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/3f/a5bb76c766205c3e7615200f81d570/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/a5bb76c766205c3e7615200f81d570/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/e03d778989310adaea80d7dc46c6ab/aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)
Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bam --METRICS_FILE aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
08:21:00.636 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 08:21:00 GMT 2026] MarkDuplicates --INPUT aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bam --METRICS_FILE aih-tih-sc-0ce15f-R1_A23WJ53LT4_1.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 08:21:00 GMT 2026] Executing as ?@nf-3fa5bb76c766205c3e7615200f81d570-b587f-sqmzz 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 08:21:00 MarkDuplicates Start of doWork freeMemory: 105826800; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 08:21:00 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 08:21:00 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 08:21:04 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:2,184,597
INFO 2026-06-08 08:21:04 MarkDuplicates Tracking 1708 as yet unmatched pairs. 26 records in RAM.
INFO 2026-06-08 08:21:07 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 2s. Last read position: chr1:8,866,480
INFO 2026-06-08 08:21:07 MarkDuplicates Tracking 3580 as yet unmatched pairs. 79 records in RAM.
INFO 2026-06-08 08:21:09 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: chr1:12,282,744
INFO 2026-06-08 08:21:09 MarkDuplicates Tracking 5521 as yet unmatched pairs. 148 records in RAM.
INFO 2026-06-08 08:21:11 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 2s. Last read position: chr1:17,664,533
INFO 2026-06-08 08:21:11 MarkDuplicates Tracking 7070 as yet unmatched pairs. 42 records in RAM.
INFO 2026-06-08 08:21:14 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 2s. Last read position: chr1:21,862,003
INFO 2026-06-08 08:21:14 MarkDuplicates Tracking 9036 as yet unmatched pairs. 203 records in RAM.
INFO 2026-06-08 08:21:16 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: chr1:24,655,001
INFO 2026-06-08 08:21:16 MarkDuplicates Tracking 10562 as yet unmatched pairs. 102 records in RAM.
INFO 2026-06-08 08:21:18 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: chr1:26,942,755
INFO 2026-06-08 08:21:18 MarkDuplicates Tracking 12278 as yet unmatched pairs. 74 records in RAM.
INFO 2026-06-08 08:21:21 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 2s. Last read position: chr1:31,666,039
INFO 2026-06-08 08:21:21 MarkDuplicates Tracking 14228 as yet unmatched pairs. 238 records in RAM.
INFO 2026-06-08 08:21:23 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: chr1:35,761,186
INFO 2026-06-08 08:21:23 MarkDuplicates Tracking 15617 as yet unmatched pairs. 19 records in RAM.
INFO 2026-06-08 08:21:25 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 2s. Last read position: chr1:39,424,027
INFO 2026-06-08 08:21:25 MarkDuplicates Tracking 17391 as yet unmatched pairs. 115 records in RAM.
INFO 2026-06-08 08:21:28 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 3s. Last read position: chr1:43,445,973
INFO 2026-06-08 08:21:28 MarkDuplicates Tracking 19115 as yet unmatched pairs. 32 records in RAM.
INFO 2026-06-08 08:21:31 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 2s. Last read position: chr1:51,468,511
INFO 2026-06-08 08:21:31 MarkDuplicates Tracking 20991 as yet unmatched pairs. 327 records in RAM.
INFO 2026-06-08 08:21:33 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 2s. Last read position: chr1:67,424,276
INFO 2026-06-08 08:21:33 MarkDuplicates Tracking 22404 as yet unmatched pairs. 128 records in RAM.
INFO 2026-06-08 08:21:35 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 2s. Last read position: chr1:91,328,855
INFO 2026-06-08 08:21:35 MarkDuplicates Tracking 23796 as yet unmatched pairs. 5 records in RAM.
INFO 2026-06-08 08:21:37 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 2s. Last read position: chr1:109,495,145
INFO 2026-06-08 08:21:37 MarkDuplicates Tracking 25331 as yet unmatched pairs. 55 records in RAM.
INFO 2026-06-08 08:21:40 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 2s. Last read position: chr1:115,664,241
INFO 2026-06-08 08:21:40 MarkDuplicates Tracking 26842 as yet unmatched pairs. 8 records in RAM.
INFO 2026-06-08 08:21:43 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 2s. Last read position: chr1:119,969,712
INFO 2026-06-08 08:21:43 MarkDuplicates Tracking 29012 as yet unmatched pairs. 430 records in RAM.
INFO 2026-06-08 08:21:45 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 1s. Last read position: chr1:146,136,442
INFO 2026-06-08 08:21:45 MarkDuplicates Tracking 29628 as yet unmatched pairs. 252 records in RAM.
INFO 2026-06-08 08:21:46 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 1s. Last read position: chr1:149,455,466
INFO 2026-06-08 08:21:46 MarkDuplicates Tracking 30362 as yet unmatched pairs. 252 records in RAM.
INFO 2026-06-08 08:21:49 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 2s. Last read position: chr1:150,796,722
INFO 2026-06-08 08:21:49 MarkDuplicates Tracking 31974 as yet unmatched pairs. 623 records in RAM.
INFO 2026-06-08 08:21:51 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 2s. Last read position: chr1:152,214,415
INFO 2026-06-08 08:21:51 MarkDuplicates Tracking 34726 as yet unmatched pairs. 2146 records in RAM.
INFO 2026-06-08 08:21:53 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 1s. Last read position: chr1:152,217,719
INFO 2026-06-08 08:21:53 MarkDuplicates Tracking 34462 as yet unmatched pairs. 1011 records in RAM.
INFO 2026-06-08 08:21:55 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 1s. Last read position: chr1:152,303,817
INFO 2026-06-08 08:21:55 MarkDuplicates Tracking 39077 as yet unmatched pairs. 4498 records in RAM.
INFO 2026-06-08 08:21:57 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 2s. Last read position: chr1:152,304,689
INFO 2026-06-08 08:21:57 MarkDuplicates Tracking 39605 as yet unmatched pairs. 3898 records in RAM.
INFO 2026-06-08 08:21:58 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 1s. Last read position: chr1:152,305,464
INFO 2026-06-08 08:21:58 MarkDuplicates Tracking 39568 as yet unmatched pairs. 2917 records in RAM.
INFO 2026-06-08 08:22:00 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 1s. Last read position: chr1:152,305,901
INFO 2026-06-08 08:22:00 MarkDuplicates Tracking 42989 as yet unmatched pairs. 5387 records in RAM.
INFO 2026-06-08 08:22:02 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 1s. Last read position: chr1:152,306,353
INFO 2026-06-08 08:22:02 MarkDuplicates Tracking 41191 as yet unmatched pairs. 2604 records in RAM.
INFO 2026-06-08 08:22:03 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 1s. Last read position: chr1:152,306,780
INFO 2026-06-08 08:22:03 MarkDuplicates Tracking 45327 as yet unmatched pairs. 6254 records in RAM.
INFO 2026-06-08 08:22:05 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 1s. Last read position: chr1:152,307,283
INFO 2026-06-08 08:22:05 MarkDuplicates Tracking 41463 as yet unmatched pairs. 1648 records in RAM.
INFO 2026-06-08 08:22:07 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 1s. Last read position: chr1:152,308,312
INFO 2026-06-08 08:22:07 MarkDuplicates Tracking 43294 as yet unmatched pairs. 2439 records in RAM.
INFO 2026-06-08 08:22:10 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 2s. Last read position: chr1:152,309,601
INFO 2026-06-08 08:22:10 MarkDuplicates Tracking 44848 as yet unmatched pairs. 2407 records in RAM.
INFO 2026-06-08 08:22:12 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 2s. Last read position: chr1:152,311,235
INFO 2026-06-08 08:22:12 MarkDuplicates Tracking 47002 as yet unmatched pairs. 3092 records in RAM.
INFO 2026-06-08 08:22:15 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 2s. Last read position: chr1:152,312,293
INFO 2026-06-08 08:22:15 MarkDuplicates Tracking 48607 as yet unmatched pairs. 3364 records in RAM.
INFO 2026-06-08 08:22:16 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 1s. Last read position: chr1:152,313,621
INFO 2026-06-08 08:22:16 MarkDuplicates Tracking 48914 as yet unmatched pairs. 2294 records in RAM.
INFO 2026-06-08 08:22:18 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 1s. Last read position: chr1:152,354,924
INFO 2026-06-08 08:22:18 MarkDuplicates Tracking 49087 as yet unmatched pairs. 1184 records in RAM.
INFO 2026-06-08 08:22:20 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 1s. Last read position: chr1:152,776,555
INFO 2026-06-08 08:22:20 MarkDuplicates Tracking 49756 as yet unmatched pairs. 319 records in RAM.
INFO 2026-06-08 08:22:23 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 2s. Last read position: chr1:153,056,569
INFO 2026-06-08 08:22:23 MarkDuplicates Tracking 51414 as yet unmatched pairs. 310 records in RAM.
INFO 2026-06-08 08:22:25 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 1s. Last read position: chr1:153,563,350
INFO 2026-06-08 08:22:25 MarkDuplicates Tracking 52653 as yet unmatched pairs. 303 records in RAM.
INFO 2026-06-08 08:22:27 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 1s. Last read position: chr1:154,550,940
INFO 2026-06-08 08:22:27 MarkDuplicates Tracking 53935 as yet unmatched pairs. 123 records in RAM.
INFO 2026-06-08 08:22:29 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 2s. Last read position: chr1:155,752,103
INFO 2026-06-08 08:22:29 MarkDuplicates Tracking 55428 as yet unmatched pairs. 96 records in RAM.
INFO 2026-06-08 08:22:31 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 2s. Last read position: chr1:156,138,635
INFO 2026-06-08 08:22:31 MarkDuplicates Tracking 58224 as yet unmatched pairs. 846 records in RAM.
INFO 2026-06-08 08:22:34 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 2s. Last read position: chr1:158,952,897
INFO 2026-06-08 08:22:34 MarkDuplicates Tracking 59180 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 08:22:36 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 1s. Last read position: chr1:161,606,279
INFO 2026-06-08 08:22:36 MarkDuplicates Tracking 60623 as yet unmatched pairs. 65 records in RAM.
INFO 2026-06-08 08:22:38 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 2s. Last read position: chr1:174,278,663
INFO 2026-06-08 08:22:38 MarkDuplicates Tracking 62091 as yet unmatched pairs. 101 records in RAM.
INFO 2026-06-08 08:22:40 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 1s. Last read position: chr1:186,052,984
INFO 2026-06-08 08:22:40 MarkDuplicates Tracking 63601 as yet unmatched pairs. 104 records in RAM.
INFO 2026-06-08 08:22:42 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 1s. Last read position: chr1:201,294,034
INFO 2026-06-08 08:22:42 MarkDuplicates Tracking 65088 as yet unmatched pairs. 237 records in RAM.
INFO 2026-06-08 08:22:44 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 1s. Last read position: chr1:204,469,295
INFO 2026-06-08 08:22:44 MarkDuplicates Tracking 66408 as yet unmatched pairs. 57 records in RAM.
INFO 2026-06-08 08:22:47 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 2s. Last read position: chr1:215,620,459
INFO 2026-06-08 08:22:47 MarkDuplicates Tracking 67965 as yet unmatched pairs. 53 records in RAM.
INFO 2026-06-08 08:22:50 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 2s. Last read position: chr1:228,256,912
INFO 2026-06-08 08:22:50 MarkDuplicates Tracking 69392 as yet unmatched pairs. 20 records in RAM.
INFO 2026-06-08 08:22:53 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 3s. Last read position: chr1:236,537,504
INFO 2026-06-08 08:22:53 MarkDuplicates Tracking 71284 as yet unmatched pairs. 93 records in RAM.
INFO 2026-06-08 08:22:56 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 2s. Last read position: chr2:9,535,807
INFO 2026-06-08 08:22:56 MarkDuplicates Tracking 72745 as yet unmatched pairs. 72632 records in RAM.
INFO 2026-06-08 08:22:58 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 1s. Last read position: chr2:24,665,898
INFO 2026-06-08 08:22:58 MarkDuplicates Tracking 74716 as yet unmatched pairs. 74597 records in RAM.
INFO 2026-06-08 08:23:00 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 2s. Last read position: chr2:28,752,130
INFO 2026-06-08 08:23:00 MarkDuplicates Tracking 77621 as yet unmatched pairs. 77492 records in RAM.
INFO 2026-06-08 08:23:03 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,264
INFO 2026-06-08 08:23:03 MarkDuplicates Tracking 274621 as yet unmatched pairs. 54740 records in RAM.
INFO 2026-06-08 08:23:04 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 1s. Last read position: chr2:32,916,409
INFO 2026-06-08 08:23:04 MarkDuplicates Tracking 485099 as yet unmatched pairs. 31690 records in RAM.
INFO 2026-06-08 08:23:06 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 2s. Last read position: chr2:43,572,838
INFO 2026-06-08 08:23:06 MarkDuplicates Tracking 505398 as yet unmatched pairs. 28008 records in RAM.
INFO 2026-06-08 08:23:08 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 1s. Last read position: chr2:55,318,884
INFO 2026-06-08 08:23:08 MarkDuplicates Tracking 503972 as yet unmatched pairs. 26579 records in RAM.
INFO 2026-06-08 08:23:10 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 1s. Last read position: chr2:69,960,888
INFO 2026-06-08 08:23:10 MarkDuplicates Tracking 503038 as yet unmatched pairs. 25640 records in RAM.
INFO 2026-06-08 08:23:12 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 2s. Last read position: chr2:74,679,693
INFO 2026-06-08 08:23:12 MarkDuplicates Tracking 500301 as yet unmatched pairs. 22898 records in RAM.
INFO 2026-06-08 08:23:14 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 2s. Last read position: chr2:95,850,498
INFO 2026-06-08 08:23:14 MarkDuplicates Tracking 498912 as yet unmatched pairs. 21504 records in RAM.
INFO 2026-06-08 08:23:17 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 2s. Last read position: chr2:101,866,467
INFO 2026-06-08 08:23:17 MarkDuplicates Tracking 497702 as yet unmatched pairs. 20274 records in RAM.
INFO 2026-06-08 08:23:19 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 2s. Last read position: chr2:111,850,814
INFO 2026-06-08 08:23:19 MarkDuplicates Tracking 496346 as yet unmatched pairs. 18910 records in RAM.
INFO 2026-06-08 08:23:22 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 2s. Last read position: chr2:130,161,178
INFO 2026-06-08 08:23:22 MarkDuplicates Tracking 494920 as yet unmatched pairs. 17480 records in RAM.
INFO 2026-06-08 08:23:24 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 2s. Last read position: chr2:157,780,429
INFO 2026-06-08 08:23:24 MarkDuplicates Tracking 493410 as yet unmatched pairs. 15968 records in RAM.
INFO 2026-06-08 08:23:27 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 2s. Last read position: chr2:174,719,893
INFO 2026-06-08 08:23:27 MarkDuplicates Tracking 491899 as yet unmatched pairs. 14454 records in RAM.
INFO 2026-06-08 08:23:29 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 2s. Last read position: chr2:188,985,231
INFO 2026-06-08 08:23:29 MarkDuplicates Tracking 490738 as yet unmatched pairs. 13291 records in RAM.
INFO 2026-06-08 08:23:31 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 2s. Last read position: chr2:197,495,333
INFO 2026-06-08 08:23:31 MarkDuplicates Tracking 489101 as yet unmatched pairs. 11653 records in RAM.
INFO 2026-06-08 08:23:33 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 2s. Last read position: chr2:208,347,960
INFO 2026-06-08 08:23:33 MarkDuplicates Tracking 487559 as yet unmatched pairs. 10109 records in RAM.
INFO 2026-06-08 08:23:36 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 3s. Last read position: chr2:215,379,128
INFO 2026-06-08 08:23:36 MarkDuplicates Tracking 487277 as yet unmatched pairs. 9824 records in RAM.
INFO 2026-06-08 08:23:38 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 1s. Last read position: chr2:215,409,974
INFO 2026-06-08 08:23:38 MarkDuplicates Tracking 485814 as yet unmatched pairs. 8360 records in RAM.
INFO 2026-06-08 08:23:41 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 2s. Last read position: chr2:218,239,400
INFO 2026-06-08 08:23:41 MarkDuplicates Tracking 483429 as yet unmatched pairs. 5975 records in RAM.
INFO 2026-06-08 08:23:43 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 2s. Last read position: chr2:222,298,531
INFO 2026-06-08 08:23:43 MarkDuplicates Tracking 481859 as yet unmatched pairs. 4405 records in RAM.
INFO 2026-06-08 08:23:45 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 2s. Last read position: chr2:232,300,069
INFO 2026-06-08 08:23:45 MarkDuplicates Tracking 479997 as yet unmatched pairs. 2537 records in RAM.
INFO 2026-06-08 08:23:48 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 2s. Last read position: chr2:240,575,519
INFO 2026-06-08 08:23:48 MarkDuplicates Tracking 478400 as yet unmatched pairs. 940 records in RAM.
INFO 2026-06-08 08:23:50 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 2s. Last read position: chr3:10,073,286
INFO 2026-06-08 08:23:50 MarkDuplicates Tracking 476689 as yet unmatched pairs. 23902 records in RAM.
INFO 2026-06-08 08:23:52 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 1s. Last read position: chr3:25,612,565
INFO 2026-06-08 08:23:52 MarkDuplicates Tracking 475110 as yet unmatched pairs. 22320 records in RAM.
INFO 2026-06-08 08:23:53 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 1s. Last read position: chr3:39,412,299
INFO 2026-06-08 08:23:53 MarkDuplicates Tracking 473476 as yet unmatched pairs. 20683 records in RAM.
INFO 2026-06-08 08:23:55 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 1s. Last read position: chr3:47,002,128
INFO 2026-06-08 08:23:55 MarkDuplicates Tracking 471875 as yet unmatched pairs. 19082 records in RAM.
INFO 2026-06-08 08:23:57 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 2s. Last read position: chr3:48,579,642
INFO 2026-06-08 08:23:57 MarkDuplicates Tracking 470288 as yet unmatched pairs. 17495 records in RAM.
INFO 2026-06-08 08:23:59 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 1s. Last read position: chr3:49,532,805
INFO 2026-06-08 08:23:59 MarkDuplicates Tracking 468609 as yet unmatched pairs. 15816 records in RAM.
INFO 2026-06-08 08:24:01 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 2s. Last read position: chr3:52,366,767
INFO 2026-06-08 08:24:01 MarkDuplicates Tracking 466817 as yet unmatched pairs. 14023 records in RAM.
INFO 2026-06-08 08:24:03 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 2s. Last read position: chr3:62,003,467
INFO 2026-06-08 08:24:03 MarkDuplicates Tracking 465143 as yet unmatched pairs. 12343 records in RAM.
INFO 2026-06-08 08:24:05 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 1s. Last read position: chr3:100,748,205
INFO 2026-06-08 08:24:05 MarkDuplicates Tracking 464224 as yet unmatched pairs. 11414 records in RAM.
INFO 2026-06-08 08:24:07 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 1s. Last read position: chr3:121,696,183
INFO 2026-06-08 08:24:07 MarkDuplicates Tracking 462303 as yet unmatched pairs. 9492 records in RAM.
INFO 2026-06-08 08:24:09 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 1s. Last read position: chr3:128,644,943
INFO 2026-06-08 08:24:09 MarkDuplicates Tracking 460616 as yet unmatched pairs. 7802 records in RAM.
INFO 2026-06-08 08:24:10 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 1s. Last read position: chr3:138,452,043
INFO 2026-06-08 08:24:10 MarkDuplicates Tracking 458824 as yet unmatched pairs. 6009 records in RAM.
INFO 2026-06-08 08:24:12 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 1s. Last read position: chr3:158,807,394
INFO 2026-06-08 08:24:12 MarkDuplicates Tracking 457223 as yet unmatched pairs. 4407 records in RAM.
INFO 2026-06-08 08:24:14 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 1s. Last read position: chr3:184,181,147
INFO 2026-06-08 08:24:14 MarkDuplicates Tracking 455874 as yet unmatched pairs. 3058 records in RAM.
INFO 2026-06-08 08:24:16 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 1s. Last read position: chr3:189,867,835
INFO 2026-06-08 08:24:16 MarkDuplicates Tracking 454413 as yet unmatched pairs. 1593 records in RAM.
INFO 2026-06-08 08:24:18 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 1s. Last read position: chr4:768,992
INFO 2026-06-08 08:24:18 MarkDuplicates Tracking 452718 as yet unmatched pairs. 13467 records in RAM.
INFO 2026-06-08 08:24:19 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 1s. Last read position: chr4:2,944,078
INFO 2026-06-08 08:24:19 MarkDuplicates Tracking 450533 as yet unmatched pairs. 11282 records in RAM.
INFO 2026-06-08 08:24:21 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 1s. Last read position: chr4:15,935,930
INFO 2026-06-08 08:24:21 MarkDuplicates Tracking 448865 as yet unmatched pairs. 9612 records in RAM.
INFO 2026-06-08 08:24:23 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 1s. Last read position: chr4:48,557,564
INFO 2026-06-08 08:24:23 MarkDuplicates Tracking 447441 as yet unmatched pairs. 8183 records in RAM.
INFO 2026-06-08 08:24:25 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 1s. Last read position: chr4:76,001,955
INFO 2026-06-08 08:24:25 MarkDuplicates Tracking 446156 as yet unmatched pairs. 6895 records in RAM.
INFO 2026-06-08 08:24:27 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 1s. Last read position: chr4:88,065,470
INFO 2026-06-08 08:24:27 MarkDuplicates Tracking 444319 as yet unmatched pairs. 5055 records in RAM.
INFO 2026-06-08 08:24:29 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 2s. Last read position: chr4:119,501,103
INFO 2026-06-08 08:24:29 MarkDuplicates Tracking 442886 as yet unmatched pairs. 3611 records in RAM.
INFO 2026-06-08 08:24:31 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 1s. Last read position: chr4:150,735,331
INFO 2026-06-08 08:24:31 MarkDuplicates Tracking 441517 as yet unmatched pairs. 2239 records in RAM.
INFO 2026-06-08 08:24:33 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 1s. Last read position: chr4:184,803,383
INFO 2026-06-08 08:24:33 MarkDuplicates Tracking 439942 as yet unmatched pairs. 657 records in RAM.
INFO 2026-06-08 08:24:35 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 2s. Last read position: chr5:14,462,781
INFO 2026-06-08 08:24:35 MarkDuplicates Tracking 438359 as yet unmatched pairs. 25222 records in RAM.
INFO 2026-06-08 08:24:37 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 1s. Last read position: chr5:40,680,446
INFO 2026-06-08 08:24:37 MarkDuplicates Tracking 436488 as yet unmatched pairs. 23344 records in RAM.
INFO 2026-06-08 08:24:39 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 1s. Last read position: chr5:68,293,810
INFO 2026-06-08 08:24:39 MarkDuplicates Tracking 434913 as yet unmatched pairs. 21768 records in RAM.
INFO 2026-06-08 08:24:40 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 1s. Last read position: chr5:78,227,393
INFO 2026-06-08 08:24:40 MarkDuplicates Tracking 433837 as yet unmatched pairs. 20689 records in RAM.
INFO 2026-06-08 08:24:42 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 1s. Last read position: chr5:98,892,573
INFO 2026-06-08 08:24:42 MarkDuplicates Tracking 432173 as yet unmatched pairs. 19023 records in RAM.
INFO 2026-06-08 08:24:44 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 1s. Last read position: chr5:132,716,945
INFO 2026-06-08 08:24:44 MarkDuplicates Tracking 430609 as yet unmatched pairs. 17456 records in RAM.
INFO 2026-06-08 08:24:46 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 1s. Last read position: chr5:138,571,088
INFO 2026-06-08 08:24:46 MarkDuplicates Tracking 429211 as yet unmatched pairs. 16055 records in RAM.
INFO 2026-06-08 08:24:47 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 1s. Last read position: chr5:141,432,134
INFO 2026-06-08 08:24:47 MarkDuplicates Tracking 427634 as yet unmatched pairs. 14465 records in RAM.
INFO 2026-06-08 08:24:49 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 1s. Last read position: chr5:149,525,125
INFO 2026-06-08 08:24:49 MarkDuplicates Tracking 426132 as yet unmatched pairs. 12958 records in RAM.
INFO 2026-06-08 08:24:51 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 1s. Last read position: chr5:150,402,206
INFO 2026-06-08 08:24:51 MarkDuplicates Tracking 444579 as yet unmatched pairs. 31405 records in RAM.
INFO 2026-06-08 08:24:53 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 1s. Last read position: chr5:150,405,082
INFO 2026-06-08 08:24:53 MarkDuplicates Tracking 430372 as yet unmatched pairs. 17198 records in RAM.
INFO 2026-06-08 08:24:54 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 1s. Last read position: chr5:150,407,152
INFO 2026-06-08 08:24:54 MarkDuplicates Tracking 425514 as yet unmatched pairs. 12340 records in RAM.
INFO 2026-06-08 08:24:56 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 1s. Last read position: chr5:151,566,029
INFO 2026-06-08 08:24:56 MarkDuplicates Tracking 418920 as yet unmatched pairs. 5740 records in RAM.
INFO 2026-06-08 08:24:58 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 1s. Last read position: chr5:171,391,304
INFO 2026-06-08 08:24:58 MarkDuplicates Tracking 418429 as yet unmatched pairs. 5248 records in RAM.
INFO 2026-06-08 08:25:00 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 1s. Last read position: chr5:177,435,041
INFO 2026-06-08 08:25:00 MarkDuplicates Tracking 415905 as yet unmatched pairs. 2715 records in RAM.
INFO 2026-06-08 08:25:02 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 1s. Last read position: chr5:179,836,443
INFO 2026-06-08 08:25:02 MarkDuplicates Tracking 414985 as yet unmatched pairs. 1794 records in RAM.
INFO 2026-06-08 08:25:04 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 2s. Last read position: chr6:3,225,089
INFO 2026-06-08 08:25:04 MarkDuplicates Tracking 412872 as yet unmatched pairs. 33916 records in RAM.
INFO 2026-06-08 08:25:06 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 1s. Last read position: chr6:7,579,585
INFO 2026-06-08 08:25:06 MarkDuplicates Tracking 411271 as yet unmatched pairs. 32315 records in RAM.
INFO 2026-06-08 08:25:08 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:04:05s. Time for last 1,000,000: 1s. Last read position: chr6:13,622,329
INFO 2026-06-08 08:25:08 MarkDuplicates Tracking 409288 as yet unmatched pairs. 30321 records in RAM.
INFO 2026-06-08 08:25:10 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 1s. Last read position: chr6:26,156,921
INFO 2026-06-08 08:25:10 MarkDuplicates Tracking 407627 as yet unmatched pairs. 28655 records in RAM.
INFO 2026-06-08 08:25:12 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 2s. Last read position: chr6:29,889,477
INFO 2026-06-08 08:25:12 MarkDuplicates Tracking 406795 as yet unmatched pairs. 27823 records in RAM.
INFO 2026-06-08 08:25:14 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 1s. Last read position: chr6:30,679,341
INFO 2026-06-08 08:25:14 MarkDuplicates Tracking 404688 as yet unmatched pairs. 25716 records in RAM.
INFO 2026-06-08 08:25:16 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 2s. Last read position: chr6:31,271,998
INFO 2026-06-08 08:25:16 MarkDuplicates Tracking 402970 as yet unmatched pairs. 23994 records in RAM.
INFO 2026-06-08 08:25:18 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 1s. Last read position: chr6:31,642,136
INFO 2026-06-08 08:25:18 MarkDuplicates Tracking 401385 as yet unmatched pairs. 22409 records in RAM.
INFO 2026-06-08 08:25:19 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 1s. Last read position: chr6:32,061,543
INFO 2026-06-08 08:25:19 MarkDuplicates Tracking 399691 as yet unmatched pairs. 20714 records in RAM.
INFO 2026-06-08 08:25:21 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 1s. Last read position: chr6:32,746,306
INFO 2026-06-08 08:25:21 MarkDuplicates Tracking 398244 as yet unmatched pairs. 19262 records in RAM.
INFO 2026-06-08 08:25:23 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 1s. Last read position: chr6:33,201,815
INFO 2026-06-08 08:25:23 MarkDuplicates Tracking 396581 as yet unmatched pairs. 17599 records in RAM.
INFO 2026-06-08 08:25:25 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 1s. Last read position: chr6:33,691,666
INFO 2026-06-08 08:25:25 MarkDuplicates Tracking 394755 as yet unmatched pairs. 15773 records in RAM.
INFO 2026-06-08 08:25:27 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 1s. Last read position: chr6:38,402,816
INFO 2026-06-08 08:25:27 MarkDuplicates Tracking 392954 as yet unmatched pairs. 13967 records in RAM.
INFO 2026-06-08 08:25:28 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr6:43,520,951
INFO 2026-06-08 08:25:28 MarkDuplicates Tracking 391251 as yet unmatched pairs. 12253 records in RAM.
INFO 2026-06-08 08:25:30 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr6:56,473,877
INFO 2026-06-08 08:25:30 MarkDuplicates Tracking 389546 as yet unmatched pairs. 10540 records in RAM.
INFO 2026-06-08 08:25:32 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 1s. Last read position: chr6:75,914,087
INFO 2026-06-08 08:25:32 MarkDuplicates Tracking 387959 as yet unmatched pairs. 8953 records in RAM.
INFO 2026-06-08 08:25:34 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 1s. Last read position: chr6:106,105,354
INFO 2026-06-08 08:25:34 MarkDuplicates Tracking 386574 as yet unmatched pairs. 7564 records in RAM.
INFO 2026-06-08 08:25:36 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 1s. Last read position: chr6:118,566,038
INFO 2026-06-08 08:25:36 MarkDuplicates Tracking 384908 as yet unmatched pairs. 5898 records in RAM.
INFO 2026-06-08 08:25:37 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 1s. Last read position: chr6:138,912,879
INFO 2026-06-08 08:25:37 MarkDuplicates Tracking 383419 as yet unmatched pairs. 4409 records in RAM.
INFO 2026-06-08 08:25:39 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 1s. Last read position: chr6:152,233,905
INFO 2026-06-08 08:25:39 MarkDuplicates Tracking 381852 as yet unmatched pairs. 2841 records in RAM.
INFO 2026-06-08 08:25:41 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 1s. Last read position: chr6:160,010,686
INFO 2026-06-08 08:25:41 MarkDuplicates Tracking 380271 as yet unmatched pairs. 1258 records in RAM.
INFO 2026-06-08 08:25:43 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 2s. Last read position: chr7:1,745,490
INFO 2026-06-08 08:25:43 MarkDuplicates Tracking 378419 as yet unmatched pairs. 26728 records in RAM.
INFO 2026-06-08 08:25:45 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 1s. Last read position: chr7:5,528,282
INFO 2026-06-08 08:25:45 MarkDuplicates Tracking 378366 as yet unmatched pairs. 26666 records in RAM.
INFO 2026-06-08 08:25:47 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 1s. Last read position: chr7:13,935,797
INFO 2026-06-08 08:25:47 MarkDuplicates Tracking 374879 as yet unmatched pairs. 23174 records in RAM.
INFO 2026-06-08 08:25:49 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 2s. Last read position: chr7:32,869,736
INFO 2026-06-08 08:25:49 MarkDuplicates Tracking 373344 as yet unmatched pairs. 21638 records in RAM.
INFO 2026-06-08 08:25:51 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 2s. Last read position: chr7:44,208,154
INFO 2026-06-08 08:25:51 MarkDuplicates Tracking 371910 as yet unmatched pairs. 20203 records in RAM.
INFO 2026-06-08 08:25:53 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 2s. Last read position: chr7:66,081,821
INFO 2026-06-08 08:25:53 MarkDuplicates Tracking 370111 as yet unmatched pairs. 18402 records in RAM.
INFO 2026-06-08 08:25:55 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 1s. Last read position: chr7:74,254,270
INFO 2026-06-08 08:25:55 MarkDuplicates Tracking 368987 as yet unmatched pairs. 17277 records in RAM.
INFO 2026-06-08 08:25:56 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 1s. Last read position: chr7:76,302,901
INFO 2026-06-08 08:25:56 MarkDuplicates Tracking 369577 as yet unmatched pairs. 17865 records in RAM.
INFO 2026-06-08 08:25:58 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 1s. Last read position: chr7:91,941,120
INFO 2026-06-08 08:25:58 MarkDuplicates Tracking 366405 as yet unmatched pairs. 14683 records in RAM.
INFO 2026-06-08 08:26:00 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 1s. Last read position: chr7:98,230,999
INFO 2026-06-08 08:26:00 MarkDuplicates Tracking 364733 as yet unmatched pairs. 13005 records in RAM.
INFO 2026-06-08 08:26:02 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 1s. Last read position: chr7:100,319,746
INFO 2026-06-08 08:26:02 MarkDuplicates Tracking 363163 as yet unmatched pairs. 11431 records in RAM.
INFO 2026-06-08 08:26:03 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 1s. Last read position: chr7:101,212,264
INFO 2026-06-08 08:26:03 MarkDuplicates Tracking 361143 as yet unmatched pairs. 9409 records in RAM.
INFO 2026-06-08 08:26:05 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 1s. Last read position: chr7:106,251,098
INFO 2026-06-08 08:26:05 MarkDuplicates Tracking 360180 as yet unmatched pairs. 8446 records in RAM.
INFO 2026-06-08 08:26:07 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 1s. Last read position: chr7:123,709,133
INFO 2026-06-08 08:26:07 MarkDuplicates Tracking 358515 as yet unmatched pairs. 6776 records in RAM.
INFO 2026-06-08 08:26:09 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 1s. Last read position: chr7:131,506,596
INFO 2026-06-08 08:26:09 MarkDuplicates Tracking 356977 as yet unmatched pairs. 5238 records in RAM.
INFO 2026-06-08 08:26:10 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 1s. Last read position: chr7:140,781,595
INFO 2026-06-08 08:26:10 MarkDuplicates Tracking 355833 as yet unmatched pairs. 4093 records in RAM.
INFO 2026-06-08 08:26:12 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 1s. Last read position: chr7:150,371,538
INFO 2026-06-08 08:26:12 MarkDuplicates Tracking 354259 as yet unmatched pairs. 2518 records in RAM.
INFO 2026-06-08 08:26:14 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 1s. Last read position: chr7:155,738,342
INFO 2026-06-08 08:26:14 MarkDuplicates Tracking 352329 as yet unmatched pairs. 586 records in RAM.
INFO 2026-06-08 08:26:16 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 1s. Last read position: chr8:16,139,422
INFO 2026-06-08 08:26:16 MarkDuplicates Tracking 350552 as yet unmatched pairs. 17344 records in RAM.
INFO 2026-06-08 08:26:17 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 1s. Last read position: chr8:22,629,977
INFO 2026-06-08 08:26:17 MarkDuplicates Tracking 348833 as yet unmatched pairs. 15625 records in RAM.
INFO 2026-06-08 08:26:19 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 1s. Last read position: chr8:38,177,113
INFO 2026-06-08 08:26:19 MarkDuplicates Tracking 347307 as yet unmatched pairs. 14072 records in RAM.
INFO 2026-06-08 08:26:21 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 1s. Last read position: chr8:47,817,450
INFO 2026-06-08 08:26:21 MarkDuplicates Tracking 345513 as yet unmatched pairs. 12277 records in RAM.
INFO 2026-06-08 08:26:23 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 2s. Last read position: chr8:70,144,707
INFO 2026-06-08 08:26:23 MarkDuplicates Tracking 344139 as yet unmatched pairs. 10901 records in RAM.
INFO 2026-06-08 08:26:25 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 1s. Last read position: chr8:98,045,022
INFO 2026-06-08 08:26:25 MarkDuplicates Tracking 342500 as yet unmatched pairs. 9262 records in RAM.
INFO 2026-06-08 08:26:27 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 2s. Last read position: chr8:115,604,877
INFO 2026-06-08 08:26:27 MarkDuplicates Tracking 341196 as yet unmatched pairs. 7958 records in RAM.
INFO 2026-06-08 08:26:29 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 1s. Last read position: chr8:133,264,585
INFO 2026-06-08 08:26:29 MarkDuplicates Tracking 340066 as yet unmatched pairs. 6828 records in RAM.
INFO 2026-06-08 08:26:31 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 1s. Last read position: chr8:143,858,519
INFO 2026-06-08 08:26:31 MarkDuplicates Tracking 337890 as yet unmatched pairs. 4652 records in RAM.
INFO 2026-06-08 08:26:32 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 1s. Last read position: chr8:143,863,837
INFO 2026-06-08 08:26:32 MarkDuplicates Tracking 337116 as yet unmatched pairs. 3878 records in RAM.
INFO 2026-06-08 08:26:33 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 1s. Last read position: chr8:143,921,941
INFO 2026-06-08 08:26:33 MarkDuplicates Tracking 336114 as yet unmatched pairs. 2876 records in RAM.
INFO 2026-06-08 08:26:35 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 1s. Last read position: chr8:144,450,548
INFO 2026-06-08 08:26:35 MarkDuplicates Tracking 333904 as yet unmatched pairs. 666 records in RAM.
INFO 2026-06-08 08:26:37 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 2s. Last read position: chr9:6,420,913
INFO 2026-06-08 08:26:37 MarkDuplicates Tracking 332162 as yet unmatched pairs. 21234 records in RAM.
INFO 2026-06-08 08:26:39 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 1s. Last read position: chr9:32,543,126
INFO 2026-06-08 08:26:39 MarkDuplicates Tracking 330670 as yet unmatched pairs. 19741 records in RAM.
INFO 2026-06-08 08:26:41 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 1s. Last read position: chr9:35,707,137
INFO 2026-06-08 08:26:41 MarkDuplicates Tracking 329321 as yet unmatched pairs. 18392 records in RAM.
INFO 2026-06-08 08:26:42 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 1s. Last read position: chr9:73,162,832
INFO 2026-06-08 08:26:42 MarkDuplicates Tracking 328385 as yet unmatched pairs. 17441 records in RAM.
INFO 2026-06-08 08:26:44 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 1s. Last read position: chr9:92,719,500
INFO 2026-06-08 08:26:44 MarkDuplicates Tracking 326585 as yet unmatched pairs. 15638 records in RAM.
INFO 2026-06-08 08:26:46 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 1s. Last read position: chr9:105,335,620
INFO 2026-06-08 08:26:46 MarkDuplicates Tracking 324984 as yet unmatched pairs. 14034 records in RAM.
INFO 2026-06-08 08:26:48 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 1s. Last read position: chr9:114,406,767
INFO 2026-06-08 08:26:48 MarkDuplicates Tracking 323436 as yet unmatched pairs. 12486 records in RAM.
INFO 2026-06-08 08:26:49 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 1s. Last read position: chr9:115,086,213
INFO 2026-06-08 08:26:49 MarkDuplicates Tracking 322865 as yet unmatched pairs. 11915 records in RAM.
INFO 2026-06-08 08:26:51 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 1s. Last read position: chr9:122,858,986
INFO 2026-06-08 08:26:51 MarkDuplicates Tracking 320174 as yet unmatched pairs. 9224 records in RAM.
INFO 2026-06-08 08:26:53 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 1s. Last read position: chr9:128,166,301
INFO 2026-06-08 08:26:53 MarkDuplicates Tracking 318501 as yet unmatched pairs. 7549 records in RAM.
INFO 2026-06-08 08:26:56 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 2s. Last read position: chr9:130,630,757
INFO 2026-06-08 08:26:56 MarkDuplicates Tracking 316584 as yet unmatched pairs. 5617 records in RAM.
INFO 2026-06-08 08:26:58 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 2s. Last read position: chr9:133,107,128
INFO 2026-06-08 08:26:58 MarkDuplicates Tracking 315115 as yet unmatched pairs. 4145 records in RAM.
INFO 2026-06-08 08:26:59 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 1s. Last read position: chr9:136,505,068
INFO 2026-06-08 08:26:59 MarkDuplicates Tracking 313274 as yet unmatched pairs. 2293 records in RAM.
INFO 2026-06-08 08:27:01 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 1s. Last read position: chr9:137,614,681
INFO 2026-06-08 08:27:01 MarkDuplicates Tracking 311200 as yet unmatched pairs. 219 records in RAM.
INFO 2026-06-08 08:27:03 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 1s. Last read position: chr10:5,766,503
INFO 2026-06-08 08:27:03 MarkDuplicates Tracking 309403 as yet unmatched pairs. 14795 records in RAM.
INFO 2026-06-08 08:27:05 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 1s. Last read position: chr10:20,217,442
INFO 2026-06-08 08:27:05 MarkDuplicates Tracking 307584 as yet unmatched pairs. 12973 records in RAM.
INFO 2026-06-08 08:27:07 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 1s. Last read position: chr10:32,926,013
INFO 2026-06-08 08:27:07 MarkDuplicates Tracking 306157 as yet unmatched pairs. 11542 records in RAM.
INFO 2026-06-08 08:27:08 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 1s. Last read position: chr10:48,010,247
INFO 2026-06-08 08:27:08 MarkDuplicates Tracking 304694 as yet unmatched pairs. 10077 records in RAM.
INFO 2026-06-08 08:27:10 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 1s. Last read position: chr10:70,152,500
INFO 2026-06-08 08:27:10 MarkDuplicates Tracking 303192 as yet unmatched pairs. 8571 records in RAM.
INFO 2026-06-08 08:27:12 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:06:09s. Time for last 1,000,000: 1s. Last read position: chr10:78,040,216
INFO 2026-06-08 08:27:12 MarkDuplicates Tracking 301717 as yet unmatched pairs. 7092 records in RAM.
INFO 2026-06-08 08:27:13 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 1s. Last read position: chr10:92,531,793
INFO 2026-06-08 08:27:13 MarkDuplicates Tracking 300529 as yet unmatched pairs. 5899 records in RAM.
INFO 2026-06-08 08:27:15 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 1s. Last read position: chr10:101,002,699
INFO 2026-06-08 08:27:15 MarkDuplicates Tracking 298926 as yet unmatched pairs. 4296 records in RAM.
INFO 2026-06-08 08:27:17 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 1s. Last read position: chr10:109,865,182
INFO 2026-06-08 08:27:17 MarkDuplicates Tracking 297088 as yet unmatched pairs. 2457 records in RAM.
INFO 2026-06-08 08:27:19 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:06:16s. Time for last 1,000,000: 1s. Last read position: chr10:124,045,840
INFO 2026-06-08 08:27:19 MarkDuplicates Tracking 295686 as yet unmatched pairs. 1043 records in RAM.
INFO 2026-06-08 08:27:21 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 2s. Last read position: chr11:397,105
INFO 2026-06-08 08:27:21 MarkDuplicates Tracking 294213 as yet unmatched pairs. 32760 records in RAM.
INFO 2026-06-08 08:27:22 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 1s. Last read position: chr11:1,761,324
INFO 2026-06-08 08:27:22 MarkDuplicates Tracking 292995 as yet unmatched pairs. 31539 records in RAM.
INFO 2026-06-08 08:27:24 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 1s. Last read position: chr11:7,987,364
INFO 2026-06-08 08:27:24 MarkDuplicates Tracking 290379 as yet unmatched pairs. 28918 records in RAM.
INFO 2026-06-08 08:27:26 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 1s. Last read position: chr11:17,074,444
INFO 2026-06-08 08:27:26 MarkDuplicates Tracking 289599 as yet unmatched pairs. 28137 records in RAM.
INFO 2026-06-08 08:27:28 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 1s. Last read position: chr11:34,154,287
INFO 2026-06-08 08:27:28 MarkDuplicates Tracking 287018 as yet unmatched pairs. 25555 records in RAM.
INFO 2026-06-08 08:27:30 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 1s. Last read position: chr11:47,260,498
INFO 2026-06-08 08:27:30 MarkDuplicates Tracking 285494 as yet unmatched pairs. 24026 records in RAM.
INFO 2026-06-08 08:27:33 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:06:31s. Time for last 1,000,000: 3s. Last read position: chr11:57,806,949
INFO 2026-06-08 08:27:33 MarkDuplicates Tracking 284038 as yet unmatched pairs. 22569 records in RAM.
INFO 2026-06-08 08:27:35 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:06:33s. Time for last 1,000,000: 1s. Last read position: chr11:61,967,323
INFO 2026-06-08 08:27:35 MarkDuplicates Tracking 282607 as yet unmatched pairs. 21135 records in RAM.
INFO 2026-06-08 08:27:37 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:06:35s. Time for last 1,000,000: 2s. Last read position: chr11:62,528,535
INFO 2026-06-08 08:27:37 MarkDuplicates Tracking 281387 as yet unmatched pairs. 19912 records in RAM.
INFO 2026-06-08 08:27:39 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 1s. Last read position: chr11:62,787,426
INFO 2026-06-08 08:27:39 MarkDuplicates Tracking 279243 as yet unmatched pairs. 17768 records in RAM.
INFO 2026-06-08 08:27:41 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 1s. Last read position: chr11:64,860,058
INFO 2026-06-08 08:27:41 MarkDuplicates Tracking 277483 as yet unmatched pairs. 16007 records in RAM.
INFO 2026-06-08 08:27:42 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 1s. Last read position: chr11:65,654,373
INFO 2026-06-08 08:27:42 MarkDuplicates Tracking 275963 as yet unmatched pairs. 14480 records in RAM.
INFO 2026-06-08 08:27:44 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 1s. Last read position: chr11:66,688,192
INFO 2026-06-08 08:27:44 MarkDuplicates Tracking 273818 as yet unmatched pairs. 12330 records in RAM.
INFO 2026-06-08 08:27:46 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:06:44s. Time for last 1,000,000: 1s. Last read position: chr11:68,613,119
INFO 2026-06-08 08:27:46 MarkDuplicates Tracking 272054 as yet unmatched pairs. 10561 records in RAM.
INFO 2026-06-08 08:27:48 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 1s. Last read position: chr11:72,824,749
INFO 2026-06-08 08:27:48 MarkDuplicates Tracking 270120 as yet unmatched pairs. 8626 records in RAM.
INFO 2026-06-08 08:27:49 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:06:47s. Time for last 1,000,000: 1s. Last read position: chr11:85,695,172
INFO 2026-06-08 08:27:49 MarkDuplicates Tracking 268530 as yet unmatched pairs. 7035 records in RAM.
INFO 2026-06-08 08:27:51 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 1s. Last read position: chr11:102,797,313
INFO 2026-06-08 08:27:51 MarkDuplicates Tracking 267010 as yet unmatched pairs. 5514 records in RAM.
INFO 2026-06-08 08:27:53 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:06:51s. Time for last 1,000,000: 1s. Last read position: chr11:118,212,406
INFO 2026-06-08 08:27:53 MarkDuplicates Tracking 265444 as yet unmatched pairs. 3948 records in RAM.
INFO 2026-06-08 08:27:55 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 1s. Last read position: chr11:119,359,601
INFO 2026-06-08 08:27:55 MarkDuplicates Tracking 263757 as yet unmatched pairs. 2261 records in RAM.
INFO 2026-06-08 08:27:56 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:06:54s. Time for last 1,000,000: 1s. Last read position: chr11:128,758,252
INFO 2026-06-08 08:27:56 MarkDuplicates Tracking 262316 as yet unmatched pairs. 819 records in RAM.
INFO 2026-06-08 08:27:59 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 2s. Last read position: chr12:2,874,303
INFO 2026-06-08 08:27:59 MarkDuplicates Tracking 260673 as yet unmatched pairs. 36995 records in RAM.
INFO 2026-06-08 08:28:00 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 1s. Last read position: chr12:6,944,513
INFO 2026-06-08 08:28:00 MarkDuplicates Tracking 258988 as yet unmatched pairs. 35309 records in RAM.
INFO 2026-06-08 08:28:02 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:07:00s. Time for last 1,000,000: 1s. Last read position: chr12:10,723,021
INFO 2026-06-08 08:28:02 MarkDuplicates Tracking 257462 as yet unmatched pairs. 33783 records in RAM.
INFO 2026-06-08 08:28:04 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 1s. Last read position: chr12:26,483,698
INFO 2026-06-08 08:28:04 MarkDuplicates Tracking 255515 as yet unmatched pairs. 31836 records in RAM.
INFO 2026-06-08 08:28:06 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:07:03s. Time for last 1,000,000: 1s. Last read position: chr12:47,751,739
INFO 2026-06-08 08:28:06 MarkDuplicates Tracking 254030 as yet unmatched pairs. 30350 records in RAM.
INFO 2026-06-08 08:28:08 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 2s. Last read position: chr12:49,269,963
INFO 2026-06-08 08:28:08 MarkDuplicates Tracking 252766 as yet unmatched pairs. 29086 records in RAM.
INFO 2026-06-08 08:28:10 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 2s. Last read position: chr12:52,447,350
INFO 2026-06-08 08:28:10 MarkDuplicates Tracking 254521 as yet unmatched pairs. 30840 records in RAM.
INFO 2026-06-08 08:28:12 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 1s. Last read position: chr12:52,451,959
INFO 2026-06-08 08:28:12 MarkDuplicates Tracking 252985 as yet unmatched pairs. 29304 records in RAM.
INFO 2026-06-08 08:28:14 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:07:11s. Time for last 1,000,000: 1s. Last read position: chr12:52,473,477
INFO 2026-06-08 08:28:14 MarkDuplicates Tracking 251207 as yet unmatched pairs. 27526 records in RAM.
INFO 2026-06-08 08:28:15 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 1s. Last read position: chr12:52,490,015
INFO 2026-06-08 08:28:15 MarkDuplicates Tracking 250075 as yet unmatched pairs. 26394 records in RAM.
INFO 2026-06-08 08:28:17 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:07:15s. Time for last 1,000,000: 1s. Last read position: chr12:52,493,112
INFO 2026-06-08 08:28:17 MarkDuplicates Tracking 246479 as yet unmatched pairs. 22798 records in RAM.
INFO 2026-06-08 08:28:19 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:07:16s. Time for last 1,000,000: 1s. Last read position: chr12:52,646,749
INFO 2026-06-08 08:28:19 MarkDuplicates Tracking 245334 as yet unmatched pairs. 21653 records in RAM.
INFO 2026-06-08 08:28:20 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:07:18s. Time for last 1,000,000: 1s. Last read position: chr12:52,679,793
INFO 2026-06-08 08:28:20 MarkDuplicates Tracking 244943 as yet unmatched pairs. 21262 records in RAM.
INFO 2026-06-08 08:28:22 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:07:20s. Time for last 1,000,000: 1s. Last read position: chr12:53,665,337
INFO 2026-06-08 08:28:22 MarkDuplicates Tracking 241976 as yet unmatched pairs. 18295 records in RAM.
INFO 2026-06-08 08:28:24 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:07:21s. Time for last 1,000,000: 1s. Last read position: chr12:55,957,945
INFO 2026-06-08 08:28:24 MarkDuplicates Tracking 240804 as yet unmatched pairs. 17123 records in RAM.
INFO 2026-06-08 08:28:25 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:07:23s. Time for last 1,000,000: 1s. Last read position: chr12:56,432,412
INFO 2026-06-08 08:28:25 MarkDuplicates Tracking 238263 as yet unmatched pairs. 14581 records in RAM.
INFO 2026-06-08 08:28:27 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:07:25s. Time for last 1,000,000: 1s. Last read position: chr12:57,107,302
INFO 2026-06-08 08:28:27 MarkDuplicates Tracking 236906 as yet unmatched pairs. 13224 records in RAM.
INFO 2026-06-08 08:28:29 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 1s. Last read position: chr12:58,874,284
INFO 2026-06-08 08:28:29 MarkDuplicates Tracking 235016 as yet unmatched pairs. 11333 records in RAM.
INFO 2026-06-08 08:28:31 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:07:28s. Time for last 1,000,000: 1s. Last read position: chr12:76,031,256
INFO 2026-06-08 08:28:31 MarkDuplicates Tracking 233743 as yet unmatched pairs. 10056 records in RAM.
INFO 2026-06-08 08:28:32 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:07:30s. Time for last 1,000,000: 1s. Last read position: chr12:100,312,546
INFO 2026-06-08 08:28:32 MarkDuplicates Tracking 231965 as yet unmatched pairs. 8270 records in RAM.
INFO 2026-06-08 08:28:34 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:07:32s. Time for last 1,000,000: 1s. Last read position: chr12:109,857,593
INFO 2026-06-08 08:28:34 MarkDuplicates Tracking 230740 as yet unmatched pairs. 7045 records in RAM.
INFO 2026-06-08 08:28:36 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:07:34s. Time for last 1,000,000: 1s. Last read position: chr12:113,295,955
INFO 2026-06-08 08:28:36 MarkDuplicates Tracking 228865 as yet unmatched pairs. 5169 records in RAM.
INFO 2026-06-08 08:28:38 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:07:35s. Time for last 1,000,000: 1s. Last read position: chr12:121,255,792
INFO 2026-06-08 08:28:38 MarkDuplicates Tracking 227321 as yet unmatched pairs. 3625 records in RAM.
INFO 2026-06-08 08:28:39 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:07:37s. Time for last 1,000,000: 1s. Last read position: chr12:124,336,889
INFO 2026-06-08 08:28:39 MarkDuplicates Tracking 225911 as yet unmatched pairs. 2212 records in RAM.
INFO 2026-06-08 08:28:41 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:07:39s. Time for last 1,000,000: 1s. Last read position: chr12:132,754,995
INFO 2026-06-08 08:28:41 MarkDuplicates Tracking 224120 as yet unmatched pairs. 420 records in RAM.
INFO 2026-06-08 08:28:43 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:07:41s. Time for last 1,000,000: 1s. Last read position: chr13:23,331,945
INFO 2026-06-08 08:28:43 MarkDuplicates Tracking 222428 as yet unmatched pairs. 7236 records in RAM.
INFO 2026-06-08 08:28:45 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:07:42s. Time for last 1,000,000: 1s. Last read position: chr13:40,559,579
INFO 2026-06-08 08:28:45 MarkDuplicates Tracking 221127 as yet unmatched pairs. 5933 records in RAM.
INFO 2026-06-08 08:28:47 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:07:44s. Time for last 1,000,000: 2s. Last read position: chr13:49,191,220
INFO 2026-06-08 08:28:47 MarkDuplicates Tracking 219455 as yet unmatched pairs. 4257 records in RAM.
INFO 2026-06-08 08:28:49 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:07:47s. Time for last 1,000,000: 2s. Last read position: chr13:77,918,313
INFO 2026-06-08 08:28:49 MarkDuplicates Tracking 218969 as yet unmatched pairs. 3771 records in RAM.
INFO 2026-06-08 08:28:51 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:07:49s. Time for last 1,000,000: 1s. Last read position: chr13:110,206,664
INFO 2026-06-08 08:28:51 MarkDuplicates Tracking 216459 as yet unmatched pairs. 1258 records in RAM.
INFO 2026-06-08 08:28:53 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:07:51s. Time for last 1,000,000: 1s. Last read position: chr14:21,017,552
INFO 2026-06-08 08:28:53 MarkDuplicates Tracking 214825 as yet unmatched pairs. 18262 records in RAM.
INFO 2026-06-08 08:28:55 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:07:52s. Time for last 1,000,000: 1s. Last read position: chr14:24,062,474
INFO 2026-06-08 08:28:55 MarkDuplicates Tracking 213160 as yet unmatched pairs. 16584 records in RAM.
INFO 2026-06-08 08:28:57 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:07:54s. Time for last 1,000,000: 1s. Last read position: chr14:32,091,952
INFO 2026-06-08 08:28:57 MarkDuplicates Tracking 211624 as yet unmatched pairs. 15047 records in RAM.
INFO 2026-06-08 08:28:58 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:07:56s. Time for last 1,000,000: 1s. Last read position: chr14:51,715,364
INFO 2026-06-08 08:28:58 MarkDuplicates Tracking 210173 as yet unmatched pairs. 13596 records in RAM.
INFO 2026-06-08 08:29:00 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:07:58s. Time for last 1,000,000: 1s. Last read position: chr14:64,122,359
INFO 2026-06-08 08:29:00 MarkDuplicates Tracking 208669 as yet unmatched pairs. 12092 records in RAM.
INFO 2026-06-08 08:29:02 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:08:00s. Time for last 1,000,000: 1s. Last read position: chr14:70,342,697
INFO 2026-06-08 08:29:02 MarkDuplicates Tracking 207088 as yet unmatched pairs. 10510 records in RAM.
INFO 2026-06-08 08:29:04 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:08:02s. Time for last 1,000,000: 2s. Last read position: chr14:77,026,206
INFO 2026-06-08 08:29:04 MarkDuplicates Tracking 205515 as yet unmatched pairs. 8932 records in RAM.
INFO 2026-06-08 08:29:06 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:08:04s. Time for last 1,000,000: 2s. Last read position: chr14:94,497,894
INFO 2026-06-08 08:29:06 MarkDuplicates Tracking 203891 as yet unmatched pairs. 7304 records in RAM.
INFO 2026-06-08 08:29:08 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:08:06s. Time for last 1,000,000: 1s. Last read position: chr14:102,034,105
INFO 2026-06-08 08:29:08 MarkDuplicates Tracking 202447 as yet unmatched pairs. 5851 records in RAM.
INFO 2026-06-08 08:29:10 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:08:08s. Time for last 1,000,000: 1s. Last read position: chr14:104,940,112
INFO 2026-06-08 08:29:10 MarkDuplicates Tracking 200670 as yet unmatched pairs. 4074 records in RAM.
INFO 2026-06-08 08:29:12 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:08:09s. Time for last 1,000,000: 1s. Last read position: chr14:104,954,270
INFO 2026-06-08 08:29:12 MarkDuplicates Tracking 199477 as yet unmatched pairs. 2881 records in RAM.
INFO 2026-06-08 08:29:14 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:08:11s. Time for last 1,000,000: 1s. Last read position: chr14:105,708,371
INFO 2026-06-08 08:29:14 MarkDuplicates Tracking 198913 as yet unmatched pairs. 2317 records in RAM.
INFO 2026-06-08 08:30:22 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 68s. Last read position: chr14:105,770,311
INFO 2026-06-08 08:30:22 MarkDuplicates Tracking 197630 as yet unmatched pairs. 1033 records in RAM.
INFO 2026-06-08 08:30:25 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 2s. Last read position: chr15:30,558,302
INFO 2026-06-08 08:30:25 MarkDuplicates Tracking 195787 as yet unmatched pairs. 15248 records in RAM.
INFO 2026-06-08 08:30:26 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:09:24s. Time for last 1,000,000: 1s. Last read position: chr15:40,008,045
INFO 2026-06-08 08:30:26 MarkDuplicates Tracking 194476 as yet unmatched pairs. 13937 records in RAM.
INFO 2026-06-08 08:30:28 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:09:26s. Time for last 1,000,000: 1s. Last read position: chr15:42,450,283
INFO 2026-06-08 08:30:28 MarkDuplicates Tracking 192898 as yet unmatched pairs. 12357 records in RAM.
INFO 2026-06-08 08:30:30 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:09:28s. Time for last 1,000,000: 1s. Last read position: chr15:45,151,928
INFO 2026-06-08 08:30:30 MarkDuplicates Tracking 191431 as yet unmatched pairs. 10890 records in RAM.
INFO 2026-06-08 08:30:32 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:09:29s. Time for last 1,000,000: 1s. Last read position: chr15:56,919,966
INFO 2026-06-08 08:30:32 MarkDuplicates Tracking 190077 as yet unmatched pairs. 9534 records in RAM.
INFO 2026-06-08 08:30:34 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:09:31s. Time for last 1,000,000: 1s. Last read position: chr15:64,160,170
INFO 2026-06-08 08:30:34 MarkDuplicates Tracking 188513 as yet unmatched pairs. 7970 records in RAM.
INFO 2026-06-08 08:30:35 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:09:33s. Time for last 1,000,000: 1s. Last read position: chr15:72,200,563
INFO 2026-06-08 08:30:35 MarkDuplicates Tracking 186904 as yet unmatched pairs. 6361 records in RAM.
INFO 2026-06-08 08:30:37 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:09:34s. Time for last 1,000,000: 1s. Last read position: chr15:75,208,383
INFO 2026-06-08 08:30:37 MarkDuplicates Tracking 184951 as yet unmatched pairs. 4408 records in RAM.
INFO 2026-06-08 08:30:38 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:09:36s. Time for last 1,000,000: 1s. Last read position: chr15:82,539,993
INFO 2026-06-08 08:30:38 MarkDuplicates Tracking 183439 as yet unmatched pairs. 2894 records in RAM.
INFO 2026-06-08 08:30:40 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 1s. Last read position: chr15:90,466,297
INFO 2026-06-08 08:30:40 MarkDuplicates Tracking 182005 as yet unmatched pairs. 1455 records in RAM.
INFO 2026-06-08 08:30:41 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:09:39s. Time for last 1,000,000: 1s. Last read position: chr16:298,045
INFO 2026-06-08 08:30:41 MarkDuplicates Tracking 180287 as yet unmatched pairs. 27942 records in RAM.
INFO 2026-06-08 08:30:43 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:09:41s. Time for last 1,000,000: 1s. Last read position: chr16:1,827,684
INFO 2026-06-08 08:30:43 MarkDuplicates Tracking 178246 as yet unmatched pairs. 25901 records in RAM.
INFO 2026-06-08 08:30:45 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:09:42s. Time for last 1,000,000: 1s. Last read position: chr16:2,763,231
INFO 2026-06-08 08:30:45 MarkDuplicates Tracking 176658 as yet unmatched pairs. 24310 records in RAM.
INFO 2026-06-08 08:30:47 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 1s. Last read position: chr16:4,382,559
INFO 2026-06-08 08:30:47 MarkDuplicates Tracking 174917 as yet unmatched pairs. 22569 records in RAM.
INFO 2026-06-08 08:30:48 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:09:46s. Time for last 1,000,000: 1s. Last read position: chr16:11,885,181
INFO 2026-06-08 08:30:48 MarkDuplicates Tracking 173191 as yet unmatched pairs. 20843 records in RAM.
INFO 2026-06-08 08:30:50 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:09:48s. Time for last 1,000,000: 1s. Last read position: chr16:16,052,777
INFO 2026-06-08 08:30:50 MarkDuplicates Tracking 172204 as yet unmatched pairs. 19856 records in RAM.
INFO 2026-06-08 08:30:52 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:09:49s. Time for last 1,000,000: 1s. Last read position: chr16:18,431,908
INFO 2026-06-08 08:30:52 MarkDuplicates Tracking 171655 as yet unmatched pairs. 19307 records in RAM.
INFO 2026-06-08 08:30:53 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:09:51s. Time for last 1,000,000: 1s. Last read position: chr16:21,405,002
INFO 2026-06-08 08:30:53 MarkDuplicates Tracking 170946 as yet unmatched pairs. 18598 records in RAM.
INFO 2026-06-08 08:30:54 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:09:52s. Time for last 1,000,000: 1s. Last read position: chr16:21,851,022
INFO 2026-06-08 08:30:54 MarkDuplicates Tracking 170206 as yet unmatched pairs. 17858 records in RAM.
INFO 2026-06-08 08:30:56 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:09:53s. Time for last 1,000,000: 1s. Last read position: chr16:22,535,008
INFO 2026-06-08 08:30:56 MarkDuplicates Tracking 170358 as yet unmatched pairs. 18010 records in RAM.
INFO 2026-06-08 08:30:57 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:09:55s. Time for last 1,000,000: 1s. Last read position: chr16:28,605,865
INFO 2026-06-08 08:30:57 MarkDuplicates Tracking 168424 as yet unmatched pairs. 16071 records in RAM.
INFO 2026-06-08 08:30:58 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:09:56s. Time for last 1,000,000: 1s. Last read position: chr16:29,483,920
INFO 2026-06-08 08:30:58 MarkDuplicates Tracking 168474 as yet unmatched pairs. 16121 records in RAM.
INFO 2026-06-08 08:31:00 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:09:58s. Time for last 1,000,000: 1s. Last read position: chr16:30,070,254
INFO 2026-06-08 08:31:00 MarkDuplicates Tracking 166646 as yet unmatched pairs. 14293 records in RAM.
INFO 2026-06-08 08:31:01 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 1s. Last read position: chr16:30,665,062
INFO 2026-06-08 08:31:01 MarkDuplicates Tracking 165420 as yet unmatched pairs. 13067 records in RAM.
INFO 2026-06-08 08:31:03 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:10:00s. Time for last 1,000,000: 1s. Last read position: chr16:31,202,540
INFO 2026-06-08 08:31:03 MarkDuplicates Tracking 163780 as yet unmatched pairs. 11425 records in RAM.
INFO 2026-06-08 08:31:04 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:10:02s. Time for last 1,000,000: 1s. Last read position: chr16:56,389,212
INFO 2026-06-08 08:31:04 MarkDuplicates Tracking 162064 as yet unmatched pairs. 9709 records in RAM.
INFO 2026-06-08 08:31:06 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:10:04s. Time for last 1,000,000: 1s. Last read position: chr16:66,604,802
INFO 2026-06-08 08:31:06 MarkDuplicates Tracking 160407 as yet unmatched pairs. 8046 records in RAM.
INFO 2026-06-08 08:31:08 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:10:05s. Time for last 1,000,000: 1s. Last read position: chr16:68,819,316
INFO 2026-06-08 08:31:08 MarkDuplicates Tracking 158500 as yet unmatched pairs. 6139 records in RAM.
INFO 2026-06-08 08:31:09 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:10:07s. Time for last 1,000,000: 1s. Last read position: chr16:72,959,375
INFO 2026-06-08 08:31:09 MarkDuplicates Tracking 156915 as yet unmatched pairs. 4554 records in RAM.
INFO 2026-06-08 08:31:11 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:10:08s. Time for last 1,000,000: 1s. Last read position: chr16:85,918,604
INFO 2026-06-08 08:31:11 MarkDuplicates Tracking 155195 as yet unmatched pairs. 2833 records in RAM.
INFO 2026-06-08 08:31:13 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:10:10s. Time for last 1,000,000: 1s. Last read position: chr16:89,561,289
INFO 2026-06-08 08:31:13 MarkDuplicates Tracking 154583 as yet unmatched pairs. 2221 records in RAM.
INFO 2026-06-08 08:31:15 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:10:12s. Time for last 1,000,000: 2s. Last read position: chr17:1,553,059
INFO 2026-06-08 08:31:15 MarkDuplicates Tracking 151515 as yet unmatched pairs. 48427 records in RAM.
INFO 2026-06-08 08:31:16 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:10:14s. Time for last 1,000,000: 1s. Last read position: chr17:4,307,063
INFO 2026-06-08 08:31:16 MarkDuplicates Tracking 149782 as yet unmatched pairs. 46694 records in RAM.
INFO 2026-06-08 08:31:18 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:10:16s. Time for last 1,000,000: 1s. Last read position: chr17:7,220,128
INFO 2026-06-08 08:31:18 MarkDuplicates Tracking 148040 as yet unmatched pairs. 44952 records in RAM.
INFO 2026-06-08 08:31:20 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:10:18s. Time for last 1,000,000: 1s. Last read position: chr17:7,577,120
INFO 2026-06-08 08:31:20 MarkDuplicates Tracking 146614 as yet unmatched pairs. 43526 records in RAM.
INFO 2026-06-08 08:31:22 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:10:19s. Time for last 1,000,000: 1s. Last read position: chr17:11,977,920
INFO 2026-06-08 08:31:22 MarkDuplicates Tracking 144623 as yet unmatched pairs. 41535 records in RAM.
INFO 2026-06-08 08:31:23 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:10:21s. Time for last 1,000,000: 1s. Last read position: chr17:17,819,618
INFO 2026-06-08 08:31:23 MarkDuplicates Tracking 143292 as yet unmatched pairs. 40204 records in RAM.
INFO 2026-06-08 08:31:25 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:10:23s. Time for last 1,000,000: 1s. Last read position: chr17:27,642,244
INFO 2026-06-08 08:31:25 MarkDuplicates Tracking 141996 as yet unmatched pairs. 38907 records in RAM.
INFO 2026-06-08 08:31:26 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:10:24s. Time for last 1,000,000: 1s. Last read position: chr17:30,427,417
INFO 2026-06-08 08:31:26 MarkDuplicates Tracking 140182 as yet unmatched pairs. 37093 records in RAM.
INFO 2026-06-08 08:31:28 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 1s. Last read position: chr17:36,333,939
INFO 2026-06-08 08:31:28 MarkDuplicates Tracking 138839 as yet unmatched pairs. 35750 records in RAM.
INFO 2026-06-08 08:31:30 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:10:28s. Time for last 1,000,000: 1s. Last read position: chr17:39,201,304
INFO 2026-06-08 08:31:30 MarkDuplicates Tracking 138332 as yet unmatched pairs. 35242 records in RAM.
INFO 2026-06-08 08:31:31 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:10:29s. Time for last 1,000,000: 1s. Last read position: chr17:40,818,323
INFO 2026-06-08 08:31:31 MarkDuplicates Tracking 138496 as yet unmatched pairs. 35405 records in RAM.
INFO 2026-06-08 08:31:33 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:10:31s. Time for last 1,000,000: 1s. Last read position: chr17:40,822,009
INFO 2026-06-08 08:31:33 MarkDuplicates Tracking 141149 as yet unmatched pairs. 38058 records in RAM.
INFO 2026-06-08 08:31:35 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:10:33s. Time for last 1,000,000: 1s. Last read position: chr17:41,583,393
INFO 2026-06-08 08:31:35 MarkDuplicates Tracking 137285 as yet unmatched pairs. 34194 records in RAM.
INFO 2026-06-08 08:31:37 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:10:34s. Time for last 1,000,000: 1s. Last read position: chr17:41,586,661
INFO 2026-06-08 08:31:37 MarkDuplicates Tracking 132998 as yet unmatched pairs. 29907 records in RAM.
INFO 2026-06-08 08:31:38 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:10:36s. Time for last 1,000,000: 1s. Last read position: chr17:41,619,444
INFO 2026-06-08 08:31:38 MarkDuplicates Tracking 129807 as yet unmatched pairs. 26716 records in RAM.
INFO 2026-06-08 08:31:40 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:10:37s. Time for last 1,000,000: 1s. Last read position: chr17:41,689,059
INFO 2026-06-08 08:31:40 MarkDuplicates Tracking 127617 as yet unmatched pairs. 24526 records in RAM.
INFO 2026-06-08 08:31:42 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:10:39s. Time for last 1,000,000: 1s. Last read position: chr17:42,693,370
INFO 2026-06-08 08:31:42 MarkDuplicates Tracking 125466 as yet unmatched pairs. 22375 records in RAM.
INFO 2026-06-08 08:31:44 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:10:41s. Time for last 1,000,000: 2s. Last read position: chr17:45,102,969
INFO 2026-06-08 08:31:44 MarkDuplicates Tracking 123890 as yet unmatched pairs. 20798 records in RAM.
INFO 2026-06-08 08:31:45 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:10:43s. Time for last 1,000,000: 1s. Last read position: chr17:48,051,360
INFO 2026-06-08 08:31:45 MarkDuplicates Tracking 122587 as yet unmatched pairs. 19490 records in RAM.
INFO 2026-06-08 08:31:47 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:10:45s. Time for last 1,000,000: 1s. Last read position: chr17:50,188,533
INFO 2026-06-08 08:31:47 MarkDuplicates Tracking 122161 as yet unmatched pairs. 19064 records in RAM.
INFO 2026-06-08 08:31:49 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 1s. Last read position: chr17:50,192,804
INFO 2026-06-08 08:31:49 MarkDuplicates Tracking 121581 as yet unmatched pairs. 18484 records in RAM.
INFO 2026-06-08 08:31:51 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:10:48s. Time for last 1,000,000: 1s. Last read position: chr17:50,197,179
INFO 2026-06-08 08:31:51 MarkDuplicates Tracking 120130 as yet unmatched pairs. 17033 records in RAM.
INFO 2026-06-08 08:31:52 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:10:50s. Time for last 1,000,000: 1s. Last read position: chr17:58,006,450
INFO 2026-06-08 08:31:52 MarkDuplicates Tracking 115354 as yet unmatched pairs. 12257 records in RAM.
INFO 2026-06-08 08:31:54 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:10:52s. Time for last 1,000,000: 1s. Last read position: chr17:62,690,693
INFO 2026-06-08 08:31:54 MarkDuplicates Tracking 113847 as yet unmatched pairs. 10749 records in RAM.
INFO 2026-06-08 08:31:56 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:10:53s. Time for last 1,000,000: 1s. Last read position: chr17:67,944,258
INFO 2026-06-08 08:31:56 MarkDuplicates Tracking 112397 as yet unmatched pairs. 9298 records in RAM.
INFO 2026-06-08 08:31:57 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:10:55s. Time for last 1,000,000: 1s. Last read position: chr17:75,570,063
INFO 2026-06-08 08:31:57 MarkDuplicates Tracking 110802 as yet unmatched pairs. 7695 records in RAM.
INFO 2026-06-08 08:31:59 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:10:57s. Time for last 1,000,000: 1s. Last read position: chr17:76,736,398
INFO 2026-06-08 08:31:59 MarkDuplicates Tracking 109253 as yet unmatched pairs. 6146 records in RAM.
INFO 2026-06-08 08:32:01 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 1s. Last read position: chr17:80,288,205
INFO 2026-06-08 08:32:01 MarkDuplicates Tracking 106971 as yet unmatched pairs. 3863 records in RAM.
INFO 2026-06-08 08:32:02 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:11:00s. Time for last 1,000,000: 1s. Last read position: chr17:81,687,077
INFO 2026-06-08 08:32:02 MarkDuplicates Tracking 105248 as yet unmatched pairs. 2140 records in RAM.
INFO 2026-06-08 08:32:04 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:11:01s. Time for last 1,000,000: 1s. Last read position: chr17:82,831,627
INFO 2026-06-08 08:32:04 MarkDuplicates Tracking 103387 as yet unmatched pairs. 279 records in RAM.
INFO 2026-06-08 08:32:05 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:11:03s. Time for last 1,000,000: 1s. Last read position: chr18:12,329,133
INFO 2026-06-08 08:32:05 MarkDuplicates Tracking 101642 as yet unmatched pairs. 5903 records in RAM.
INFO 2026-06-08 08:32:07 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:11:05s. Time for last 1,000,000: 1s. Last read position: chr18:31,162,537
INFO 2026-06-08 08:32:07 MarkDuplicates Tracking 100127 as yet unmatched pairs. 4388 records in RAM.
INFO 2026-06-08 08:32:09 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:11:06s. Time for last 1,000,000: 1s. Last read position: chr18:48,758,358
INFO 2026-06-08 08:32:09 MarkDuplicates Tracking 98533 as yet unmatched pairs. 2793 records in RAM.
INFO 2026-06-08 08:32:10 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:11:08s. Time for last 1,000,000: 1s. Last read position: chr18:63,403,745
INFO 2026-06-08 08:32:10 MarkDuplicates Tracking 96933 as yet unmatched pairs. 1193 records in RAM.
INFO 2026-06-08 08:32:12 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:11:10s. Time for last 1,000,000: 1s. Last read position: chr19:807,874
INFO 2026-06-08 08:32:12 MarkDuplicates Tracking 95197 as yet unmatched pairs. 43505 records in RAM.
INFO 2026-06-08 08:32:14 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:11:12s. Time for last 1,000,000: 1s. Last read position: chr19:1,466,745
INFO 2026-06-08 08:32:14 MarkDuplicates Tracking 93189 as yet unmatched pairs. 41497 records in RAM.
INFO 2026-06-08 08:32:16 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:11:14s. Time for last 1,000,000: 1s. Last read position: chr19:3,452,607
INFO 2026-06-08 08:32:16 MarkDuplicates Tracking 91453 as yet unmatched pairs. 39761 records in RAM.
INFO 2026-06-08 08:32:17 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:11:15s. Time for last 1,000,000: 1s. Last read position: chr19:5,244,124
INFO 2026-06-08 08:32:17 MarkDuplicates Tracking 89619 as yet unmatched pairs. 37926 records in RAM.
INFO 2026-06-08 08:32:19 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:11:17s. Time for last 1,000,000: 1s. Last read position: chr19:7,682,775
INFO 2026-06-08 08:32:19 MarkDuplicates Tracking 87438 as yet unmatched pairs. 35745 records in RAM.
INFO 2026-06-08 08:32:21 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:11:19s. Time for last 1,000,000: 2s. Last read position: chr19:10,361,796
INFO 2026-06-08 08:32:21 MarkDuplicates Tracking 85836 as yet unmatched pairs. 34143 records in RAM.
INFO 2026-06-08 08:32:23 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:11:21s. Time for last 1,000,000: 2s. Last read position: chr19:12,015,022
INFO 2026-06-08 08:32:23 MarkDuplicates Tracking 84091 as yet unmatched pairs. 32398 records in RAM.
INFO 2026-06-08 08:32:25 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:11:22s. Time for last 1,000,000: 1s. Last read position: chr19:14,160,624
INFO 2026-06-08 08:32:25 MarkDuplicates Tracking 82338 as yet unmatched pairs. 30645 records in RAM.
INFO 2026-06-08 08:32:26 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:11:24s. Time for last 1,000,000: 1s. Last read position: chr19:15,264,562
INFO 2026-06-08 08:32:26 MarkDuplicates Tracking 80910 as yet unmatched pairs. 29217 records in RAM.
INFO 2026-06-08 08:32:28 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:11:26s. Time for last 1,000,000: 1s. Last read position: chr19:17,486,725
INFO 2026-06-08 08:32:28 MarkDuplicates Tracking 78672 as yet unmatched pairs. 26979 records in RAM.
INFO 2026-06-08 08:32:30 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:11:27s. Time for last 1,000,000: 1s. Last read position: chr19:18,860,844
INFO 2026-06-08 08:32:30 MarkDuplicates Tracking 76908 as yet unmatched pairs. 25214 records in RAM.
INFO 2026-06-08 08:32:31 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:11:29s. Time for last 1,000,000: 1s. Last read position: chr19:34,438,764
INFO 2026-06-08 08:32:31 MarkDuplicates Tracking 75219 as yet unmatched pairs. 23525 records in RAM.
INFO 2026-06-08 08:32:33 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:11:30s. Time for last 1,000,000: 1s. Last read position: chr19:35,524,720
INFO 2026-06-08 08:32:33 MarkDuplicates Tracking 74539 as yet unmatched pairs. 22845 records in RAM.
INFO 2026-06-08 08:32:34 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:11:32s. Time for last 1,000,000: 1s. Last read position: chr19:36,091,241
INFO 2026-06-08 08:32:34 MarkDuplicates Tracking 71231 as yet unmatched pairs. 19536 records in RAM.
INFO 2026-06-08 08:32:36 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:11:34s. Time for last 1,000,000: 1s. Last read position: chr19:39,178,471
INFO 2026-06-08 08:32:36 MarkDuplicates Tracking 69753 as yet unmatched pairs. 18057 records in RAM.
INFO 2026-06-08 08:32:37 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:11:35s. Time for last 1,000,000: 1s. Last read position: chr19:40,586,860
INFO 2026-06-08 08:32:37 MarkDuplicates Tracking 68108 as yet unmatched pairs. 16412 records in RAM.
INFO 2026-06-08 08:32:39 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:11:37s. Time for last 1,000,000: 1s. Last read position: chr19:42,272,129
INFO 2026-06-08 08:32:39 MarkDuplicates Tracking 66840 as yet unmatched pairs. 15143 records in RAM.
INFO 2026-06-08 08:32:41 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:11:38s. Time for last 1,000,000: 1s. Last read position: chr19:43,652,261
INFO 2026-06-08 08:32:41 MarkDuplicates Tracking 64465 as yet unmatched pairs. 12768 records in RAM.
INFO 2026-06-08 08:32:42 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:11:40s. Time for last 1,000,000: 1s. Last read position: chr19:45,526,162
INFO 2026-06-08 08:32:42 MarkDuplicates Tracking 62267 as yet unmatched pairs. 10569 records in RAM.
INFO 2026-06-08 08:32:44 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:11:42s. Time for last 1,000,000: 1s. Last read position: chr19:48,097,103
INFO 2026-06-08 08:32:44 MarkDuplicates Tracking 60331 as yet unmatched pairs. 8633 records in RAM.
INFO 2026-06-08 08:32:46 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:11:43s. Time for last 1,000,000: 1s. Last read position: chr19:49,487,632
INFO 2026-06-08 08:32:46 MarkDuplicates Tracking 59579 as yet unmatched pairs. 7881 records in RAM.
INFO 2026-06-08 08:32:47 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:11:45s. Time for last 1,000,000: 1s. Last read position: chr19:50,378,652
INFO 2026-06-08 08:32:47 MarkDuplicates Tracking 56846 as yet unmatched pairs. 5148 records in RAM.
INFO 2026-06-08 08:32:49 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:11:47s. Time for last 1,000,000: 1s. Last read position: chr19:54,191,456
INFO 2026-06-08 08:32:49 MarkDuplicates Tracking 55200 as yet unmatched pairs. 3501 records in RAM.
INFO 2026-06-08 08:32:51 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:11:48s. Time for last 1,000,000: 1s. Last read position: chr19:55,615,787
INFO 2026-06-08 08:32:51 MarkDuplicates Tracking 53432 as yet unmatched pairs. 1733 records in RAM.
INFO 2026-06-08 08:32:52 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:11:50s. Time for last 1,000,000: 1s. Last read position: chr19:58,556,349
INFO 2026-06-08 08:32:52 MarkDuplicates Tracking 51880 as yet unmatched pairs. 181 records in RAM.
INFO 2026-06-08 08:32:54 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:11:52s. Time for last 1,000,000: 1s. Last read position: chr20:5,106,214
INFO 2026-06-08 08:32:54 MarkDuplicates Tracking 50239 as yet unmatched pairs. 10903 records in RAM.
INFO 2026-06-08 08:32:56 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:11:53s. Time for last 1,000,000: 1s. Last read position: chr20:25,477,052
INFO 2026-06-08 08:32:56 MarkDuplicates Tracking 48489 as yet unmatched pairs. 9152 records in RAM.
INFO 2026-06-08 08:32:57 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:11:55s. Time for last 1,000,000: 1s. Last read position: chr20:35,714,184
INFO 2026-06-08 08:32:57 MarkDuplicates Tracking 46948 as yet unmatched pairs. 7599 records in RAM.
INFO 2026-06-08 08:32:59 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:11:57s. Time for last 1,000,000: 1s. Last read position: chr20:44,724,874
INFO 2026-06-08 08:32:59 MarkDuplicates Tracking 45327 as yet unmatched pairs. 5975 records in RAM.
INFO 2026-06-08 08:33:01 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:11:59s. Time for last 1,000,000: 1s. Last read position: chr20:49,135,846
INFO 2026-06-08 08:33:01 MarkDuplicates Tracking 43401 as yet unmatched pairs. 4049 records in RAM.
INFO 2026-06-08 08:33:02 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:12:00s. Time for last 1,000,000: 1s. Last read position: chr20:59,030,346
INFO 2026-06-08 08:33:02 MarkDuplicates Tracking 42136 as yet unmatched pairs. 2783 records in RAM.
INFO 2026-06-08 08:33:04 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:12:02s. Time for last 1,000,000: 1s. Last read position: chr20:63,742,926
INFO 2026-06-08 08:33:04 MarkDuplicates Tracking 39734 as yet unmatched pairs. 381 records in RAM.
INFO 2026-06-08 08:33:05 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:12:03s. Time for last 1,000,000: 1s. Last read position: chr21:8,258,931
INFO 2026-06-08 08:33:05 MarkDuplicates Tracking 38640 as yet unmatched pairs. 6960 records in RAM.
INFO 2026-06-08 08:33:07 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:12:04s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,566
INFO 2026-06-08 08:33:07 MarkDuplicates Tracking 37808 as yet unmatched pairs. 6127 records in RAM.
INFO 2026-06-08 08:33:08 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:12:06s. Time for last 1,000,000: 1s. Last read position: chr21:33,554,142
INFO 2026-06-08 08:33:08 MarkDuplicates Tracking 36466 as yet unmatched pairs. 4785 records in RAM.
INFO 2026-06-08 08:33:09 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:12:07s. Time for last 1,000,000: 1s. Last read position: chr21:43,803,588
INFO 2026-06-08 08:33:09 MarkDuplicates Tracking 34588 as yet unmatched pairs. 2907 records in RAM.
INFO 2026-06-08 08:33:11 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:12:09s. Time for last 1,000,000: 1s. Last read position: chr21:46,003,819
INFO 2026-06-08 08:33:11 MarkDuplicates Tracking 33085 as yet unmatched pairs. 1404 records in RAM.
INFO 2026-06-08 08:33:13 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:12:11s. Time for last 1,000,000: 1s. Last read position: chr22:19,962,681
INFO 2026-06-08 08:33:13 MarkDuplicates Tracking 30997 as yet unmatched pairs. 14677 records in RAM.
INFO 2026-06-08 08:33:15 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:12:12s. Time for last 1,000,000: 1s. Last read position: chr22:23,309,423
INFO 2026-06-08 08:33:15 MarkDuplicates Tracking 29348 as yet unmatched pairs. 13028 records in RAM.
INFO 2026-06-08 08:33:16 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:12:14s. Time for last 1,000,000: 1s. Last read position: chr22:29,288,743
INFO 2026-06-08 08:33:16 MarkDuplicates Tracking 27775 as yet unmatched pairs. 11455 records in RAM.
INFO 2026-06-08 08:33:18 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:12:15s. Time for last 1,000,000: 1s. Last read position: chr22:32,399,616
INFO 2026-06-08 08:33:18 MarkDuplicates Tracking 25954 as yet unmatched pairs. 9634 records in RAM.
INFO 2026-06-08 08:33:19 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:12:17s. Time for last 1,000,000: 1s. Last read position: chr22:37,231,985
INFO 2026-06-08 08:33:19 MarkDuplicates Tracking 24378 as yet unmatched pairs. 8058 records in RAM.
INFO 2026-06-08 08:33:21 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:12:18s. Time for last 1,000,000: 1s. Last read position: chr22:38,738,515
INFO 2026-06-08 08:33:21 MarkDuplicates Tracking 22590 as yet unmatched pairs. 6270 records in RAM.
INFO 2026-06-08 08:33:22 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:12:20s. Time for last 1,000,000: 1s. Last read position: chr22:41,621,970
INFO 2026-06-08 08:33:22 MarkDuplicates Tracking 20731 as yet unmatched pairs. 4411 records in RAM.
INFO 2026-06-08 08:33:24 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:12:21s. Time for last 1,000,000: 1s. Last read position: chr22:46,686,589
INFO 2026-06-08 08:33:24 MarkDuplicates Tracking 18959 as yet unmatched pairs. 2639 records in RAM.
INFO 2026-06-08 08:33:25 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:12:23s. Time for last 1,000,000: 1s. Last read position: chr22:50,529,574
INFO 2026-06-08 08:33:25 MarkDuplicates Tracking 17215 as yet unmatched pairs. 895 records in RAM.
INFO 2026-06-08 08:33:27 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:12:25s. Time for last 1,000,000: 1s. Last read position: chrX:16,736,201
INFO 2026-06-08 08:33:27 MarkDuplicates Tracking 15051 as yet unmatched pairs. 11606 records in RAM.
INFO 2026-06-08 08:33:28 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:12:26s. Time for last 1,000,000: 1s. Last read position: chrX:41,702,504
INFO 2026-06-08 08:33:28 MarkDuplicates Tracking 13577 as yet unmatched pairs. 10129 records in RAM.
INFO 2026-06-08 08:33:30 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:12:28s. Time for last 1,000,000: 1s. Last read position: chrX:51,895,267
INFO 2026-06-08 08:33:30 MarkDuplicates Tracking 12020 as yet unmatched pairs. 8571 records in RAM.
INFO 2026-06-08 08:33:32 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:12:29s. Time for last 1,000,000: 1s. Last read position: chrX:67,643,293
INFO 2026-06-08 08:33:32 MarkDuplicates Tracking 10324 as yet unmatched pairs. 6875 records in RAM.
INFO 2026-06-08 08:33:33 MarkDuplicates Read 368,000,000 records. Elapsed time: 00:12:31s. Time for last 1,000,000: 1s. Last read position: chrX:78,113,844
INFO 2026-06-08 08:33:33 MarkDuplicates Tracking 8947 as yet unmatched pairs. 5498 records in RAM.
INFO 2026-06-08 08:33:35 MarkDuplicates Read 369,000,000 records. Elapsed time: 00:12:33s. Time for last 1,000,000: 1s. Last read position: chrX:120,447,839
INFO 2026-06-08 08:33:35 MarkDuplicates Tracking 7570 as yet unmatched pairs. 4121 records in RAM.
INFO 2026-06-08 08:33:37 MarkDuplicates Read 370,000,000 records. Elapsed time: 00:12:34s. Time for last 1,000,000: 1s. Last read position: chrX:153,776,104
INFO 2026-06-08 08:33:37 MarkDuplicates Tracking 5933 as yet unmatched pairs. 2484 records in RAM.
INFO 2026-06-08 08:33:38 MarkDuplicates Read 371,000,000 records. Elapsed time: 00:12:36s. Time for last 1,000,000: 1s. Last read position: chrX:154,399,804
INFO 2026-06-08 08:33:38 MarkDuplicates Tracking 4279 as yet unmatched pairs. 830 records in RAM.
INFO 2026-06-08 08:33:40 MarkDuplicates Read 372,000,000 records. Elapsed time: 00:12:37s. Time for last 1,000,000: 1s. Last read position: GL000220.1:115,549
INFO 2026-06-08 08:33:40 MarkDuplicates Tracking 2260 as yet unmatched pairs. 64 records in RAM.
INFO 2026-06-08 08:33:41 MarkDuplicates Read 373,000,000 records. Elapsed time: 00:12:39s. Time for last 1,000,000: 1s. Last read position: KI270733.1:132,309
INFO 2026-06-08 08:33:41 MarkDuplicates Tracking 1024 as yet unmatched pairs. 1022 records in RAM.
INFO 2026-06-08 08:33:42 MarkDuplicates Read 373799256 records. 0 pairs never matched.
INFO 2026-06-08 08:34:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 33005737160; totalMemory: 47110422528; maxMemory: 63585648640
INFO 2026-06-08 08:34:18 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:34:23 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:34:41 OpticalDuplicateFinder Large duplicate set. size = 1237
INFO 2026-06-08 08:34:41 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,917
INFO 2026-06-08 08:34:41 OpticalDuplicateFinder Large duplicate set. size = 1218
INFO 2026-06-08 08:34:41 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:23,571
INFO 2026-06-08 08:34:41 OpticalDuplicateFinder Large duplicate set. size = 1363
INFO 2026-06-08 08:34:41 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,107
INFO 2026-06-08 08:34:41 OpticalDuplicateFinder Large duplicate set. size = 1645
INFO 2026-06-08 08:34:41 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,090
INFO 2026-06-08 08:34:41 OpticalDuplicateFinder Large duplicate set. size = 1390
INFO 2026-06-08 08:34:41 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,408
INFO 2026-06-08 08:35:03 MarkDuplicates Traversing fragment information and detecting duplicates.
WARNING 2026-06-08 08:35:03 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
INFO 2026-06-08 08:35:42 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:35:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300694992; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-08 08:35:51 MarkDuplicates Marking 227488314 records as duplicates.
INFO 2026-06-08 08:35:51 MarkDuplicates Found 6319950 optical duplicate clusters.
INFO 2026-06-08 08:35:51 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 08:36:07 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:16s. Time for last 10,000,000: 16s. Last read position: chr1:39,424,027
INFO 2026-06-08 08:36:23 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:32s. Time for last 10,000,000: 16s. Last read position: chr1:150,796,722
INFO 2026-06-08 08:36:38 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:47s. Time for last 10,000,000: 15s. Last read position: chr1:152,308,312
INFO 2026-06-08 08:36:53 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:02s. Time for last 10,000,000: 14s. Last read position: chr1:155,752,103
INFO 2026-06-08 08:37:09 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:18s. Time for last 10,000,000: 15s. Last read position: chr1:236,537,504
INFO 2026-06-08 08:37:25 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:33s. Time for last 10,000,000: 15s. Last read position: chr2:95,850,498
INFO 2026-06-08 08:37:41 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:01:50s. Time for last 10,000,000: 16s. Last read position: chr2:215,409,974
INFO 2026-06-08 08:37:57 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:06s. Time for last 10,000,000: 15s. Last read position: chr3:49,532,805
INFO 2026-06-08 08:38:13 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:21s. Time for last 10,000,000: 15s. Last read position: chr4:768,992
INFO 2026-06-08 08:38:29 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:38s. Time for last 10,000,000: 16s. Last read position: chr5:40,680,446
INFO 2026-06-08 08:38:45 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:02:54s. Time for last 10,000,000: 16s. Last read position: chr5:150,407,152
INFO 2026-06-08 08:39:01 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:10s. Time for last 10,000,000: 16s. Last read position: chr6:30,679,341
INFO 2026-06-08 08:39:17 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:26s. Time for last 10,000,000: 16s. Last read position: chr6:75,914,087
INFO 2026-06-08 08:39:33 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:03:42s. Time for last 10,000,000: 15s. Last read position: chr7:44,208,154
INFO 2026-06-08 08:39:49 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:03:57s. Time for last 10,000,000: 15s. Last read position: chr7:131,506,596
INFO 2026-06-08 08:40:04 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:13s. Time for last 10,000,000: 15s. Last read position: chr8:115,604,877
INFO 2026-06-08 08:40:20 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:04:29s. Time for last 10,000,000: 15s. Last read position: chr9:92,719,500
INFO 2026-06-08 08:40:35 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:04:44s. Time for last 10,000,000: 15s. Last read position: chr10:5,766,503
INFO 2026-06-08 08:40:51 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:05:00s. Time for last 10,000,000: 15s. Last read position: chr11:397,105
INFO 2026-06-08 08:41:06 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:05:15s. Time for last 10,000,000: 15s. Last read position: chr11:64,860,058
INFO 2026-06-08 08:41:21 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:05:30s. Time for last 10,000,000: 14s. Last read position: chr12:2,874,303
INFO 2026-06-08 08:41:36 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:05:45s. Time for last 10,000,000: 14s. Last read position: chr12:52,493,112
INFO 2026-06-08 08:41:51 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:06:00s. Time for last 10,000,000: 15s. Last read position: chr12:109,857,593
INFO 2026-06-08 08:42:07 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:06:16s. Time for last 10,000,000: 15s. Last read position: chr14:21,017,552
INFO 2026-06-08 08:42:23 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:06:31s. Time for last 10,000,000: 15s. Last read position: chr14:104,954,270
INFO 2026-06-08 08:42:38 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:06:47s. Time for last 10,000,000: 15s. Last read position: chr15:75,208,383
INFO 2026-06-08 08:42:54 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:07:03s. Time for last 10,000,000: 15s. Last read position: chr16:21,405,002
INFO 2026-06-08 08:43:10 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:07:18s. Time for last 10,000,000: 15s. Last read position: chr16:68,819,316
INFO 2026-06-08 08:43:25 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:07:34s. Time for last 10,000,000: 15s. Last read position: chr17:27,642,244
INFO 2026-06-08 08:43:40 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:07:49s. Time for last 10,000,000: 14s. Last read position: chr17:42,693,370
INFO 2026-06-08 08:43:55 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:08:04s. Time for last 10,000,000: 15s. Last read position: chr17:76,736,398
INFO 2026-06-08 08:44:11 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:08:20s. Time for last 10,000,000: 15s. Last read position: chr19:3,452,607
INFO 2026-06-08 08:44:27 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:08:36s. Time for last 10,000,000: 15s. Last read position: chr19:35,524,720
INFO 2026-06-08 08:44:42 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:08:51s. Time for last 10,000,000: 15s. Last read position: chr19:54,191,456
INFO 2026-06-08 08:44:57 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:09:06s. Time for last 10,000,000: 15s. Last read position: chr21:8,258,931
INFO 2026-06-08 08:45:12 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:09:21s. Time for last 10,000,000: 14s. Last read position: chr22:38,738,515
INFO 2026-06-08 08:45:28 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:09:36s. Time for last 10,000,000: 15s. Last read position: chrX:153,776,104
INFO 2026-06-08 08:45:38 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:45:38 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:45:38 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:45:38 MarkDuplicates Before output close freeMemory: 202009536; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:45:38 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:45:38 MarkDuplicates After output close freeMemory: 104163800; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 08:45:38 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 24.63 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory