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/3a/fa6c7fa7648a885684beefc18b0d92/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/fa6c7fa7648a885684beefc18b0d92/.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/58/0edd20402bf857483355320fdf3b05/659_bGW-T1-TRNA-1_B23WHTKLT4_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 659_bGW-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bGW-T1-TRNA-1_B23WHTKLT4_1.md.bam --METRICS_FILE 659_bGW-T1-TRNA-1_B23WHTKLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
23:59:05.245 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
[Wed May 27 23:59:05 GMT 2026] MarkDuplicates --INPUT 659_bGW-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bGW-T1-TRNA-1_B23WHTKLT4_1.md.bam --METRICS_FILE 659_bGW-T1-TRNA-1_B23WHTKLT4_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
[Wed May 27 23:59:05 GMT 2026] Executing as ?@nf-3afa6c7fa7648a885684beefc18b0d92-71a8d-2z5xc on Linux 6.12.83 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 2026-05-27 23:59:05 MarkDuplicates Start of doWork freeMemory: 105829088; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-05-27 23:59:05 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-05-27 23:59:05 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-05-27 23:59:10 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:3,498,486
INFO 2026-05-27 23:59:10 MarkDuplicates Tracking 1947 as yet unmatched pairs. 131 records in RAM.
INFO 2026-05-27 23:59:13 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: chr1:13,583,927
INFO 2026-05-27 23:59:13 MarkDuplicates Tracking 3639 as yet unmatched pairs. 132 records in RAM.
INFO 2026-05-27 23:59:16 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 3s. Last read position: chr1:20,969,585
INFO 2026-05-27 23:59:16 MarkDuplicates Tracking 5066 as yet unmatched pairs. 18 records in RAM.
INFO 2026-05-27 23:59:20 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 3s. Last read position: chr1:24,533,158
INFO 2026-05-27 23:59:20 MarkDuplicates Tracking 6615 as yet unmatched pairs. 87 records in RAM.
INFO 2026-05-27 23:59:23 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 3s. Last read position: chr1:31,684,220
INFO 2026-05-27 23:59:23 MarkDuplicates Tracking 8019 as yet unmatched pairs. 77 records in RAM.
INFO 2026-05-27 23:59:26 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 2s. Last read position: chr1:39,387,796
INFO 2026-05-27 23:59:26 MarkDuplicates Tracking 9580 as yet unmatched pairs. 59 records in RAM.
INFO 2026-05-27 23:59:29 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 3s. Last read position: chr1:45,511,360
INFO 2026-05-27 23:59:29 MarkDuplicates Tracking 11549 as yet unmatched pairs. 445 records in RAM.
INFO 2026-05-27 23:59:32 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 2s. Last read position: chr1:67,420,160
INFO 2026-05-27 23:59:32 MarkDuplicates Tracking 12773 as yet unmatched pairs. 160 records in RAM.
INFO 2026-05-27 23:59:35 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 3s. Last read position: chr1:109,914,216
INFO 2026-05-27 23:59:35 MarkDuplicates Tracking 13913 as yet unmatched pairs. 66 records in RAM.
INFO 2026-05-27 23:59:38 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 3s. Last read position: chr1:119,997,144
INFO 2026-05-27 23:59:38 MarkDuplicates Tracking 15682 as yet unmatched pairs. 457 records in RAM.
INFO 2026-05-27 23:59:41 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 2s. Last read position: chr1:150,267,960
INFO 2026-05-27 23:59:41 MarkDuplicates Tracking 16855 as yet unmatched pairs. 686 records in RAM.
INFO 2026-05-27 23:59:43 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 2s. Last read position: chr1:154,172,930
INFO 2026-05-27 23:59:43 MarkDuplicates Tracking 19059 as yet unmatched pairs. 1454 records in RAM.
INFO 2026-05-27 23:59:46 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 2s. Last read position: chr1:156,044,168
INFO 2026-05-27 23:59:46 MarkDuplicates Tracking 19034 as yet unmatched pairs. 76 records in RAM.
INFO 2026-05-27 23:59:48 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 2s. Last read position: chr1:161,175,899
INFO 2026-05-27 23:59:48 MarkDuplicates Tracking 20664 as yet unmatched pairs. 122 records in RAM.
INFO 2026-05-27 23:59:50 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 2s. Last read position: chr1:180,006,446
INFO 2026-05-27 23:59:50 MarkDuplicates Tracking 21931 as yet unmatched pairs. 15 records in RAM.
INFO 2026-05-27 23:59:53 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 2s. Last read position: chr1:201,490,328
INFO 2026-05-27 23:59:53 MarkDuplicates Tracking 24464 as yet unmatched pairs. 1083 records in RAM.
INFO 2026-05-27 23:59:56 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 3s. Last read position: chr1:207,560,833
INFO 2026-05-27 23:59:56 MarkDuplicates Tracking 24733 as yet unmatched pairs. 12 records in RAM.
INFO 2026-05-28 00:00:00 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 4s. Last read position: chr1:227,976,998
INFO 2026-05-28 00:00:00 MarkDuplicates Tracking 26150 as yet unmatched pairs. 0 records in RAM.
INFO 2026-05-28 00:00:04 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 3s. Last read position: chr1:244,864,108
INFO 2026-05-28 00:00:04 MarkDuplicates Tracking 28440 as yet unmatched pairs. 456 records in RAM.
INFO 2026-05-28 00:00:08 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 4s. Last read position: chr2:26,776,407
INFO 2026-05-28 00:00:08 MarkDuplicates Tracking 29473 as yet unmatched pairs. 29350 records in RAM.
INFO 2026-05-28 00:00:11 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,264
INFO 2026-05-28 00:00:11 MarkDuplicates Tracking 138900 as yet unmatched pairs. 26191 records in RAM.
INFO 2026-05-28 00:00:13 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 2s. Last read position: chr2:43,224,536
INFO 2026-05-28 00:00:13 MarkDuplicates Tracking 273783 as yet unmatched pairs. 21002 records in RAM.
INFO 2026-05-28 00:00:15 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 2s. Last read position: chr2:61,526,352
INFO 2026-05-28 00:00:15 MarkDuplicates Tracking 272131 as yet unmatched pairs. 19349 records in RAM.
INFO 2026-05-28 00:00:17 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 2s. Last read position: chr2:74,491,331
INFO 2026-05-28 00:00:17 MarkDuplicates Tracking 270735 as yet unmatched pairs. 17948 records in RAM.
INFO 2026-05-28 00:00:20 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 2s. Last read position: chr2:101,308,102
INFO 2026-05-28 00:00:20 MarkDuplicates Tracking 269377 as yet unmatched pairs. 16581 records in RAM.
INFO 2026-05-28 00:00:22 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 2s. Last read position: chr2:121,755,839
INFO 2026-05-28 00:00:22 MarkDuplicates Tracking 268245 as yet unmatched pairs. 15448 records in RAM.
INFO 2026-05-28 00:00:24 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 2s. Last read position: chr2:158,673,675
INFO 2026-05-28 00:00:24 MarkDuplicates Tracking 266836 as yet unmatched pairs. 14037 records in RAM.
INFO 2026-05-28 00:00:27 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 2s. Last read position: chr2:178,557,292
INFO 2026-05-28 00:00:27 MarkDuplicates Tracking 265741 as yet unmatched pairs. 12933 records in RAM.
INFO 2026-05-28 00:00:29 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 2s. Last read position: chr2:178,709,644
INFO 2026-05-28 00:00:29 MarkDuplicates Tracking 264611 as yet unmatched pairs. 11801 records in RAM.
INFO 2026-05-28 00:00:32 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 2s. Last read position: chr2:188,999,476
INFO 2026-05-28 00:00:32 MarkDuplicates Tracking 264596 as yet unmatched pairs. 11786 records in RAM.
INFO 2026-05-28 00:00:36 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 3s. Last read position: chr2:201,195,848
INFO 2026-05-28 00:00:36 MarkDuplicates Tracking 261750 as yet unmatched pairs. 8938 records in RAM.
INFO 2026-05-28 00:00:39 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 3s. Last read position: chr2:215,373,322
INFO 2026-05-28 00:00:39 MarkDuplicates Tracking 264550 as yet unmatched pairs. 11735 records in RAM.
INFO 2026-05-28 00:00:42 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 2s. Last read position: chr2:215,399,305
INFO 2026-05-28 00:00:42 MarkDuplicates Tracking 261714 as yet unmatched pairs. 8899 records in RAM.
INFO 2026-05-28 00:00:45 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 2s. Last read position: chr2:215,431,858
INFO 2026-05-28 00:00:45 MarkDuplicates Tracking 262518 as yet unmatched pairs. 9701 records in RAM.
INFO 2026-05-28 00:00:47 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 2s. Last read position: chr2:219,180,717
INFO 2026-05-28 00:00:47 MarkDuplicates Tracking 256917 as yet unmatched pairs. 4100 records in RAM.
INFO 2026-05-28 00:00:50 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 2s. Last read position: chr2:231,463,202
INFO 2026-05-28 00:00:50 MarkDuplicates Tracking 255629 as yet unmatched pairs. 2810 records in RAM.
INFO 2026-05-28 00:00:52 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 2s. Last read position: chr2:240,596,475
INFO 2026-05-28 00:00:52 MarkDuplicates Tracking 253369 as yet unmatched pairs. 543 records in RAM.
INFO 2026-05-28 00:00:56 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 3s. Last read position: chr3:15,414,067
INFO 2026-05-28 00:00:56 MarkDuplicates Tracking 251756 as yet unmatched pairs. 12397 records in RAM.
INFO 2026-05-28 00:00:58 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 2s. Last read position: chr3:43,347,460
INFO 2026-05-28 00:00:58 MarkDuplicates Tracking 250345 as yet unmatched pairs. 10980 records in RAM.
INFO 2026-05-28 00:01:01 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 3s. Last read position: chr3:49,096,063
INFO 2026-05-28 00:01:01 MarkDuplicates Tracking 248937 as yet unmatched pairs. 9571 records in RAM.
INFO 2026-05-28 00:01:03 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 2s. Last read position: chr3:52,503,458
INFO 2026-05-28 00:01:03 MarkDuplicates Tracking 247354 as yet unmatched pairs. 7987 records in RAM.
INFO 2026-05-28 00:01:05 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 2s. Last read position: chr3:87,245,751
INFO 2026-05-28 00:01:05 MarkDuplicates Tracking 246218 as yet unmatched pairs. 6849 records in RAM.
INFO 2026-05-28 00:01:07 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 2s. Last read position: chr3:123,648,982
INFO 2026-05-28 00:01:07 MarkDuplicates Tracking 244709 as yet unmatched pairs. 5335 records in RAM.
INFO 2026-05-28 00:01:09 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 2s. Last read position: chr3:134,366,295
INFO 2026-05-28 00:01:09 MarkDuplicates Tracking 243104 as yet unmatched pairs. 3729 records in RAM.
INFO 2026-05-28 00:01:12 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 2s. Last read position: chr3:172,710,936
INFO 2026-05-28 00:01:12 MarkDuplicates Tracking 241704 as yet unmatched pairs. 2328 records in RAM.
INFO 2026-05-28 00:01:15 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 2s. Last read position: chr3:193,593,294
INFO 2026-05-28 00:01:15 MarkDuplicates Tracking 240621 as yet unmatched pairs. 1238 records in RAM.
INFO 2026-05-28 00:01:17 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 2s. Last read position: chr3:196,782,809
INFO 2026-05-28 00:01:17 MarkDuplicates Tracking 239711 as yet unmatched pairs. 325 records in RAM.
INFO 2026-05-28 00:01:20 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 2s. Last read position: chr4:6,609,852
INFO 2026-05-28 00:01:20 MarkDuplicates Tracking 237993 as yet unmatched pairs. 6516 records in RAM.
INFO 2026-05-28 00:01:23 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 3s. Last read position: chr4:47,591,171
INFO 2026-05-28 00:01:23 MarkDuplicates Tracking 236246 as yet unmatched pairs. 4767 records in RAM.
INFO 2026-05-28 00:01:26 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 3s. Last read position: chr4:76,741,644
INFO 2026-05-28 00:01:26 MarkDuplicates Tracking 234772 as yet unmatched pairs. 3287 records in RAM.
INFO 2026-05-28 00:01:30 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 3s. Last read position: chr4:119,031,497
INFO 2026-05-28 00:01:30 MarkDuplicates Tracking 234829 as yet unmatched pairs. 3341 records in RAM.
INFO 2026-05-28 00:01:33 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 2s. Last read position: chr4:169,130,139
INFO 2026-05-28 00:01:33 MarkDuplicates Tracking 232097 as yet unmatched pairs. 602 records in RAM.
INFO 2026-05-28 00:01:36 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 3s. Last read position: chr5:14,397,102
INFO 2026-05-28 00:01:36 MarkDuplicates Tracking 230993 as yet unmatched pairs. 9680 records in RAM.
INFO 2026-05-28 00:01:39 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 3s. Last read position: chr5:62,348,139
INFO 2026-05-28 00:01:39 MarkDuplicates Tracking 229364 as yet unmatched pairs. 8046 records in RAM.
INFO 2026-05-28 00:01:42 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 2s. Last read position: chr5:95,748,394
INFO 2026-05-28 00:01:42 MarkDuplicates Tracking 228191 as yet unmatched pairs. 6867 records in RAM.
INFO 2026-05-28 00:01:44 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 2s. Last read position: chr5:136,153,782
INFO 2026-05-28 00:01:44 MarkDuplicates Tracking 226711 as yet unmatched pairs. 5380 records in RAM.
INFO 2026-05-28 00:01:46 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 2s. Last read position: chr5:149,345,612
INFO 2026-05-28 00:01:46 MarkDuplicates Tracking 225350 as yet unmatched pairs. 4015 records in RAM.
INFO 2026-05-28 00:01:49 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 2s. Last read position: chr5:154,790,339
INFO 2026-05-28 00:01:49 MarkDuplicates Tracking 224060 as yet unmatched pairs. 2723 records in RAM.
INFO 2026-05-28 00:01:52 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 2s. Last read position: chr5:178,210,216
INFO 2026-05-28 00:01:52 MarkDuplicates Tracking 222736 as yet unmatched pairs. 1392 records in RAM.
INFO 2026-05-28 00:01:55 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 3s. Last read position: chr6:7,230,004
INFO 2026-05-28 00:01:55 MarkDuplicates Tracking 221141 as yet unmatched pairs. 13804 records in RAM.
INFO 2026-05-28 00:01:57 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 2s. Last read position: chr6:27,824,304
INFO 2026-05-28 00:01:57 MarkDuplicates Tracking 219628 as yet unmatched pairs. 12286 records in RAM.
INFO 2026-05-28 00:02:00 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 2s. Last read position: chr6:31,355,374
INFO 2026-05-28 00:02:00 MarkDuplicates Tracking 219706 as yet unmatched pairs. 12362 records in RAM.
INFO 2026-05-28 00:02:02 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 1s. Last read position: chr6:31,827,899
INFO 2026-05-28 00:02:02 MarkDuplicates Tracking 219373 as yet unmatched pairs. 12026 records in RAM.
INFO 2026-05-28 00:02:04 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 2s. Last read position: chr6:32,439,915
INFO 2026-05-28 00:02:04 MarkDuplicates Tracking 216319 as yet unmatched pairs. 8970 records in RAM.
INFO 2026-05-28 00:02:06 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 2s. Last read position: chr6:36,970,094
INFO 2026-05-28 00:02:06 MarkDuplicates Tracking 215400 as yet unmatched pairs. 8050 records in RAM.
INFO 2026-05-28 00:02:09 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 2s. Last read position: chr6:52,282,696
INFO 2026-05-28 00:02:09 MarkDuplicates Tracking 213118 as yet unmatched pairs. 5765 records in RAM.
INFO 2026-05-28 00:02:11 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 2s. Last read position: chr6:89,146,149
INFO 2026-05-28 00:02:11 MarkDuplicates Tracking 211929 as yet unmatched pairs. 4575 records in RAM.
INFO 2026-05-28 00:02:15 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 3s. Last read position: chr6:130,869,785
INFO 2026-05-28 00:02:15 MarkDuplicates Tracking 210633 as yet unmatched pairs. 3279 records in RAM.
INFO 2026-05-28 00:02:17 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 2s. Last read position: chr6:157,201,039
INFO 2026-05-28 00:02:17 MarkDuplicates Tracking 209128 as yet unmatched pairs. 1771 records in RAM.
INFO 2026-05-28 00:02:19 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 2s. Last read position: chr6:169,248,919
INFO 2026-05-28 00:02:19 MarkDuplicates Tracking 208495 as yet unmatched pairs. 1137 records in RAM.
INFO 2026-05-28 00:02:22 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 2s. Last read position: chr7:5,527,735
INFO 2026-05-28 00:02:22 MarkDuplicates Tracking 209862 as yet unmatched pairs. 19904 records in RAM.
INFO 2026-05-28 00:02:25 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 2s. Last read position: chr7:17,868,450
INFO 2026-05-28 00:02:25 MarkDuplicates Tracking 204203 as yet unmatched pairs. 14243 records in RAM.
INFO 2026-05-28 00:02:27 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 2s. Last read position: chr7:44,111,860
INFO 2026-05-28 00:02:27 MarkDuplicates Tracking 203291 as yet unmatched pairs. 13330 records in RAM.
INFO 2026-05-28 00:02:29 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 2s. Last read position: chr7:73,084,142
INFO 2026-05-28 00:02:29 MarkDuplicates Tracking 201139 as yet unmatched pairs. 11177 records in RAM.
INFO 2026-05-28 00:02:31 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 2s. Last read position: chr7:76,330,009
INFO 2026-05-28 00:02:31 MarkDuplicates Tracking 199945 as yet unmatched pairs. 9982 records in RAM.
INFO 2026-05-28 00:02:34 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 2s. Last read position: chr7:94,420,558
INFO 2026-05-28 00:02:34 MarkDuplicates Tracking 199328 as yet unmatched pairs. 9362 records in RAM.
INFO 2026-05-28 00:02:37 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 2s. Last read position: chr7:100,615,168
INFO 2026-05-28 00:02:37 MarkDuplicates Tracking 196804 as yet unmatched pairs. 6837 records in RAM.
INFO 2026-05-28 00:02:38 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 1s. Last read position: chr7:100,996,636
INFO 2026-05-28 00:02:38 MarkDuplicates Tracking 197268 as yet unmatched pairs. 7301 records in RAM.
INFO 2026-05-28 00:02:40 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 1s. Last read position: chr7:101,001,326
INFO 2026-05-28 00:02:40 MarkDuplicates Tracking 197501 as yet unmatched pairs. 7534 records in RAM.
INFO 2026-05-28 00:02:43 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 2s. Last read position: chr7:107,203,461
INFO 2026-05-28 00:02:43 MarkDuplicates Tracking 194830 as yet unmatched pairs. 4860 records in RAM.
INFO 2026-05-28 00:02:46 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 3s. Last read position: chr7:128,847,764
INFO 2026-05-28 00:02:46 MarkDuplicates Tracking 193960 as yet unmatched pairs. 3988 records in RAM.
INFO 2026-05-28 00:02:48 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 1s. Last read position: chr7:143,858,842
INFO 2026-05-28 00:02:48 MarkDuplicates Tracking 192234 as yet unmatched pairs. 2262 records in RAM.
INFO 2026-05-28 00:02:50 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 2s. Last read position: chr7:151,467,179
INFO 2026-05-28 00:02:50 MarkDuplicates Tracking 190938 as yet unmatched pairs. 962 records in RAM.
INFO 2026-05-28 00:02:52 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 2s. Last read position: chr8:22,604,831
INFO 2026-05-28 00:02:52 MarkDuplicates Tracking 189440 as yet unmatched pairs. 10670 records in RAM.
INFO 2026-05-28 00:02:55 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 2s. Last read position: chr8:38,842,298
INFO 2026-05-28 00:02:55 MarkDuplicates Tracking 188050 as yet unmatched pairs. 9276 records in RAM.
INFO 2026-05-28 00:02:57 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 2s. Last read position: chr8:73,315,174
INFO 2026-05-28 00:02:57 MarkDuplicates Tracking 186222 as yet unmatched pairs. 7446 records in RAM.
INFO 2026-05-28 00:02:59 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 2s. Last read position: chr8:119,208,523
INFO 2026-05-28 00:02:59 MarkDuplicates Tracking 186215 as yet unmatched pairs. 7438 records in RAM.
INFO 2026-05-28 00:03:01 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 1s. Last read position: chr8:143,805,217
INFO 2026-05-28 00:03:01 MarkDuplicates Tracking 183361 as yet unmatched pairs. 4579 records in RAM.
INFO 2026-05-28 00:03:03 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 1s. Last read position: chr8:143,860,775
INFO 2026-05-28 00:03:03 MarkDuplicates Tracking 185156 as yet unmatched pairs. 6374 records in RAM.
INFO 2026-05-28 00:03:04 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 1s. Last read position: chr8:143,863,121
INFO 2026-05-28 00:03:04 MarkDuplicates Tracking 186152 as yet unmatched pairs. 7370 records in RAM.
INFO 2026-05-28 00:03:06 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 1s. Last read position: chr8:143,865,678
INFO 2026-05-28 00:03:06 MarkDuplicates Tracking 181364 as yet unmatched pairs. 2582 records in RAM.
INFO 2026-05-28 00:03:08 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 1s. Last read position: chr8:143,927,738
INFO 2026-05-28 00:03:08 MarkDuplicates Tracking 180756 as yet unmatched pairs. 1973 records in RAM.
INFO 2026-05-28 00:03:11 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 2s. Last read position: chr9:15,447,229
INFO 2026-05-28 00:03:11 MarkDuplicates Tracking 178343 as yet unmatched pairs. 10696 records in RAM.
INFO 2026-05-28 00:03:14 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 3s. Last read position: chr9:35,717,629
INFO 2026-05-28 00:03:14 MarkDuplicates Tracking 177092 as yet unmatched pairs. 9443 records in RAM.
INFO 2026-05-28 00:03:17 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:04:10s. Time for last 1,000,000: 2s. Last read position: chr9:92,223,377
INFO 2026-05-28 00:03:17 MarkDuplicates Tracking 175600 as yet unmatched pairs. 7944 records in RAM.
INFO 2026-05-28 00:03:19 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 2s. Last read position: chr9:111,425,743
INFO 2026-05-28 00:03:19 MarkDuplicates Tracking 174058 as yet unmatched pairs. 6399 records in RAM.
INFO 2026-05-28 00:03:23 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 3s. Last read position: chr9:127,449,624
INFO 2026-05-28 00:03:23 MarkDuplicates Tracking 173653 as yet unmatched pairs. 5987 records in RAM.
INFO 2026-05-28 00:03:26 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 3s. Last read position: chr9:130,480,426
INFO 2026-05-28 00:03:26 MarkDuplicates Tracking 171198 as yet unmatched pairs. 3530 records in RAM.
INFO 2026-05-28 00:03:28 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 2s. Last read position: chr9:135,945,084
INFO 2026-05-28 00:03:28 MarkDuplicates Tracking 169561 as yet unmatched pairs. 1892 records in RAM.
INFO 2026-05-28 00:03:30 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 2s. Last read position: chr9:137,614,757
INFO 2026-05-28 00:03:30 MarkDuplicates Tracking 168205 as yet unmatched pairs. 534 records in RAM.
INFO 2026-05-28 00:03:32 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 2s. Last read position: chr10:27,204,482
INFO 2026-05-28 00:03:32 MarkDuplicates Tracking 166516 as yet unmatched pairs. 8451 records in RAM.
INFO 2026-05-28 00:03:35 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 3s. Last read position: chr10:49,107,844
INFO 2026-05-28 00:03:35 MarkDuplicates Tracking 165214 as yet unmatched pairs. 7149 records in RAM.
INFO 2026-05-28 00:03:37 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 2s. Last read position: chr10:76,887,281
INFO 2026-05-28 00:03:37 MarkDuplicates Tracking 163973 as yet unmatched pairs. 5902 records in RAM.
INFO 2026-05-28 00:03:40 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 2s. Last read position: chr10:79,349,680
INFO 2026-05-28 00:03:40 MarkDuplicates Tracking 163866 as yet unmatched pairs. 5792 records in RAM.
INFO 2026-05-28 00:03:44 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 3s. Last read position: chr10:91,820,009
INFO 2026-05-28 00:03:44 MarkDuplicates Tracking 161089 as yet unmatched pairs. 3010 records in RAM.
INFO 2026-05-28 00:03:46 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 2s. Last read position: chr10:104,034,243
INFO 2026-05-28 00:03:46 MarkDuplicates Tracking 159709 as yet unmatched pairs. 1627 records in RAM.
INFO 2026-05-28 00:03:49 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 2s. Last read position: chr10:133,292,562
INFO 2026-05-28 00:03:49 MarkDuplicates Tracking 158319 as yet unmatched pairs. 236 records in RAM.
INFO 2026-05-28 00:03:52 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 3s. Last read position: chr11:1,083,704
INFO 2026-05-28 00:03:52 MarkDuplicates Tracking 156625 as yet unmatched pairs. 18055 records in RAM.
INFO 2026-05-28 00:03:55 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 3s. Last read position: chr11:7,994,428
INFO 2026-05-28 00:03:55 MarkDuplicates Tracking 155085 as yet unmatched pairs. 16512 records in RAM.
INFO 2026-05-28 00:03:59 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 3s. Last read position: chr11:33,339,350
INFO 2026-05-28 00:03:59 MarkDuplicates Tracking 153747 as yet unmatched pairs. 15174 records in RAM.
INFO 2026-05-28 00:04:02 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 3s. Last read position: chr11:57,302,570
INFO 2026-05-28 00:04:02 MarkDuplicates Tracking 152369 as yet unmatched pairs. 13796 records in RAM.
INFO 2026-05-28 00:04:06 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 3s. Last read position: chr11:62,519,244
INFO 2026-05-28 00:04:06 MarkDuplicates Tracking 150971 as yet unmatched pairs. 12394 records in RAM.
INFO 2026-05-28 00:04:09 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 3s. Last read position: chr11:62,671,835
INFO 2026-05-28 00:04:09 MarkDuplicates Tracking 149485 as yet unmatched pairs. 10904 records in RAM.
INFO 2026-05-28 00:04:11 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 2s. Last read position: chr11:65,120,698
INFO 2026-05-28 00:04:11 MarkDuplicates Tracking 148707 as yet unmatched pairs. 10126 records in RAM.
INFO 2026-05-28 00:04:14 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 2s. Last read position: chr11:66,070,520
INFO 2026-05-28 00:04:14 MarkDuplicates Tracking 145980 as yet unmatched pairs. 7399 records in RAM.
INFO 2026-05-28 00:04:16 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 2s. Last read position: chr11:68,438,512
INFO 2026-05-28 00:04:16 MarkDuplicates Tracking 144229 as yet unmatched pairs. 5648 records in RAM.
INFO 2026-05-28 00:04:19 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 2s. Last read position: chr11:75,441,698
INFO 2026-05-28 00:04:19 MarkDuplicates Tracking 142664 as yet unmatched pairs. 4082 records in RAM.
INFO 2026-05-28 00:04:22 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 3s. Last read position: chr11:108,304,785
INFO 2026-05-28 00:04:22 MarkDuplicates Tracking 141247 as yet unmatched pairs. 2664 records in RAM.
INFO 2026-05-28 00:04:25 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 3s. Last read position: chr11:119,311,607
INFO 2026-05-28 00:04:25 MarkDuplicates Tracking 140067 as yet unmatched pairs. 1484 records in RAM.
INFO 2026-05-28 00:04:29 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 3s. Last read position: chr12:878,259
INFO 2026-05-28 00:04:29 MarkDuplicates Tracking 138635 as yet unmatched pairs. 14541 records in RAM.
INFO 2026-05-28 00:04:32 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 2s. Last read position: chr12:7,081,177
INFO 2026-05-28 00:04:32 MarkDuplicates Tracking 137061 as yet unmatched pairs. 12960 records in RAM.
INFO 2026-05-28 00:04:34 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 2s. Last read position: chr12:32,755,396
INFO 2026-05-28 00:04:34 MarkDuplicates Tracking 135654 as yet unmatched pairs. 11551 records in RAM.
INFO 2026-05-28 00:04:38 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 4s. Last read position: chr12:49,758,229
INFO 2026-05-28 00:04:38 MarkDuplicates Tracking 135480 as yet unmatched pairs. 11376 records in RAM.
INFO 2026-05-28 00:04:40 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 2s. Last read position: chr12:53,441,782
INFO 2026-05-28 00:04:40 MarkDuplicates Tracking 133158 as yet unmatched pairs. 9045 records in RAM.
INFO 2026-05-28 00:04:43 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 2s. Last read position: chr12:56,286,462
INFO 2026-05-28 00:04:43 MarkDuplicates Tracking 131872 as yet unmatched pairs. 7756 records in RAM.
INFO 2026-05-28 00:04:45 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 2s. Last read position: chr12:57,210,047
INFO 2026-05-28 00:04:45 MarkDuplicates Tracking 130552 as yet unmatched pairs. 6435 records in RAM.
INFO 2026-05-28 00:04:48 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 2s. Last read position: chr12:76,487,518
INFO 2026-05-28 00:04:48 MarkDuplicates Tracking 128993 as yet unmatched pairs. 4876 records in RAM.
INFO 2026-05-28 00:04:51 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 2s. Last read position: chr12:108,592,040
INFO 2026-05-28 00:04:51 MarkDuplicates Tracking 127795 as yet unmatched pairs. 3678 records in RAM.
INFO 2026-05-28 00:04:54 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 3s. Last read position: chr12:120,184,182
INFO 2026-05-28 00:04:54 MarkDuplicates Tracking 126280 as yet unmatched pairs. 2152 records in RAM.
INFO 2026-05-28 00:04:58 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 3s. Last read position: chr12:124,960,390
INFO 2026-05-28 00:04:58 MarkDuplicates Tracking 124789 as yet unmatched pairs. 661 records in RAM.
INFO 2026-05-28 00:05:01 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 3s. Last read position: chr13:31,161,445
INFO 2026-05-28 00:05:01 MarkDuplicates Tracking 123336 as yet unmatched pairs. 4052 records in RAM.
INFO 2026-05-28 00:05:04 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 3s. Last read position: chr13:73,062,686
INFO 2026-05-28 00:05:04 MarkDuplicates Tracking 122439 as yet unmatched pairs. 3154 records in RAM.
INFO 2026-05-28 00:05:08 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:06:01s. Time for last 1,000,000: 3s. Last read position: chr13:110,307,891
INFO 2026-05-28 00:05:08 MarkDuplicates Tracking 120871 as yet unmatched pairs. 1586 records in RAM.
INFO 2026-05-28 00:05:11 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 3s. Last read position: chr14:22,575,175
INFO 2026-05-28 00:05:11 MarkDuplicates Tracking 119138 as yet unmatched pairs. 9322 records in RAM.
INFO 2026-05-28 00:05:14 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 2s. Last read position: chr14:31,599,324
INFO 2026-05-28 00:05:14 MarkDuplicates Tracking 117190 as yet unmatched pairs. 7374 records in RAM.
INFO 2026-05-28 00:05:16 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:06:09s. Time for last 1,000,000: 2s. Last read position: chr14:59,331,377
INFO 2026-05-28 00:05:16 MarkDuplicates Tracking 115820 as yet unmatched pairs. 6002 records in RAM.
INFO 2026-05-28 00:05:19 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 2s. Last read position: chr14:74,296,413
INFO 2026-05-28 00:05:19 MarkDuplicates Tracking 114451 as yet unmatched pairs. 4632 records in RAM.
INFO 2026-05-28 00:05:21 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 2s. Last read position: chr14:95,103,388
INFO 2026-05-28 00:05:21 MarkDuplicates Tracking 113079 as yet unmatched pairs. 3260 records in RAM.
INFO 2026-05-28 00:05:24 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 2s. Last read position: chr14:104,773,341
INFO 2026-05-28 00:05:24 MarkDuplicates Tracking 111652 as yet unmatched pairs. 1832 records in RAM.
INFO 2026-05-28 00:05:26 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 2s. Last read position: chr14:105,643,185
INFO 2026-05-28 00:05:26 MarkDuplicates Tracking 110436 as yet unmatched pairs. 616 records in RAM.
INFO 2026-05-28 00:05:30 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 3s. Last read position: chr15:34,363,660
INFO 2026-05-28 00:05:30 MarkDuplicates Tracking 109430 as yet unmatched pairs. 9226 records in RAM.
INFO 2026-05-28 00:05:32 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 2s. Last read position: chr15:43,523,276
INFO 2026-05-28 00:05:32 MarkDuplicates Tracking 107502 as yet unmatched pairs. 7296 records in RAM.
INFO 2026-05-28 00:05:35 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 2s. Last read position: chr15:52,135,691
INFO 2026-05-28 00:05:35 MarkDuplicates Tracking 106184 as yet unmatched pairs. 5976 records in RAM.
INFO 2026-05-28 00:05:38 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:06:31s. Time for last 1,000,000: 2s. Last read position: chr15:65,650,840
INFO 2026-05-28 00:05:38 MarkDuplicates Tracking 104787 as yet unmatched pairs. 4577 records in RAM.
INFO 2026-05-28 00:05:41 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:06:34s. Time for last 1,000,000: 3s. Last read position: chr15:74,802,478
INFO 2026-05-28 00:05:41 MarkDuplicates Tracking 103395 as yet unmatched pairs. 3185 records in RAM.
INFO 2026-05-28 00:05:44 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 3s. Last read position: chr15:86,079,907
INFO 2026-05-28 00:05:44 MarkDuplicates Tracking 101804 as yet unmatched pairs. 1592 records in RAM.
INFO 2026-05-28 00:05:47 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 3s. Last read position: chr15:101,272,806
INFO 2026-05-28 00:05:47 MarkDuplicates Tracking 100364 as yet unmatched pairs. 151 records in RAM.
INFO 2026-05-28 00:05:51 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:06:44s. Time for last 1,000,000: 3s. Last read position: chr16:1,777,192
INFO 2026-05-28 00:05:51 MarkDuplicates Tracking 98879 as yet unmatched pairs. 15902 records in RAM.
INFO 2026-05-28 00:05:54 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:06:47s. Time for last 1,000,000: 2s. Last read position: chr16:3,021,644
INFO 2026-05-28 00:05:54 MarkDuplicates Tracking 97045 as yet unmatched pairs. 14068 records in RAM.
INFO 2026-05-28 00:05:57 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 2s. Last read position: chr16:14,875,412
INFO 2026-05-28 00:05:57 MarkDuplicates Tracking 95280 as yet unmatched pairs. 12303 records in RAM.
INFO 2026-05-28 00:06:00 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 3s. Last read position: chr16:16,310,456
INFO 2026-05-28 00:06:00 MarkDuplicates Tracking 93997 as yet unmatched pairs. 11020 records in RAM.
INFO 2026-05-28 00:06:03 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 3s. Last read position: chr16:21,456,322
INFO 2026-05-28 00:06:03 MarkDuplicates Tracking 93257 as yet unmatched pairs. 10280 records in RAM.
INFO 2026-05-28 00:06:05 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 2s. Last read position: chr16:28,829,958
INFO 2026-05-28 00:06:05 MarkDuplicates Tracking 92510 as yet unmatched pairs. 9531 records in RAM.
INFO 2026-05-28 00:06:07 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:07:00s. Time for last 1,000,000: 2s. Last read position: chr16:30,111,412
INFO 2026-05-28 00:06:07 MarkDuplicates Tracking 91096 as yet unmatched pairs. 8117 records in RAM.
INFO 2026-05-28 00:06:09 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 2s. Last read position: chr16:31,490,537
INFO 2026-05-28 00:06:09 MarkDuplicates Tracking 89654 as yet unmatched pairs. 6675 records in RAM.
INFO 2026-05-28 00:06:12 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 3s. Last read position: chr16:58,582,848
INFO 2026-05-28 00:06:12 MarkDuplicates Tracking 88309 as yet unmatched pairs. 5330 records in RAM.
INFO 2026-05-28 00:06:15 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 3s. Last read position: chr16:69,647,229
INFO 2026-05-28 00:06:15 MarkDuplicates Tracking 86737 as yet unmatched pairs. 3757 records in RAM.
INFO 2026-05-28 00:06:19 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:07:12s. Time for last 1,000,000: 3s. Last read position: chr16:84,657,566
INFO 2026-05-28 00:06:19 MarkDuplicates Tracking 85248 as yet unmatched pairs. 2267 records in RAM.
INFO 2026-05-28 00:06:22 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:07:15s. Time for last 1,000,000: 3s. Last read position: chr16:89,575,869
INFO 2026-05-28 00:06:22 MarkDuplicates Tracking 83447 as yet unmatched pairs. 464 records in RAM.
INFO 2026-05-28 00:06:24 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:07:17s. Time for last 1,000,000: 2s. Last read position: chr17:4,558,077
INFO 2026-05-28 00:06:24 MarkDuplicates Tracking 81932 as yet unmatched pairs. 25233 records in RAM.
INFO 2026-05-28 00:06:28 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:07:21s. Time for last 1,000,000: 3s. Last read position: chr17:7,900,569
INFO 2026-05-28 00:06:28 MarkDuplicates Tracking 80240 as yet unmatched pairs. 23541 records in RAM.
INFO 2026-05-28 00:06:30 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:07:23s. Time for last 1,000,000: 2s. Last read position: chr17:21,011,259
INFO 2026-05-28 00:06:30 MarkDuplicates Tracking 78872 as yet unmatched pairs. 22173 records in RAM.
INFO 2026-05-28 00:06:33 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:07:26s. Time for last 1,000,000: 2s. Last read position: chr17:38,510,683
INFO 2026-05-28 00:06:33 MarkDuplicates Tracking 77481 as yet unmatched pairs. 20782 records in RAM.
INFO 2026-05-28 00:06:35 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:07:28s. Time for last 1,000,000: 2s. Last read position: chr17:41,764,971
INFO 2026-05-28 00:06:35 MarkDuplicates Tracking 76174 as yet unmatched pairs. 19475 records in RAM.
INFO 2026-05-28 00:06:38 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:07:31s. Time for last 1,000,000: 2s. Last read position: chr17:45,404,960
INFO 2026-05-28 00:06:38 MarkDuplicates Tracking 74530 as yet unmatched pairs. 17831 records in RAM.
INFO 2026-05-28 00:06:40 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:07:33s. Time for last 1,000,000: 2s. Last read position: chr17:50,186,745
INFO 2026-05-28 00:06:40 MarkDuplicates Tracking 79034 as yet unmatched pairs. 22333 records in RAM.
INFO 2026-05-28 00:06:44 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:07:37s. Time for last 1,000,000: 3s. Last read position: chr17:50,188,617
INFO 2026-05-28 00:06:44 MarkDuplicates Tracking 90071 as yet unmatched pairs. 33369 records in RAM.
INFO 2026-05-28 00:06:47 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:07:39s. Time for last 1,000,000: 2s. Last read position: chr17:50,190,005
INFO 2026-05-28 00:06:47 MarkDuplicates Tracking 88443 as yet unmatched pairs. 31741 records in RAM.
INFO 2026-05-28 00:06:50 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:07:43s. Time for last 1,000,000: 3s. Last read position: chr17:50,192,485
INFO 2026-05-28 00:06:50 MarkDuplicates Tracking 89293 as yet unmatched pairs. 32591 records in RAM.
INFO 2026-05-28 00:06:53 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:07:46s. Time for last 1,000,000: 3s. Last read position: chr17:50,194,396
INFO 2026-05-28 00:06:53 MarkDuplicates Tracking 90256 as yet unmatched pairs. 33554 records in RAM.
INFO 2026-05-28 00:06:56 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:07:49s. Time for last 1,000,000: 3s. Last read position: chr17:50,195,947
INFO 2026-05-28 00:06:56 MarkDuplicates Tracking 84195 as yet unmatched pairs. 27493 records in RAM.
INFO 2026-05-28 00:07:00 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:07:53s. Time for last 1,000,000: 3s. Last read position: chr17:50,198,167
INFO 2026-05-28 00:07:00 MarkDuplicates Tracking 74739 as yet unmatched pairs. 18037 records in RAM.
INFO 2026-05-28 00:07:03 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:07:56s. Time for last 1,000,000: 2s. Last read position: chr17:58,007,027
INFO 2026-05-28 00:07:03 MarkDuplicates Tracking 62027 as yet unmatched pairs. 5325 records in RAM.
INFO 2026-05-28 00:07:06 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:07:59s. Time for last 1,000,000: 3s. Last read position: chr17:73,286,094
INFO 2026-05-28 00:07:06 MarkDuplicates Tracking 60689 as yet unmatched pairs. 3987 records in RAM.
INFO 2026-05-28 00:07:09 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:08:02s. Time for last 1,000,000: 3s. Last read position: chr17:78,855,519
INFO 2026-05-28 00:07:09 MarkDuplicates Tracking 58793 as yet unmatched pairs. 2090 records in RAM.
INFO 2026-05-28 00:07:12 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:08:05s. Time for last 1,000,000: 3s. Last read position: chr17:82,087,062
INFO 2026-05-28 00:07:12 MarkDuplicates Tracking 57218 as yet unmatched pairs. 510 records in RAM.
INFO 2026-05-28 00:07:16 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:08:09s. Time for last 1,000,000: 3s. Last read position: chr18:41,955,279
INFO 2026-05-28 00:07:16 MarkDuplicates Tracking 55657 as yet unmatched pairs. 993 records in RAM.
INFO 2026-05-28 00:07:20 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:08:13s. Time for last 1,000,000: 4s. Last read position: chr19:804,332
INFO 2026-05-28 00:07:20 MarkDuplicates Tracking 54387 as yet unmatched pairs. 24637 records in RAM.
INFO 2026-05-28 00:07:24 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:08:17s. Time for last 1,000,000: 3s. Last read position: chr19:2,477,195
INFO 2026-05-28 00:07:24 MarkDuplicates Tracking 52389 as yet unmatched pairs. 22639 records in RAM.
INFO 2026-05-28 00:07:28 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 3s. Last read position: chr19:6,684,812
INFO 2026-05-28 00:07:28 MarkDuplicates Tracking 50933 as yet unmatched pairs. 21183 records in RAM.
INFO 2026-05-28 00:07:31 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:08:24s. Time for last 1,000,000: 3s. Last read position: chr19:10,783,076
INFO 2026-05-28 00:07:31 MarkDuplicates Tracking 48952 as yet unmatched pairs. 19202 records in RAM.
INFO 2026-05-28 00:07:35 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:08:28s. Time for last 1,000,000: 3s. Last read position: chr19:14,388,443
INFO 2026-05-28 00:07:35 MarkDuplicates Tracking 47627 as yet unmatched pairs. 17877 records in RAM.
INFO 2026-05-28 00:07:39 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 4s. Last read position: chr19:17,727,892
INFO 2026-05-28 00:07:39 MarkDuplicates Tracking 45539 as yet unmatched pairs. 15789 records in RAM.
INFO 2026-05-28 00:07:43 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 3s. Last read position: chr19:34,352,666
INFO 2026-05-28 00:07:43 MarkDuplicates Tracking 43923 as yet unmatched pairs. 14172 records in RAM.
INFO 2026-05-28 00:07:46 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:08:39s. Time for last 1,000,000: 3s. Last read position: chr19:38,383,276
INFO 2026-05-28 00:07:46 MarkDuplicates Tracking 42297 as yet unmatched pairs. 12545 records in RAM.
INFO 2026-05-28 00:07:49 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:08:42s. Time for last 1,000,000: 2s. Last read position: chr19:40,192,626
INFO 2026-05-28 00:07:49 MarkDuplicates Tracking 40781 as yet unmatched pairs. 11029 records in RAM.
INFO 2026-05-28 00:07:51 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:08:44s. Time for last 1,000,000: 2s. Last read position: chr19:41,715,690
INFO 2026-05-28 00:07:51 MarkDuplicates Tracking 42710 as yet unmatched pairs. 12958 records in RAM.
INFO 2026-05-28 00:07:54 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:08:47s. Time for last 1,000,000: 2s. Last read position: chr19:42,287,824
INFO 2026-05-28 00:07:54 MarkDuplicates Tracking 38364 as yet unmatched pairs. 8610 records in RAM.
INFO 2026-05-28 00:07:57 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 2s. Last read position: chr19:45,711,688
INFO 2026-05-28 00:07:57 MarkDuplicates Tracking 36362 as yet unmatched pairs. 6607 records in RAM.
INFO 2026-05-28 00:08:00 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:08:53s. Time for last 1,000,000: 3s. Last read position: chr19:48,873,395
INFO 2026-05-28 00:08:00 MarkDuplicates Tracking 34783 as yet unmatched pairs. 5028 records in RAM.
INFO 2026-05-28 00:08:03 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:08:56s. Time for last 1,000,000: 3s. Last read position: chr19:50,210,598
INFO 2026-05-28 00:08:03 MarkDuplicates Tracking 33723 as yet unmatched pairs. 3968 records in RAM.
INFO 2026-05-28 00:08:07 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:09:00s. Time for last 1,000,000: 3s. Last read position: chr19:55,236,749
INFO 2026-05-28 00:08:07 MarkDuplicates Tracking 31262 as yet unmatched pairs. 1507 records in RAM.
INFO 2026-05-28 00:08:10 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:09:03s. Time for last 1,000,000: 3s. Last read position: chr20:3,209,555
INFO 2026-05-28 00:08:10 MarkDuplicates Tracking 29471 as yet unmatched pairs. 8543 records in RAM.
INFO 2026-05-28 00:08:13 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:09:06s. Time for last 1,000,000: 2s. Last read position: chr20:31,792,807
INFO 2026-05-28 00:08:13 MarkDuplicates Tracking 28017 as yet unmatched pairs. 7089 records in RAM.
INFO 2026-05-28 00:08:16 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:09:09s. Time for last 1,000,000: 3s. Last read position: chr20:37,179,354
INFO 2026-05-28 00:08:16 MarkDuplicates Tracking 26865 as yet unmatched pairs. 5937 records in RAM.
INFO 2026-05-28 00:08:20 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:09:13s. Time for last 1,000,000: 3s. Last read position: chr20:45,899,832
INFO 2026-05-28 00:08:20 MarkDuplicates Tracking 25496 as yet unmatched pairs. 4568 records in RAM.
INFO 2026-05-28 00:08:24 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:09:17s. Time for last 1,000,000: 3s. Last read position: chr20:58,891,804
INFO 2026-05-28 00:08:24 MarkDuplicates Tracking 24825 as yet unmatched pairs. 3897 records in RAM.
INFO 2026-05-28 00:08:27 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 3s. Last read position: chr20:63,521,562
INFO 2026-05-28 00:08:27 MarkDuplicates Tracking 23859 as yet unmatched pairs. 2931 records in RAM.
INFO 2026-05-28 00:08:30 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 2s. Last read position: chr21:8,443,199
INFO 2026-05-28 00:08:30 MarkDuplicates Tracking 20796 as yet unmatched pairs. 3899 records in RAM.
INFO 2026-05-28 00:08:32 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 2s. Last read position: chr21:41,168,565
INFO 2026-05-28 00:08:32 MarkDuplicates Tracking 19129 as yet unmatched pairs. 2232 records in RAM.
INFO 2026-05-28 00:08:34 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:09:27s. Time for last 1,000,000: 2s. Last read position: chr21:46,118,612
INFO 2026-05-28 00:08:34 MarkDuplicates Tracking 17576 as yet unmatched pairs. 679 records in RAM.
INFO 2026-05-28 00:08:37 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:09:30s. Time for last 1,000,000: 2s. Last read position: chr22:23,800,986
INFO 2026-05-28 00:08:37 MarkDuplicates Tracking 15571 as yet unmatched pairs. 5476 records in RAM.
INFO 2026-05-28 00:08:40 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:09:33s. Time for last 1,000,000: 3s. Last read position: chr22:36,285,132
INFO 2026-05-28 00:08:40 MarkDuplicates Tracking 14350 as yet unmatched pairs. 4255 records in RAM.
INFO 2026-05-28 00:08:44 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 3s. Last read position: chr22:39,875,543
INFO 2026-05-28 00:08:44 MarkDuplicates Tracking 12392 as yet unmatched pairs. 2297 records in RAM.
INFO 2026-05-28 00:08:47 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:09:40s. Time for last 1,000,000: 3s. Last read position: chr22:50,287,129
INFO 2026-05-28 00:08:47 MarkDuplicates Tracking 11298 as yet unmatched pairs. 1203 records in RAM.
INFO 2026-05-28 00:08:50 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:09:43s. Time for last 1,000,000: 2s. Last read position: chrX:23,682,474
INFO 2026-05-28 00:08:50 MarkDuplicates Tracking 9193 as yet unmatched pairs. 7587 records in RAM.
INFO 2026-05-28 00:08:52 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:09:45s. Time for last 1,000,000: 2s. Last read position: chrX:48,934,856
INFO 2026-05-28 00:08:52 MarkDuplicates Tracking 7880 as yet unmatched pairs. 6274 records in RAM.
INFO 2026-05-28 00:08:54 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:09:47s. Time for last 1,000,000: 2s. Last read position: chrX:71,224,079
INFO 2026-05-28 00:08:54 MarkDuplicates Tracking 6438 as yet unmatched pairs. 4832 records in RAM.
INFO 2026-05-28 00:08:57 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:09:50s. Time for last 1,000,000: 2s. Last read position: chrX:119,452,050
INFO 2026-05-28 00:08:57 MarkDuplicates Tracking 5119 as yet unmatched pairs. 3513 records in RAM.
INFO 2026-05-28 00:09:00 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:09:53s. Time for last 1,000,000: 3s. Last read position: chrX:153,952,888
INFO 2026-05-28 00:09:00 MarkDuplicates Tracking 3999 as yet unmatched pairs. 2393 records in RAM.
INFO 2026-05-28 00:09:02 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:09:55s. Time for last 1,000,000: 2s. Last read position: chrX:154,367,964
INFO 2026-05-28 00:09:02 MarkDuplicates Tracking 4248 as yet unmatched pairs. 2642 records in RAM.
INFO 2026-05-28 00:09:04 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:09:57s. Time for last 1,000,000: 1s. Last read position: KI270733.1:131,104
INFO 2026-05-28 00:09:04 MarkDuplicates Tracking 474 as yet unmatched pairs. 470 records in RAM.
INFO 2026-05-28 00:09:05 MarkDuplicates Read 212377412 records. 0 pairs never matched.
INFO 2026-05-28 00:09:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 32799235192; totalMemory: 57747177472; maxMemory: 63585648640
INFO 2026-05-28 00:09:13 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-05-28 00:09:14 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-05-28 00:09:49 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-05-28 00:10:06 MarkDuplicates Sorting list of duplicate records.
INFO 2026-05-28 00:10:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300845096; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-05-28 00:10:11 MarkDuplicates Marking 106226050 records as duplicates.
INFO 2026-05-28 00:10:11 MarkDuplicates Found 6296283 optical duplicate clusters.
INFO 2026-05-28 00:10:11 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-05-28 00:10:39 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:27s. Time for last 10,000,000: 27s. Last read position: chr1:119,997,144
INFO 2026-05-28 00:11:00 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:48s. Time for last 10,000,000: 20s. Last read position: chr2:26,776,407
INFO 2026-05-28 00:11:19 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:07s. Time for last 10,000,000: 18s. Last read position: chr2:188,999,476
INFO 2026-05-28 00:11:37 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:25s. Time for last 10,000,000: 17s. Last read position: chr3:49,096,063
INFO 2026-05-28 00:11:54 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:43s. Time for last 10,000,000: 17s. Last read position: chr4:76,741,644
INFO 2026-05-28 00:12:11 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:00s. Time for last 10,000,000: 16s. Last read position: chr6:7,230,004
INFO 2026-05-28 00:12:29 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:17s. Time for last 10,000,000: 17s. Last read position: chr6:169,248,919
INFO 2026-05-28 00:12:45 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:34s. Time for last 10,000,000: 16s. Last read position: chr7:107,203,461
INFO 2026-05-28 00:13:02 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:50s. Time for last 10,000,000: 16s. Last read position: chr8:143,863,121
INFO 2026-05-28 00:13:20 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:03:08s. Time for last 10,000,000: 17s. Last read position: chr9:137,614,757
INFO 2026-05-28 00:13:41 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:03:29s. Time for last 10,000,000: 20s. Last read position: chr11:33,339,350
INFO 2026-05-28 00:14:02 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:50s. Time for last 10,000,000: 21s. Last read position: chr12:878,259
INFO 2026-05-28 00:14:21 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:04:09s. Time for last 10,000,000: 18s. Last read position: chr12:124,960,390
INFO 2026-05-28 00:14:40 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:04:28s. Time for last 10,000,000: 18s. Last read position: chr14:105,643,185
INFO 2026-05-28 00:14:57 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:04:46s. Time for last 10,000,000: 17s. Last read position: chr16:14,875,412
INFO 2026-05-28 00:15:15 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:05:03s. Time for last 10,000,000: 17s. Last read position: chr17:4,558,077
INFO 2026-05-28 00:15:32 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:05:20s. Time for last 10,000,000: 17s. Last read position: chr17:50,194,396
INFO 2026-05-28 00:15:51 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:05:39s. Time for last 10,000,000: 18s. Last read position: chr19:6,684,812
INFO 2026-05-28 00:16:09 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:05:57s. Time for last 10,000,000: 18s. Last read position: chr19:48,873,395
INFO 2026-05-28 00:16:27 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:06:15s. Time for last 10,000,000: 17s. Last read position: chr21:41,168,565
INFO 2026-05-28 00:16:44 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:06:33s. Time for last 10,000,000: 17s. Last read position: chrX:153,952,888
INFO 2026-05-28 00:16:52 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-05-28 00:16:52 MarkDuplicates Duplicate Index cleanup.
INFO 2026-05-28 00:16:52 MarkDuplicates Getting Memory Stats.
INFO 2026-05-28 00:16:52 MarkDuplicates Before output close freeMemory: 201501456; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-05-28 00:16:52 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-05-28 00:16:52 MarkDuplicates After output close freeMemory: 104314240; totalMemory: 134217728; maxMemory: 63585648640
[Thu May 28 00:16:52 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 17.79 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory