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/e9/a1ca6f575e72c11c925044f36fb13c/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/cbf3ac48f19c81b003c31925dd4901/dna_s772.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/a1ca6f575e72c11c925044f36fb13c/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai
==> STAGING COMPLETE (5 inputs)
Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT dna_s772.Aligned.sortedByCoord.out.bam --OUTPUT dna_s772.md.bam --METRICS_FILE dna_s772.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:49:56.247 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Jun 08 07:49:56 GMT 2026] MarkDuplicates --INPUT dna_s772.Aligned.sortedByCoord.out.bam --OUTPUT dna_s772.md.bam --METRICS_FILE dna_s772.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 07:49:56 GMT 2026] Executing as ?@nf-e9a1ca6f575e72c11c925044f36fb13c-c1fff-4xdhp on Linux 6.12.88 amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0
INFO 2026-06-08 07:49:56 MarkDuplicates Start of doWork freeMemory: 105829144; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:49:56 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:49:56 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:50:01 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:3,507,702
INFO 2026-06-08 07:50:01 MarkDuplicates Tracking 2365 as yet unmatched pairs. 229 records in RAM.
INFO 2026-06-08 07:50:04 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 3s. Last read position: chr1:11,130,333
INFO 2026-06-08 07:50:04 MarkDuplicates Tracking 5690 as yet unmatched pairs. 500 records in RAM.
INFO 2026-06-08 07:50:08 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 3s. Last read position: chr1:15,382,029
INFO 2026-06-08 07:50:08 MarkDuplicates Tracking 8178 as yet unmatched pairs. 695 records in RAM.
INFO 2026-06-08 07:50:11 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 3s. Last read position: chr1:16,961,115
INFO 2026-06-08 07:50:11 MarkDuplicates Tracking 10379 as yet unmatched pairs. 665 records in RAM.
INFO 2026-06-08 07:50:14 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 3s. Last read position: chr1:22,953,599
INFO 2026-06-08 07:50:14 MarkDuplicates Tracking 13330 as yet unmatched pairs. 933 records in RAM.
INFO 2026-06-08 07:50:17 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 3s. Last read position: chr1:28,237,914
INFO 2026-06-08 07:50:17 MarkDuplicates Tracking 16147 as yet unmatched pairs. 934 records in RAM.
INFO 2026-06-08 07:50:20 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 3s. Last read position: chr1:36,320,988
INFO 2026-06-08 07:50:20 MarkDuplicates Tracking 19695 as yet unmatched pairs. 1252 records in RAM.
INFO 2026-06-08 07:50:23 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 2s. Last read position: chr1:42,642,108
INFO 2026-06-08 07:50:23 MarkDuplicates Tracking 22471 as yet unmatched pairs. 1144 records in RAM.
INFO 2026-06-08 07:50:26 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 3s. Last read position: chr1:46,272,425
INFO 2026-06-08 07:50:26 MarkDuplicates Tracking 25511 as yet unmatched pairs. 1613 records in RAM.
INFO 2026-06-08 07:50:28 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 2s. Last read position: chr1:56,707,463
INFO 2026-06-08 07:50:28 MarkDuplicates Tracking 28898 as yet unmatched pairs. 1460 records in RAM.
INFO 2026-06-08 07:50:32 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 3s. Last read position: chr1:71,402,362
INFO 2026-06-08 07:50:32 MarkDuplicates Tracking 34964 as yet unmatched pairs. 3077 records in RAM.
INFO 2026-06-08 07:50:35 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 3s. Last read position: chr1:89,777,581
INFO 2026-06-08 07:50:35 MarkDuplicates Tracking 38506 as yet unmatched pairs. 1595 records in RAM.
INFO 2026-06-08 07:50:38 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 2s. Last read position: chr1:103,695,115
INFO 2026-06-08 07:50:38 MarkDuplicates Tracking 42779 as yet unmatched pairs. 1694 records in RAM.
INFO 2026-06-08 07:50:40 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chr1:113,391,215
INFO 2026-06-08 07:50:40 MarkDuplicates Tracking 46092 as yet unmatched pairs. 1835 records in RAM.
INFO 2026-06-08 07:50:43 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: chr1:119,968,133
INFO 2026-06-08 07:50:43 MarkDuplicates Tracking 49792 as yet unmatched pairs. 2349 records in RAM.
INFO 2026-06-08 07:50:46 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 2s. Last read position: chr1:145,961,047
INFO 2026-06-08 07:50:46 MarkDuplicates Tracking 52035 as yet unmatched pairs. 1802 records in RAM.
INFO 2026-06-08 07:50:48 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 2s. Last read position: chr1:150,504,853
INFO 2026-06-08 07:50:48 MarkDuplicates Tracking 54058 as yet unmatched pairs. 1714 records in RAM.
INFO 2026-06-08 07:50:51 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 2s. Last read position: chr1:152,909,996
INFO 2026-06-08 07:50:51 MarkDuplicates Tracking 56382 as yet unmatched pairs. 1924 records in RAM.
INFO 2026-06-08 07:50:54 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 2s. Last read position: chr1:156,528,029
INFO 2026-06-08 07:50:54 MarkDuplicates Tracking 58592 as yet unmatched pairs. 1691 records in RAM.
INFO 2026-06-08 07:50:56 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 2s. Last read position: chr1:160,042,262
INFO 2026-06-08 07:50:56 MarkDuplicates Tracking 61225 as yet unmatched pairs. 1667 records in RAM.
INFO 2026-06-08 07:50:59 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 3s. Last read position: chr1:169,111,288
INFO 2026-06-08 07:50:59 MarkDuplicates Tracking 64518 as yet unmatched pairs. 1525 records in RAM.
INFO 2026-06-08 07:51:01 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 1s. Last read position: chr1:179,588,655
INFO 2026-06-08 07:51:01 MarkDuplicates Tracking 68166 as yet unmatched pairs. 1418 records in RAM.
INFO 2026-06-08 07:51:04 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 2s. Last read position: chr1:197,340,975
INFO 2026-06-08 07:51:04 MarkDuplicates Tracking 72492 as yet unmatched pairs. 1161 records in RAM.
INFO 2026-06-08 07:51:06 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 2s. Last read position: chr1:204,468,934
INFO 2026-06-08 07:51:06 MarkDuplicates Tracking 76263 as yet unmatched pairs. 1912 records in RAM.
INFO 2026-06-08 07:51:08 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 2s. Last read position: chr1:206,772,619
INFO 2026-06-08 07:51:08 MarkDuplicates Tracking 78872 as yet unmatched pairs. 1988 records in RAM.
INFO 2026-06-08 07:51:11 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 2s. Last read position: chr1:222,654,854
INFO 2026-06-08 07:51:11 MarkDuplicates Tracking 81855 as yet unmatched pairs. 709 records in RAM.
INFO 2026-06-08 07:51:13 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 2s. Last read position: chr1:228,464,427
INFO 2026-06-08 07:51:13 MarkDuplicates Tracking 84690 as yet unmatched pairs. 585 records in RAM.
INFO 2026-06-08 07:51:17 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 3s. Last read position: chr1:243,500,667
INFO 2026-06-08 07:51:17 MarkDuplicates Tracking 90506 as yet unmatched pairs. 1943 records in RAM.
INFO 2026-06-08 07:51:20 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 3s. Last read position: chr2:5,698,016
INFO 2026-06-08 07:51:20 MarkDuplicates Tracking 93153 as yet unmatched pairs. 25757 records in RAM.
INFO 2026-06-08 07:51:22 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 2s. Last read position: chr2:24,122,478
INFO 2026-06-08 07:51:22 MarkDuplicates Tracking 96711 as yet unmatched pairs. 25492 records in RAM.
INFO 2026-06-08 07:51:26 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 3s. Last read position: chr2:27,472,410
INFO 2026-06-08 07:51:26 MarkDuplicates Tracking 99022 as yet unmatched pairs. 26116 records in RAM.
INFO 2026-06-08 07:51:29 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 3s. Last read position: chr2:32,916,264
INFO 2026-06-08 07:51:29 MarkDuplicates Tracking 180114 as yet unmatched pairs. 22838 records in RAM.
INFO 2026-06-08 07:51:32 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 2s. Last read position: chr2:40,856,044
INFO 2026-06-08 07:51:32 MarkDuplicates Tracking 268075 as yet unmatched pairs. 18327 records in RAM.
INFO 2026-06-08 07:51:34 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 2s. Last read position: chr2:48,687,737
INFO 2026-06-08 07:51:34 MarkDuplicates Tracking 269932 as yet unmatched pairs. 17718 records in RAM.
INFO 2026-06-08 07:51:37 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 2s. Last read position: chr2:63,890,136
INFO 2026-06-08 07:51:37 MarkDuplicates Tracking 272366 as yet unmatched pairs. 16799 records in RAM.
INFO 2026-06-08 07:51:40 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 2s. Last read position: chr2:74,417,260
INFO 2026-06-08 07:51:40 MarkDuplicates Tracking 274073 as yet unmatched pairs. 15893 records in RAM.
INFO 2026-06-08 07:51:42 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 1s. Last read position: chr2:87,816,780
INFO 2026-06-08 07:51:42 MarkDuplicates Tracking 276508 as yet unmatched pairs. 15467 records in RAM.
INFO 2026-06-08 07:51:45 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 2s. Last read position: chr2:97,030,292
INFO 2026-06-08 07:51:45 MarkDuplicates Tracking 277745 as yet unmatched pairs. 14575 records in RAM.
INFO 2026-06-08 07:51:48 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 3s. Last read position: chr2:105,277,776
INFO 2026-06-08 07:51:48 MarkDuplicates Tracking 279285 as yet unmatched pairs. 13712 records in RAM.
INFO 2026-06-08 07:51:50 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 2s. Last read position: chr2:110,543,604
INFO 2026-06-08 07:51:50 MarkDuplicates Tracking 280441 as yet unmatched pairs. 13143 records in RAM.
INFO 2026-06-08 07:51:54 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 3s. Last read position: chr2:113,229,935
INFO 2026-06-08 07:51:54 MarkDuplicates Tracking 282982 as yet unmatched pairs. 14216 records in RAM.
INFO 2026-06-08 07:51:57 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 3s. Last read position: chr2:128,152,915
INFO 2026-06-08 07:51:57 MarkDuplicates Tracking 283323 as yet unmatched pairs. 11413 records in RAM.
INFO 2026-06-08 07:52:00 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 2s. Last read position: chr2:140,231,972
INFO 2026-06-08 07:52:00 MarkDuplicates Tracking 285898 as yet unmatched pairs. 11352 records in RAM.
INFO 2026-06-08 07:52:03 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 3s. Last read position: chr2:158,854,031
INFO 2026-06-08 07:52:03 MarkDuplicates Tracking 287738 as yet unmatched pairs. 9312 records in RAM.
INFO 2026-06-08 07:52:06 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 2s. Last read position: chr2:172,595,893
INFO 2026-06-08 07:52:06 MarkDuplicates Tracking 290667 as yet unmatched pairs. 8987 records in RAM.
INFO 2026-06-08 07:52:08 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 2s. Last read position: chr2:178,654,926
INFO 2026-06-08 07:52:08 MarkDuplicates Tracking 291559 as yet unmatched pairs. 7512 records in RAM.
INFO 2026-06-08 07:52:11 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 2s. Last read position: chr2:190,514,520
INFO 2026-06-08 07:52:11 MarkDuplicates Tracking 293268 as yet unmatched pairs. 6334 records in RAM.
INFO 2026-06-08 07:52:13 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 2s. Last read position: chr2:203,315,333
INFO 2026-06-08 07:52:13 MarkDuplicates Tracking 295319 as yet unmatched pairs. 5274 records in RAM.
INFO 2026-06-08 07:52:16 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 3s. Last read position: chr2:215,383,337
INFO 2026-06-08 07:52:16 MarkDuplicates Tracking 297436 as yet unmatched pairs. 4232 records in RAM.
INFO 2026-06-08 07:52:20 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 3s. Last read position: chr2:222,209,546
INFO 2026-06-08 07:52:20 MarkDuplicates Tracking 298543 as yet unmatched pairs. 3188 records in RAM.
INFO 2026-06-08 07:52:22 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 2s. Last read position: chr2:230,573,822
INFO 2026-06-08 07:52:22 MarkDuplicates Tracking 299908 as yet unmatched pairs. 1990 records in RAM.
INFO 2026-06-08 07:52:25 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 2s. Last read position: chr2:239,068,725
INFO 2026-06-08 07:52:25 MarkDuplicates Tracking 301565 as yet unmatched pairs. 1326 records in RAM.
INFO 2026-06-08 07:52:27 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 2s. Last read position: chr3:8,985,771
INFO 2026-06-08 07:52:27 MarkDuplicates Tracking 302536 as yet unmatched pairs. 21830 records in RAM.
INFO 2026-06-08 07:52:30 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 2s. Last read position: chr3:12,316,829
INFO 2026-06-08 07:52:30 MarkDuplicates Tracking 304259 as yet unmatched pairs. 21807 records in RAM.
INFO 2026-06-08 07:52:33 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 2s. Last read position: chr3:12,377,214
INFO 2026-06-08 07:52:33 MarkDuplicates Tracking 305372 as yet unmatched pairs. 21368 records in RAM.
INFO 2026-06-08 07:52:35 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 2s. Last read position: chr3:23,893,115
INFO 2026-06-08 07:52:35 MarkDuplicates Tracking 305694 as yet unmatched pairs. 19012 records in RAM.
INFO 2026-06-08 07:52:38 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 2s. Last read position: chr3:38,605,200
INFO 2026-06-08 07:52:38 MarkDuplicates Tracking 307585 as yet unmatched pairs. 17754 records in RAM.
INFO 2026-06-08 07:52:39 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 1s. Last read position: chr3:47,004,905
INFO 2026-06-08 07:52:39 MarkDuplicates Tracking 309026 as yet unmatched pairs. 16875 records in RAM.
INFO 2026-06-08 07:52:42 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 2s. Last read position: chr3:49,687,723
INFO 2026-06-08 07:52:42 MarkDuplicates Tracking 310021 as yet unmatched pairs. 16447 records in RAM.
INFO 2026-06-08 07:52:44 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 2s. Last read position: chr3:52,545,586
INFO 2026-06-08 07:52:44 MarkDuplicates Tracking 311108 as yet unmatched pairs. 16042 records in RAM.
INFO 2026-06-08 07:52:46 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 1s. Last read position: chr3:64,603,846
INFO 2026-06-08 07:52:46 MarkDuplicates Tracking 311430 as yet unmatched pairs. 13649 records in RAM.
INFO 2026-06-08 07:52:49 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 3s. Last read position: chr3:84,201,713
INFO 2026-06-08 07:52:49 MarkDuplicates Tracking 313878 as yet unmatched pairs. 12149 records in RAM.
INFO 2026-06-08 07:52:52 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 2s. Last read position: chr3:111,112,000
INFO 2026-06-08 07:52:52 MarkDuplicates Tracking 316820 as yet unmatched pairs. 10560 records in RAM.
INFO 2026-06-08 07:52:56 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 3s. Last read position: chr3:122,687,078
INFO 2026-06-08 07:52:56 MarkDuplicates Tracking 318349 as yet unmatched pairs. 9341 records in RAM.
INFO 2026-06-08 07:52:59 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 3s. Last read position: chr3:130,469,189
INFO 2026-06-08 07:52:59 MarkDuplicates Tracking 319933 as yet unmatched pairs. 8944 records in RAM.
INFO 2026-06-08 07:53:02 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 2s. Last read position: chr3:139,462,140
INFO 2026-06-08 07:53:02 MarkDuplicates Tracking 320357 as yet unmatched pairs. 7007 records in RAM.
INFO 2026-06-08 07:53:04 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 1s. Last read position: chr3:156,927,428
INFO 2026-06-08 07:53:04 MarkDuplicates Tracking 322278 as yet unmatched pairs. 5460 records in RAM.
INFO 2026-06-08 07:53:06 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 2s. Last read position: chr3:179,239,917
INFO 2026-06-08 07:53:06 MarkDuplicates Tracking 325305 as yet unmatched pairs. 4282 records in RAM.
INFO 2026-06-08 07:53:08 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 2s. Last read position: chr3:185,484,152
INFO 2026-06-08 07:53:08 MarkDuplicates Tracking 326652 as yet unmatched pairs. 3589 records in RAM.
INFO 2026-06-08 07:53:11 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 2s. Last read position: chr3:194,405,926
INFO 2026-06-08 07:53:11 MarkDuplicates Tracking 326544 as yet unmatched pairs. 858 records in RAM.
INFO 2026-06-08 07:53:13 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 2s. Last read position: chr4:1,799,486
INFO 2026-06-08 07:53:13 MarkDuplicates Tracking 327784 as yet unmatched pairs. 18995 records in RAM.
INFO 2026-06-08 07:53:15 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 1s. Last read position: chr4:7,001,147
INFO 2026-06-08 07:53:15 MarkDuplicates Tracking 327766 as yet unmatched pairs. 17263 records in RAM.
INFO 2026-06-08 07:53:17 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 2s. Last read position: chr4:20,253,221
INFO 2026-06-08 07:53:17 MarkDuplicates Tracking 330516 as yet unmatched pairs. 17508 records in RAM.
INFO 2026-06-08 07:53:20 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 2s. Last read position: chr4:41,744,692
INFO 2026-06-08 07:53:20 MarkDuplicates Tracking 332387 as yet unmatched pairs. 15585 records in RAM.
INFO 2026-06-08 07:53:23 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 2s. Last read position: chr4:55,087,502
INFO 2026-06-08 07:53:23 MarkDuplicates Tracking 332619 as yet unmatched pairs. 12994 records in RAM.
INFO 2026-06-08 07:53:25 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 1s. Last read position: chr4:72,548,608
INFO 2026-06-08 07:53:25 MarkDuplicates Tracking 334129 as yet unmatched pairs. 11305 records in RAM.
INFO 2026-06-08 07:53:28 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 3s. Last read position: chr4:86,772,755
INFO 2026-06-08 07:53:28 MarkDuplicates Tracking 335235 as yet unmatched pairs. 9590 records in RAM.
INFO 2026-06-08 07:53:30 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 2s. Last read position: chr4:105,275,640
INFO 2026-06-08 07:53:30 MarkDuplicates Tracking 337607 as yet unmatched pairs. 8660 records in RAM.
INFO 2026-06-08 07:53:33 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 2s. Last read position: chr4:122,896,516
INFO 2026-06-08 07:53:33 MarkDuplicates Tracking 339861 as yet unmatched pairs. 7510 records in RAM.
INFO 2026-06-08 07:53:36 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 2s. Last read position: chr4:147,561,399
INFO 2026-06-08 07:53:36 MarkDuplicates Tracking 340255 as yet unmatched pairs. 3940 records in RAM.
INFO 2026-06-08 07:53:39 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 2s. Last read position: chr4:169,731,647
INFO 2026-06-08 07:53:39 MarkDuplicates Tracking 342345 as yet unmatched pairs. 2113 records in RAM.
INFO 2026-06-08 07:53:42 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 2s. Last read position: chr5:211,876
INFO 2026-06-08 07:53:42 MarkDuplicates Tracking 343873 as yet unmatched pairs. 22162 records in RAM.
INFO 2026-06-08 07:53:45 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 3s. Last read position: chr5:17,655,410
INFO 2026-06-08 07:53:45 MarkDuplicates Tracking 344973 as yet unmatched pairs. 20292 records in RAM.
INFO 2026-06-08 07:53:47 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 2s. Last read position: chr5:38,981,919
INFO 2026-06-08 07:53:47 MarkDuplicates Tracking 347058 as yet unmatched pairs. 18934 records in RAM.
INFO 2026-06-08 07:53:50 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 2s. Last read position: chr5:58,458,417
INFO 2026-06-08 07:53:50 MarkDuplicates Tracking 348435 as yet unmatched pairs. 16761 records in RAM.
INFO 2026-06-08 07:53:52 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 2s. Last read position: chr5:71,222,140
INFO 2026-06-08 07:53:52 MarkDuplicates Tracking 348973 as yet unmatched pairs. 14947 records in RAM.
INFO 2026-06-08 07:53:54 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 2s. Last read position: chr5:87,268,753
INFO 2026-06-08 07:53:54 MarkDuplicates Tracking 351543 as yet unmatched pairs. 14591 records in RAM.
INFO 2026-06-08 07:53:57 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 2s. Last read position: chr5:112,838,390
INFO 2026-06-08 07:53:57 MarkDuplicates Tracking 352691 as yet unmatched pairs. 11924 records in RAM.
INFO 2026-06-08 07:54:00 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 2s. Last read position: chr5:132,294,953
INFO 2026-06-08 07:54:00 MarkDuplicates Tracking 353301 as yet unmatched pairs. 9343 records in RAM.
INFO 2026-06-08 07:54:03 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 2s. Last read position: chr5:140,360,387
INFO 2026-06-08 07:54:03 MarkDuplicates Tracking 353555 as yet unmatched pairs. 7686 records in RAM.
INFO 2026-06-08 07:54:06 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 3s. Last read position: chr5:144,165,439
INFO 2026-06-08 07:54:06 MarkDuplicates Tracking 353540 as yet unmatched pairs. 6316 records in RAM.
INFO 2026-06-08 07:54:09 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 2s. Last read position: chr5:151,253,391
INFO 2026-06-08 07:54:09 MarkDuplicates Tracking 353772 as yet unmatched pairs. 4644 records in RAM.
INFO 2026-06-08 07:54:11 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 2s. Last read position: chr5:171,392,793
INFO 2026-06-08 07:54:11 MarkDuplicates Tracking 355710 as yet unmatched pairs. 3302 records in RAM.
INFO 2026-06-08 07:54:14 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 3s. Last read position: chr5:177,732,047
INFO 2026-06-08 07:54:14 MarkDuplicates Tracking 355036 as yet unmatched pairs. 1054 records in RAM.
INFO 2026-06-08 07:54:18 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 3s. Last read position: chr6:4,258,383
INFO 2026-06-08 07:54:18 MarkDuplicates Tracking 355218 as yet unmatched pairs. 27736 records in RAM.
INFO 2026-06-08 07:54:21 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 3s. Last read position: chr6:25,915,710
INFO 2026-06-08 07:54:21 MarkDuplicates Tracking 356468 as yet unmatched pairs. 25823 records in RAM.
INFO 2026-06-08 07:54:24 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 2s. Last read position: chr6:30,329,599
INFO 2026-06-08 07:54:24 MarkDuplicates Tracking 356491 as yet unmatched pairs. 24494 records in RAM.
INFO 2026-06-08 07:54:27 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 2s. Last read position: chr6:31,998,879
INFO 2026-06-08 07:54:27 MarkDuplicates Tracking 356191 as yet unmatched pairs. 23264 records in RAM.
INFO 2026-06-08 07:54:30 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 3s. Last read position: chr6:33,007,526
INFO 2026-06-08 07:54:30 MarkDuplicates Tracking 356521 as yet unmatched pairs. 22681 records in RAM.
INFO 2026-06-08 07:54:32 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 2s. Last read position: chr6:37,218,495
INFO 2026-06-08 07:54:32 MarkDuplicates Tracking 356077 as yet unmatched pairs. 20926 records in RAM.
INFO 2026-06-08 07:54:34 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 2s. Last read position: chr6:43,783,936
INFO 2026-06-08 07:54:34 MarkDuplicates Tracking 356147 as yet unmatched pairs. 19466 records in RAM.
INFO 2026-06-08 07:54:38 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 3s. Last read position: chr6:59,348,609
INFO 2026-06-08 07:54:38 MarkDuplicates Tracking 356561 as yet unmatched pairs. 17466 records in RAM.
INFO 2026-06-08 07:54:41 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 2s. Last read position: chr6:84,762,556
INFO 2026-06-08 07:54:41 MarkDuplicates Tracking 357706 as yet unmatched pairs. 15204 records in RAM.
INFO 2026-06-08 07:54:43 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 2s. Last read position: chr6:103,802,320
INFO 2026-06-08 07:54:43 MarkDuplicates Tracking 358282 as yet unmatched pairs. 12756 records in RAM.
INFO 2026-06-08 07:54:46 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 2s. Last read position: chr6:116,693,575
INFO 2026-06-08 07:54:46 MarkDuplicates Tracking 358622 as yet unmatched pairs. 10749 records in RAM.
INFO 2026-06-08 07:54:48 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 2s. Last read position: chr6:127,128,943
INFO 2026-06-08 07:54:48 MarkDuplicates Tracking 359481 as yet unmatched pairs. 9495 records in RAM.
INFO 2026-06-08 07:54:51 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 3s. Last read position: chr6:135,210,896
INFO 2026-06-08 07:54:51 MarkDuplicates Tracking 360274 as yet unmatched pairs. 8359 records in RAM.
INFO 2026-06-08 07:54:54 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 3s. Last read position: chr6:147,382,799
INFO 2026-06-08 07:54:54 MarkDuplicates Tracking 359171 as yet unmatched pairs. 5079 records in RAM.
INFO 2026-06-08 07:54:57 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 2s. Last read position: chr6:155,254,275
INFO 2026-06-08 07:54:57 MarkDuplicates Tracking 359099 as yet unmatched pairs. 3157 records in RAM.
INFO 2026-06-08 07:55:00 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 3s. Last read position: chr6:161,349,809
INFO 2026-06-08 07:55:00 MarkDuplicates Tracking 360053 as yet unmatched pairs. 2587 records in RAM.
INFO 2026-06-08 07:55:04 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 3s. Last read position: chr7:2,702,834
INFO 2026-06-08 07:55:04 MarkDuplicates Tracking 359091 as yet unmatched pairs. 30504 records in RAM.
INFO 2026-06-08 07:55:07 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 2s. Last read position: chr7:11,469,597
INFO 2026-06-08 07:55:07 MarkDuplicates Tracking 358880 as yet unmatched pairs. 28735 records in RAM.
INFO 2026-06-08 07:55:10 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 3s. Last read position: chr7:13,975,022
INFO 2026-06-08 07:55:10 MarkDuplicates Tracking 359487 as yet unmatched pairs. 27975 records in RAM.
INFO 2026-06-08 07:55:13 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 2s. Last read position: chr7:30,923,408
INFO 2026-06-08 07:55:13 MarkDuplicates Tracking 359142 as yet unmatched pairs. 25004 records in RAM.
INFO 2026-06-08 07:55:16 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 3s. Last read position: chr7:45,686,038
INFO 2026-06-08 07:55:16 MarkDuplicates Tracking 359344 as yet unmatched pairs. 23002 records in RAM.
INFO 2026-06-08 07:55:19 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 3s. Last read position: chr7:55,178,957
INFO 2026-06-08 07:55:19 MarkDuplicates Tracking 360474 as yet unmatched pairs. 22246 records in RAM.
INFO 2026-06-08 07:55:22 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 2s. Last read position: chr7:70,790,401
INFO 2026-06-08 07:55:22 MarkDuplicates Tracking 359252 as yet unmatched pairs. 18651 records in RAM.
INFO 2026-06-08 07:55:25 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 2s. Last read position: chr7:75,347,689
INFO 2026-06-08 07:55:25 MarkDuplicates Tracking 359017 as yet unmatched pairs. 17500 records in RAM.
INFO 2026-06-08 07:55:28 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 3s. Last read position: chr7:87,059,434
INFO 2026-06-08 07:55:28 MarkDuplicates Tracking 359080 as yet unmatched pairs. 15704 records in RAM.
INFO 2026-06-08 07:55:31 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 2s. Last read position: chr7:98,949,533
INFO 2026-06-08 07:55:31 MarkDuplicates Tracking 359099 as yet unmatched pairs. 13661 records in RAM.
INFO 2026-06-08 07:55:34 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 2s. Last read position: chr7:101,034,061
INFO 2026-06-08 07:55:34 MarkDuplicates Tracking 359464 as yet unmatched pairs. 13255 records in RAM.
INFO 2026-06-08 07:55:37 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 3s. Last read position: chr7:105,125,494
INFO 2026-06-08 07:55:37 MarkDuplicates Tracking 358154 as yet unmatched pairs. 10862 records in RAM.
INFO 2026-06-08 07:55:40 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 2s. Last read position: chr7:117,119,586
INFO 2026-06-08 07:55:40 MarkDuplicates Tracking 358103 as yet unmatched pairs. 8718 records in RAM.
INFO 2026-06-08 07:55:42 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 2s. Last read position: chr7:131,488,026
INFO 2026-06-08 07:55:42 MarkDuplicates Tracking 358959 as yet unmatched pairs. 7309 records in RAM.
INFO 2026-06-08 07:55:46 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 3s. Last read position: chr7:140,786,312
INFO 2026-06-08 07:55:46 MarkDuplicates Tracking 359088 as yet unmatched pairs. 5623 records in RAM.
INFO 2026-06-08 07:55:48 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 2s. Last read position: chr7:148,430,471
INFO 2026-06-08 07:55:48 MarkDuplicates Tracking 357745 as yet unmatched pairs. 2847 records in RAM.
INFO 2026-06-08 07:55:51 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 2s. Last read position: chr7:152,221,939
INFO 2026-06-08 07:55:51 MarkDuplicates Tracking 357419 as yet unmatched pairs. 1336 records in RAM.
INFO 2026-06-08 07:55:54 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 3s. Last read position: chr8:7,267,242
INFO 2026-06-08 07:55:54 MarkDuplicates Tracking 357573 as yet unmatched pairs. 28979 records in RAM.
INFO 2026-06-08 07:55:55 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 1s. Last read position: chr8:7,763,795
INFO 2026-06-08 07:55:55 MarkDuplicates Tracking 357777 as yet unmatched pairs. 28960 records in RAM.
INFO 2026-06-08 07:55:57 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 1s. Last read position: chr8:17,755,065
INFO 2026-06-08 07:55:57 MarkDuplicates Tracking 356603 as yet unmatched pairs. 26369 records in RAM.
INFO 2026-06-08 07:55:59 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 2s. Last read position: chr8:28,859,433
INFO 2026-06-08 07:55:59 MarkDuplicates Tracking 356234 as yet unmatched pairs. 24274 records in RAM.
INFO 2026-06-08 07:56:01 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 2s. Last read position: chr8:32,651,006
INFO 2026-06-08 07:56:01 MarkDuplicates Tracking 356575 as yet unmatched pairs. 23370 records in RAM.
INFO 2026-06-08 07:56:04 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 2s. Last read position: chr8:32,723,775
INFO 2026-06-08 07:56:04 MarkDuplicates Tracking 356081 as yet unmatched pairs. 21906 records in RAM.
INFO 2026-06-08 07:56:06 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 2s. Last read position: chr8:37,830,675
INFO 2026-06-08 07:56:06 MarkDuplicates Tracking 355244 as yet unmatched pairs. 19693 records in RAM.
INFO 2026-06-08 07:56:08 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 2s. Last read position: chr8:38,453,214
INFO 2026-06-08 07:56:08 MarkDuplicates Tracking 355687 as yet unmatched pairs. 19215 records in RAM.
INFO 2026-06-08 07:56:10 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 2s. Last read position: chr8:47,830,566
INFO 2026-06-08 07:56:10 MarkDuplicates Tracking 354149 as yet unmatched pairs. 16103 records in RAM.
INFO 2026-06-08 07:56:13 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 2s. Last read position: chr8:67,287,989
INFO 2026-06-08 07:56:13 MarkDuplicates Tracking 353296 as yet unmatched pairs. 12736 records in RAM.
INFO 2026-06-08 07:56:15 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 2s. Last read position: chr8:89,934,632
INFO 2026-06-08 07:56:15 MarkDuplicates Tracking 353955 as yet unmatched pairs. 10774 records in RAM.
INFO 2026-06-08 07:56:17 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 2s. Last read position: chr8:105,444,397
INFO 2026-06-08 07:56:17 MarkDuplicates Tracking 352362 as yet unmatched pairs. 7041 records in RAM.
INFO 2026-06-08 07:56:19 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 2s. Last read position: chr8:127,740,629
INFO 2026-06-08 07:56:19 MarkDuplicates Tracking 352933 as yet unmatched pairs. 5000 records in RAM.
INFO 2026-06-08 07:56:21 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 2s. Last read position: chr8:143,860,020
INFO 2026-06-08 07:56:21 MarkDuplicates Tracking 351866 as yet unmatched pairs. 1930 records in RAM.
INFO 2026-06-08 07:56:24 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 2s. Last read position: chr9:156,376
INFO 2026-06-08 07:56:24 MarkDuplicates Tracking 350663 as yet unmatched pairs. 30913 records in RAM.
INFO 2026-06-08 07:56:27 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 2s. Last read position: chr9:8,317,791
INFO 2026-06-08 07:56:27 MarkDuplicates Tracking 350617 as yet unmatched pairs. 29354 records in RAM.
INFO 2026-06-08 07:56:30 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 3s. Last read position: chr9:22,003,886
INFO 2026-06-08 07:56:30 MarkDuplicates Tracking 350296 as yet unmatched pairs. 27132 records in RAM.
INFO 2026-06-08 07:56:33 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:06:35s. Time for last 1,000,000: 3s. Last read position: chr9:35,697,771
INFO 2026-06-08 07:56:33 MarkDuplicates Tracking 348750 as yet unmatched pairs. 23787 records in RAM.
INFO 2026-06-08 07:56:36 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 2s. Last read position: chr9:41,908,467
INFO 2026-06-08 07:56:36 MarkDuplicates Tracking 348412 as yet unmatched pairs. 22443 records in RAM.
INFO 2026-06-08 07:56:39 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 2s. Last read position: chr9:64,394,697
INFO 2026-06-08 07:56:39 MarkDuplicates Tracking 347828 as yet unmatched pairs. 21087 records in RAM.
INFO 2026-06-08 07:56:41 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 2s. Last read position: chr9:77,339,331
INFO 2026-06-08 07:56:41 MarkDuplicates Tracking 347415 as yet unmatched pairs. 19245 records in RAM.
INFO 2026-06-08 07:56:44 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:06:46s. Time for last 1,000,000: 2s. Last read position: chr9:84,813,245
INFO 2026-06-08 07:56:44 MarkDuplicates Tracking 347781 as yet unmatched pairs. 18272 records in RAM.
INFO 2026-06-08 07:56:47 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 2s. Last read position: chr9:84,915,082
INFO 2026-06-08 07:56:47 MarkDuplicates Tracking 347497 as yet unmatched pairs. 17092 records in RAM.
INFO 2026-06-08 07:56:50 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 3s. Last read position: chr9:92,314,843
INFO 2026-06-08 07:56:50 MarkDuplicates Tracking 345146 as yet unmatched pairs. 13330 records in RAM.
INFO 2026-06-08 07:56:53 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 2s. Last read position: chr9:99,105,097
INFO 2026-06-08 07:56:53 MarkDuplicates Tracking 345168 as yet unmatched pairs. 12139 records in RAM.
INFO 2026-06-08 07:56:55 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:06:57s. Time for last 1,000,000: 1s. Last read position: chr9:113,297,900
INFO 2026-06-08 07:56:55 MarkDuplicates Tracking 343586 as yet unmatched pairs. 8646 records in RAM.
INFO 2026-06-08 07:56:58 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:07:00s. Time for last 1,000,000: 3s. Last read position: chr9:127,397,268
INFO 2026-06-08 07:56:58 MarkDuplicates Tracking 342945 as yet unmatched pairs. 6217 records in RAM.
INFO 2026-06-08 07:57:01 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:07:03s. Time for last 1,000,000: 3s. Last read position: chr9:130,887,423
INFO 2026-06-08 07:57:01 MarkDuplicates Tracking 343061 as yet unmatched pairs. 5449 records in RAM.
INFO 2026-06-08 07:57:04 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 2s. Last read position: chr9:134,439,457
INFO 2026-06-08 07:57:04 MarkDuplicates Tracking 342614 as yet unmatched pairs. 4102 records in RAM.
INFO 2026-06-08 07:57:07 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:07:09s. Time for last 1,000,000: 3s. Last read position: chr9:137,099,962
INFO 2026-06-08 07:57:07 MarkDuplicates Tracking 339856 as yet unmatched pairs. 596 records in RAM.
INFO 2026-06-08 07:57:11 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 3s. Last read position: chr10:12,814,129
INFO 2026-06-08 07:57:11 MarkDuplicates Tracking 339013 as yet unmatched pairs. 26869 records in RAM.
INFO 2026-06-08 07:57:14 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:07:16s. Time for last 1,000,000: 3s. Last read position: chr10:30,322,212
INFO 2026-06-08 07:57:14 MarkDuplicates Tracking 338074 as yet unmatched pairs. 24042 records in RAM.
INFO 2026-06-08 07:57:17 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:07:19s. Time for last 1,000,000: 3s. Last read position: chr10:43,117,896
INFO 2026-06-08 07:57:17 MarkDuplicates Tracking 339074 as yet unmatched pairs. 23388 records in RAM.
INFO 2026-06-08 07:57:19 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:07:21s. Time for last 1,000,000: 2s. Last read position: chr10:49,459,031
INFO 2026-06-08 07:57:19 MarkDuplicates Tracking 336434 as yet unmatched pairs. 19830 records in RAM.
INFO 2026-06-08 07:57:22 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:07:24s. Time for last 1,000,000: 2s. Last read position: chr10:68,574,107
INFO 2026-06-08 07:57:22 MarkDuplicates Tracking 335688 as yet unmatched pairs. 16973 records in RAM.
INFO 2026-06-08 07:57:24 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:07:26s. Time for last 1,000,000: 2s. Last read position: chr10:77,796,356
INFO 2026-06-08 07:57:24 MarkDuplicates Tracking 334473 as yet unmatched pairs. 14482 records in RAM.
INFO 2026-06-08 07:57:26 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:07:28s. Time for last 1,000,000: 1s. Last read position: chr10:88,831,948
INFO 2026-06-08 07:57:26 MarkDuplicates Tracking 333485 as yet unmatched pairs. 11977 records in RAM.
INFO 2026-06-08 07:57:29 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:07:31s. Time for last 1,000,000: 2s. Last read position: chr10:96,984,381
INFO 2026-06-08 07:57:29 MarkDuplicates Tracking 332608 as yet unmatched pairs. 9842 records in RAM.
INFO 2026-06-08 07:57:32 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:07:34s. Time for last 1,000,000: 3s. Last read position: chr10:102,631,350
INFO 2026-06-08 07:57:32 MarkDuplicates Tracking 333196 as yet unmatched pairs. 9527 records in RAM.
INFO 2026-06-08 07:57:35 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:07:36s. Time for last 1,000,000: 2s. Last read position: chr10:116,621,125
INFO 2026-06-08 07:57:35 MarkDuplicates Tracking 330155 as yet unmatched pairs. 4870 records in RAM.
INFO 2026-06-08 07:57:38 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:07:40s. Time for last 1,000,000: 3s. Last read position: chr10:121,591,841
INFO 2026-06-08 07:57:38 MarkDuplicates Tracking 330721 as yet unmatched pairs. 4422 records in RAM.
INFO 2026-06-08 07:57:41 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:07:42s. Time for last 1,000,000: 2s. Last read position: chr10:133,273,975
INFO 2026-06-08 07:57:41 MarkDuplicates Tracking 327910 as yet unmatched pairs. 335 records in RAM.
INFO 2026-06-08 07:57:43 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:07:45s. Time for last 1,000,000: 2s. Last read position: chr11:1,445,427
INFO 2026-06-08 07:57:43 MarkDuplicates Tracking 327034 as yet unmatched pairs. 33952 records in RAM.
INFO 2026-06-08 07:57:46 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:07:48s. Time for last 1,000,000: 2s. Last read position: chr11:6,639,797
INFO 2026-06-08 07:57:46 MarkDuplicates Tracking 325842 as yet unmatched pairs. 31972 records in RAM.
INFO 2026-06-08 07:57:49 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:07:51s. Time for last 1,000,000: 3s. Last read position: chr11:17,721,715
INFO 2026-06-08 07:57:49 MarkDuplicates Tracking 325893 as yet unmatched pairs. 30754 records in RAM.
INFO 2026-06-08 07:57:52 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:07:54s. Time for last 1,000,000: 2s. Last read position: chr11:34,658,715
INFO 2026-06-08 07:57:52 MarkDuplicates Tracking 323340 as yet unmatched pairs. 26530 records in RAM.
INFO 2026-06-08 07:57:55 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:07:57s. Time for last 1,000,000: 3s. Last read position: chr11:54,707,247
INFO 2026-06-08 07:57:55 MarkDuplicates Tracking 322081 as yet unmatched pairs. 23560 records in RAM.
INFO 2026-06-08 07:57:58 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:08:00s. Time for last 1,000,000: 3s. Last read position: chr11:61,741,336
INFO 2026-06-08 07:57:58 MarkDuplicates Tracking 321078 as yet unmatched pairs. 21528 records in RAM.
INFO 2026-06-08 07:58:01 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:08:03s. Time for last 1,000,000: 2s. Last read position: chr11:64,833,477
INFO 2026-06-08 07:58:01 MarkDuplicates Tracking 319966 as yet unmatched pairs. 19692 records in RAM.
INFO 2026-06-08 07:58:04 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:08:06s. Time for last 1,000,000: 3s. Last read position: chr11:67,504,063
INFO 2026-06-08 07:58:04 MarkDuplicates Tracking 318756 as yet unmatched pairs. 17884 records in RAM.
INFO 2026-06-08 07:58:08 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:08:09s. Time for last 1,000,000: 3s. Last read position: chr11:74,273,583
INFO 2026-06-08 07:58:08 MarkDuplicates Tracking 317502 as yet unmatched pairs. 15658 records in RAM.
INFO 2026-06-08 07:58:10 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:08:12s. Time for last 1,000,000: 2s. Last read position: chr11:89,768,164
INFO 2026-06-08 07:58:10 MarkDuplicates Tracking 315936 as yet unmatched pairs. 12587 records in RAM.
INFO 2026-06-08 07:58:13 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:08:15s. Time for last 1,000,000: 2s. Last read position: chr11:102,205,841
INFO 2026-06-08 07:58:13 MarkDuplicates Tracking 315049 as yet unmatched pairs. 10398 records in RAM.
INFO 2026-06-08 07:58:17 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:08:18s. Time for last 1,000,000: 3s. Last read position: chr11:111,306,550
INFO 2026-06-08 07:58:17 MarkDuplicates Tracking 313054 as yet unmatched pairs. 7155 records in RAM.
INFO 2026-06-08 07:58:19 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 2s. Last read position: chr11:118,523,369
INFO 2026-06-08 07:58:19 MarkDuplicates Tracking 313048 as yet unmatched pairs. 6103 records in RAM.
INFO 2026-06-08 07:58:22 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:08:24s. Time for last 1,000,000: 2s. Last read position: chr11:124,774,857
INFO 2026-06-08 07:58:22 MarkDuplicates Tracking 310413 as yet unmatched pairs. 2510 records in RAM.
INFO 2026-06-08 07:58:26 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:08:28s. Time for last 1,000,000: 3s. Last read position: chr12:293,127
INFO 2026-06-08 07:58:26 MarkDuplicates Tracking 309184 as yet unmatched pairs. 40274 records in RAM.
INFO 2026-06-08 07:58:29 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:08:31s. Time for last 1,000,000: 3s. Last read position: chr12:6,600,039
INFO 2026-06-08 07:58:29 MarkDuplicates Tracking 308082 as yet unmatched pairs. 38312 records in RAM.
INFO 2026-06-08 07:58:32 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 2s. Last read position: chr12:11,757,053
INFO 2026-06-08 07:58:32 MarkDuplicates Tracking 307790 as yet unmatched pairs. 37272 records in RAM.
INFO 2026-06-08 07:58:35 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 3s. Last read position: chr12:11,812,813
INFO 2026-06-08 07:58:35 MarkDuplicates Tracking 306794 as yet unmatched pairs. 35640 records in RAM.
INFO 2026-06-08 07:58:38 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 3s. Last read position: chr12:11,881,440
INFO 2026-06-08 07:58:38 MarkDuplicates Tracking 305265 as yet unmatched pairs. 33534 records in RAM.
INFO 2026-06-08 07:58:41 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:08:43s. Time for last 1,000,000: 2s. Last read position: chr12:24,583,842
INFO 2026-06-08 07:58:41 MarkDuplicates Tracking 302206 as yet unmatched pairs. 29166 records in RAM.
INFO 2026-06-08 07:58:44 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:08:46s. Time for last 1,000,000: 2s. Last read position: chr12:43,383,975
INFO 2026-06-08 07:58:44 MarkDuplicates Tracking 300378 as yet unmatched pairs. 25908 records in RAM.
INFO 2026-06-08 07:58:46 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 2s. Last read position: chr12:49,044,807
INFO 2026-06-08 07:58:46 MarkDuplicates Tracking 299490 as yet unmatched pairs. 24138 records in RAM.
INFO 2026-06-08 07:58:48 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:08:50s. Time for last 1,000,000: 2s. Last read position: chr12:52,451,664
INFO 2026-06-08 07:58:48 MarkDuplicates Tracking 298120 as yet unmatched pairs. 22142 records in RAM.
INFO 2026-06-08 07:58:51 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:08:53s. Time for last 1,000,000: 2s. Last read position: chr12:56,236,378
INFO 2026-06-08 07:58:51 MarkDuplicates Tracking 296411 as yet unmatched pairs. 19779 records in RAM.
INFO 2026-06-08 07:58:53 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:08:55s. Time for last 1,000,000: 2s. Last read position: chr12:57,809,600
INFO 2026-06-08 07:58:53 MarkDuplicates Tracking 295161 as yet unmatched pairs. 17970 records in RAM.
INFO 2026-06-08 07:58:56 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:08:58s. Time for last 1,000,000: 3s. Last read position: chr12:75,964,904
INFO 2026-06-08 07:58:56 MarkDuplicates Tracking 293154 as yet unmatched pairs. 14393 records in RAM.
INFO 2026-06-08 07:59:00 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:09:02s. Time for last 1,000,000: 3s. Last read position: chr12:99,812,253
INFO 2026-06-08 07:59:00 MarkDuplicates Tracking 290788 as yet unmatched pairs. 10184 records in RAM.
INFO 2026-06-08 07:59:03 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 3s. Last read position: chr12:109,803,020
INFO 2026-06-08 07:59:03 MarkDuplicates Tracking 289330 as yet unmatched pairs. 7665 records in RAM.
INFO 2026-06-08 07:59:06 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 2s. Last read position: chr12:117,174,631
INFO 2026-06-08 07:59:06 MarkDuplicates Tracking 287654 as yet unmatched pairs. 5105 records in RAM.
INFO 2026-06-08 07:59:09 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:09:11s. Time for last 1,000,000: 3s. Last read position: chr12:123,161,106
INFO 2026-06-08 07:59:09 MarkDuplicates Tracking 286063 as yet unmatched pairs. 2757 records in RAM.
INFO 2026-06-08 07:59:11 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:09:13s. Time for last 1,000,000: 2s. Last read position: chr13:18,261,928
INFO 2026-06-08 07:59:11 MarkDuplicates Tracking 284510 as yet unmatched pairs. 19964 records in RAM.
INFO 2026-06-08 07:59:13 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:09:15s. Time for last 1,000,000: 1s. Last read position: chr13:28,300,859
INFO 2026-06-08 07:59:13 MarkDuplicates Tracking 283529 as yet unmatched pairs. 17933 records in RAM.
INFO 2026-06-08 07:59:16 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:09:17s. Time for last 1,000,000: 2s. Last read position: chr13:40,556,180
INFO 2026-06-08 07:59:16 MarkDuplicates Tracking 281883 as yet unmatched pairs. 15189 records in RAM.
INFO 2026-06-08 07:59:17 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:09:19s. Time for last 1,000,000: 1s. Last read position: chr13:57,147,766
INFO 2026-06-08 07:59:17 MarkDuplicates Tracking 278458 as yet unmatched pairs. 10468 records in RAM.
INFO 2026-06-08 07:59:20 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 3s. Last read position: chr13:98,213,263
INFO 2026-06-08 07:59:20 MarkDuplicates Tracking 274831 as yet unmatched pairs. 4181 records in RAM.
INFO 2026-06-08 07:59:23 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 3s. Last read position: chr13:110,938,866
INFO 2026-06-08 07:59:23 MarkDuplicates Tracking 272646 as yet unmatched pairs. 948 records in RAM.
INFO 2026-06-08 07:59:27 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:09:29s. Time for last 1,000,000: 3s. Last read position: chr14:22,006,667
INFO 2026-06-08 07:59:27 MarkDuplicates Tracking 270864 as yet unmatched pairs. 20216 records in RAM.
INFO 2026-06-08 07:59:30 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:09:32s. Time for last 1,000,000: 3s. Last read position: chr14:35,076,515
INFO 2026-06-08 07:59:30 MarkDuplicates Tracking 268925 as yet unmatched pairs. 17227 records in RAM.
INFO 2026-06-08 07:59:33 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 3s. Last read position: chr14:52,384,677
INFO 2026-06-08 07:59:33 MarkDuplicates Tracking 266452 as yet unmatched pairs. 13489 records in RAM.
INFO 2026-06-08 07:59:36 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:09:38s. Time for last 1,000,000: 2s. Last read position: chr14:68,274,898
INFO 2026-06-08 07:59:36 MarkDuplicates Tracking 264204 as yet unmatched pairs. 10128 records in RAM.
INFO 2026-06-08 07:59:38 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:09:40s. Time for last 1,000,000: 2s. Last read position: chr14:80,785,294
INFO 2026-06-08 07:59:38 MarkDuplicates Tracking 262116 as yet unmatched pairs. 7099 records in RAM.
INFO 2026-06-08 07:59:42 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 3s. Last read position: chr14:95,692,414
INFO 2026-06-08 07:59:42 MarkDuplicates Tracking 261541 as yet unmatched pairs. 5338 records in RAM.
INFO 2026-06-08 07:59:45 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:09:47s. Time for last 1,000,000: 3s. Last read position: chr14:104,794,640
INFO 2026-06-08 07:59:45 MarkDuplicates Tracking 257885 as yet unmatched pairs. 905 records in RAM.
INFO 2026-06-08 07:59:47 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:09:49s. Time for last 1,000,000: 2s. Last read position: chr15:23,160,116
INFO 2026-06-08 07:59:47 MarkDuplicates Tracking 256427 as yet unmatched pairs. 34856 records in RAM.
INFO 2026-06-08 07:59:49 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:09:51s. Time for last 1,000,000: 2s. Last read position: chr15:30,815,397
INFO 2026-06-08 07:59:49 MarkDuplicates Tracking 255062 as yet unmatched pairs. 32998 records in RAM.
INFO 2026-06-08 07:59:52 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:09:54s. Time for last 1,000,000: 2s. Last read position: chr15:38,501,031
INFO 2026-06-08 07:59:52 MarkDuplicates Tracking 253075 as yet unmatched pairs. 30399 records in RAM.
INFO 2026-06-08 07:59:54 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:09:56s. Time for last 1,000,000: 2s. Last read position: chr15:42,735,229
INFO 2026-06-08 07:59:54 MarkDuplicates Tracking 251282 as yet unmatched pairs. 28109 records in RAM.
INFO 2026-06-08 07:59:57 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 2s. Last read position: chr15:49,485,431
INFO 2026-06-08 07:59:57 MarkDuplicates Tracking 250380 as yet unmatched pairs. 26638 records in RAM.
INFO 2026-06-08 08:00:01 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:10:03s. Time for last 1,000,000: 3s. Last read position: chr15:63,774,841
INFO 2026-06-08 08:00:01 MarkDuplicates Tracking 246723 as yet unmatched pairs. 22086 records in RAM.
INFO 2026-06-08 08:00:04 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:10:06s. Time for last 1,000,000: 2s. Last read position: chr15:73,711,612
INFO 2026-06-08 08:00:04 MarkDuplicates Tracking 245690 as yet unmatched pairs. 20313 records in RAM.
INFO 2026-06-08 08:00:07 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 3s. Last read position: chr15:81,585,073
INFO 2026-06-08 08:00:07 MarkDuplicates Tracking 242552 as yet unmatched pairs. 16477 records in RAM.
INFO 2026-06-08 08:00:09 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:10:11s. Time for last 1,000,000: 2s. Last read position: chr15:87,941,434
INFO 2026-06-08 08:00:09 MarkDuplicates Tracking 242166 as yet unmatched pairs. 15558 records in RAM.
INFO 2026-06-08 08:00:12 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:10:14s. Time for last 1,000,000: 2s. Last read position: chr15:87,998,779
INFO 2026-06-08 08:00:12 MarkDuplicates Tracking 240366 as yet unmatched pairs. 13390 records in RAM.
INFO 2026-06-08 08:00:14 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:10:16s. Time for last 1,000,000: 2s. Last read position: chr15:88,042,958
INFO 2026-06-08 08:00:14 MarkDuplicates Tracking 239059 as yet unmatched pairs. 11670 records in RAM.
INFO 2026-06-08 08:00:16 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:10:18s. Time for last 1,000,000: 2s. Last read position: chr15:88,085,307
INFO 2026-06-08 08:00:16 MarkDuplicates Tracking 236962 as yet unmatched pairs. 9199 records in RAM.
INFO 2026-06-08 08:00:19 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:10:21s. Time for last 1,000,000: 2s. Last read position: chr15:88,131,708
INFO 2026-06-08 08:00:19 MarkDuplicates Tracking 234975 as yet unmatched pairs. 6801 records in RAM.
INFO 2026-06-08 08:00:21 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:10:23s. Time for last 1,000,000: 1s. Last read position: chr15:90,907,518
INFO 2026-06-08 08:00:21 MarkDuplicates Tracking 231820 as yet unmatched pairs. 3182 records in RAM.
INFO 2026-06-08 08:00:24 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 3s. Last read position: chr16:260,064
INFO 2026-06-08 08:00:24 MarkDuplicates Tracking 229375 as yet unmatched pairs. 31923 records in RAM.
INFO 2026-06-08 08:00:28 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:10:30s. Time for last 1,000,000: 3s. Last read position: chr16:2,088,059
INFO 2026-06-08 08:00:28 MarkDuplicates Tracking 228794 as yet unmatched pairs. 31041 records in RAM.
INFO 2026-06-08 08:00:31 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:10:33s. Time for last 1,000,000: 3s. Last read position: chr16:3,590,313
INFO 2026-06-08 08:00:31 MarkDuplicates Tracking 226906 as yet unmatched pairs. 28858 records in RAM.
INFO 2026-06-08 08:00:34 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:10:36s. Time for last 1,000,000: 3s. Last read position: chr16:11,255,845
INFO 2026-06-08 08:00:34 MarkDuplicates Tracking 225439 as yet unmatched pairs. 26806 records in RAM.
INFO 2026-06-08 08:00:36 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:10:38s. Time for last 1,000,000: 2s. Last read position: chr16:16,356,717
INFO 2026-06-08 08:00:36 MarkDuplicates Tracking 222365 as yet unmatched pairs. 23357 records in RAM.
INFO 2026-06-08 08:00:39 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:10:41s. Time for last 1,000,000: 2s. Last read position: chr16:21,839,038
INFO 2026-06-08 08:00:39 MarkDuplicates Tracking 220965 as yet unmatched pairs. 21628 records in RAM.
INFO 2026-06-08 08:00:41 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:10:43s. Time for last 1,000,000: 2s. Last read position: chr16:28,735,293
INFO 2026-06-08 08:00:41 MarkDuplicates Tracking 219999 as yet unmatched pairs. 20199 records in RAM.
INFO 2026-06-08 08:00:44 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 3s. Last read position: chr16:30,965,091
INFO 2026-06-08 08:00:44 MarkDuplicates Tracking 217933 as yet unmatched pairs. 17877 records in RAM.
INFO 2026-06-08 08:00:47 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:10:49s. Time for last 1,000,000: 2s. Last read position: chr16:47,650,481
INFO 2026-06-08 08:00:47 MarkDuplicates Tracking 215741 as yet unmatched pairs. 15128 records in RAM.
INFO 2026-06-08 08:00:51 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:10:53s. Time for last 1,000,000: 3s. Last read position: chr16:57,769,687
INFO 2026-06-08 08:00:51 MarkDuplicates Tracking 213411 as yet unmatched pairs. 12157 records in RAM.
INFO 2026-06-08 08:00:53 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:10:55s. Time for last 1,000,000: 2s. Last read position: chr16:68,315,973
INFO 2026-06-08 08:00:53 MarkDuplicates Tracking 210813 as yet unmatched pairs. 8939 records in RAM.
INFO 2026-06-08 08:00:56 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 2s. Last read position: chr16:72,889,548
INFO 2026-06-08 08:00:56 MarkDuplicates Tracking 208857 as yet unmatched pairs. 6554 records in RAM.
INFO 2026-06-08 08:00:58 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:11:00s. Time for last 1,000,000: 2s. Last read position: chr16:84,873,027
INFO 2026-06-08 08:00:58 MarkDuplicates Tracking 206261 as yet unmatched pairs. 3196 records in RAM.
INFO 2026-06-08 08:01:01 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:11:03s. Time for last 1,000,000: 2s. Last read position: chr16:89,737,648
INFO 2026-06-08 08:01:01 MarkDuplicates Tracking 205239 as yet unmatched pairs. 1748 records in RAM.
INFO 2026-06-08 08:01:04 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:11:06s. Time for last 1,000,000: 2s. Last read position: chr17:3,589,725
INFO 2026-06-08 08:01:04 MarkDuplicates Tracking 202245 as yet unmatched pairs. 42460 records in RAM.
INFO 2026-06-08 08:01:06 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:11:08s. Time for last 1,000,000: 2s. Last read position: chr17:7,427,273
INFO 2026-06-08 08:01:06 MarkDuplicates Tracking 200512 as yet unmatched pairs. 40401 records in RAM.
INFO 2026-06-08 08:01:08 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:11:10s. Time for last 1,000,000: 2s. Last read position: chr17:10,398,702
INFO 2026-06-08 08:01:08 MarkDuplicates Tracking 198527 as yet unmatched pairs. 38126 records in RAM.
INFO 2026-06-08 08:01:11 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:11:13s. Time for last 1,000,000: 2s. Last read position: chr17:17,214,423
INFO 2026-06-08 08:01:11 MarkDuplicates Tracking 196108 as yet unmatched pairs. 35272 records in RAM.
INFO 2026-06-08 08:01:14 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:11:16s. Time for last 1,000,000: 3s. Last read position: chr17:21,300,582
INFO 2026-06-08 08:01:14 MarkDuplicates Tracking 194190 as yet unmatched pairs. 33050 records in RAM.
INFO 2026-06-08 08:01:17 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:11:19s. Time for last 1,000,000: 3s. Last read position: chr17:31,325,819
INFO 2026-06-08 08:01:17 MarkDuplicates Tracking 192152 as yet unmatched pairs. 30558 records in RAM.
INFO 2026-06-08 08:01:20 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:11:22s. Time for last 1,000,000: 2s. Last read position: chr17:36,377,823
INFO 2026-06-08 08:01:20 MarkDuplicates Tracking 189642 as yet unmatched pairs. 27697 records in RAM.
INFO 2026-06-08 08:01:22 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:11:24s. Time for last 1,000,000: 2s. Last read position: chr17:39,711,728
INFO 2026-06-08 08:01:22 MarkDuplicates Tracking 188510 as yet unmatched pairs. 26318 records in RAM.
INFO 2026-06-08 08:01:24 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:11:26s. Time for last 1,000,000: 2s. Last read position: chr17:40,495,996
INFO 2026-06-08 08:01:24 MarkDuplicates Tracking 186494 as yet unmatched pairs. 24016 records in RAM.
INFO 2026-06-08 08:02:36 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:12:38s. Time for last 1,000,000: 71s. Last read position: chr17:42,306,324
INFO 2026-06-08 08:02:36 MarkDuplicates Tracking 185139 as yet unmatched pairs. 22362 records in RAM.
INFO 2026-06-08 08:02:39 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:12:41s. Time for last 1,000,000: 3s. Last read position: chr17:43,532,024
INFO 2026-06-08 08:02:39 MarkDuplicates Tracking 182958 as yet unmatched pairs. 19841 records in RAM.
INFO 2026-06-08 08:02:42 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:12:44s. Time for last 1,000,000: 2s. Last read position: chr17:46,248,046
INFO 2026-06-08 08:02:42 MarkDuplicates Tracking 180777 as yet unmatched pairs. 17344 records in RAM.
INFO 2026-06-08 08:02:44 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:12:46s. Time for last 1,000,000: 2s. Last read position: chr17:50,170,445
INFO 2026-06-08 08:02:44 MarkDuplicates Tracking 178793 as yet unmatched pairs. 15058 records in RAM.
INFO 2026-06-08 08:02:46 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:12:48s. Time for last 1,000,000: 2s. Last read position: chr17:59,588,635
INFO 2026-06-08 08:02:46 MarkDuplicates Tracking 176077 as yet unmatched pairs. 11863 records in RAM.
INFO 2026-06-08 08:02:49 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:12:51s. Time for last 1,000,000: 2s. Last read position: chr17:64,214,018
INFO 2026-06-08 08:02:49 MarkDuplicates Tracking 174074 as yet unmatched pairs. 9462 records in RAM.
INFO 2026-06-08 08:02:52 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:12:54s. Time for last 1,000,000: 2s. Last read position: chr17:72,125,539
INFO 2026-06-08 08:02:52 MarkDuplicates Tracking 172397 as yet unmatched pairs. 7361 records in RAM.
INFO 2026-06-08 08:02:55 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:12:57s. Time for last 1,000,000: 3s. Last read position: chr17:76,626,355
INFO 2026-06-08 08:02:55 MarkDuplicates Tracking 169113 as yet unmatched pairs. 3715 records in RAM.
INFO 2026-06-08 08:02:58 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:13:00s. Time for last 1,000,000: 3s. Last read position: chr17:81,682,055
INFO 2026-06-08 08:02:58 MarkDuplicates Tracking 166827 as yet unmatched pairs. 1048 records in RAM.
INFO 2026-06-08 08:03:00 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:13:02s. Time for last 1,000,000: 2s. Last read position: chr18:11,884,542
INFO 2026-06-08 08:03:00 MarkDuplicates Tracking 163657 as yet unmatched pairs. 17145 records in RAM.
INFO 2026-06-08 08:03:02 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:13:04s. Time for last 1,000,000: 1s. Last read position: chr18:34,838,759
INFO 2026-06-08 08:03:02 MarkDuplicates Tracking 159962 as yet unmatched pairs. 12725 records in RAM.
INFO 2026-06-08 08:03:05 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:13:07s. Time for last 1,000,000: 3s. Last read position: chr18:47,815,529
INFO 2026-06-08 08:03:05 MarkDuplicates Tracking 157923 as yet unmatched pairs. 10199 records in RAM.
INFO 2026-06-08 08:03:08 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:13:10s. Time for last 1,000,000: 2s. Last read position: chr18:58,751,924
INFO 2026-06-08 08:03:08 MarkDuplicates Tracking 154418 as yet unmatched pairs. 6201 records in RAM.
INFO 2026-06-08 08:03:11 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:13:13s. Time for last 1,000,000: 3s. Last read position: chr19:156,881
INFO 2026-06-08 08:03:11 MarkDuplicates Tracking 149953 as yet unmatched pairs. 37416 records in RAM.
INFO 2026-06-08 08:03:14 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:13:16s. Time for last 1,000,000: 2s. Last read position: chr19:2,231,673
INFO 2026-06-08 08:03:14 MarkDuplicates Tracking 148906 as yet unmatched pairs. 36210 records in RAM.
INFO 2026-06-08 08:03:17 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:13:19s. Time for last 1,000,000: 3s. Last read position: chr19:5,244,459
INFO 2026-06-08 08:03:17 MarkDuplicates Tracking 144957 as yet unmatched pairs. 32063 records in RAM.
INFO 2026-06-08 08:03:19 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:13:21s. Time for last 1,000,000: 2s. Last read position: chr19:8,603,824
INFO 2026-06-08 08:03:19 MarkDuplicates Tracking 142484 as yet unmatched pairs. 29375 records in RAM.
INFO 2026-06-08 08:03:22 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:13:24s. Time for last 1,000,000: 2s. Last read position: chr19:10,224,520
INFO 2026-06-08 08:03:22 MarkDuplicates Tracking 141181 as yet unmatched pairs. 27875 records in RAM.
INFO 2026-06-08 08:03:25 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:13:27s. Time for last 1,000,000: 3s. Last read position: chr19:12,948,626
INFO 2026-06-08 08:03:25 MarkDuplicates Tracking 138294 as yet unmatched pairs. 24791 records in RAM.
INFO 2026-06-08 08:03:28 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:13:30s. Time for last 1,000,000: 2s. Last read position: chr19:15,373,574
INFO 2026-06-08 08:03:28 MarkDuplicates Tracking 136026 as yet unmatched pairs. 22311 records in RAM.
INFO 2026-06-08 08:03:31 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:13:33s. Time for last 1,000,000: 2s. Last read position: chr19:18,938,788
INFO 2026-06-08 08:03:31 MarkDuplicates Tracking 134015 as yet unmatched pairs. 20064 records in RAM.
INFO 2026-06-08 08:03:34 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:13:36s. Time for last 1,000,000: 3s. Last read position: chr19:35,555,260
INFO 2026-06-08 08:03:34 MarkDuplicates Tracking 130587 as yet unmatched pairs. 16221 records in RAM.
INFO 2026-06-08 08:03:37 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:13:39s. Time for last 1,000,000: 2s. Last read position: chr19:39,199,066
INFO 2026-06-08 08:03:37 MarkDuplicates Tracking 128282 as yet unmatched pairs. 13697 records in RAM.
INFO 2026-06-08 08:03:39 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:13:41s. Time for last 1,000,000: 1s. Last read position: chr19:42,021,056
INFO 2026-06-08 08:03:39 MarkDuplicates Tracking 125986 as yet unmatched pairs. 11189 records in RAM.
INFO 2026-06-08 08:03:41 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:13:43s. Time for last 1,000,000: 2s. Last read position: chr19:45,370,097
INFO 2026-06-08 08:03:41 MarkDuplicates Tracking 124466 as yet unmatched pairs. 9481 records in RAM.
INFO 2026-06-08 08:03:43 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:13:45s. Time for last 1,000,000: 2s. Last read position: chr19:48,861,195
INFO 2026-06-08 08:03:43 MarkDuplicates Tracking 121602 as yet unmatched pairs. 6420 records in RAM.
INFO 2026-06-08 08:03:45 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:13:47s. Time for last 1,000,000: 1s. Last read position: chr19:51,891,439
INFO 2026-06-08 08:03:45 MarkDuplicates Tracking 119791 as yet unmatched pairs. 4412 records in RAM.
INFO 2026-06-08 08:03:47 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:13:49s. Time for last 1,000,000: 2s. Last read position: chr19:55,455,743
INFO 2026-06-08 08:03:47 MarkDuplicates Tracking 117426 as yet unmatched pairs. 1848 records in RAM.
INFO 2026-06-08 08:03:49 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:13:51s. Time for last 1,000,000: 2s. Last read position: chr20:3,027,401
INFO 2026-06-08 08:03:49 MarkDuplicates Tracking 114774 as yet unmatched pairs. 21273 records in RAM.
INFO 2026-06-08 08:03:52 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:13:54s. Time for last 1,000,000: 2s. Last read position: chr20:20,712,384
INFO 2026-06-08 08:03:52 MarkDuplicates Tracking 110696 as yet unmatched pairs. 16780 records in RAM.
INFO 2026-06-08 08:03:55 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:13:57s. Time for last 1,000,000: 3s. Last read position: chr20:32,808,321
INFO 2026-06-08 08:03:55 MarkDuplicates Tracking 108818 as yet unmatched pairs. 14577 records in RAM.
INFO 2026-06-08 08:03:58 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:14:00s. Time for last 1,000,000: 3s. Last read position: chr20:38,637,270
INFO 2026-06-08 08:03:58 MarkDuplicates Tracking 104819 as yet unmatched pairs. 10375 records in RAM.
INFO 2026-06-08 08:04:01 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:14:03s. Time for last 1,000,000: 2s. Last read position: chr20:45,968,287
INFO 2026-06-08 08:04:01 MarkDuplicates Tracking 102190 as yet unmatched pairs. 7478 records in RAM.
INFO 2026-06-08 08:04:04 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:14:06s. Time for last 1,000,000: 3s. Last read position: chr20:57,340,058
INFO 2026-06-08 08:04:04 MarkDuplicates Tracking 98563 as yet unmatched pairs. 3509 records in RAM.
INFO 2026-06-08 08:04:06 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:14:08s. Time for last 1,000,000: 2s. Last read position: chr20:63,699,992
INFO 2026-06-08 08:04:06 MarkDuplicates Tracking 97640 as yet unmatched pairs. 2392 records in RAM.
INFO 2026-06-08 08:04:09 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:14:11s. Time for last 1,000,000: 2s. Last read position: chr21:8,425,454
INFO 2026-06-08 08:04:09 MarkDuplicates Tracking 94573 as yet unmatched pairs. 13694 records in RAM.
INFO 2026-06-08 08:04:12 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:14:13s. Time for last 1,000,000: 2s. Last read position: chr21:30,613,662
INFO 2026-06-08 08:04:12 MarkDuplicates Tracking 89841 as yet unmatched pairs. 8544 records in RAM.
INFO 2026-06-08 08:04:15 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:14:17s. Time for last 1,000,000: 3s. Last read position: chr21:40,271,178
INFO 2026-06-08 08:04:15 MarkDuplicates Tracking 86311 as yet unmatched pairs. 4767 records in RAM.
INFO 2026-06-08 08:04:18 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:14:20s. Time for last 1,000,000: 3s. Last read position: chr21:43,416,979
INFO 2026-06-08 08:04:18 MarkDuplicates Tracking 83958 as yet unmatched pairs. 2258 records in RAM.
INFO 2026-06-08 08:04:21 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:14:23s. Time for last 1,000,000: 3s. Last read position: chr22:11,903,803
INFO 2026-06-08 08:04:21 MarkDuplicates Tracking 81519 as yet unmatched pairs. 21886 records in RAM.
INFO 2026-06-08 08:04:23 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:14:25s. Time for last 1,000,000: 2s. Last read position: chr22:19,233,391
INFO 2026-06-08 08:04:23 MarkDuplicates Tracking 79711 as yet unmatched pairs. 19959 records in RAM.
INFO 2026-06-08 08:04:26 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:14:28s. Time for last 1,000,000: 2s. Last read position: chr22:21,288,290
INFO 2026-06-08 08:04:26 MarkDuplicates Tracking 77821 as yet unmatched pairs. 17951 records in RAM.
INFO 2026-06-08 08:04:29 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:14:31s. Time for last 1,000,000: 2s. Last read position: chr22:23,267,972
INFO 2026-06-08 08:04:29 MarkDuplicates Tracking 78020 as yet unmatched pairs. 18068 records in RAM.
INFO 2026-06-08 08:04:32 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:14:34s. Time for last 1,000,000: 3s. Last read position: chr22:23,698,215
INFO 2026-06-08 08:04:32 MarkDuplicates Tracking 73942 as yet unmatched pairs. 13880 records in RAM.
INFO 2026-06-08 08:04:34 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:14:36s. Time for last 1,000,000: 2s. Last read position: chr22:28,786,060
INFO 2026-06-08 08:04:34 MarkDuplicates Tracking 71370 as yet unmatched pairs. 11178 records in RAM.
INFO 2026-06-08 08:04:37 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:14:39s. Time for last 1,000,000: 2s. Last read position: chr22:31,713,341
INFO 2026-06-08 08:04:37 MarkDuplicates Tracking 68884 as yet unmatched pairs. 8563 records in RAM.
INFO 2026-06-08 08:04:39 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:14:41s. Time for last 1,000,000: 2s. Last read position: chr22:39,223,585
INFO 2026-06-08 08:04:39 MarkDuplicates Tracking 67190 as yet unmatched pairs. 6711 records in RAM.
INFO 2026-06-08 08:04:41 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:14:43s. Time for last 1,000,000: 2s. Last read position: chr22:45,025,777
INFO 2026-06-08 08:04:41 MarkDuplicates Tracking 62985 as yet unmatched pairs. 2387 records in RAM.
INFO 2026-06-08 08:04:43 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:14:45s. Time for last 1,000,000: 2s. Last read position: chrX:1,599,332
INFO 2026-06-08 08:04:43 MarkDuplicates Tracking 60339 as yet unmatched pairs. 54092 records in RAM.
INFO 2026-06-08 08:04:46 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:14:48s. Time for last 1,000,000: 2s. Last read position: chrX:19,302,691
INFO 2026-06-08 08:04:46 MarkDuplicates Tracking 55437 as yet unmatched pairs. 49167 records in RAM.
INFO 2026-06-08 08:04:49 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:14:51s. Time for last 1,000,000: 2s. Last read position: chrX:40,055,346
INFO 2026-06-08 08:04:49 MarkDuplicates Tracking 51303 as yet unmatched pairs. 45011 records in RAM.
INFO 2026-06-08 08:04:52 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:14:54s. Time for last 1,000,000: 2s. Last read position: chrX:47,569,003
INFO 2026-06-08 08:04:52 MarkDuplicates Tracking 47345 as yet unmatched pairs. 41042 records in RAM.
INFO 2026-06-08 08:04:54 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:14:56s. Time for last 1,000,000: 2s. Last read position: chrX:49,571,609
INFO 2026-06-08 08:04:54 MarkDuplicates Tracking 45475 as yet unmatched pairs. 39167 records in RAM.
INFO 2026-06-08 08:04:57 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:14:59s. Time for last 1,000,000: 3s. Last read position: chrX:53,430,388
INFO 2026-06-08 08:04:57 MarkDuplicates Tracking 42843 as yet unmatched pairs. 36522 records in RAM.
INFO 2026-06-08 08:05:00 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:15:02s. Time for last 1,000,000: 2s. Last read position: chrX:67,687,478
INFO 2026-06-08 08:05:00 MarkDuplicates Tracking 40581 as yet unmatched pairs. 34233 records in RAM.
INFO 2026-06-08 08:05:03 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:15:05s. Time for last 1,000,000: 2s. Last read position: chrX:70,519,220
INFO 2026-06-08 08:05:03 MarkDuplicates Tracking 36138 as yet unmatched pairs. 29771 records in RAM.
INFO 2026-06-08 08:05:05 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:15:07s. Time for last 1,000,000: 2s. Last read position: chrX:75,421,916
INFO 2026-06-08 08:05:05 MarkDuplicates Tracking 33404 as yet unmatched pairs. 27013 records in RAM.
INFO 2026-06-08 08:05:07 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:15:09s. Time for last 1,000,000: 1s. Last read position: chrX:100,802,434
INFO 2026-06-08 08:05:07 MarkDuplicates Tracking 27384 as yet unmatched pairs. 20959 records in RAM.
INFO 2026-06-08 08:05:08 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:15:10s. Time for last 1,000,000: 1s. Last read position: chrX:109,404,400
INFO 2026-06-08 08:05:08 MarkDuplicates Tracking 23878 as yet unmatched pairs. 17436 records in RAM.
INFO 2026-06-08 08:05:11 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:15:13s. Time for last 1,000,000: 2s. Last read position: chrX:120,969,178
INFO 2026-06-08 08:05:11 MarkDuplicates Tracking 19841 as yet unmatched pairs. 13376 records in RAM.
INFO 2026-06-08 08:05:13 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:15:15s. Time for last 1,000,000: 2s. Last read position: chrX:131,279,285
INFO 2026-06-08 08:05:13 MarkDuplicates Tracking 15964 as yet unmatched pairs. 9492 records in RAM.
INFO 2026-06-08 08:05:16 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:15:18s. Time for last 1,000,000: 2s. Last read position: chrX:139,528,270
INFO 2026-06-08 08:05:16 MarkDuplicates Tracking 12872 as yet unmatched pairs. 6386 records in RAM.
INFO 2026-06-08 08:05:19 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:15:21s. Time for last 1,000,000: 2s. Last read position: chrX:153,671,297
INFO 2026-06-08 08:05:19 MarkDuplicates Tracking 9002 as yet unmatched pairs. 2505 records in RAM.
INFO 2026-06-08 08:05:21 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:15:23s. Time for last 1,000,000: 2s. Last read position: chrX:154,886,948
INFO 2026-06-08 08:05:21 MarkDuplicates Tracking 7890 as yet unmatched pairs. 1382 records in RAM.
INFO 2026-06-08 08:05:23 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:15:25s. Time for last 1,000,000: 2s. Last read position: KI270719.1:105,529
INFO 2026-06-08 08:05:23 MarkDuplicates Tracking 3003 as yet unmatched pairs. 431 records in RAM.
INFO 2026-06-08 08:05:25 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:15:27s. Time for last 1,000,000: 1s. Last read position: KI270742.1:29,160
INFO 2026-06-08 08:05:25 MarkDuplicates Tracking 1218 as yet unmatched pairs. 375 records in RAM.
INFO 2026-06-08 08:05:26 MarkDuplicates Read 315237707 records. 0 pairs never matched.
INFO 2026-06-08 08:05:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 28842282928; totalMemory: 41171288064; maxMemory: 63585648640
INFO 2026-06-08 08:05:46 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:05:48 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:06:07 MarkDuplicates Traversing fragment information and detecting duplicates.
WARNING 2026-06-08 08:06:07 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.