Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/af15205b816de8ba91fc11855d08b8/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/0f14dcd1e97d5fa480dbbabe1485b4/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/0f14dcd1e97d5fa480dbbabe1485b4/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai
==> STAGING COMPLETE (5 inputs)
Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bam --METRICS_FILE BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:45:13.245 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Jun 08 07:45:13 GMT 2026] MarkDuplicates --INPUT BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bam --METRICS_FILE BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 07:45:13 GMT 2026] Executing as ?@nf-6b0f14dcd1e97d5fa480dbbabe1485b4-f1797-c5dgw on Linux 6.12.88 amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0
INFO 2026-06-08 07:45:13 MarkDuplicates Start of doWork freeMemory: 105829960; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:45:13 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:45:13 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:45:20 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 4s. Last read position: chr1:1,525,246
INFO 2026-06-08 07:45:20 MarkDuplicates Tracking 3147 as yet unmatched pairs. 41 records in RAM.
INFO 2026-06-08 07:45:23 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 3s. Last read position: chr1:11,286,013
INFO 2026-06-08 07:45:23 MarkDuplicates Tracking 5771 as yet unmatched pairs. 12 records in RAM.
INFO 2026-06-08 07:45:25 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 2s. Last read position: chr1:20,779,812
INFO 2026-06-08 07:45:25 MarkDuplicates Tracking 8823 as yet unmatched pairs. 19 records in RAM.
INFO 2026-06-08 07:45:28 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 2s. Last read position: chr1:26,344,930
INFO 2026-06-08 07:45:28 MarkDuplicates Tracking 11799 as yet unmatched pairs. 124 records in RAM.
INFO 2026-06-08 07:45:30 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 2s. Last read position: chr1:32,366,558
INFO 2026-06-08 07:45:30 MarkDuplicates Tracking 14494 as yet unmatched pairs. 48 records in RAM.
INFO 2026-06-08 07:45:33 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 3s. Last read position: chr1:39,955,300
INFO 2026-06-08 07:45:33 MarkDuplicates Tracking 17289 as yet unmatched pairs. 34 records in RAM.
INFO 2026-06-08 07:45:36 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 2s. Last read position: chr1:48,384,250
INFO 2026-06-08 07:45:36 MarkDuplicates Tracking 20235 as yet unmatched pairs. 20 records in RAM.
INFO 2026-06-08 07:45:39 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 3s. Last read position: chr1:100,022,330
INFO 2026-06-08 07:45:39 MarkDuplicates Tracking 23020 as yet unmatched pairs. 62 records in RAM.
INFO 2026-06-08 07:45:42 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 3s. Last read position: chr1:117,402,253
INFO 2026-06-08 07:45:42 MarkDuplicates Tracking 25489 as yet unmatched pairs. 79 records in RAM.
INFO 2026-06-08 07:45:44 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 2s. Last read position: chr1:149,813,352
INFO 2026-06-08 07:45:44 MarkDuplicates Tracking 27086 as yet unmatched pairs. 100 records in RAM.
INFO 2026-06-08 07:45:47 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 2s. Last read position: chr1:151,404,795
INFO 2026-06-08 07:45:47 MarkDuplicates Tracking 29313 as yet unmatched pairs. 21 records in RAM.
INFO 2026-06-08 07:45:49 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 2s. Last read position: chr1:155,053,969
INFO 2026-06-08 07:45:49 MarkDuplicates Tracking 31984 as yet unmatched pairs. 121 records in RAM.
INFO 2026-06-08 07:45:52 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 2s. Last read position: chr1:156,312,152
INFO 2026-06-08 07:45:52 MarkDuplicates Tracking 34910 as yet unmatched pairs. 34 records in RAM.
INFO 2026-06-08 07:45:55 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 2s. Last read position: chr1:166,840,954
INFO 2026-06-08 07:45:55 MarkDuplicates Tracking 37339 as yet unmatched pairs. 50 records in RAM.
INFO 2026-06-08 07:45:57 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chr1:186,344,562
INFO 2026-06-08 07:45:57 MarkDuplicates Tracking 39941 as yet unmatched pairs. 118 records in RAM.
INFO 2026-06-08 07:46:00 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: chr1:206,538,284
INFO 2026-06-08 07:46:00 MarkDuplicates Tracking 42549 as yet unmatched pairs. 31 records in RAM.
INFO 2026-06-08 07:46:03 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 2s. Last read position: chr1:228,148,371
INFO 2026-06-08 07:46:03 MarkDuplicates Tracking 45252 as yet unmatched pairs. 154 records in RAM.
INFO 2026-06-08 07:46:07 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 3s. Last read position: chr1:247,159,032
INFO 2026-06-08 07:46:07 MarkDuplicates Tracking 48061 as yet unmatched pairs. 30 records in RAM.
INFO 2026-06-08 07:46:10 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 3s. Last read position: chr2:24,820,708
INFO 2026-06-08 07:46:10 MarkDuplicates Tracking 50962 as yet unmatched pairs. 50144 records in RAM.
INFO 2026-06-08 07:46:14 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 3s. Last read position: chr2:32,916,264
INFO 2026-06-08 07:46:14 MarkDuplicates Tracking 141604 as yet unmatched pairs. 44311 records in RAM.
INFO 2026-06-08 07:46:18 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 4s. Last read position: chr2:32,916,408
INFO 2026-06-08 07:46:18 MarkDuplicates Tracking 425117 as yet unmatched pairs. 20287 records in RAM.
INFO 2026-06-08 07:46:20 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 2s. Last read position: chr2:55,049,867
INFO 2026-06-08 07:46:20 MarkDuplicates Tracking 440849 as yet unmatched pairs. 16665 records in RAM.
INFO 2026-06-08 07:46:23 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 2s. Last read position: chr2:74,885,542
INFO 2026-06-08 07:46:23 MarkDuplicates Tracking 437851 as yet unmatched pairs. 13642 records in RAM.
INFO 2026-06-08 07:46:27 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 4s. Last read position: chr2:108,765,898
INFO 2026-06-08 07:46:27 MarkDuplicates Tracking 435378 as yet unmatched pairs. 11110 records in RAM.
INFO 2026-06-08 07:46:30 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 3s. Last read position: chr2:156,326,257
INFO 2026-06-08 07:46:30 MarkDuplicates Tracking 433044 as yet unmatched pairs. 8757 records in RAM.
INFO 2026-06-08 07:46:32 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 2s. Last read position: chr2:189,006,420
INFO 2026-06-08 07:46:32 MarkDuplicates Tracking 430631 as yet unmatched pairs. 6326 records in RAM.
INFO 2026-06-08 07:46:36 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 3s. Last read position: chr2:215,434,803
INFO 2026-06-08 07:46:36 MarkDuplicates Tracking 428306 as yet unmatched pairs. 3968 records in RAM.
INFO 2026-06-08 07:46:38 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 2s. Last read position: chr2:237,365,826
INFO 2026-06-08 07:46:38 MarkDuplicates Tracking 425400 as yet unmatched pairs. 1012 records in RAM.
INFO 2026-06-08 07:46:42 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 4s. Last read position: chr3:15,227,911
INFO 2026-06-08 07:46:42 MarkDuplicates Tracking 422681 as yet unmatched pairs. 19924 records in RAM.
INFO 2026-06-08 07:46:45 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 2s. Last read position: chr3:40,461,468
INFO 2026-06-08 07:46:45 MarkDuplicates Tracking 420363 as yet unmatched pairs. 17537 records in RAM.
INFO 2026-06-08 07:46:48 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 2s. Last read position: chr3:48,583,137
INFO 2026-06-08 07:46:48 MarkDuplicates Tracking 417369 as yet unmatched pairs. 14492 records in RAM.
INFO 2026-06-08 07:46:50 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 2s. Last read position: chr3:52,533,506
INFO 2026-06-08 07:46:50 MarkDuplicates Tracking 414418 as yet unmatched pairs. 11523 records in RAM.
INFO 2026-06-08 07:46:53 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 2s. Last read position: chr3:119,826,842
INFO 2026-06-08 07:46:53 MarkDuplicates Tracking 412082 as yet unmatched pairs. 9125 records in RAM.
INFO 2026-06-08 07:46:56 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 3s. Last read position: chr3:136,338,208
INFO 2026-06-08 07:46:56 MarkDuplicates Tracking 409433 as yet unmatched pairs. 6435 records in RAM.
INFO 2026-06-08 07:46:59 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 2s. Last read position: chr3:183,921,371
INFO 2026-06-08 07:46:59 MarkDuplicates Tracking 407045 as yet unmatched pairs. 3865 records in RAM.
INFO 2026-06-08 07:47:01 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 2s. Last read position: chr3:195,725,115
INFO 2026-06-08 07:47:01 MarkDuplicates Tracking 404843 as yet unmatched pairs. 1642 records in RAM.
INFO 2026-06-08 07:47:04 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 3s. Last read position: chr4:1,739,702
INFO 2026-06-08 07:47:04 MarkDuplicates Tracking 402415 as yet unmatched pairs. 18088 records in RAM.
INFO 2026-06-08 07:47:07 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 2s. Last read position: chr4:1,801,444
INFO 2026-06-08 07:47:07 MarkDuplicates Tracking 401037 as yet unmatched pairs. 16595 records in RAM.
INFO 2026-06-08 07:47:10 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 2s. Last read position: chr4:1,805,891
INFO 2026-06-08 07:47:10 MarkDuplicates Tracking 397906 as yet unmatched pairs. 13436 records in RAM.
INFO 2026-06-08 07:47:12 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 2s. Last read position: chr4:4,391,520
INFO 2026-06-08 07:47:12 MarkDuplicates Tracking 392384 as yet unmatched pairs. 7899 records in RAM.
INFO 2026-06-08 07:47:14 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 1s. Last read position: chr4:48,540,883
INFO 2026-06-08 07:47:14 MarkDuplicates Tracking 390383 as yet unmatched pairs. 5823 records in RAM.
INFO 2026-06-08 07:47:17 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 3s. Last read position: chr4:90,849,221
INFO 2026-06-08 07:47:17 MarkDuplicates Tracking 387796 as yet unmatched pairs. 3176 records in RAM.
INFO 2026-06-08 07:47:20 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 2s. Last read position: chr4:169,704,065
INFO 2026-06-08 07:47:20 MarkDuplicates Tracking 385389 as yet unmatched pairs. 715 records in RAM.
INFO 2026-06-08 07:47:22 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 2s. Last read position: chr5:32,126,560
INFO 2026-06-08 07:47:22 MarkDuplicates Tracking 382587 as yet unmatched pairs. 15475 records in RAM.
INFO 2026-06-08 07:47:25 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 2s. Last read position: chr5:77,691,351
INFO 2026-06-08 07:47:25 MarkDuplicates Tracking 380236 as yet unmatched pairs. 13084 records in RAM.
INFO 2026-06-08 07:47:27 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 2s. Last read position: chr5:134,649,075
INFO 2026-06-08 07:47:27 MarkDuplicates Tracking 377785 as yet unmatched pairs. 10580 records in RAM.
INFO 2026-06-08 07:47:29 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 2s. Last read position: chr5:142,005,056
INFO 2026-06-08 07:47:29 MarkDuplicates Tracking 375347 as yet unmatched pairs. 8021 records in RAM.
INFO 2026-06-08 07:47:32 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 2s. Last read position: chr5:154,865,237
INFO 2026-06-08 07:47:32 MarkDuplicates Tracking 372904 as yet unmatched pairs. 5552 records in RAM.
INFO 2026-06-08 07:47:35 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 2s. Last read position: chr5:178,210,144
INFO 2026-06-08 07:47:35 MarkDuplicates Tracking 370095 as yet unmatched pairs. 2737 records in RAM.
INFO 2026-06-08 07:47:38 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 2s. Last read position: chr6:3,515,185
INFO 2026-06-08 07:47:38 MarkDuplicates Tracking 366664 as yet unmatched pairs. 21450 records in RAM.
INFO 2026-06-08 07:47:40 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 2s. Last read position: chr6:27,133,375
INFO 2026-06-08 07:47:40 MarkDuplicates Tracking 363815 as yet unmatched pairs. 18591 records in RAM.
INFO 2026-06-08 07:47:42 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 2s. Last read position: chr6:31,531,055
INFO 2026-06-08 07:47:42 MarkDuplicates Tracking 361102 as yet unmatched pairs. 15859 records in RAM.
INFO 2026-06-08 07:47:44 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 2s. Last read position: chr6:32,116,784
INFO 2026-06-08 07:47:44 MarkDuplicates Tracking 358879 as yet unmatched pairs. 13625 records in RAM.
INFO 2026-06-08 07:47:47 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 2s. Last read position: chr6:41,806,227
INFO 2026-06-08 07:47:47 MarkDuplicates Tracking 356067 as yet unmatched pairs. 10806 records in RAM.
INFO 2026-06-08 07:47:49 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 2s. Last read position: chr6:75,090,279
INFO 2026-06-08 07:47:49 MarkDuplicates Tracking 353263 as yet unmatched pairs. 7897 records in RAM.
INFO 2026-06-08 07:47:51 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 1s. Last read position: chr6:119,189,668
INFO 2026-06-08 07:47:51 MarkDuplicates Tracking 350726 as yet unmatched pairs. 5294 records in RAM.
INFO 2026-06-08 07:47:53 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 2s. Last read position: chr6:158,605,311
INFO 2026-06-08 07:47:53 MarkDuplicates Tracking 348089 as yet unmatched pairs. 2613 records in RAM.
INFO 2026-06-08 07:47:56 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 2s. Last read position: chr7:873,252
INFO 2026-06-08 07:47:56 MarkDuplicates Tracking 345218 as yet unmatched pairs. 24859 records in RAM.
INFO 2026-06-08 07:47:59 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 3s. Last read position: chr7:5,528,678
INFO 2026-06-08 07:47:59 MarkDuplicates Tracking 342258 as yet unmatched pairs. 21823 records in RAM.
INFO 2026-06-08 07:48:01 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 2s. Last read position: chr7:43,869,062
INFO 2026-06-08 07:48:01 MarkDuplicates Tracking 339141 as yet unmatched pairs. 18660 records in RAM.
INFO 2026-06-08 07:48:03 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 2s. Last read position: chr7:72,942,927
INFO 2026-06-08 07:48:03 MarkDuplicates Tracking 336885 as yet unmatched pairs. 16358 records in RAM.
INFO 2026-06-08 07:48:06 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 2s. Last read position: chr7:76,302,969
INFO 2026-06-08 07:48:06 MarkDuplicates Tracking 335743 as yet unmatched pairs. 15192 records in RAM.
INFO 2026-06-08 07:48:08 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 2s. Last read position: chr7:94,422,973
INFO 2026-06-08 07:48:08 MarkDuplicates Tracking 332638 as yet unmatched pairs. 12071 records in RAM.
INFO 2026-06-08 07:48:10 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 2s. Last read position: chr7:100,870,408
INFO 2026-06-08 07:48:10 MarkDuplicates Tracking 329407 as yet unmatched pairs. 8806 records in RAM.
INFO 2026-06-08 07:48:12 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 2s. Last read position: chr7:107,975,306
INFO 2026-06-08 07:48:12 MarkDuplicates Tracking 327483 as yet unmatched pairs. 6872 records in RAM.
INFO 2026-06-08 07:48:14 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 2s. Last read position: chr7:138,581,702
INFO 2026-06-08 07:48:14 MarkDuplicates Tracking 325363 as yet unmatched pairs. 4690 records in RAM.
INFO 2026-06-08 07:48:17 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 2s. Last read position: chr7:150,372,219
INFO 2026-06-08 07:48:17 MarkDuplicates Tracking 322521 as yet unmatched pairs. 1835 records in RAM.
INFO 2026-06-08 07:48:20 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 2s. Last read position: chr8:22,629,928
INFO 2026-06-08 07:48:20 MarkDuplicates Tracking 319667 as yet unmatched pairs. 17705 records in RAM.
INFO 2026-06-08 07:48:22 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 2s. Last read position: chr8:47,830,619
INFO 2026-06-08 07:48:22 MarkDuplicates Tracking 316620 as yet unmatched pairs. 14652 records in RAM.
INFO 2026-06-08 07:48:25 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 2s. Last read position: chr8:90,645,367
INFO 2026-06-08 07:48:25 MarkDuplicates Tracking 313978 as yet unmatched pairs. 11948 records in RAM.
INFO 2026-06-08 07:48:27 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 2s. Last read position: chr8:127,736,524
INFO 2026-06-08 07:48:27 MarkDuplicates Tracking 311467 as yet unmatched pairs. 9387 records in RAM.
INFO 2026-06-08 07:48:30 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 2s. Last read position: chr8:143,858,098
INFO 2026-06-08 07:48:30 MarkDuplicates Tracking 308076 as yet unmatched pairs. 5927 records in RAM.
INFO 2026-06-08 07:48:32 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 1s. Last read position: chr8:143,863,779
INFO 2026-06-08 07:48:32 MarkDuplicates Tracking 306675 as yet unmatched pairs. 4526 records in RAM.
INFO 2026-06-08 07:48:34 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 2s. Last read position: chr8:143,930,111
INFO 2026-06-08 07:48:34 MarkDuplicates Tracking 304663 as yet unmatched pairs. 2484 records in RAM.
INFO 2026-06-08 07:48:37 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 2s. Last read position: chr9:9,442,103
INFO 2026-06-08 07:48:37 MarkDuplicates Tracking 301732 as yet unmatched pairs. 16130 records in RAM.
INFO 2026-06-08 07:48:39 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 2s. Last read position: chr9:39,809,974
INFO 2026-06-08 07:48:39 MarkDuplicates Tracking 298959 as yet unmatched pairs. 13309 records in RAM.
INFO 2026-06-08 07:48:41 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 1s. Last read position: chr9:96,147,390
INFO 2026-06-08 07:48:41 MarkDuplicates Tracking 296785 as yet unmatched pairs. 11103 records in RAM.
INFO 2026-06-08 07:48:43 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 1s. Last read position: chr9:124,356,798
INFO 2026-06-08 07:48:43 MarkDuplicates Tracking 294143 as yet unmatched pairs. 8390 records in RAM.
INFO 2026-06-08 07:48:45 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 2s. Last read position: chr9:130,884,204
INFO 2026-06-08 07:48:45 MarkDuplicates Tracking 291343 as yet unmatched pairs. 5584 records in RAM.
INFO 2026-06-08 07:48:47 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 2s. Last read position: chr9:136,475,817
INFO 2026-06-08 07:48:47 MarkDuplicates Tracking 288497 as yet unmatched pairs. 2698 records in RAM.
INFO 2026-06-08 07:48:49 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 1s. Last read position: chr10:4,972,237
INFO 2026-06-08 07:48:49 MarkDuplicates Tracking 285367 as yet unmatched pairs. 12413 records in RAM.
INFO 2026-06-08 07:48:51 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 2s. Last read position: chr10:32,019,884
INFO 2026-06-08 07:48:51 MarkDuplicates Tracking 282885 as yet unmatched pairs. 9912 records in RAM.
INFO 2026-06-08 07:48:53 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 2s. Last read position: chr10:70,120,539
INFO 2026-06-08 07:48:53 MarkDuplicates Tracking 280600 as yet unmatched pairs. 7606 records in RAM.
INFO 2026-06-08 07:48:55 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 2s. Last read position: chr10:91,997,632
INFO 2026-06-08 07:48:55 MarkDuplicates Tracking 278204 as yet unmatched pairs. 5162 records in RAM.
INFO 2026-06-08 07:48:57 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 2s. Last read position: chr10:114,126,000
INFO 2026-06-08 07:48:57 MarkDuplicates Tracking 275322 as yet unmatched pairs. 2248 records in RAM.
INFO 2026-06-08 07:49:00 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 2s. Last read position: chr11:315,059
INFO 2026-06-08 07:49:00 MarkDuplicates Tracking 273078 as yet unmatched pairs. 32104 records in RAM.
INFO 2026-06-08 07:49:03 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 3s. Last read position: chr11:2,133,203
INFO 2026-06-08 07:49:03 MarkDuplicates Tracking 273035 as yet unmatched pairs. 32020 records in RAM.
INFO 2026-06-08 07:49:06 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 2s. Last read position: chr11:10,799,228
INFO 2026-06-08 07:49:06 MarkDuplicates Tracking 266596 as yet unmatched pairs. 25508 records in RAM.
INFO 2026-06-08 07:49:08 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 2s. Last read position: chr11:47,584,357
INFO 2026-06-08 07:49:08 MarkDuplicates Tracking 263830 as yet unmatched pairs. 22734 records in RAM.
INFO 2026-06-08 07:49:11 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 2s. Last read position: chr11:62,534,041
INFO 2026-06-08 07:49:11 MarkDuplicates Tracking 261475 as yet unmatched pairs. 20350 records in RAM.
INFO 2026-06-08 07:49:13 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 2s. Last read position: chr11:65,130,002
INFO 2026-06-08 07:49:13 MarkDuplicates Tracking 258284 as yet unmatched pairs. 17155 records in RAM.
INFO 2026-06-08 07:49:15 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 2s. Last read position: chr11:66,315,630
INFO 2026-06-08 07:49:15 MarkDuplicates Tracking 255494 as yet unmatched pairs. 14330 records in RAM.
INFO 2026-06-08 07:49:17 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 2s. Last read position: chr11:68,042,685
INFO 2026-06-08 07:49:17 MarkDuplicates Tracking 252660 as yet unmatched pairs. 11436 records in RAM.
INFO 2026-06-08 07:49:20 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 2s. Last read position: chr11:71,593,562
INFO 2026-06-08 07:49:20 MarkDuplicates Tracking 250240 as yet unmatched pairs. 8969 records in RAM.
INFO 2026-06-08 07:49:22 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 2s. Last read position: chr11:74,852,000
INFO 2026-06-08 07:49:22 MarkDuplicates Tracking 247442 as yet unmatched pairs. 6154 records in RAM.
INFO 2026-06-08 07:49:24 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 2s. Last read position: chr11:118,436,692
INFO 2026-06-08 07:49:24 MarkDuplicates Tracking 244728 as yet unmatched pairs. 3346 records in RAM.
INFO 2026-06-08 07:49:26 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 2s. Last read position: chr11:129,869,652
INFO 2026-06-08 07:49:26 MarkDuplicates Tracking 242055 as yet unmatched pairs. 649 records in RAM.
INFO 2026-06-08 07:49:30 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 3s. Last read position: chr12:6,770,411
INFO 2026-06-08 07:49:30 MarkDuplicates Tracking 239489 as yet unmatched pairs. 23180 records in RAM.
INFO 2026-06-08 07:49:32 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 2s. Last read position: chr12:31,981,230
INFO 2026-06-08 07:49:32 MarkDuplicates Tracking 237084 as yet unmatched pairs. 20773 records in RAM.
INFO 2026-06-08 07:49:34 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 2s. Last read position: chr12:49,272,290
INFO 2026-06-08 07:49:34 MarkDuplicates Tracking 234899 as yet unmatched pairs. 18588 records in RAM.
INFO 2026-06-08 07:49:37 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 2s. Last read position: chr12:53,297,859
INFO 2026-06-08 07:49:37 MarkDuplicates Tracking 232241 as yet unmatched pairs. 15913 records in RAM.
INFO 2026-06-08 07:49:39 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 2s. Last read position: chr12:56,645,200
INFO 2026-06-08 07:49:39 MarkDuplicates Tracking 229571 as yet unmatched pairs. 13227 records in RAM.
INFO 2026-06-08 07:49:41 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 2s. Last read position: chr12:68,553,470
INFO 2026-06-08 07:49:41 MarkDuplicates Tracking 226816 as yet unmatched pairs. 10463 records in RAM.
INFO 2026-06-08 07:49:43 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 2s. Last read position: chr12:109,451,642
INFO 2026-06-08 07:49:43 MarkDuplicates Tracking 224019 as yet unmatched pairs. 7661 records in RAM.
INFO 2026-06-08 07:49:47 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 3s. Last read position: chr12:117,186,532
INFO 2026-06-08 07:49:47 MarkDuplicates Tracking 221106 as yet unmatched pairs. 4738 records in RAM.
INFO 2026-06-08 07:49:49 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 2s. Last read position: chr12:124,344,621
INFO 2026-06-08 07:49:49 MarkDuplicates Tracking 218453 as yet unmatched pairs. 2080 records in RAM.
INFO 2026-06-08 07:49:52 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 2s. Last read position: chr13:26,682,695
INFO 2026-06-08 07:49:52 MarkDuplicates Tracking 215532 as yet unmatched pairs. 5842 records in RAM.
INFO 2026-06-08 07:49:54 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 2s. Last read position: chr13:95,071,754
INFO 2026-06-08 07:49:54 MarkDuplicates Tracking 213050 as yet unmatched pairs. 3353 records in RAM.
INFO 2026-06-08 07:49:56 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 2s. Last read position: chr13:113,096,601
INFO 2026-06-08 07:49:56 MarkDuplicates Tracking 210280 as yet unmatched pairs. 518 records in RAM.
INFO 2026-06-08 07:49:59 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 2s. Last read position: chr14:23,644,874
INFO 2026-06-08 07:49:59 MarkDuplicates Tracking 207915 as yet unmatched pairs. 11294 records in RAM.
INFO 2026-06-08 07:50:01 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 2s. Last read position: chr14:55,350,623
INFO 2026-06-08 07:50:01 MarkDuplicates Tracking 204882 as yet unmatched pairs. 8234 records in RAM.
INFO 2026-06-08 07:50:04 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 2s. Last read position: chr14:75,126,813
INFO 2026-06-08 07:50:04 MarkDuplicates Tracking 202233 as yet unmatched pairs. 5581 records in RAM.
INFO 2026-06-08 07:50:07 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 3s. Last read position: chr14:102,000,331
INFO 2026-06-08 07:50:07 MarkDuplicates Tracking 199496 as yet unmatched pairs. 2792 records in RAM.
INFO 2026-06-08 07:50:10 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 2s. Last read position: chr15:22,556,065
INFO 2026-06-08 07:50:10 MarkDuplicates Tracking 196659 as yet unmatched pairs. 12341 records in RAM.
INFO 2026-06-08 07:50:12 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 2s. Last read position: chr15:42,439,275
INFO 2026-06-08 07:50:12 MarkDuplicates Tracking 194222 as yet unmatched pairs. 9853 records in RAM.
INFO 2026-06-08 07:50:14 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 2s. Last read position: chr15:63,057,038
INFO 2026-06-08 07:50:14 MarkDuplicates Tracking 191686 as yet unmatched pairs. 7302 records in RAM.
INFO 2026-06-08 07:50:16 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 1s. Last read position: chr15:74,839,564
INFO 2026-06-08 07:50:16 MarkDuplicates Tracking 188768 as yet unmatched pairs. 4366 records in RAM.
INFO 2026-06-08 07:50:18 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 2s. Last read position: chr15:89,575,814
INFO 2026-06-08 07:50:18 MarkDuplicates Tracking 186027 as yet unmatched pairs. 1602 records in RAM.
INFO 2026-06-08 07:50:20 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 2s. Last read position: chr16:672,997
INFO 2026-06-08 07:50:20 MarkDuplicates Tracking 183192 as yet unmatched pairs. 26264 records in RAM.
INFO 2026-06-08 07:50:23 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 2s. Last read position: chr16:2,519,232
INFO 2026-06-08 07:50:23 MarkDuplicates Tracking 179669 as yet unmatched pairs. 22738 records in RAM.
INFO 2026-06-08 07:50:25 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 2s. Last read position: chr16:11,838,091
INFO 2026-06-08 07:50:25 MarkDuplicates Tracking 176680 as yet unmatched pairs. 19717 records in RAM.
INFO 2026-06-08 07:50:27 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 1s. Last read position: chr16:16,372,008
INFO 2026-06-08 07:50:27 MarkDuplicates Tracking 175325 as yet unmatched pairs. 18348 records in RAM.
INFO 2026-06-08 07:50:29 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 1s. Last read position: chr16:21,836,473
INFO 2026-06-08 07:50:29 MarkDuplicates Tracking 173715 as yet unmatched pairs. 16709 records in RAM.
INFO 2026-06-08 07:50:30 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 1s. Last read position: chr16:28,844,772
INFO 2026-06-08 07:50:30 MarkDuplicates Tracking 171909 as yet unmatched pairs. 14902 records in RAM.
INFO 2026-06-08 07:50:32 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 1s. Last read position: chr16:30,225,603
INFO 2026-06-08 07:50:32 MarkDuplicates Tracking 170064 as yet unmatched pairs. 13004 records in RAM.
INFO 2026-06-08 07:50:34 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 2s. Last read position: chr16:47,454,081
INFO 2026-06-08 07:50:34 MarkDuplicates Tracking 167629 as yet unmatched pairs. 10566 records in RAM.
INFO 2026-06-08 07:50:37 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 2s. Last read position: chr16:67,909,463
INFO 2026-06-08 07:50:37 MarkDuplicates Tracking 164786 as yet unmatched pairs. 7719 records in RAM.
INFO 2026-06-08 07:50:39 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 2s. Last read position: chr16:72,959,450
INFO 2026-06-08 07:50:39 MarkDuplicates Tracking 161986 as yet unmatched pairs. 4897 records in RAM.
INFO 2026-06-08 07:50:41 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 2s. Last read position: chr16:88,826,806
INFO 2026-06-08 07:50:41 MarkDuplicates Tracking 158816 as yet unmatched pairs. 1700 records in RAM.
INFO 2026-06-08 07:50:45 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 3s. Last read position: chr17:3,663,773
INFO 2026-06-08 07:50:45 MarkDuplicates Tracking 155814 as yet unmatched pairs. 41549 records in RAM.
INFO 2026-06-08 07:50:47 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 2s. Last read position: chr17:7,893,403
INFO 2026-06-08 07:50:47 MarkDuplicates Tracking 152723 as yet unmatched pairs. 38452 records in RAM.
INFO 2026-06-08 07:50:49 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 2s. Last read position: chr17:28,556,165
INFO 2026-06-08 07:50:49 MarkDuplicates Tracking 150223 as yet unmatched pairs. 35952 records in RAM.
INFO 2026-06-08 07:50:51 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 1s. Last read position: chr17:35,259,579
INFO 2026-06-08 07:50:51 MarkDuplicates Tracking 147337 as yet unmatched pairs. 33057 records in RAM.
INFO 2026-06-08 07:50:53 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 2s. Last read position: chr17:38,716,387
INFO 2026-06-08 07:50:53 MarkDuplicates Tracking 145139 as yet unmatched pairs. 30836 records in RAM.
INFO 2026-06-08 07:50:56 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 2s. Last read position: chr17:39,719,803
INFO 2026-06-08 07:50:56 MarkDuplicates Tracking 143730 as yet unmatched pairs. 29426 records in RAM.
INFO 2026-06-08 07:50:58 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:05:43s. Time for last 1,000,000: 2s. Last read position: chr17:41,503,716
INFO 2026-06-08 07:50:58 MarkDuplicates Tracking 139639 as yet unmatched pairs. 25331 records in RAM.
INFO 2026-06-08 07:51:00 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 2s. Last read position: chr17:44,398,864
INFO 2026-06-08 07:51:00 MarkDuplicates Tracking 136240 as yet unmatched pairs. 21930 records in RAM.
INFO 2026-06-08 07:51:03 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 2s. Last read position: chr17:50,188,758
INFO 2026-06-08 07:51:03 MarkDuplicates Tracking 134973 as yet unmatched pairs. 20629 records in RAM.
INFO 2026-06-08 07:51:05 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 2s. Last read position: chr17:50,194,150
INFO 2026-06-08 07:51:05 MarkDuplicates Tracking 134504 as yet unmatched pairs. 20124 records in RAM.
INFO 2026-06-08 07:51:08 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 2s. Last read position: chr17:50,199,432
INFO 2026-06-08 07:51:08 MarkDuplicates Tracking 128680 as yet unmatched pairs. 14299 records in RAM.
INFO 2026-06-08 07:51:10 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 2s. Last read position: chr17:64,098,225
INFO 2026-06-08 07:51:10 MarkDuplicates Tracking 125207 as yet unmatched pairs. 10812 records in RAM.
INFO 2026-06-08 07:51:12 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 2s. Last read position: chr17:75,779,046
INFO 2026-06-08 07:51:12 MarkDuplicates Tracking 122448 as yet unmatched pairs. 7986 records in RAM.
INFO 2026-06-08 07:51:15 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 2s. Last read position: chr17:80,334,217
INFO 2026-06-08 07:51:15 MarkDuplicates Tracking 119412 as yet unmatched pairs. 4949 records in RAM.
INFO 2026-06-08 07:51:17 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 2s. Last read position: chr17:82,057,072
INFO 2026-06-08 07:51:17 MarkDuplicates Tracking 116445 as yet unmatched pairs. 1956 records in RAM.
INFO 2026-06-08 07:51:20 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 2s. Last read position: chr18:12,326,044
INFO 2026-06-08 07:51:20 MarkDuplicates Tracking 113705 as yet unmatched pairs. 3549 records in RAM.
INFO 2026-06-08 07:51:22 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 2s. Last read position: chr18:62,716,636
INFO 2026-06-08 07:51:22 MarkDuplicates Tracking 111078 as yet unmatched pairs. 910 records in RAM.
INFO 2026-06-08 07:51:25 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 2s. Last read position: chr19:1,278,841
INFO 2026-06-08 07:51:25 MarkDuplicates Tracking 107756 as yet unmatched pairs. 46196 records in RAM.
INFO 2026-06-08 07:51:27 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 1s. Last read position: chr19:3,053,817
INFO 2026-06-08 07:51:27 MarkDuplicates Tracking 104255 as yet unmatched pairs. 42692 records in RAM.
INFO 2026-06-08 07:51:29 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 2s. Last read position: chr19:6,380,587
INFO 2026-06-08 07:51:29 MarkDuplicates Tracking 101027 as yet unmatched pairs. 39420 records in RAM.
INFO 2026-06-08 07:51:32 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:06:16s. Time for last 1,000,000: 2s. Last read position: chr19:10,362,316
INFO 2026-06-08 07:51:32 MarkDuplicates Tracking 97666 as yet unmatched pairs. 36059 records in RAM.
INFO 2026-06-08 07:51:34 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 2s. Last read position: chr19:12,938,656
INFO 2026-06-08 07:51:34 MarkDuplicates Tracking 94830 as yet unmatched pairs. 33222 records in RAM.
INFO 2026-06-08 07:51:36 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 2s. Last read position: chr19:15,179,247
INFO 2026-06-08 07:51:36 MarkDuplicates Tracking 91623 as yet unmatched pairs. 30011 records in RAM.
INFO 2026-06-08 07:51:38 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 2s. Last read position: chr19:17,194,751
INFO 2026-06-08 07:51:38 MarkDuplicates Tracking 88139 as yet unmatched pairs. 26511 records in RAM.
INFO 2026-06-08 07:51:41 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 2s. Last read position: chr19:19,145,921
INFO 2026-06-08 07:51:41 MarkDuplicates Tracking 84913 as yet unmatched pairs. 23284 records in RAM.
INFO 2026-06-08 07:51:43 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 2s. Last read position: chr19:35,270,556
INFO 2026-06-08 07:51:43 MarkDuplicates Tracking 81851 as yet unmatched pairs. 20202 records in RAM.
INFO 2026-06-08 07:51:46 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:06:30s. Time for last 1,000,000: 2s. Last read position: chr19:38,838,415
INFO 2026-06-08 07:51:46 MarkDuplicates Tracking 78780 as yet unmatched pairs. 17129 records in RAM.
INFO 2026-06-08 07:51:48 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:06:33s. Time for last 1,000,000: 2s. Last read position: chr19:40,255,174
INFO 2026-06-08 07:51:48 MarkDuplicates Tracking 76034 as yet unmatched pairs. 14382 records in RAM.
INFO 2026-06-08 07:51:51 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:06:35s. Time for last 1,000,000: 2s. Last read position: chr19:43,461,565
INFO 2026-06-08 07:51:51 MarkDuplicates Tracking 73191 as yet unmatched pairs. 11530 records in RAM.
INFO 2026-06-08 07:51:53 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 2s. Last read position: chr19:47,275,061
INFO 2026-06-08 07:51:53 MarkDuplicates Tracking 69818 as yet unmatched pairs. 8144 records in RAM.
INFO 2026-06-08 07:51:56 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 2s. Last read position: chr19:49,615,977
INFO 2026-06-08 07:51:56 MarkDuplicates Tracking 66863 as yet unmatched pairs. 5189 records in RAM.
INFO 2026-06-08 07:51:58 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 2s. Last read position: chr19:55,045,059
INFO 2026-06-08 07:51:58 MarkDuplicates Tracking 64096 as yet unmatched pairs. 2406 records in RAM.
INFO 2026-06-08 07:52:00 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 2s. Last read position: chr20:2,463,161
INFO 2026-06-08 07:52:00 MarkDuplicates Tracking 60912 as yet unmatched pairs. 13942 records in RAM.
INFO 2026-06-08 07:52:03 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 2s. Last read position: chr20:25,057,909
INFO 2026-06-08 07:52:03 MarkDuplicates Tracking 58093 as yet unmatched pairs. 11104 records in RAM.
INFO 2026-06-08 07:52:06 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:06:51s. Time for last 1,000,000: 2s. Last read position: chr20:35,954,010
INFO 2026-06-08 07:52:06 MarkDuplicates Tracking 55334 as yet unmatched pairs. 8340 records in RAM.
INFO 2026-06-08 07:52:08 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 2s. Last read position: chr20:45,812,663
INFO 2026-06-08 07:52:08 MarkDuplicates Tracking 52779 as yet unmatched pairs. 5783 records in RAM.
INFO 2026-06-08 07:52:11 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 2s. Last read position: chr20:58,692,940
INFO 2026-06-08 07:52:11 MarkDuplicates Tracking 50004 as yet unmatched pairs. 2990 records in RAM.
INFO 2026-06-08 07:52:13 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:06:57s. Time for last 1,000,000: 2s. Last read position: chr21:6,120,613
INFO 2026-06-08 07:52:13 MarkDuplicates Tracking 47011 as yet unmatched pairs. 9162 records in RAM.
INFO 2026-06-08 07:52:15 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 1s. Last read position: chr21:8,260,797
INFO 2026-06-08 07:52:15 MarkDuplicates Tracking 45364 as yet unmatched pairs. 7506 records in RAM.
INFO 2026-06-08 07:52:16 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,609
INFO 2026-06-08 07:52:16 MarkDuplicates Tracking 43625 as yet unmatched pairs. 5764 records in RAM.
INFO 2026-06-08 07:52:18 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:07:03s. Time for last 1,000,000: 2s. Last read position: chr21:41,953,548
INFO 2026-06-08 07:52:18 MarkDuplicates Tracking 40882 as yet unmatched pairs. 3018 records in RAM.
INFO 2026-06-08 07:52:21 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 2s. Last read position: chr21:46,311,497
INFO 2026-06-08 07:52:21 MarkDuplicates Tracking 38055 as yet unmatched pairs. 191 records in RAM.
INFO 2026-06-08 07:52:24 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 2s. Last read position: chr22:21,962,466
INFO 2026-06-08 07:52:24 MarkDuplicates Tracking 35167 as yet unmatched pairs. 17558 records in RAM.
INFO 2026-06-08 07:52:26 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:07:11s. Time for last 1,000,000: 2s. Last read position: chr22:24,568,053
INFO 2026-06-08 07:52:26 MarkDuplicates Tracking 32530 as yet unmatched pairs. 14919 records in RAM.
INFO 2026-06-08 07:52:28 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 2s. Last read position: chr22:29,310,697
INFO 2026-06-08 07:52:28 MarkDuplicates Tracking 29588 as yet unmatched pairs. 11977 records in RAM.
INFO 2026-06-08 07:52:30 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:07:15s. Time for last 1,000,000: 2s. Last read position: chr22:31,427,134
INFO 2026-06-08 07:52:30 MarkDuplicates Tracking 27080 as yet unmatched pairs. 9459 records in RAM.
INFO 2026-06-08 07:52:33 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:07:17s. Time for last 1,000,000: 2s. Last read position: chr22:37,643,709
INFO 2026-06-08 07:52:33 MarkDuplicates Tracking 23865 as yet unmatched pairs. 6244 records in RAM.
INFO 2026-06-08 07:52:35 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:07:19s. Time for last 1,000,000: 2s. Last read position: chr22:42,571,091
INFO 2026-06-08 07:52:35 MarkDuplicates Tracking 20771 as yet unmatched pairs. 3150 records in RAM.
INFO 2026-06-08 07:52:38 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:07:23s. Time for last 1,000,000: 3s. Last read position: chrX:1,386,595
INFO 2026-06-08 07:52:38 MarkDuplicates Tracking 17636 as yet unmatched pairs. 12953 records in RAM.
INFO 2026-06-08 07:52:40 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:07:25s. Time for last 1,000,000: 2s. Last read position: chrX:47,145,390
INFO 2026-06-08 07:52:40 MarkDuplicates Tracking 15187 as yet unmatched pairs. 10499 records in RAM.
INFO 2026-06-08 07:52:42 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 2s. Last read position: chrX:53,627,845
INFO 2026-06-08 07:52:42 MarkDuplicates Tracking 12404 as yet unmatched pairs. 7716 records in RAM.
INFO 2026-06-08 07:52:44 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:07:29s. Time for last 1,000,000: 1s. Last read position: chrX:103,377,602
INFO 2026-06-08 07:52:44 MarkDuplicates Tracking 9982 as yet unmatched pairs. 5293 records in RAM.
INFO 2026-06-08 07:52:47 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:07:31s. Time for last 1,000,000: 2s. Last read position: chrX:153,693,918
INFO 2026-06-08 07:52:47 MarkDuplicates Tracking 7623 as yet unmatched pairs. 2933 records in RAM.
INFO 2026-06-08 07:52:49 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:07:34s. Time for last 1,000,000: 2s. Last read position: chrY:12,912,987
INFO 2026-06-08 07:52:49 MarkDuplicates Tracking 4577 as yet unmatched pairs. 234 records in RAM.
INFO 2026-06-08 07:52:51 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:07:35s. Time for last 1,000,000: 1s. Last read position: GL000220.1:159,466
INFO 2026-06-08 07:52:51 MarkDuplicates Tracking 2935 as yet unmatched pairs. 47 records in RAM.
INFO 2026-06-08 07:52:53 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:07:38s. Time for last 1,000,000: 2s. Last read position: KI270733.1:176,125
INFO 2026-06-08 07:52:53 MarkDuplicates Tracking 68 as yet unmatched pairs. 42 records in RAM.
INFO 2026-06-08 07:52:54 MarkDuplicates Read 185397617 records. 0 pairs never matched.
INFO 2026-06-08 07:53:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 41974234520; totalMemory: 63585648640; maxMemory: 63585648640
INFO 2026-06-08 07:53:10 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 07:53:18 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 07:54:00 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 07:54:28 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 07:54:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300853408; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-08 07:54:35 MarkDuplicates Marking 139376984 records as duplicates.
INFO 2026-06-08 07:54:35 MarkDuplicates Found 3120924 optical duplicate clusters.
INFO 2026-06-08 07:54:35 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 07:55:09 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:34s. Time for last 10,000,000: 34s. Last read position: chr1:149,813,352
INFO 2026-06-08 07:55:41 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:01:06s. Time for last 10,000,000: 31s. Last read position: chr2:32,916,264
INFO 2026-06-08 07:56:10 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:35s. Time for last 10,000,000: 28s. Last read position: chr3:40,461,468
INFO 2026-06-08 07:56:40 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:02:04s. Time for last 10,000,000: 29s. Last read position: chr4:4,391,520
INFO 2026-06-08 07:57:08 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:02:33s. Time for last 10,000,000: 28s. Last read position: chr6:3,515,185
INFO 2026-06-08 07:57:35 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:03:00s. Time for last 10,000,000: 26s. Last read position: chr7:43,869,062
INFO 2026-06-08 07:58:03 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:03:28s. Time for last 10,000,000: 28s. Last read position: chr8:90,645,367
INFO 2026-06-08 07:58:32 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:03:57s. Time for last 10,000,000: 29s. Last read position: chr9:136,475,817
INFO 2026-06-08 07:59:01 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:04:25s. Time for last 10,000,000: 28s. Last read position: chr11:62,534,041
INFO 2026-06-08 07:59:28 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:04:53s. Time for last 10,000,000: 27s. Last read position: chr12:49,272,290
INFO 2026-06-08 07:59:57 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:05:22s. Time for last 10,000,000: 28s. Last read position: chr14:23,644,874
INFO 2026-06-08 08:00:23 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:05:48s. Time for last 10,000,000: 26s. Last read position: chr16:2,519,232
INFO 2026-06-08 08:00:50 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:06:15s. Time for last 10,000,000: 26s. Last read position: chr17:3,663,773
INFO 2026-06-08 08:01:17 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:06:42s. Time for last 10,000,000: 26s. Last read position: chr17:50,199,432
INFO 2026-06-08 08:01:46 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:07:11s. Time for last 10,000,000: 28s. Last read position: chr19:10,362,316
INFO 2026-06-08 08:02:12 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:07:37s. Time for last 10,000,000: 26s. Last read position: chr19:49,615,977
INFO 2026-06-08 08:02:38 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:08:03s. Time for last 10,000,000: 25s. Last read position: chr21:41,953,548
INFO 2026-06-08 08:03:07 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:08:32s. Time for last 10,000,000: 29s. Last read position: chrX:53,627,845
INFO 2026-06-08 08:03:31 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:03:31 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:03:31 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:03:32 MarkDuplicates Before output close freeMemory: 201791640; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:03:32 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:03:32 MarkDuplicates After output close freeMemory: 104312032; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 08:03:32 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 18.32 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory