119,915,450 INFO 2026-06-08 09:28:44 MarkDuplicates Tracking 77694 as yet unmatched pairs. 2878 records in RAM. INFO 2026-06-08 09:28:47 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 2s. Last read position: chr1:119,950,680 INFO 2026-06-08 09:28:47 MarkDuplicates Tracking 80272 as yet unmatched pairs. 2828 records in RAM. INFO 2026-06-08 09:28:49 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 2s. Last read position: chr1:121,366,696 INFO 2026-06-08 09:28:49 MarkDuplicates Tracking 79477 as yet unmatched pairs. 111 records in RAM. INFO 2026-06-08 09:28:52 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 2s. Last read position: chr1:146,078,241 INFO 2026-06-08 09:28:52 MarkDuplicates Tracking 81725 as yet unmatched pairs. 607 records in RAM. INFO 2026-06-08 09:28:53 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 1s. Last read position: chr1:147,186,886 INFO 2026-06-08 09:28:53 MarkDuplicates Tracking 82880 as yet unmatched pairs. 783 records in RAM. INFO 2026-06-08 09:28:56 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 2s. Last read position: chr1:148,564,553 INFO 2026-06-08 09:28:56 MarkDuplicates Tracking 84296 as yet unmatched pairs. 923 records in RAM. INFO 2026-06-08 09:28:58 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 2s. Last read position: chr1:149,455,348 INFO 2026-06-08 09:28:58 MarkDuplicates Tracking 88246 as yet unmatched pairs. 3695 records in RAM. INFO 2026-06-08 09:29:00 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 2s. Last read position: chr1:149,842,471 INFO 2026-06-08 09:29:00 MarkDuplicates Tracking 90241 as yet unmatched pairs. 3955 records in RAM. INFO 2026-06-08 09:29:02 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 2s. Last read position: chr1:149,959,775 INFO 2026-06-08 09:29:02 MarkDuplicates Tracking 88451 as yet unmatched pairs. 331 records in RAM. INFO 2026-06-08 09:29:04 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 2s. Last read position: chr1:150,509,707 INFO 2026-06-08 09:29:04 MarkDuplicates Tracking 105760 as yet unmatched pairs. 15201 records in RAM. INFO 2026-06-08 09:29:07 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 2s. Last read position: chr1:150,511,584 INFO 2026-06-08 09:29:07 MarkDuplicates Tracking 95254 as yet unmatched pairs. 2222 records in RAM. INFO 2026-06-08 09:29:09 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 2s. Last read position: chr1:150,627,554 INFO 2026-06-08 09:29:09 MarkDuplicates Tracking 99452 as yet unmatched pairs. 3881 records in RAM. INFO 2026-06-08 09:29:12 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 2s. Last read position: chr1:151,055,677 INFO 2026-06-08 09:29:12 MarkDuplicates Tracking 99486 as yet unmatched pairs. 1239 records in RAM. INFO 2026-06-08 09:29:14 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 2s. Last read position: chr1:151,411,701 INFO 2026-06-08 09:29:14 MarkDuplicates Tracking 102428 as yet unmatched pairs. 1378 records in RAM. INFO 2026-06-08 09:29:16 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 2s. Last read position: chr1:153,948,094 INFO 2026-06-08 09:29:16 MarkDuplicates Tracking 103893 as yet unmatched pairs. 274 records in RAM. INFO 2026-06-08 09:29:19 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 2s. Last read position: chr1:154,183,014 INFO 2026-06-08 09:29:19 MarkDuplicates Tracking 109354 as yet unmatched pairs. 3185 records in RAM. INFO 2026-06-08 09:29:22 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 2s. Last read position: chr1:154,966,200 INFO 2026-06-08 09:29:22 MarkDuplicates Tracking 109523 as yet unmatched pairs. 752 records in RAM. INFO 2026-06-08 09:29:25 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 3s. Last read position: chr1:155,172,743 INFO 2026-06-08 09:29:25 MarkDuplicates Tracking 114617 as yet unmatched pairs. 2999 records in RAM. INFO 2026-06-08 09:29:28 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 2s. Last read position: chr1:155,188,021 INFO 2026-06-08 09:29:28 MarkDuplicates Tracking 121051 as yet unmatched pairs. 6609 records in RAM. INFO 2026-06-08 09:29:31 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 2s. Last read position: chr1:155,190,054 INFO 2026-06-08 09:29:31 MarkDuplicates Tracking 118395 as yet unmatched pairs. 2203 records in RAM. INFO 2026-06-08 09:29:33 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 2s. Last read position: chr1:155,192,064 INFO 2026-06-08 09:29:33 MarkDuplicates Tracking 132760 as yet unmatched pairs. 14933 records in RAM. INFO 2026-06-08 09:29:36 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 2s. Last read position: chr1:155,253,931 INFO 2026-06-08 09:29:36 MarkDuplicates Tracking 120808 as yet unmatched pairs. 702 records in RAM. INFO 2026-06-08 09:29:39 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 3s. Last read position: chr1:155,479,010 INFO 2026-06-08 09:29:39 MarkDuplicates Tracking 124413 as yet unmatched pairs. 1573 records in RAM. INFO 2026-06-08 09:29:42 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 2s. Last read position: chr1:155,721,516 INFO 2026-06-08 09:29:42 MarkDuplicates Tracking 127817 as yet unmatched pairs. 2649 records in RAM. INFO 2026-06-08 09:29:44 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 2s. Last read position: chr1:156,114,953 INFO 2026-06-08 09:29:44 MarkDuplicates Tracking 128524 as yet unmatched pairs. 679 records in RAM. INFO 2026-06-08 09:29:47 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 2s. Last read position: chr1:156,469,003 INFO 2026-06-08 09:29:47 MarkDuplicates Tracking 131462 as yet unmatched pairs. 363 records in RAM. INFO 2026-06-08 09:29:50 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 2s. Last read position: chr1:159,049,576 INFO 2026-06-08 09:29:50 MarkDuplicates Tracking 133983 as yet unmatched pairs. 313 records in RAM. INFO 2026-06-08 09:29:53 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 2s. Last read position: chr1:161,089,283 INFO 2026-06-08 09:29:53 MarkDuplicates Tracking 136631 as yet unmatched pairs. 123 records in RAM. INFO 2026-06-08 09:29:55 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 2s. Last read position: chr1:162,365,547 INFO 2026-06-08 09:29:55 MarkDuplicates Tracking 139503 as yet unmatched pairs. 397 records in RAM. INFO 2026-06-08 09:29:58 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 2s. Last read position: chr1:165,662,995 INFO 2026-06-08 09:29:58 MarkDuplicates Tracking 143383 as yet unmatched pairs. 1622 records in RAM. INFO 2026-06-08 09:30:01 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 2s. Last read position: chr1:169,127,277 INFO 2026-06-08 09:30:01 MarkDuplicates Tracking 149090 as yet unmatched pairs. 4426 records in RAM. INFO 2026-06-08 09:30:04 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 2s. Last read position: chr1:171,579,393 INFO 2026-06-08 09:30:04 MarkDuplicates Tracking 147976 as yet unmatched pairs. 890 records in RAM. INFO 2026-06-08 09:30:06 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 2s. Last read position: chr1:178,457,805 INFO 2026-06-08 09:30:06 MarkDuplicates Tracking 150212 as yet unmatched pairs. 498 records in RAM. INFO 2026-06-08 09:30:09 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 2s. Last read position: chr1:180,092,762 INFO 2026-06-08 09:30:09 MarkDuplicates Tracking 152550 as yet unmatched pairs. 342 records in RAM. INFO 2026-06-08 09:30:12 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 2s. Last read position: chr1:182,876,500 INFO 2026-06-08 09:30:12 MarkDuplicates Tracking 155791 as yet unmatched pairs. 819 records in RAM. INFO 2026-06-08 09:30:15 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 3s. Last read position: chr1:186,318,577 INFO 2026-06-08 09:30:15 MarkDuplicates Tracking 159785 as yet unmatched pairs. 2225 records in RAM. INFO 2026-06-08 09:30:18 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 2s. Last read position: chr1:186,356,301 INFO 2026-06-08 09:30:18 MarkDuplicates Tracking 162634 as yet unmatched pairs. 2854 records in RAM. INFO 2026-06-08 09:30:20 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 2s. Last read position: chr1:197,645,706 INFO 2026-06-08 09:30:20 MarkDuplicates Tracking 163706 as yet unmatched pairs. 1591 records in RAM. INFO 2026-06-08 09:30:23 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 2s. Last read position: chr1:201,848,462 INFO 2026-06-08 09:30:23 MarkDuplicates Tracking 165927 as yet unmatched pairs. 1102 records in RAM. INFO 2026-06-08 09:30:25 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 2s. Last read position: chr1:202,766,925 INFO 2026-06-08 09:30:25 MarkDuplicates Tracking 168208 as yet unmatched pairs. 578 records in RAM. INFO 2026-06-08 09:30:28 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 2s. Last read position: chr1:203,708,005 INFO 2026-06-08 09:30:28 MarkDuplicates Tracking 170795 as yet unmatched pairs. 538 records in RAM. INFO 2026-06-08 09:30:30 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 2s. Last read position: chr1:203,849,790 INFO 2026-06-08 09:30:30 MarkDuplicates Tracking 175550 as yet unmatched pairs. 2990 records in RAM. INFO 2026-06-08 09:30:33 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 2s. Last read position: chr1:204,410,955 INFO 2026-06-08 09:30:33 MarkDuplicates Tracking 176757 as yet unmatched pairs. 1408 records in RAM. INFO 2026-06-08 09:30:36 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 2s. Last read position: chr1:205,723,963 INFO 2026-06-08 09:30:36 MarkDuplicates Tracking 184576 as yet unmatched pairs. 6826 records in RAM. INFO 2026-06-08 09:30:38 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 2s. Last read position: chr1:207,340,519 INFO 2026-06-08 09:30:38 MarkDuplicates Tracking 181924 as yet unmatched pairs. 1608 records in RAM. INFO 2026-06-08 09:30:40 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 2s. Last read position: chr1:207,887,414 INFO 2026-06-08 09:30:40 MarkDuplicates Tracking 183530 as yet unmatched pairs. 479 records in RAM. INFO 2026-06-08 09:30:43 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 3s. Last read position: chr1:214,334,252 INFO 2026-06-08 09:30:43 MarkDuplicates Tracking 185926 as yet unmatched pairs. 223 records in RAM. INFO 2026-06-08 09:30:46 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 2s. Last read position: chr1:222,665,331 INFO 2026-06-08 09:30:46 MarkDuplicates Tracking 188408 as yet unmatched pairs. 253 records in RAM. INFO 2026-06-08 09:30:49 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 2s. Last read position: chr1:225,517,912 INFO 2026-06-08 09:30:49 MarkDuplicates Tracking 191215 as yet unmatched pairs. 404 records in RAM. INFO 2026-06-08 09:30:51 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 2s. Last read position: chr1:228,271,933 INFO 2026-06-08 09:30:51 MarkDuplicates Tracking 193706 as yet unmatched pairs. 127 records in RAM. INFO 2026-06-08 09:30:53 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 2s. Last read position: chr1:234,607,118 INFO 2026-06-08 09:30:53 MarkDuplicates Tracking 197864 as yet unmatched pairs. 1304 records in RAM. INFO 2026-06-08 09:30:56 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 2s. Last read position: chr1:241,885,318 INFO 2026-06-08 09:30:56 MarkDuplicates Tracking 199454 as yet unmatched pairs. 37 records in RAM. INFO 2026-06-08 09:30:58 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 2s. Last read position: chr1:247,434,110 INFO 2026-06-08 09:30:58 MarkDuplicates Tracking 201930 as yet unmatched pairs. 24 records in RAM. INFO 2026-06-08 09:31:03 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 5s. Last read position: chr2:10,789,751 INFO 2026-06-08 09:31:03 MarkDuplicates Tracking 205288 as yet unmatched pairs. 203398 records in RAM. INFO 2026-06-08 09:31:06 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 2s. Last read position: chr2:20,263,336 INFO 2026-06-08 09:31:06 MarkDuplicates Tracking 207924 as yet unmatched pairs. 205995 records in RAM. INFO 2026-06-08 09:31:09 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 2s. Last read position: chr2:24,790,379 INFO 2026-06-08 09:31:09 MarkDuplicates Tracking 210420 as yet unmatched pairs. 208459 records in RAM. INFO 2026-06-08 09:31:12 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 3s. Last read position: chr2:27,312,983 INFO 2026-06-08 09:31:12 MarkDuplicates Tracking 213891 as yet unmatched pairs. 211894 records in RAM. INFO 2026-06-08 09:31:15 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 3s. Last read position: chr2:32,029,657 INFO 2026-06-08 09:31:15 MarkDuplicates Tracking 216817 as yet unmatched pairs. 214792 records in RAM. INFO 2026-06-08 09:31:18 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,259 INFO 2026-06-08 09:31:18 MarkDuplicates Tracking 297392 as yet unmatched pairs. 209475 records in RAM. INFO 2026-06-08 09:31:21 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 3s. Last read position: chr2:32,916,264 INFO 2026-06-08 09:31:21 MarkDuplicates Tracking 714731 as yet unmatched pairs. 180286 records in RAM. INFO 2026-06-08 09:31:24 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 3s. Last read position: chr2:32,916,360 INFO 2026-06-08 09:31:24 MarkDuplicates Tracking 1265523 as yet unmatched pairs. 140896 records in RAM. INFO 2026-06-08 09:31:26 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,406 INFO 2026-06-08 09:31:26 MarkDuplicates Tracking 1356995 as yet unmatched pairs. 134084 records in RAM. INFO 2026-06-08 09:31:28 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,430 INFO 2026-06-08 09:31:28 MarkDuplicates Tracking 1435588 as yet unmatched pairs. 128569 records in RAM. INFO 2026-06-08 09:31:31 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 2s. Last read position: chr2:39,265,233 INFO 2026-06-08 09:31:31 MarkDuplicates Tracking 1444653 as yet unmatched pairs. 125817 records in RAM. INFO 2026-06-08 09:31:33 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 2s. Last read position: chr2:43,995,827 INFO 2026-06-08 09:31:33 MarkDuplicates Tracking 1441986 as yet unmatched pairs. 123125 records in RAM. INFO 2026-06-08 09:31:36 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 2s. Last read position: chr2:54,115,607 INFO 2026-06-08 09:31:36 MarkDuplicates Tracking 1439325 as yet unmatched pairs. 120435 records in RAM. INFO 2026-06-08 09:31:39 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 2s. Last read position: chr2:58,221,999 INFO 2026-06-08 09:31:39 MarkDuplicates Tracking 1436985 as yet unmatched pairs. 118063 records in RAM. INFO 2026-06-08 09:31:41 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 2s. Last read position: chr2:65,098,011 INFO 2026-06-08 09:31:41 MarkDuplicates Tracking 1435468 as yet unmatched pairs. 116521 records in RAM. INFO 2026-06-08 09:31:44 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 2s. Last read position: chr2:70,820,463 INFO 2026-06-08 09:31:44 MarkDuplicates Tracking 1431737 as yet unmatched pairs. 112765 records in RAM. INFO 2026-06-08 09:31:46 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 2s. Last read position: chr2:74,365,231 INFO 2026-06-08 09:31:46 MarkDuplicates Tracking 1429120 as yet unmatched pairs. 110133 records in RAM. INFO 2026-06-08 09:31:49 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 2s. Last read position: chr2:85,401,550 INFO 2026-06-08 09:31:49 MarkDuplicates Tracking 1427224 as yet unmatched pairs. 108221 records in RAM. INFO 2026-06-08 09:31:52 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 3s. Last read position: chr2:88,857,483 INFO 2026-06-08 09:31:52 MarkDuplicates Tracking 1425425 as yet unmatched pairs. 106399 records in RAM. INFO 2026-06-08 09:31:55 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 2s. Last read position: chr2:96,865,460 INFO 2026-06-08 09:31:55 MarkDuplicates Tracking 1422009 as yet unmatched pairs. 102958 records in RAM. INFO 2026-06-08 09:31:58 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 2s. Last read position: chr2:99,727,091 INFO 2026-06-08 09:31:58 MarkDuplicates Tracking 1420270 as yet unmatched pairs. 101193 records in RAM. INFO 2026-06-08 09:32:00 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 2s. Last read position: chr2:108,749,102 INFO 2026-06-08 09:32:00 MarkDuplicates Tracking 1417980 as yet unmatched pairs. 98879 records in RAM. INFO 2026-06-08 09:32:02 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 2s. Last read position: chr2:111,783,950 INFO 2026-06-08 09:32:02 MarkDuplicates Tracking 1415186 as yet unmatched pairs. 96081 records in RAM. INFO 2026-06-08 09:32:05 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 2s. Last read position: chr2:119,437,274 INFO 2026-06-08 09:32:05 MarkDuplicates Tracking 1413101 as yet unmatched pairs. 93979 records in RAM. INFO 2026-06-08 09:32:07 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 2s. Last read position: chr2:130,115,298 INFO 2026-06-08 09:32:07 MarkDuplicates Tracking 1410917 as yet unmatched pairs. 91759 records in RAM. INFO 2026-06-08 09:32:09 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 1s. Last read position: chr2:130,638,667 INFO 2026-06-08 09:32:09 MarkDuplicates Tracking 1409792 as yet unmatched pairs. 90606 records in RAM. INFO 2026-06-08 09:32:11 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 2s. Last read position: chr2:131,531,670 INFO 2026-06-08 09:32:11 MarkDuplicates Tracking 1408044 as yet unmatched pairs. 88834 records in RAM. INFO 2026-06-08 09:32:13 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 2s. Last read position: chr2:144,007,512 INFO 2026-06-08 09:32:13 MarkDuplicates Tracking 1405644 as yet unmatched pairs. 86366 records in RAM. INFO 2026-06-08 09:32:16 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 2s. Last read position: chr2:159,230,210 INFO 2026-06-08 09:32:16 MarkDuplicates Tracking 1403275 as yet unmatched pairs. 83955 records in RAM. INFO 2026-06-08 09:32:18 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 2s. Last read position: chr2:169,156,391 INFO 2026-06-08 09:32:18 MarkDuplicates Tracking 1402582 as yet unmatched pairs. 83236 records in RAM. INFO 2026-06-08 09:32:20 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 2s. Last read position: chr2:170,996,656 INFO 2026-06-08 09:32:20 MarkDuplicates Tracking 1398778 as yet unmatched pairs. 79407 records in RAM. INFO 2026-06-08 09:32:22 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 2s. Last read position: chr2:176,328,344 INFO 2026-06-08 09:32:22 MarkDuplicates Tracking 1396276 as yet unmatched pairs. 76860 records in RAM. INFO 2026-06-08 09:32:25 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 2s. Last read position: chr2:182,759,159 INFO 2026-06-08 09:32:25 MarkDuplicates Tracking 1394412 as yet unmatched pairs. 74965 records in RAM. INFO 2026-06-08 09:32:27 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 2s. Last read position: chr2:188,994,237 INFO 2026-06-08 09:32:27 MarkDuplicates Tracking 1394559 as yet unmatched pairs. 75089 records in RAM. INFO 2026-06-08 09:32:29 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 2s. Last read position: chr2:189,035,114 INFO 2026-06-08 09:32:29 MarkDuplicates Tracking 1390226 as yet unmatched pairs. 70728 records in RAM. INFO 2026-06-08 09:32:32 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 2s. Last read position: chr2:195,680,039 INFO 2026-06-08 09:32:32 MarkDuplicates Tracking 1385416 as yet unmatched pairs. 65876 records in RAM. INFO 2026-06-08 09:32:34 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 2s. Last read position: chr2:201,380,818 INFO 2026-06-08 09:32:34 MarkDuplicates Tracking 1382979 as yet unmatched pairs. 63416 records in RAM. INFO 2026-06-08 09:32:37 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 2s. Last read position: chr2:207,567,459 INFO 2026-06-08 09:32:37 MarkDuplicates Tracking 1382568 as yet unmatched pairs. 62996 records in RAM. INFO 2026-06-08 09:32:39 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 2s. Last read position: chr2:212,124,767 INFO 2026-06-08 09:32:39 MarkDuplicates Tracking 1380925 as yet unmatched pairs. 61331 records in RAM. INFO 2026-06-08 09:32:41 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 2s. Last read position: chr2:215,361,624 INFO 2026-06-08 09:32:41 MarkDuplicates Tracking 1403492 as yet unmatched pairs. 83857 records in RAM. INFO 2026-06-08 09:32:43 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 2s. Last read position: chr2:215,370,343 INFO 2026-06-08 09:32:43 MarkDuplicates Tracking 1403152 as yet unmatched pairs. 83498 records in RAM. INFO 2026-06-08 09:32:46 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 2s. Last read position: chr2:215,372,173 INFO 2026-06-08 09:32:46 MarkDuplicates Tracking 1414419 as yet unmatched pairs. 94762 records in RAM. INFO 2026-06-08 09:32:49 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 2s. Last read position: chr2:215,375,280 INFO 2026-06-08 09:32:49 MarkDuplicates Tracking 1388508 as yet unmatched pairs. 68849 records in RAM. INFO 2026-06-08 09:32:51 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 2s. Last read position: chr2:215,376,600 INFO 2026-06-08 09:32:51 MarkDuplicates Tracking 1391449 as yet unmatched pairs. 71767 records in RAM. INFO 2026-06-08 09:32:54 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 2s. Last read position: chr2:215,379,296 INFO 2026-06-08 09:32:54 MarkDuplicates Tracking 1402524 as yet unmatched pairs. 82841 records in RAM. INFO 2026-06-08 09:32:56 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 2s. Last read position: chr2:215,384,859 INFO 2026-06-08 09:32:56 MarkDuplicates Tracking 1373165 as yet unmatched pairs. 53479 records in RAM. INFO 2026-06-08 09:32:58 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 2s. Last read position: chr2:215,391,651 INFO 2026-06-08 09:32:58 MarkDuplicates Tracking 1382462 as yet unmatched pairs. 62767 records in RAM. INFO 2026-06-08 09:33:01 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 2s. Last read position: chr2:215,397,222 INFO 2026-06-08 09:33:01 MarkDuplicates Tracking 1380075 as yet unmatched pairs. 60376 records in RAM. INFO 2026-06-08 09:33:03 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 2s. Last read position: chr2:215,406,255 INFO 2026-06-08 09:33:03 MarkDuplicates Tracking 1374695 as yet unmatched pairs. 54986 records in RAM. INFO 2026-06-08 09:33:05 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 2s. Last read position: chr2:215,408,302 INFO 2026-06-08 09:33:05 MarkDuplicates Tracking 1374356 as yet unmatched pairs. 54633 records in RAM. INFO 2026-06-08 09:33:08 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 2s. Last read position: chr2:215,414,837 INFO 2026-06-08 09:33:08 MarkDuplicates Tracking 1362251 as yet unmatched pairs. 42504 records in RAM. INFO 2026-06-08 09:33:10 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 2s. Last read position: chr2:215,423,397 INFO 2026-06-08 09:33:10 MarkDuplicates Tracking 1357171 as yet unmatched pairs. 37423 records in RAM. INFO 2026-06-08 09:33:13 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 2s. Last read position: chr2:215,428,322 INFO 2026-06-08 09:33:13 MarkDuplicates Tracking 1364712 as yet unmatched pairs. 44945 records in RAM. INFO 2026-06-08 09:33:15 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 2s. Last read position: chr2:216,116,755 INFO 2026-06-08 09:33:15 MarkDuplicates Tracking 1342088 as yet unmatched pairs. 22288 records in RAM. INFO 2026-06-08 09:33:17 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 2s. Last read position: chr2:218,075,190 INFO 2026-06-08 09:33:17 MarkDuplicates Tracking 1337751 as yet unmatched pairs. 17923 records in RAM. INFO 2026-06-08 09:33:19 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 2s. Last read position: chr2:219,543,411 INFO 2026-06-08 09:33:19 MarkDuplicates Tracking 1334991 as yet unmatched pairs. 15139 records in RAM. INFO 2026-06-08 09:33:22 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 2s. Last read position: chr2:230,359,015 INFO 2026-06-08 09:33:22 MarkDuplicates Tracking 1332332 as yet unmatched pairs. 12451 records in RAM. INFO 2026-06-08 09:33:24 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 2s. Last read position: chr2:233,204,373 INFO 2026-06-08 09:33:24 MarkDuplicates Tracking 1329654 as yet unmatched pairs. 9750 records in RAM. INFO 2026-06-08 09:33:26 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 2s. Last read position: chr2:237,365,771 INFO 2026-06-08 09:33:26 MarkDuplicates Tracking 1327233 as yet unmatched pairs. 7306 records in RAM. INFO 2026-06-08 09:33:28 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 2s. Last read position: chr2:237,762,950 INFO 2026-06-08 09:33:28 MarkDuplicates Tracking 1324950 as yet unmatched pairs. 5003 records in RAM. INFO 2026-06-08 09:33:30 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 2s. Last read position: chr2:241,256,693 INFO 2026-06-08 09:33:30 MarkDuplicates Tracking 1322000 as yet unmatched pairs. 2026 records in RAM. INFO 2026-06-08 09:33:33 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 2s. Last read position: chr3:9,435,763 INFO 2026-06-08 09:33:33 MarkDuplicates Tracking 1318516 as yet unmatched pairs. 74541 records in RAM. INFO 2026-06-08 09:33:35 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 2s. Last read position: chr3:12,606,264 INFO 2026-06-08 09:33:35 MarkDuplicates Tracking 1318486 as yet unmatched pairs. 74491 records in RAM. INFO 2026-06-08 09:33:38 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 2s. Last read position: chr3:17,372,093 INFO 2026-06-08 09:33:38 MarkDuplicates Tracking 1313033 as yet unmatched pairs. 69011 records in RAM. INFO 2026-06-08 09:33:40 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 2s. Last read position: chr3:33,124,477 INFO 2026-06-08 09:33:40 MarkDuplicates Tracking 1310649 as yet unmatched pairs. 66585 records in RAM. INFO 2026-06-08 09:33:42 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 2s. Last read position: chr3:39,394,501 INFO 2026-06-08 09:33:42 MarkDuplicates Tracking 1307660 as yet unmatched pairs. 63557 records in RAM. INFO 2026-06-08 09:33:44 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 2s. Last read position: chr3:43,347,378 INFO 2026-06-08 09:33:44 MarkDuplicates Tracking 1304921 as yet unmatched pairs. 60809 records in RAM. INFO 2026-06-08 09:33:46 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 2s. Last read position: chr3:47,406,502 INFO 2026-06-08 09:33:46 MarkDuplicates Tracking 1302201 as yet unmatched pairs. 58059 records in RAM. INFO 2026-06-08 09:33:48 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:06:16s. Time for last 1,000,000: 2s. Last read position: chr3:48,501,174 INFO 2026-06-08 09:33:48 MarkDuplicates Tracking 1299827 as yet unmatched pairs. 55668 records in RAM. INFO 2026-06-08 09:33:51 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 2s. Last read position: chr3:49,117,975 INFO 2026-06-08 09:33:51 MarkDuplicates Tracking 1296396 as yet unmatched pairs. 52216 records in RAM. INFO 2026-06-08 09:33:53 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 2s. Last read position: chr3:49,683,273 INFO 2026-06-08 09:33:53 MarkDuplicates Tracking 1293441 as yet unmatched pairs. 49214 records in RAM. INFO 2026-06-08 09:33:55 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 2s. Last read position: chr3:51,387,752 INFO 2026-06-08 09:33:55 MarkDuplicates Tracking 1290637 as yet unmatched pairs. 46378 records in RAM. INFO 2026-06-08 09:33:57 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 2s. Last read position: chr3:52,548,105 INFO 2026-06-08 09:33:57 MarkDuplicates Tracking 1287730 as yet unmatched pairs. 43449 records in RAM. INFO 2026-06-08 09:34:00 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 2s. Last read position: chr3:58,081,690 INFO 2026-06-08 09:34:00 MarkDuplicates Tracking 1285519 as yet unmatched pairs. 41229 records in RAM. INFO 2026-06-08 09:34:02 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:06:30s. Time for last 1,000,000: 2s. Last read position: chr3:65,356,498 INFO 2026-06-08 09:34:02 MarkDuplicates Tracking 1282488 as yet unmatched pairs. 38164 records in RAM. INFO 2026-06-08 09:34:04 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 1s. Last read position: chr3:94,056,275 INFO 2026-06-08 09:34:04 MarkDuplicates Tracking 1279803 as yet unmatched pairs. 35452 records in RAM. INFO 2026-06-08 09:34:06 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 2s. Last read position: chr3:101,821,564 INFO 2026-06-08 09:34:06 MarkDuplicates Tracking 1277410 as yet unmatched pairs. 33035 records in RAM. INFO 2026-06-08 09:34:08 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 2s. Last read position: chr3:113,626,190 INFO 2026-06-08 09:34:08 MarkDuplicates Tracking 1275191 as yet unmatched pairs. 30782 records in RAM. INFO 2026-06-08 09:34:10 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 2s. Last read position: chr3:121,698,652 INFO 2026-06-08 09:34:10 MarkDuplicates Tracking 1272923 as yet unmatched pairs. 28447 records in RAM. INFO 2026-06-08 09:34:13 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 2s. Last read position: chr3:125,279,213 INFO 2026-06-08 09:34:13 MarkDuplicates Tracking 1270317 as yet unmatched pairs. 25825 records in RAM. INFO 2026-06-08 09:34:16 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 2s. Last read position: chr3:129,268,505 INFO 2026-06-08 09:34:16 MarkDuplicates Tracking 1267015 as yet unmatched pairs. 22487 records in RAM. INFO 2026-06-08 09:34:18 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:06:46s. Time for last 1,000,000: 2s. Last read position: chr3:134,371,144 INFO 2026-06-08 09:34:18 MarkDuplicates Tracking 1264203 as yet unmatched pairs. 19646 records in RAM. INFO 2026-06-08 09:34:20 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 2s. Last read position: chr3:142,356,909 INFO 2026-06-08 09:34:20 MarkDuplicates Tracking 1261862 as yet unmatched pairs. 17261 records in RAM. INFO 2026-06-08 09:34:22 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 2s. Last read position: chr3:150,583,265 INFO 2026-06-08 09:34:22 MarkDuplicates Tracking 1259481 as yet unmatched pairs. 14858 records in RAM. INFO 2026-06-08 09:34:24 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 2s. Last read position: chr3:168,032,636 INFO 2026-06-08 09:34:24 MarkDuplicates Tracking 1256689 as yet unmatched pairs. 12030 records in RAM. INFO 2026-06-08 09:34:26 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 2s. Last read position: chr3:179,401,250 INFO 2026-06-08 09:34:26 MarkDuplicates Tracking 1254495 as yet unmatched pairs. 9799 records in RAM. INFO 2026-06-08 09:34:29 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 2s. Last read position: chr3:184,322,023 INFO 2026-06-08 09:34:29 MarkDuplicates Tracking 1251617 as yet unmatched pairs. 6895 records in RAM. INFO 2026-06-08 09:34:31 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 1s. Last read position: chr3:188,609,320 INFO 2026-06-08 09:34:31 MarkDuplicates Tracking 1250147 as yet unmatched pairs. 5398 records in RAM. INFO 2026-06-08 09:34:33 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 2s. Last read position: chr3:196,239,706 INFO 2026-06-08 09:34:33 MarkDuplicates Tracking 1246334 as yet unmatched pairs. 1548 records in RAM. INFO 2026-06-08 09:34:36 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:07:04s. Time for last 1,000,000: 2s. Last read position: chr4:987,808 INFO 2026-06-08 09:34:36 MarkDuplicates Tracking 1243604 as yet unmatched pairs. 47506 records in RAM. INFO 2026-06-08 09:34:38 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 2s. Last read position: chr4:2,663,246 INFO 2026-06-08 09:34:38 MarkDuplicates Tracking 1240656 as yet unmatched pairs. 44516 records in RAM. INFO 2026-06-08 09:34:40 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 2s. Last read position: chr4:6,861,981 INFO 2026-06-08 09:34:40 MarkDuplicates Tracking 1237245 as yet unmatched pairs. 41080 records in RAM. INFO 2026-06-08 09:34:42 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 1s. Last read position: chr4:16,176,186 INFO 2026-06-08 09:34:42 MarkDuplicates Tracking 1234677 as yet unmatched pairs. 38476 records in RAM. INFO 2026-06-08 09:34:44 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:07:12s. Time for last 1,000,000: 2s. Last read position: chr4:39,467,549 INFO 2026-06-08 09:34:44 MarkDuplicates Tracking 1231765 as yet unmatched pairs. 35532 records in RAM. INFO 2026-06-08 09:34:46 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:07:14s. Time for last 1,000,000: 2s. Last read position: chr4:48,857,227 INFO 2026-06-08 09:34:46 MarkDuplicates Tracking 1229678 as yet unmatched pairs. 33407 records in RAM. INFO 2026-06-08 09:34:49 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:07:17s. Time for last 1,000,000: 2s. Last read position: chr4:57,031,144 INFO 2026-06-08 09:34:49 MarkDuplicates Tracking 1228087 as yet unmatched pairs. 31797 records in RAM. INFO 2026-06-08 09:34:51 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:07:19s. Time for last 1,000,000: 2s. Last read position: chr4:75,914,907 INFO 2026-06-08 09:34:51 MarkDuplicates Tracking 1224032 as yet unmatched pairs. 27689 records in RAM. INFO 2026-06-08 09:34:53 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:07:21s. Time for last 1,000,000: 2s. Last read position: chr4:82,427,206 INFO 2026-06-08 09:34:53 MarkDuplicates Tracking 1221769 as yet unmatched pairs. 25401 records in RAM. INFO 2026-06-08 09:34:55 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:07:23s. Time for last 1,000,000: 2s. Last read position: chr4:87,422,988 INFO 2026-06-08 09:34:55 MarkDuplicates Tracking 1218894 as yet unmatched pairs. 22505 records in RAM. INFO 2026-06-08 09:34:57 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:07:25s. Time for last 1,000,000: 2s. Last read position: chr4:95,154,812 INFO 2026-06-08 09:34:57 MarkDuplicates Tracking 1220927 as yet unmatched pairs. 24521 records in RAM. INFO 2026-06-08 09:35:00 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 2s. Last read position: chr4:104,491,836 INFO 2026-06-08 09:35:00 MarkDuplicates Tracking 1214087 as yet unmatched pairs. 17657 records in RAM. INFO 2026-06-08 09:35:02 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:07:29s. Time for last 1,000,000: 2s. Last read position: chr4:112,560,850 INFO 2026-06-08 09:35:02 MarkDuplicates Tracking 1211444 as yet unmatched pairs. 14997 records in RAM. INFO 2026-06-08 09:35:04 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:07:32s. Time for last 1,000,000: 2s. Last read position: chr4:122,239,907 INFO 2026-06-08 09:35:04 MarkDuplicates Tracking 1209160 as yet unmatched pairs. 12666 records in RAM. INFO 2026-06-08 09:35:06 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:07:34s. Time for last 1,000,000: 2s. Last read position: chr4:140,622,632 INFO 2026-06-08 09:35:06 MarkDuplicates Tracking 1207443 as yet unmatched pairs. 10910 records in RAM. INFO 2026-06-08 09:35:08 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:07:36s. Time for last 1,000,000: 2s. Last read position: chr4:149,986,915 INFO 2026-06-08 09:35:08 MarkDuplicates Tracking 1204013 as yet unmatched pairs. 7428 records in RAM. INFO 2026-06-08 09:35:10 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:07:38s. Time for last 1,000,000: 2s. Last read position: chr4:153,788,407 INFO 2026-06-08 09:35:10 MarkDuplicates Tracking 1206170 as yet unmatched pairs. 9565 records in RAM. INFO 2026-06-08 09:35:13 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:07:40s. Time for last 1,000,000: 2s. Last read position: chr4:173,207,429 INFO 2026-06-08 09:35:13 MarkDuplicates Tracking 1199326 as yet unmatched pairs. 2695 records in RAM. INFO 2026-06-08 09:35:15 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:07:43s. Time for last 1,000,000: 2s. Last read position: chr5:462,202 INFO 2026-06-08 09:35:15 MarkDuplicates Tracking 1196271 as yet unmatched pairs. 74610 records in RAM. INFO 2026-06-08 09:35:18 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:07:46s. Time for last 1,000,000: 2s. Last read position: chr5:14,330,789 INFO 2026-06-08 09:35:18 MarkDuplicates Tracking 1193766 as yet unmatched pairs. 72091 records in RAM. INFO 2026-06-08 09:35:20 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:07:48s. Time for last 1,000,000: 2s. Last read position: chr5:21,491,476 INFO 2026-06-08 09:35:20 MarkDuplicates Tracking 1190641 as yet unmatched pairs. 68934 records in RAM. INFO 2026-06-08 09:35:22 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:07:50s. Time for last 1,000,000: 2s. Last read position: chr5:35,089,599 INFO 2026-06-08 09:35:22 MarkDuplicates Tracking 1188862 as yet unmatched pairs. 67134 records in RAM. INFO 2026-06-08 09:35:24 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:07:52s. Time for last 1,000,000: 2s. Last read position: chr5:42,800,722 INFO 2026-06-08 09:35:24 MarkDuplicates Tracking 1187257 as yet unmatched pairs. 65515 records in RAM. INFO 2026-06-08 09:35:27 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:07:54s. Time for last 1,000,000: 2s. Last read position: chr5:55,951,508 INFO 2026-06-08 09:35:27 MarkDuplicates Tracking 1186950 as yet unmatched pairs. 65173 records in RAM. INFO 2026-06-08 09:35:29 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:07:57s. Time for last 1,000,000: 2s. Last read position: chr5:65,542,823 INFO 2026-06-08 09:35:29 MarkDuplicates Tracking 1181221 as yet unmatched pairs. 59437 records in RAM. INFO 2026-06-08 09:35:31 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:07:59s. Time for last 1,000,000: 2s. Last read position: chr5:69,590,354 INFO 2026-06-08 09:35:31 MarkDuplicates Tracking 1178741 as yet unmatched pairs. 56947 records in RAM. INFO 2026-06-08 09:35:33 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:08:01s. Time for last 1,000,000: 1s. Last read position: chr5:71,035,713 INFO 2026-06-08 09:35:33 MarkDuplicates Tracking 1179876 as yet unmatched pairs. 58067 records in RAM. INFO 2026-06-08 09:35:35 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:08:03s. Time for last 1,000,000: 2s. Last read position: chr5:74,720,698 INFO 2026-06-08 09:35:35 MarkDuplicates Tracking 1175829 as yet unmatched pairs. 54003 records in RAM. INFO 2026-06-08 09:35:38 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 2s. Last read position: chr5:81,420,398 INFO 2026-06-08 09:35:38 MarkDuplicates Tracking 1174027 as yet unmatched pairs. 52171 records in RAM. INFO 2026-06-08 09:35:40 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:08:07s. Time for last 1,000,000: 2s. Last read position: chr5:87,363,386 INFO 2026-06-08 09:35:40 MarkDuplicates Tracking 1170971 as yet unmatched pairs. 49103 records in RAM. INFO 2026-06-08 09:35:42 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:08:10s. Time for last 1,000,000: 2s. Last read position: chr5:98,894,655 INFO 2026-06-08 09:35:42 MarkDuplicates Tracking 1168438 as yet unmatched pairs. 46508 records in RAM. INFO 2026-06-08 09:35:44 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:08:12s. Time for last 1,000,000: 2s. Last read position: chr5:115,870,100 INFO 2026-06-08 09:35:44 MarkDuplicates Tracking 1166259 as yet unmatched pairs. 44307 records in RAM. INFO 2026-06-08 09:35:46 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:08:14s. Time for last 1,000,000: 2s. Last read position: chr5:131,435,938 INFO 2026-06-08 09:35:46 MarkDuplicates Tracking 1163433 as yet unmatched pairs. 41459 records in RAM. INFO 2026-06-08 09:35:48 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 2s. Last read position: chr5:134,609,610 INFO 2026-06-08 09:35:48 MarkDuplicates Tracking 1161221 as yet unmatched pairs. 39228 records in RAM. INFO 2026-06-08 09:35:51 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 2s. Last read position: chr5:138,567,117 INFO 2026-06-08 09:35:51 MarkDuplicates Tracking 1158819 as yet unmatched pairs. 36809 records in RAM. INFO 2026-06-08 09:35:53 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 2s. Last read position: chr5:140,632,617 INFO 2026-06-08 09:35:53 MarkDuplicates Tracking 1155463 as yet unmatched pairs. 33428 records in RAM. INFO 2026-06-08 09:35:55 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 2s. Last read position: chr5:143,400,101 INFO 2026-06-08 09:35:55 MarkDuplicates Tracking 1152804 as yet unmatched pairs. 30748 records in RAM. INFO 2026-06-08 09:35:58 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 2s. Last read position: chr5:150,120,915 INFO 2026-06-08 09:35:58 MarkDuplicates Tracking 1152943 as yet unmatched pairs. 30870 records in RAM. INFO 2026-06-08 09:36:00 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:08:28s. Time for last 1,000,000: 2s. Last read position: chr5:150,402,209 INFO 2026-06-08 09:36:00 MarkDuplicates Tracking 1189635 as yet unmatched pairs. 67546 records in RAM. INFO 2026-06-08 09:36:02 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:08:30s. Time for last 1,000,000: 2s. Last read position: chr5:150,405,122 INFO 2026-06-08 09:36:02 MarkDuplicates Tracking 1170835 as yet unmatched pairs. 48733 records in RAM. INFO 2026-06-08 09:36:05 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 2s. Last read position: chr5:150,649,460 INFO 2026-06-08 09:36:05 MarkDuplicates Tracking 1140826 as yet unmatched pairs. 18712 records in RAM. INFO 2026-06-08 09:36:07 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 2s. Last read position: chr5:154,033,861 INFO 2026-06-08 09:36:07 MarkDuplicates Tracking 1137844 as yet unmatched pairs. 15711 records in RAM. INFO 2026-06-08 09:36:09 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 2s. Last read position: chr5:169,803,104 INFO 2026-06-08 09:36:09 MarkDuplicates Tracking 1135166 as yet unmatched pairs. 13014 records in RAM. INFO 2026-06-08 09:36:11 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:08:39s. Time for last 1,000,000: 2s. Last read position: chr5:171,410,662 INFO 2026-06-08 09:36:11 MarkDuplicates Tracking 1134342 as yet unmatched pairs. 12172 records in RAM. INFO 2026-06-08 09:36:13 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:08:41s. Time for last 1,000,000: 2s. Last read position: chr5:176,969,549 INFO 2026-06-08 09:36:13 MarkDuplicates Tracking 1130624 as yet unmatched pairs. 8426 records in RAM. INFO 2026-06-08 09:36:16 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:08:44s. Time for last 1,000,000: 2s. Last read position: chr5:179,313,823 INFO 2026-06-08 09:36:16 MarkDuplicates Tracking 1127340 as yet unmatched pairs. 5130 records in RAM. INFO 2026-06-08 09:36:18 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:08:46s. Time for last 1,000,000: 2s. Last read position: chr5:179,833,606 INFO 2026-06-08 09:36:18 MarkDuplicates Tracking 1128759 as yet unmatched pairs. 6538 records in RAM. INFO 2026-06-08 09:36:21 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 2s. Last read position: chr6:2,948,269 INFO 2026-06-08 09:36:21 MarkDuplicates Tracking 1121940 as yet unmatched pairs. 71960 records in RAM. INFO 2026-06-08 09:36:23 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 2s. Last read position: chr6:7,240,360 INFO 2026-06-08 09:36:23 MarkDuplicates Tracking 1119998 as yet unmatched pairs. 69997 records in RAM. INFO 2026-06-08 09:36:26 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:08:53s. Time for last 1,000,000: 2s. Last read position: chr6:13,632,382 INFO 2026-06-08 09:36:26 MarkDuplicates Tracking 1116828 as yet unmatched pairs. 66813 records in RAM. INFO 2026-06-08 09:36:28 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:08:55s. Time for last 1,000,000: 2s. Last read position: chr6:25,966,468 INFO 2026-06-08 09:36:28 MarkDuplicates Tracking 1114047 as yet unmatched pairs. 63994 records in RAM. INFO 2026-06-08 09:36:30 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:08:57s. Time for last 1,000,000: 2s. Last read position: chr6:27,814,375 INFO 2026-06-08 09:36:30 MarkDuplicates Tracking 1112201 as yet unmatched pairs. 62136 records in RAM. INFO 2026-06-08 09:36:32 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:09:00s. Time for last 1,000,000: 2s. Last read position: chr6:30,604,199 INFO 2026-06-08 09:36:32 MarkDuplicates Tracking 1108795 as yet unmatched pairs. 58724 records in RAM. INFO 2026-06-08 09:36:34 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:09:02s. Time for last 1,000,000: 2s. Last read position: chr6:31,356,704 INFO 2026-06-08 09:36:34 MarkDuplicates Tracking 1106182 as yet unmatched pairs. 56096 records in RAM. INFO 2026-06-08 09:36:36 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:09:04s. Time for last 1,000,000: 2s. Last read position: chr6:31,791,718 INFO 2026-06-08 09:36:36 MarkDuplicates Tracking 1103167 as yet unmatched pairs. 53067 records in RAM. INFO 2026-06-08 09:36:38 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:09:06s. Time for last 1,000,000: 2s. Last read position: chr6:31,948,390 INFO 2026-06-08 09:36:38 MarkDuplicates Tracking 1101575 as yet unmatched pairs. 51471 records in RAM. INFO 2026-06-08 09:36:40 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 1s. Last read position: chr6:32,442,447 INFO 2026-06-08 09:36:40 MarkDuplicates Tracking 1099540 as yet unmatched pairs. 49422 records in RAM. INFO 2026-06-08 09:36:42 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:09:10s. Time for last 1,000,000: 2s. Last read position: chr6:33,287,639 INFO 2026-06-08 09:36:42 MarkDuplicates Tracking 1096062 as yet unmatched pairs. 45942 records in RAM. INFO 2026-06-08 09:36:45 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:09:12s. Time for last 1,000,000: 2s. Last read position: chr6:34,341,905 INFO 2026-06-08 09:36:45 MarkDuplicates Tracking 1093524 as yet unmatched pairs. 43392 records in RAM. INFO 2026-06-08 09:36:47 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 2s. Last read position: chr6:36,968,899 INFO 2026-06-08 09:36:47 MarkDuplicates Tracking 1092516 as yet unmatched pairs. 42363 records in RAM. INFO 2026-06-08 09:36:49 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:09:17s. Time for last 1,000,000: 2s. Last read position: chr6:43,009,085 INFO 2026-06-08 09:36:49 MarkDuplicates Tracking 1087857 as yet unmatched pairs. 37672 records in RAM. INFO 2026-06-08 09:36:51 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:09:19s. Time for last 1,000,000: 2s. Last read position: chr6:44,247,159 INFO 2026-06-08 09:36:51 MarkDuplicates Tracking 1085994 as yet unmatched pairs. 35792 records in RAM. INFO 2026-06-08 09:36:53 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:09:21s. Time for last 1,000,000: 2s. Last read position: chr6:53,013,702 INFO 2026-06-08 09:36:53 MarkDuplicates Tracking 1082535 as yet unmatched pairs. 32261 records in RAM. INFO 2026-06-08 09:36:55 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:09:23s. Time for last 1,000,000: 2s. Last read position: chr6:63,691,884 INFO 2026-06-08 09:36:55 MarkDuplicates Tracking 1080103 as yet unmatched pairs. 29809 records in RAM. INFO 2026-06-08 09:36:58 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 2s. Last read position: chr6:75,165,524 INFO 2026-06-08 09:36:58 MarkDuplicates Tracking 1080258 as yet unmatched pairs. 29946 records in RAM. INFO 2026-06-08 09:37:00 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:09:27s. Time for last 1,000,000: 2s. Last read position: chr6:87,218,635 INFO 2026-06-08 09:37:00 MarkDuplicates Tracking 1075032 as yet unmatched pairs. 24706 records in RAM. INFO 2026-06-08 09:37:02 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:09:30s. Time for last 1,000,000: 2s. Last read position: chr6:108,214,611 INFO 2026-06-08 09:37:02 MarkDuplicates Tracking 1072548 as yet unmatched pairs. 22217 records in RAM. INFO 2026-06-08 09:37:04 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:09:32s. Time for last 1,000,000: 2s. Last read position: chr6:116,692,052 INFO 2026-06-08 09:37:04 MarkDuplicates Tracking 1069865 as yet unmatched pairs. 19530 records in RAM. INFO 2026-06-08 09:37:06 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:09:34s. Time for last 1,000,000: 2s. Last read position: chr6:132,816,536 INFO 2026-06-08 09:37:06 MarkDuplicates Tracking 1067774 as yet unmatched pairs. 17426 records in RAM. INFO 2026-06-08 09:37:08 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:09:36s. Time for last 1,000,000: 2s. Last read position: chr6:138,905,034 INFO 2026-06-08 09:37:08 MarkDuplicates Tracking 1064645 as yet unmatched pairs. 14278 records in RAM. INFO 2026-06-08 09:37:11 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:09:38s. Time for last 1,000,000: 2s. Last read position: chr6:151,350,718 INFO 2026-06-08 09:37:11 MarkDuplicates Tracking 1062002 as yet unmatched pairs. 11622 records in RAM. INFO 2026-06-08 09:37:13 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:09:40s. Time for last 1,000,000: 1s. Last read position: chr6:152,011,653 INFO 2026-06-08 09:37:13 MarkDuplicates Tracking 1063747 as yet unmatched pairs. 13324 records in RAM. INFO 2026-06-08 09:37:15 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:09:43s. Time for last 1,000,000: 2s. Last read position: chr6:158,767,323 INFO 2026-06-08 09:37:15 MarkDuplicates Tracking 1060095 as yet unmatched pairs. 9655 records in RAM. INFO 2026-06-08 09:37:17 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:09:45s. Time for last 1,000,000: 2s. Last read position: chr6:161,049,089 INFO 2026-06-08 09:37:17 MarkDuplicates Tracking 1053588 as yet unmatched pairs. 3128 records in RAM. INFO 2026-06-08 09:37:20 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:09:47s. Time for last 1,000,000: 2s. Last read position: chr6:170,317,849 INFO 2026-06-08 09:37:20 MarkDuplicates Tracking 1051024 as yet unmatched pairs. 555 records in RAM. INFO 2026-06-08 09:37:23 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:09:51s. Time for last 1,000,000: 3s. Last read position: chr7:5,357,082 INFO 2026-06-08 09:37:23 MarkDuplicates Tracking 1047872 as yet unmatched pairs. 74166 records in RAM. INFO 2026-06-08 09:37:25 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:09:53s. Time for last 1,000,000: 2s. Last read position: chr7:5,528,467 INFO 2026-06-08 09:37:25 MarkDuplicates Tracking 1048955 as yet unmatched pairs. 75245 records in RAM. INFO 2026-06-08 09:37:27 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:09:55s. Time for last 1,000,000: 1s. Last read position: chr7:6,387,213 INFO 2026-06-08 09:37:27 MarkDuplicates Tracking 1043392 as yet unmatched pairs. 69663 records in RAM. INFO 2026-06-08 09:37:29 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:09:57s. Time for last 1,000,000: 2s. Last read position: chr7:20,158,489 INFO 2026-06-08 09:37:29 MarkDuplicates Tracking 1039781 as yet unmatched pairs. 66039 records in RAM. INFO 2026-06-08 09:37:31 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 2s. Last read position: chr7:30,601,158 INFO 2026-06-08 09:37:31 MarkDuplicates Tracking 1037207 as yet unmatched pairs. 63447 records in RAM. INFO 2026-06-08 09:37:34 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:10:01s. Time for last 1,000,000: 2s. Last read position: chr7:43,866,810 INFO 2026-06-08 09:37:34 MarkDuplicates Tracking 1035435 as yet unmatched pairs. 61661 records in RAM. INFO 2026-06-08 09:37:36 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:10:04s. Time for last 1,000,000: 2s. Last read position: chr7:44,114,789 INFO 2026-06-08 09:37:36 MarkDuplicates Tracking 1031764 as yet unmatched pairs. 57978 records in RAM. INFO 2026-06-08 09:37:38 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 2s. Last read position: chr7:55,151,305 INFO 2026-06-08 09:37:38 MarkDuplicates Tracking 1028933 as yet unmatched pairs. 55120 records in RAM. INFO 2026-06-08 09:37:40 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:10:08s. Time for last 1,000,000: 1s. Last read position: chr7:72,942,161 INFO 2026-06-08 09:37:40 MarkDuplicates Tracking 1026508 as yet unmatched pairs. 52678 records in RAM. INFO 2026-06-08 09:37:42 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:10:10s. Time for last 1,000,000: 2s. Last read position: chr7:74,195,205 INFO 2026-06-08 09:37:42 MarkDuplicates Tracking 1024835 as yet unmatched pairs. 50995 records in RAM. INFO 2026-06-08 09:37:44 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 1s. Last read position: chr7:75,495,097 INFO 2026-06-08 09:37:44 MarkDuplicates Tracking 1023081 as yet unmatched pairs. 49235 records in RAM. INFO 2026-06-08 09:37:46 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:10:14s. Time for last 1,000,000: 2s. Last read position: chr7:76,303,064 INFO 2026-06-08 09:37:46 MarkDuplicates Tracking 1035600 as yet unmatched pairs. 61742 records in RAM. INFO 2026-06-08 09:37:48 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:10:16s. Time for last 1,000,000: 2s. Last read position: chr7:77,627,425 INFO 2026-06-08 09:37:48 MarkDuplicates Tracking 1017585 as yet unmatched pairs. 43704 records in RAM. INFO 2026-06-08 09:37:50 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:10:18s. Time for last 1,000,000: 2s. Last read position: chr7:92,015,807 INFO 2026-06-08 09:37:50 MarkDuplicates Tracking 1016552 as yet unmatched pairs. 42639 records in RAM. INFO 2026-06-08 09:37:53 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:10:21s. Time for last 1,000,000: 2s. Last read position: chr7:92,089,514 INFO 2026-06-08 09:37:53 MarkDuplicates Tracking 1014508 as yet unmatched pairs. 40591 records in RAM. INFO 2026-06-08 09:37:55 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:10:23s. Time for last 1,000,000: 2s. Last read position: chr7:94,400,206 INFO 2026-06-08 09:37:55 MarkDuplicates Tracking 1014005 as yet unmatched pairs. 40067 records in RAM. INFO 2026-06-08 09:37:58 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 2s. Last read position: chr7:94,420,558 INFO 2026-06-08 09:37:58 MarkDuplicates Tracking 1009223 as yet unmatched pairs. 35272 records in RAM. INFO 2026-06-08 09:38:00 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:10:28s. Time for last 1,000,000: 2s. Last read position: chr7:96,184,317 INFO 2026-06-08 09:38:00 MarkDuplicates Tracking 1004447 as yet unmatched pairs. 30483 records in RAM. INFO 2026-06-08 09:38:02 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:10:30s. Time for last 1,000,000: 2s. Last read position: chr7:100,023,570 INFO 2026-06-08 09:38:02 MarkDuplicates Tracking 1001811 as yet unmatched pairs. 27827 records in RAM. INFO 2026-06-08 09:38:05 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:10:32s. Time for last 1,000,000: 2s. Last read position: chr7:100,819,652 INFO 2026-06-08 09:38:05 MarkDuplicates Tracking 998748 as yet unmatched pairs. 24758 records in RAM. INFO 2026-06-08 09:38:06 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:10:34s. Time for last 1,000,000: 1s. Last read position: chr7:102,640,229 INFO 2026-06-08 09:38:06 MarkDuplicates Tracking 996937 as yet unmatched pairs. 22930 records in RAM. INFO 2026-06-08 09:38:09 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:10:37s. Time for last 1,000,000: 2s. Last read position: chr7:107,600,421 INFO 2026-06-08 09:38:09 MarkDuplicates Tracking 994683 as yet unmatched pairs. 20640 records in RAM. INFO 2026-06-08 09:38:11 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:10:39s. Time for last 1,000,000: 2s. Last read position: chr7:127,374,611 INFO 2026-06-08 09:38:11 MarkDuplicates Tracking 992286 as yet unmatched pairs. 18202 records in RAM. INFO 2026-06-08 09:38:14 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:10:41s. Time for last 1,000,000: 2s. Last read position: chr7:128,947,309 INFO 2026-06-08 09:38:14 MarkDuplicates Tracking 989319 as yet unmatched pairs. 15218 records in RAM. INFO 2026-06-08 09:38:16 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:10:44s. Time for last 1,000,000: 2s. Last read position: chr7:137,908,288 INFO 2026-06-08 09:38:16 MarkDuplicates Tracking 987268 as yet unmatched pairs. 13137 records in RAM. INFO 2026-06-08 09:38:18 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 2s. Last read position: chr7:140,455,883 INFO 2026-06-08 09:38:18 MarkDuplicates Tracking 984753 as yet unmatched pairs. 10605 records in RAM. INFO 2026-06-08 09:38:20 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:10:48s. Time for last 1,000,000: 2s. Last read position: chr7:143,862,862 INFO 2026-06-08 09:38:20 MarkDuplicates Tracking 982048 as yet unmatched pairs. 7888 records in RAM. INFO 2026-06-08 09:38:22 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:10:50s. Time for last 1,000,000: 1s. Last read position: chr7:150,857,550 INFO 2026-06-08 09:38:22 MarkDuplicates Tracking 979020 as yet unmatched pairs. 4852 records in RAM. INFO 2026-06-08 09:38:25 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:10:52s. Time for last 1,000,000: 2s. Last read position: chr7:152,229,923 INFO 2026-06-08 09:38:25 MarkDuplicates Tracking 976803 as yet unmatched pairs. 2627 records in RAM. INFO 2026-06-08 09:38:27 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:10:55s. Time for last 1,000,000: 2s. Last read position: chr8:9,029,815 INFO 2026-06-08 09:38:27 MarkDuplicates Tracking 973638 as yet unmatched pairs. 55468 records in RAM. INFO 2026-06-08 09:38:30 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:10:57s. Time for last 1,000,000: 2s. Last read position: chr8:17,754,684 INFO 2026-06-08 09:38:30 MarkDuplicates Tracking 971093 as yet unmatched pairs. 52919 records in RAM. INFO 2026-06-08 09:38:32 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:11:00s. Time for last 1,000,000: 2s. Last read position: chr8:22,606,980 INFO 2026-06-08 09:38:32 MarkDuplicates Tracking 971317 as yet unmatched pairs. 53136 records in RAM. INFO 2026-06-08 09:38:34 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:11:02s. Time for last 1,000,000: 2s. Last read position: chr8:27,598,089 INFO 2026-06-08 09:38:34 MarkDuplicates Tracking 966639 as yet unmatched pairs. 48441 records in RAM. INFO 2026-06-08 09:38:36 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:11:04s. Time for last 1,000,000: 2s. Last read position: chr8:29,337,065 INFO 2026-06-08 09:38:36 MarkDuplicates Tracking 963575 as yet unmatched pairs. 45360 records in RAM. INFO 2026-06-08 09:38:39 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:11:07s. Time for last 1,000,000: 2s. Last read position: chr8:37,871,468 INFO 2026-06-08 09:38:39 MarkDuplicates Tracking 959564 as yet unmatched pairs. 41336 records in RAM. INFO 2026-06-08 09:38:41 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:11:09s. Time for last 1,000,000: 2s. Last read position: chr8:38,440,281 INFO 2026-06-08 09:38:41 MarkDuplicates Tracking 957710 as yet unmatched pairs. 39466 records in RAM. INFO 2026-06-08 09:38:43 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:11:11s. Time for last 1,000,000: 2s. Last read position: chr8:47,700,401 INFO 2026-06-08 09:38:43 MarkDuplicates Tracking 954379 as yet unmatched pairs. 36126 records in RAM. INFO 2026-06-08 09:38:46 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:11:13s. Time for last 1,000,000: 2s. Last read position: chr8:56,993,318 INFO 2026-06-08 09:38:46 MarkDuplicates Tracking 951188 as yet unmatched pairs. 32921 records in RAM. INFO 2026-06-08 09:38:48 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:11:15s. Time for last 1,000,000: 2s. Last read position: chr8:70,124,841 INFO 2026-06-08 09:38:48 MarkDuplicates Tracking 949985 as yet unmatched pairs. 31684 records in RAM. INFO 2026-06-08 09:38:50 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:11:18s. Time for last 1,000,000: 2s. Last read position: chr8:79,765,275 INFO 2026-06-08 09:38:50 MarkDuplicates Tracking 946346 as yet unmatched pairs. 28033 records in RAM. INFO 2026-06-08 09:38:52 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:11:20s. Time for last 1,000,000: 2s. Last read position: chr8:94,827,766 INFO 2026-06-08 09:38:52 MarkDuplicates Tracking 943937 as yet unmatched pairs. 25609 records in RAM. INFO 2026-06-08 09:38:54 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:11:22s. Time for last 1,000,000: 2s. Last read position: chr8:100,706,708 INFO 2026-06-08 09:38:54 MarkDuplicates Tracking 942238 as yet unmatched pairs. 23897 records in RAM. INFO 2026-06-08 09:38:57 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:11:24s. Time for last 1,000,000: 2s. Last read position: chr8:104,429,570 INFO 2026-06-08 09:38:57 MarkDuplicates Tracking 938724 as yet unmatched pairs. 20364 records in RAM. INFO 2026-06-08 09:38:59 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:11:27s. Time for last 1,000,000: 2s. Last read position: chr8:115,604,787 INFO 2026-06-08 09:38:59 MarkDuplicates Tracking 938479 as yet unmatched pairs. 20081 records in RAM. INFO 2026-06-08 09:39:01 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:11:29s. Time for last 1,000,000: 1s. Last read position: chr8:123,105,428 INFO 2026-06-08 09:39:01 MarkDuplicates Tracking 933818 as yet unmatched pairs. 15390 records in RAM. INFO 2026-06-08 09:39:03 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:11:31s. Time for last 1,000,000: 2s. Last read position: chr8:133,227,614 INFO 2026-06-08 09:39:03 MarkDuplicates Tracking 931332 as yet unmatched pairs. 12884 records in RAM. INFO 2026-06-08 09:39:05 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:11:33s. Time for last 1,000,000: 2s. Last read position: chr8:143,730,178 INFO 2026-06-08 09:39:05 MarkDuplicates Tracking 928128 as yet unmatched pairs. 9660 records in RAM. INFO 2026-06-08 09:39:07 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:11:35s. Time for last 1,000,000: 1s. Last read position: chr8:143,864,584 INFO 2026-06-08 09:39:07 MarkDuplicates Tracking 926691 as yet unmatched pairs. 8222 records in RAM. INFO 2026-06-08 09:39:09 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:11:37s. Time for last 1,000,000: 1s. Last read position: chr8:143,930,037 INFO 2026-06-08 09:39:09 MarkDuplicates Tracking 924121 as yet unmatched pairs. 5637 records in RAM. INFO 2026-06-08 09:39:11 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:11:39s. Time for last 1,000,000: 2s. Last read position: chr8:144,467,040 INFO 2026-06-08 09:39:11 MarkDuplicates Tracking 920236 as yet unmatched pairs. 1739 records in RAM. INFO 2026-06-08 09:39:14 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:11:42s. Time for last 1,000,000: 2s. Last read position: chr9:5,746,079 INFO 2026-06-08 09:39:14 MarkDuplicates Tracking 917131 as yet unmatched pairs. 55249 records in RAM. INFO 2026-06-08 09:39:16 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:11:44s. Time for last 1,000,000: 2s. Last read position: chr9:16,727,978 INFO 2026-06-08 09:39:16 MarkDuplicates Tracking 914536 as yet unmatched pairs. 52635 records in RAM. INFO 2026-06-08 09:39:18 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:11:46s. Time for last 1,000,000: 2s. Last read position: chr9:33,264,253 INFO 2026-06-08 09:39:18 MarkDuplicates Tracking 913409 as yet unmatched pairs. 51476 records in RAM. INFO 2026-06-08 09:39:21 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:11:48s. Time for last 1,000,000: 2s. Last read position: chr9:35,609,603 INFO 2026-06-08 09:39:21 MarkDuplicates Tracking 908800 as yet unmatched pairs. 46855 records in RAM. INFO 2026-06-08 09:39:23 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:11:50s. Time for last 1,000,000: 2s. Last read position: chr9:39,461,781 INFO 2026-06-08 09:39:23 MarkDuplicates Tracking 905836 as yet unmatched pairs. 43865 records in RAM. INFO 2026-06-08 09:39:25 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:11:53s. Time for last 1,000,000: 2s. Last read position: chr9:82,997,046 INFO 2026-06-08 09:39:25 MarkDuplicates Tracking 904355 as yet unmatched pairs. 42343 records in RAM. INFO 2026-06-08 09:39:27 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:11:55s. Time for last 1,000,000: 2s. Last read position: chr9:89,338,463 INFO 2026-06-08 09:39:27 MarkDuplicates Tracking 901580 as yet unmatched pairs. 39551 records in RAM. INFO 2026-06-08 09:39:29 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:11:57s. Time for last 1,000,000: 2s. Last read position: chr9:93,673,729 INFO 2026-06-08 09:39:29 MarkDuplicates Tracking 898952 as yet unmatched pairs. 36902 records in RAM. INFO 2026-06-08 09:39:32 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:11:59s. Time for last 1,000,000: 2s. Last read position: chr9:101,562,338 INFO 2026-06-08 09:39:32 MarkDuplicates Tracking 895877 as yet unmatched pairs. 33799 records in RAM. INFO 2026-06-08 09:39:34 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:12:02s. Time for last 1,000,000: 2s. Last read position: chr9:111,914,631 INFO 2026-06-08 09:39:34 MarkDuplicates Tracking 894852 as yet unmatched pairs. 32751 records in RAM. INFO 2026-06-08 09:39:36 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:12:04s. Time for last 1,000,000: 2s. Last read position: chr9:114,283,744 INFO 2026-06-08 09:39:36 MarkDuplicates Tracking 890412 as yet unmatched pairs. 28301 records in RAM. INFO 2026-06-08 09:39:38 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:12:06s. Time for last 1,000,000: 2s. Last read position: chr9:121,301,941 INFO 2026-06-08 09:39:38 MarkDuplicates Tracking 888725 as yet unmatched pairs. 26590 records in RAM. INFO 2026-06-08 09:39:41 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:12:08s. Time for last 1,000,000: 2s. Last read position: chr9:125,240,197 INFO 2026-06-08 09:39:41 MarkDuplicates Tracking 886548 as yet unmatched pairs. 24396 records in RAM. INFO 2026-06-08 09:39:43 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:12:10s. Time for last 1,000,000: 2s. Last read position: chr9:128,180,433 INFO 2026-06-08 09:39:43 MarkDuplicates Tracking 881563 as yet unmatched pairs. 19366 records in RAM. INFO 2026-06-08 09:39:45 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:12:13s. Time for last 1,000,000: 2s. Last read position: chr9:128,803,983 INFO 2026-06-08 09:39:45 MarkDuplicates Tracking 878385 as yet unmatched pairs. 16173 records in RAM. INFO 2026-06-08 09:39:47 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:12:15s. Time for last 1,000,000: 2s. Last read position: chr9:130,885,067 INFO 2026-06-08 09:39:47 MarkDuplicates Tracking 876368 as yet unmatched pairs. 14143 records in RAM. INFO 2026-06-08 09:39:49 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:12:17s. Time for last 1,000,000: 1s. Last read position: chr9:133,341,553 INFO 2026-06-08 09:39:49 MarkDuplicates Tracking 873109 as yet unmatched pairs. 10875 records in RAM. INFO 2026-06-08 09:39:51 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:12:19s. Time for last 1,000,000: 2s. Last read position: chr9:135,095,929 INFO 2026-06-08 09:39:51 MarkDuplicates Tracking 869794 as yet unmatched pairs. 7535 records in RAM. INFO 2026-06-08 09:39:54 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:12:21s. Time for last 1,000,000: 2s. Last read position: chr9:136,839,076 INFO 2026-06-08 09:39:54 MarkDuplicates Tracking 867373 as yet unmatched pairs. 5110 records in RAM. INFO 2026-06-08 09:39:56 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:12:23s. Time for last 1,000,000: 2s. Last read position: chr9:137,464,352 INFO 2026-06-08 09:39:56 MarkDuplicates Tracking 863498 as yet unmatched pairs. 1232 records in RAM. INFO 2026-06-08 09:39:59 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:12:26s. Time for last 1,000,000: 2s. Last read position: chr10:5,684,991 INFO 2026-06-08 09:39:59 MarkDuplicates Tracking 860593 as yet unmatched pairs. 53056 records in RAM. INFO 2026-06-08 09:40:01 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:12:29s. Time for last 1,000,000: 2s. Last read position: chr10:8,064,018 INFO 2026-06-08 09:40:01 MarkDuplicates Tracking 860413 as yet unmatched pairs. 52865 records in RAM. INFO 2026-06-08 09:40:03 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:12:31s. Time for last 1,000,000: 1s. Last read position: chr10:17,233,592 INFO 2026-06-08 09:40:03 MarkDuplicates Tracking 857260 as yet unmatched pairs. 49700 records in RAM. INFO 2026-06-08 09:40:05 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:12:33s. Time for last 1,000,000: 2s. Last read position: chr10:25,175,702 INFO 2026-06-08 09:40:05 MarkDuplicates Tracking 852686 as yet unmatched pairs. 45105 records in RAM. INFO 2026-06-08 09:40:08 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:12:35s. Time for last 1,000,000: 2s. Last read position: chr10:32,018,121 INFO 2026-06-08 09:40:08 MarkDuplicates Tracking 853247 as yet unmatched pairs. 45643 records in RAM. INFO 2026-06-08 09:40:10 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:12:37s. Time for last 1,000,000: 2s. Last read position: chr10:32,923,594 INFO 2026-06-08 09:40:10 MarkDuplicates Tracking 848866 as yet unmatched pairs. 41249 records in RAM. INFO 2026-06-08 09:40:12 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:12:40s. Time for last 1,000,000: 2s. Last read position: chr10:43,109,034 INFO 2026-06-08 09:40:12 MarkDuplicates Tracking 846496 as yet unmatched pairs. 38846 records in RAM. INFO 2026-06-08 09:40:14 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:12:42s. Time for last 1,000,000: 2s. Last read position: chr10:46,010,655 INFO 2026-06-08 09:40:14 MarkDuplicates Tracking 845368 as yet unmatched pairs. 37707 records in RAM. INFO 2026-06-08 09:40:16 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:12:44s. Time for last 1,000,000: 1s. Last read position: chr10:51,698,949 INFO 2026-06-08 09:40:16 MarkDuplicates Tracking 841479 as yet unmatched pairs. 33803 records in RAM. INFO 2026-06-08 09:40:18 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:12:46s. Time for last 1,000,000: 2s. Last read position: chr10:63,222,260 INFO 2026-06-08 09:40:18 MarkDuplicates Tracking 838981 as yet unmatched pairs. 31288 records in RAM. INFO 2026-06-08 09:40:21 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:12:49s. Time for last 1,000,000: 2s. Last read position: chr10:71,291,098 INFO 2026-06-08 09:40:21 MarkDuplicates Tracking 835954 as yet unmatched pairs. 28237 records in RAM. INFO 2026-06-08 09:40:23 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:12:51s. Time for last 1,000,000: 2s. Last read position: chr10:73,807,754 INFO 2026-06-08 09:40:23 MarkDuplicates Tracking 833412 as yet unmatched pairs. 25677 records in RAM. INFO 2026-06-08 09:40:25 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:12:53s. Time for last 1,000,000: 2s. Last read position: chr10:79,712,813 INFO 2026-06-08 09:40:25 MarkDuplicates Tracking 830702 as yet unmatched pairs. 22952 records in RAM. INFO 2026-06-08 09:40:27 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:12:55s. Time for last 1,000,000: 2s. Last read position: chr10:87,957,938 INFO 2026-06-08 09:40:27 MarkDuplicates Tracking 829430 as yet unmatched pairs. 21654 records in RAM. INFO 2026-06-08 09:40:29 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:12:57s. Time for last 1,000,000: 2s. Last read position: chr10:94,441,900 INFO 2026-06-08 09:40:29 MarkDuplicates Tracking 825870 as yet unmatched pairs. 18081 records in RAM. INFO 2026-06-08 09:40:32 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:12:59s. Time for last 1,000,000: 2s. Last read position: chr10:99,726,967 INFO 2026-06-08 09:40:32 MarkDuplicates Tracking 823172 as yet unmatched pairs. 15374 records in RAM. INFO 2026-06-08 09:40:34 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:13:02s. Time for last 1,000,000: 2s. Last read position: chr10:102,149,934 INFO 2026-06-08 09:40:34 MarkDuplicates Tracking 820302 as yet unmatched pairs. 12482 records in RAM. INFO 2026-06-08 09:40:36 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:13:04s. Time for last 1,000,000: 2s. Last read position: chr10:110,510,181 INFO 2026-06-08 09:40:36 MarkDuplicates Tracking 817674 as yet unmatched pairs. 9845 records in RAM. INFO 2026-06-08 09:40:39 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:13:06s. Time for last 1,000,000: 2s. Last read position: chr10:116,927,814 INFO 2026-06-08 09:40:39 MarkDuplicates Tracking 818841 as yet unmatched pairs. 10996 records in RAM. INFO 2026-06-08 09:40:41 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:13:09s. Time for last 1,000,000: 2s. Last read position: chr10:121,770,976 INFO 2026-06-08 09:40:41 MarkDuplicates Tracking 812749 as yet unmatched pairs. 4888 records in RAM. INFO 2026-06-08 09:40:43 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:13:11s. Time for last 1,000,000: 2s. Last read position: chr10:127,362,181 INFO 2026-06-08 09:40:43 MarkDuplicates Tracking 810061 as yet unmatched pairs. 2185 records in RAM. INFO 2026-06-08 09:40:47 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:13:14s. Time for last 1,000,000: 3s. Last read position: chr11:292,594 INFO 2026-06-08 09:40:47 MarkDuplicates Tracking 808648 as yet unmatched pairs. 113487 records in RAM. INFO 2026-06-08 09:40:49 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:13:17s. Time for last 1,000,000: 2s. Last read position: chr11:320,601 INFO 2026-06-08 09:40:49 MarkDuplicates Tracking 806843 as yet unmatched pairs. 111679 records in RAM. INFO 2026-06-08 09:40:51 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:13:19s. Time for last 1,000,000: 2s. Last read position: chr11:828,908 INFO 2026-06-08 09:40:51 MarkDuplicates Tracking 801135 as yet unmatched pairs. 105963 records in RAM. INFO 2026-06-08 09:40:53 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:13:21s. Time for last 1,000,000: 2s. Last read position: chr11:2,396,806 INFO 2026-06-08 09:40:53 MarkDuplicates Tracking 799070 as yet unmatched pairs. 103882 records in RAM. INFO 2026-06-08 09:40:55 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:13:23s. Time for last 1,000,000: 2s. Last read position: chr11:6,610,220 INFO 2026-06-08 09:40:55 MarkDuplicates Tracking 795534 as yet unmatched pairs. 100324 records in RAM. INFO 2026-06-08 09:40:57 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:13:25s. Time for last 1,000,000: 2s. Last read position: chr11:9,586,784 INFO 2026-06-08 09:40:57 MarkDuplicates Tracking 792208 as yet unmatched pairs. 96975 records in RAM. INFO 2026-06-08 09:41:00 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:13:28s. Time for last 1,000,000: 2s. Last read position: chr11:14,513,636 INFO 2026-06-08 09:41:00 MarkDuplicates Tracking 789746 as yet unmatched pairs. 94503 records in RAM. INFO 2026-06-08 09:41:02 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:13:30s. Time for last 1,000,000: 2s. Last read position: chr11:27,357,425 INFO 2026-06-08 09:41:02 MarkDuplicates Tracking 786707 as yet unmatched pairs. 91453 records in RAM. INFO 2026-06-08 09:41:04 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:13:32s. Time for last 1,000,000: 2s. Last read position: chr11:35,139,182 INFO 2026-06-08 09:41:04 MarkDuplicates Tracking 784364 as yet unmatched pairs. 89091 records in RAM. INFO 2026-06-08 09:41:06 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:13:34s. Time for last 1,000,000: 2s. Last read position: chr11:45,933,999 INFO 2026-06-08 09:41:06 MarkDuplicates Tracking 781750 as yet unmatched pairs. 86464 records in RAM. INFO 2026-06-08 09:41:08 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:13:36s. Time for last 1,000,000: 2s. Last read position: chr11:47,329,051 INFO 2026-06-08 09:41:08 MarkDuplicates Tracking 778839 as yet unmatched pairs. 83539 records in RAM. INFO 2026-06-08 09:41:11 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:13:39s. Time for last 1,000,000: 2s. Last read position: chr11:57,528,854 INFO 2026-06-08 09:41:11 MarkDuplicates Tracking 776855 as yet unmatched pairs. 81518 records in RAM. INFO 2026-06-08 09:41:13 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:13:41s. Time for last 1,000,000: 2s. Last read position: chr11:59,151,895 INFO 2026-06-08 09:41:13 MarkDuplicates Tracking 774005 as yet unmatched pairs. 78661 records in RAM. INFO 2026-06-08 09:41:16 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:13:43s. Time for last 1,000,000: 2s. Last read position: chr11:61,415,714 INFO 2026-06-08 09:41:16 MarkDuplicates Tracking 771398 as yet unmatched pairs. 76039 records in RAM. INFO 2026-06-08 09:41:18 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:13:46s. Time for last 1,000,000: 2s. Last read position: chr11:61,967,411 INFO 2026-06-08 09:41:18 MarkDuplicates Tracking 768637 as yet unmatched pairs. 73260 records in RAM. INFO 2026-06-08 09:41:21 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:13:48s. Time for last 1,000,000: 2s. Last read position: chr11:62,522,381 INFO 2026-06-08 09:41:21 MarkDuplicates Tracking 768653 as yet unmatched pairs. 73272 records in RAM. INFO 2026-06-08 09:41:23 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:13:51s. Time for last 1,000,000: 2s. Last read position: chr11:62,527,872 INFO 2026-06-08 09:41:23 MarkDuplicates Tracking 766277 as yet unmatched pairs. 70893 records in RAM. INFO 2026-06-08 09:41:25 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:13:53s. Time for last 1,000,000: 2s. Last read position: chr11:62,533,486 INFO 2026-06-08 09:41:25 MarkDuplicates Tracking 764048 as yet unmatched pairs. 68661 records in RAM. INFO 2026-06-08 09:41:27 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:13:55s. Time for last 1,000,000: 2s. Last read position: chr11:63,904,117 INFO 2026-06-08 09:41:27 MarkDuplicates Tracking 759088 as yet unmatched pairs. 63700 records in RAM. INFO 2026-06-08 09:41:30 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:13:57s. Time for last 1,000,000: 2s. Last read position: chr11:65,321,114 INFO 2026-06-08 09:41:30 MarkDuplicates Tracking 756136 as yet unmatched pairs. 60733 records in RAM. INFO 2026-06-08 09:41:32 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:14:00s. Time for last 1,000,000: 2s. Last read position: chr11:65,580,349 INFO 2026-06-08 09:41:32 MarkDuplicates Tracking 753412 as yet unmatched pairs. 57872 records in RAM. INFO 2026-06-08 09:41:34 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:14:02s. Time for last 1,000,000: 2s. Last read position: chr11:65,658,803 INFO 2026-06-08 09:41:34 MarkDuplicates Tracking 750808 as yet unmatched pairs. 55261 records in RAM. INFO 2026-06-08 09:41:36 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:14:04s. Time for last 1,000,000: 2s. Last read position: chr11:65,921,378 INFO 2026-06-08 09:41:36 MarkDuplicates Tracking 747001 as yet unmatched pairs. 51444 records in RAM.