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/1e/1fa9c0d6df1b042f69b9ef839ad0b9/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/1fa9c0d6df1b042f69b9ef839ad0b9/.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/0e/470633ec6875aa44e851b44cd7b6c7/tih_rna_sample_00104_23H5VFLT4_s20.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 tih_rna_sample_00104_23H5VFLT4_s20.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00104_23H5VFLT4_s20.md.bam --METRICS_FILE tih_rna_sample_00104_23H5VFLT4_s20.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:59:22.030 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 07:59:22 GMT 2026] MarkDuplicates --INPUT tih_rna_sample_00104_23H5VFLT4_s20.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00104_23H5VFLT4_s20.md.bam --METRICS_FILE tih_rna_sample_00104_23H5VFLT4_s20.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 07:59:22 GMT 2026] Executing as ?@nf-1e1fa9c0d6df1b042f69b9ef839ad0b9-8a3b3-mhq4p 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 07:59:22 MarkDuplicates Start of doWork freeMemory: 105828320; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:59:22 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:59:22 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:59:28 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:1,308,709
INFO 2026-06-08 07:59:28 MarkDuplicates Tracking 781 as yet unmatched pairs. 10 records in RAM.
INFO 2026-06-08 07:59:31 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 3s. Last read position: chr1:1,959,923
INFO 2026-06-08 07:59:31 MarkDuplicates Tracking 1533 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 07:59:35 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 3s. Last read position: chr1:6,451,823
INFO 2026-06-08 07:59:35 MarkDuplicates Tracking 2655 as yet unmatched pairs. 103 records in RAM.
INFO 2026-06-08 07:59:39 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 4s. Last read position: chr1:8,867,118
INFO 2026-06-08 07:59:39 MarkDuplicates Tracking 3456 as yet unmatched pairs. 83 records in RAM.
INFO 2026-06-08 07:59:42 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 2s. Last read position: chr1:11,998,795
INFO 2026-06-08 07:59:42 MarkDuplicates Tracking 4254 as yet unmatched pairs. 108 records in RAM.
INFO 2026-06-08 07:59:44 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 2s. Last read position: chr1:16,148,797
INFO 2026-06-08 07:59:44 MarkDuplicates Tracking 4917 as yet unmatched pairs. 70 records in RAM.
INFO 2026-06-08 07:59:48 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 3s. Last read position: chr1:17,687,684
INFO 2026-06-08 07:59:48 MarkDuplicates Tracking 5809 as yet unmatched pairs. 234 records in RAM.
INFO 2026-06-08 07:59:51 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 3s. Last read position: chr1:21,854,699
INFO 2026-06-08 07:59:51 MarkDuplicates Tracking 6475 as yet unmatched pairs. 65 records in RAM.
INFO 2026-06-08 07:59:54 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 3s. Last read position: chr1:24,902,252
INFO 2026-06-08 07:59:54 MarkDuplicates Tracking 7205 as yet unmatched pairs. 4 records in RAM.
INFO 2026-06-08 07:59:57 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 2s. Last read position: chr1:28,529,866
INFO 2026-06-08 07:59:57 MarkDuplicates Tracking 8052 as yet unmatched pairs. 125 records in RAM.
INFO 2026-06-08 08:00:00 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 3s. Last read position: chr1:32,741,996
INFO 2026-06-08 08:00:00 MarkDuplicates Tracking 8853 as yet unmatched pairs. 165 records in RAM.
INFO 2026-06-08 08:00:03 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 2s. Last read position: chr1:37,483,283
INFO 2026-06-08 08:00:03 MarkDuplicates Tracking 9791 as yet unmatched pairs. 226 records in RAM.
INFO 2026-06-08 08:00:05 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 2s. Last read position: chr1:42,746,779
INFO 2026-06-08 08:00:05 MarkDuplicates Tracking 10422 as yet unmatched pairs. 39 records in RAM.
INFO 2026-06-08 08:00:08 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 2s. Last read position: chr1:46,303,749
INFO 2026-06-08 08:00:08 MarkDuplicates Tracking 11377 as yet unmatched pairs. 278 records in RAM.
INFO 2026-06-08 08:00:11 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 2s. Last read position: chr1:60,865,446
INFO 2026-06-08 08:00:11 MarkDuplicates Tracking 11856 as yet unmatched pairs. 24 records in RAM.
INFO 2026-06-08 08:00:14 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 2s. Last read position: chr1:86,734,604
INFO 2026-06-08 08:00:14 MarkDuplicates Tracking 12577 as yet unmatched pairs. 156 records in RAM.
INFO 2026-06-08 08:00:16 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 2s. Last read position: chr1:100,896,249
INFO 2026-06-08 08:00:16 MarkDuplicates Tracking 13112 as yet unmatched pairs. 28 records in RAM.
INFO 2026-06-08 08:00:18 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 1s. Last read position: chr1:110,341,445
INFO 2026-06-08 08:00:18 MarkDuplicates Tracking 13956 as yet unmatched pairs. 95 records in RAM.
INFO 2026-06-08 08:00:21 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 3s. Last read position: chr1:116,389,484
INFO 2026-06-08 08:00:21 MarkDuplicates Tracking 14790 as yet unmatched pairs. 256 records in RAM.
INFO 2026-06-08 08:00:25 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 3s. Last read position: chr1:120,912,275
INFO 2026-06-08 08:00:25 MarkDuplicates Tracking 15089 as yet unmatched pairs. 3 records in RAM.
INFO 2026-06-08 08:00:28 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 3s. Last read position: chr1:148,038,784
INFO 2026-06-08 08:00:28 MarkDuplicates Tracking 15454 as yet unmatched pairs. 5 records in RAM.
INFO 2026-06-08 08:00:30 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 2s. Last read position: chr1:149,923,601
INFO 2026-06-08 08:00:30 MarkDuplicates Tracking 15963 as yet unmatched pairs. 93 records in RAM.
INFO 2026-06-08 08:00:33 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 2s. Last read position: chr1:151,287,861
INFO 2026-06-08 08:00:33 MarkDuplicates Tracking 16582 as yet unmatched pairs. 35 records in RAM.
INFO 2026-06-08 08:00:36 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 2s. Last read position: chr1:152,306,694
INFO 2026-06-08 08:00:36 MarkDuplicates Tracking 17328 as yet unmatched pairs. 23 records in RAM.
INFO 2026-06-08 08:00:38 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 2s. Last read position: chr1:154,588,165
INFO 2026-06-08 08:00:38 MarkDuplicates Tracking 18085 as yet unmatched pairs. 80 records in RAM.
INFO 2026-06-08 08:00:41 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 2s. Last read position: chr1:155,618,944
INFO 2026-06-08 08:00:41 MarkDuplicates Tracking 18767 as yet unmatched pairs. 4 records in RAM.
INFO 2026-06-08 08:00:43 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 2s. Last read position: chr1:156,468,004
INFO 2026-06-08 08:00:43 MarkDuplicates Tracking 19859 as yet unmatched pairs. 198 records in RAM.
INFO 2026-06-08 08:00:45 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 1s. Last read position: chr1:160,996,290
INFO 2026-06-08 08:00:45 MarkDuplicates Tracking 20421 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 08:00:48 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 3s. Last read position: chr1:169,121,034
INFO 2026-06-08 08:00:48 MarkDuplicates Tracking 22225 as yet unmatched pairs. 1039 records in RAM.
INFO 2026-06-08 08:00:51 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 2s. Last read position: chr1:180,094,139
INFO 2026-06-08 08:00:51 MarkDuplicates Tracking 21824 as yet unmatched pairs. 19 records in RAM.
INFO 2026-06-08 08:00:54 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 3s. Last read position: chr1:195,178,284
INFO 2026-06-08 08:00:54 MarkDuplicates Tracking 22608 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 08:00:57 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 2s. Last read position: chr1:202,013,140
INFO 2026-06-08 08:00:57 MarkDuplicates Tracking 23561 as yet unmatched pairs. 256 records in RAM.
INFO 2026-06-08 08:01:00 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 3s. Last read position: chr1:204,981,856
INFO 2026-06-08 08:01:00 MarkDuplicates Tracking 24031 as yet unmatched pairs. 48 records in RAM.
INFO 2026-06-08 08:01:03 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 3s. Last read position: chr1:209,623,629
INFO 2026-06-08 08:01:03 MarkDuplicates Tracking 24835 as yet unmatched pairs. 117 records in RAM.
INFO 2026-06-08 08:01:05 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 2s. Last read position: chr1:224,153,207
INFO 2026-06-08 08:01:05 MarkDuplicates Tracking 25422 as yet unmatched pairs. 41 records in RAM.
INFO 2026-06-08 08:01:07 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 1s. Last read position: chr1:228,293,503
INFO 2026-06-08 08:01:07 MarkDuplicates Tracking 26222 as yet unmatched pairs. 0 records in RAM.
INFO 2026-06-08 08:01:09 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 1s. Last read position: chr1:234,609,130
INFO 2026-06-08 08:01:09 MarkDuplicates Tracking 27367 as yet unmatched pairs. 40 records in RAM.
INFO 2026-06-08 08:01:11 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 1s. Last read position: chr1:247,155,566
INFO 2026-06-08 08:01:11 MarkDuplicates Tracking 28127 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 08:01:13 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 2s. Last read position: chr2:11,344,029
INFO 2026-06-08 08:01:13 MarkDuplicates Tracking 29450 as yet unmatched pairs. 29163 records in RAM.
INFO 2026-06-08 08:01:16 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 2s. Last read position: chr2:25,239,132
INFO 2026-06-08 08:01:16 MarkDuplicates Tracking 29820 as yet unmatched pairs. 29526 records in RAM.
INFO 2026-06-08 08:01:19 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 3s. Last read position: chr2:27,661,210
INFO 2026-06-08 08:01:19 MarkDuplicates Tracking 30449 as yet unmatched pairs. 30152 records in RAM.
INFO 2026-06-08 08:01:24 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 4s. Last read position: chr2:32,916,264
INFO 2026-06-08 08:01:24 MarkDuplicates Tracking 182148 as yet unmatched pairs. 24034 records in RAM.
INFO 2026-06-08 08:01:26 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 2s. Last read position: chr2:36,877,907
INFO 2026-06-08 08:01:26 MarkDuplicates Tracking 331593 as yet unmatched pairs. 17833 records in RAM.
INFO 2026-06-08 08:01:28 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 2s. Last read position: chr2:43,224,878
INFO 2026-06-08 08:01:28 MarkDuplicates Tracking 330576 as yet unmatched pairs. 16813 records in RAM.
INFO 2026-06-08 08:01:31 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 2s. Last read position: chr2:54,624,928
INFO 2026-06-08 08:01:31 MarkDuplicates Tracking 329794 as yet unmatched pairs. 16023 records in RAM.
INFO 2026-06-08 08:01:33 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 1s. Last read position: chr2:64,552,111
INFO 2026-06-08 08:01:33 MarkDuplicates Tracking 328850 as yet unmatched pairs. 15071 records in RAM.
INFO 2026-06-08 08:01:35 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 2s. Last read position: chr2:73,913,491
INFO 2026-06-08 08:01:35 MarkDuplicates Tracking 328056 as yet unmatched pairs. 14270 records in RAM.
INFO 2026-06-08 08:01:38 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 2s. Last read position: chr2:84,970,497
INFO 2026-06-08 08:01:38 MarkDuplicates Tracking 327255 as yet unmatched pairs. 13464 records in RAM.
INFO 2026-06-08 08:01:40 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 2s. Last read position: chr2:95,274,722
INFO 2026-06-08 08:01:40 MarkDuplicates Tracking 326672 as yet unmatched pairs. 12875 records in RAM.
INFO 2026-06-08 08:01:43 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 2s. Last read position: chr2:100,397,619
INFO 2026-06-08 08:01:43 MarkDuplicates Tracking 326026 as yet unmatched pairs. 12221 records in RAM.
INFO 2026-06-08 08:01:45 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 2s. Last read position: chr2:109,585,299
INFO 2026-06-08 08:01:45 MarkDuplicates Tracking 325563 as yet unmatched pairs. 11750 records in RAM.
INFO 2026-06-08 08:01:47 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 2s. Last read position: chr2:113,719,239
INFO 2026-06-08 08:01:47 MarkDuplicates Tracking 325056 as yet unmatched pairs. 11239 records in RAM.
INFO 2026-06-08 08:01:50 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 3s. Last read position: chr2:130,154,419
INFO 2026-06-08 08:01:50 MarkDuplicates Tracking 324324 as yet unmatched pairs. 10501 records in RAM.
INFO 2026-06-08 08:01:53 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 2s. Last read position: chr2:156,115,199
INFO 2026-06-08 08:01:53 MarkDuplicates Tracking 323484 as yet unmatched pairs. 9647 records in RAM.
INFO 2026-06-08 08:01:56 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 2s. Last read position: chr2:171,745,893
INFO 2026-06-08 08:01:56 MarkDuplicates Tracking 322810 as yet unmatched pairs. 8960 records in RAM.
INFO 2026-06-08 08:01:59 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 3s. Last read position: chr2:179,566,933
INFO 2026-06-08 08:01:59 MarkDuplicates Tracking 322064 as yet unmatched pairs. 8210 records in RAM.
INFO 2026-06-08 08:02:02 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 3s. Last read position: chr2:189,007,540
INFO 2026-06-08 08:02:02 MarkDuplicates Tracking 321730 as yet unmatched pairs. 7871 records in RAM.
INFO 2026-06-08 08:02:06 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 3s. Last read position: chr2:199,348,841
INFO 2026-06-08 08:02:06 MarkDuplicates Tracking 320900 as yet unmatched pairs. 7035 records in RAM.
INFO 2026-06-08 08:02:09 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 3s. Last read position: chr2:207,767,011
INFO 2026-06-08 08:02:09 MarkDuplicates Tracking 319888 as yet unmatched pairs. 6018 records in RAM.
INFO 2026-06-08 08:02:12 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 3s. Last read position: chr2:215,375,321
INFO 2026-06-08 08:02:12 MarkDuplicates Tracking 319946 as yet unmatched pairs. 6072 records in RAM.
INFO 2026-06-08 08:02:15 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 2s. Last read position: chr2:215,406,359
INFO 2026-06-08 08:02:15 MarkDuplicates Tracking 319605 as yet unmatched pairs. 5731 records in RAM.
INFO 2026-06-08 08:02:17 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 2s. Last read position: chr2:215,435,700
INFO 2026-06-08 08:02:17 MarkDuplicates Tracking 318706 as yet unmatched pairs. 4829 records in RAM.
INFO 2026-06-08 08:02:20 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 2s. Last read position: chr2:218,698,664
INFO 2026-06-08 08:02:20 MarkDuplicates Tracking 317470 as yet unmatched pairs. 3591 records in RAM.
INFO 2026-06-08 08:02:23 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 2s. Last read position: chr2:227,330,634
INFO 2026-06-08 08:02:23 MarkDuplicates Tracking 316603 as yet unmatched pairs. 2644 records in RAM.
INFO 2026-06-08 08:02:26 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 3s. Last read position: chr2:233,204,138
INFO 2026-06-08 08:02:26 MarkDuplicates Tracking 316063 as yet unmatched pairs. 2100 records in RAM.
INFO 2026-06-08 08:02:29 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 3s. Last read position: chr2:238,239,487
INFO 2026-06-08 08:02:29 MarkDuplicates Tracking 315128 as yet unmatched pairs. 1163 records in RAM.
INFO 2026-06-08 08:02:32 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 2s. Last read position: chr2:241,385,566
INFO 2026-06-08 08:02:32 MarkDuplicates Tracking 314328 as yet unmatched pairs. 361 records in RAM.
INFO 2026-06-08 08:02:35 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 2s. Last read position: chr3:9,829,152
INFO 2026-06-08 08:02:35 MarkDuplicates Tracking 313593 as yet unmatched pairs. 15160 records in RAM.
INFO 2026-06-08 08:02:37 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 2s. Last read position: chr3:14,158,340
INFO 2026-06-08 08:02:37 MarkDuplicates Tracking 312794 as yet unmatched pairs. 14359 records in RAM.
INFO 2026-06-08 08:02:39 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 2s. Last read position: chr3:23,977,229
INFO 2026-06-08 08:02:39 MarkDuplicates Tracking 312165 as yet unmatched pairs. 13710 records in RAM.
INFO 2026-06-08 08:02:41 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 1s. Last read position: chr3:39,098,413
INFO 2026-06-08 08:02:41 MarkDuplicates Tracking 311544 as yet unmatched pairs. 13080 records in RAM.
INFO 2026-06-08 08:02:43 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 2s. Last read position: chr3:45,225,040
INFO 2026-06-08 08:02:43 MarkDuplicates Tracking 310651 as yet unmatched pairs. 12182 records in RAM.
INFO 2026-06-08 08:02:46 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 2s. Last read position: chr3:47,409,982
INFO 2026-06-08 08:02:46 MarkDuplicates Tracking 310135 as yet unmatched pairs. 11665 records in RAM.
INFO 2026-06-08 08:02:48 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 2s. Last read position: chr3:48,469,774
INFO 2026-06-08 08:02:48 MarkDuplicates Tracking 309205 as yet unmatched pairs. 10734 records in RAM.
INFO 2026-06-08 08:02:51 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 2s. Last read position: chr3:49,100,629
INFO 2026-06-08 08:02:51 MarkDuplicates Tracking 308389 as yet unmatched pairs. 9918 records in RAM.
INFO 2026-06-08 08:02:54 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 3s. Last read position: chr3:50,236,365
INFO 2026-06-08 08:02:54 MarkDuplicates Tracking 307707 as yet unmatched pairs. 9233 records in RAM.
INFO 2026-06-08 08:02:58 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 3s. Last read position: chr3:52,395,607
INFO 2026-06-08 08:02:58 MarkDuplicates Tracking 306595 as yet unmatched pairs. 8115 records in RAM.
INFO 2026-06-08 08:03:00 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 1s. Last read position: chr3:57,572,163
INFO 2026-06-08 08:03:00 MarkDuplicates Tracking 305830 as yet unmatched pairs. 7347 records in RAM.
INFO 2026-06-08 08:03:02 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 2s. Last read position: chr3:73,064,989
INFO 2026-06-08 08:03:02 MarkDuplicates Tracking 304982 as yet unmatched pairs. 6494 records in RAM.
INFO 2026-06-08 08:03:04 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 2s. Last read position: chr3:111,884,738
INFO 2026-06-08 08:03:04 MarkDuplicates Tracking 304378 as yet unmatched pairs. 5869 records in RAM.
INFO 2026-06-08 08:03:07 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 2s. Last read position: chr3:123,700,537
INFO 2026-06-08 08:03:07 MarkDuplicates Tracking 303629 as yet unmatched pairs. 5114 records in RAM.
INFO 2026-06-08 08:03:10 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 2s. Last read position: chr3:129,130,151
INFO 2026-06-08 08:03:10 MarkDuplicates Tracking 302666 as yet unmatched pairs. 4141 records in RAM.
INFO 2026-06-08 08:03:12 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 2s. Last read position: chr3:141,292,978
INFO 2026-06-08 08:03:12 MarkDuplicates Tracking 301838 as yet unmatched pairs. 3309 records in RAM.
INFO 2026-06-08 08:03:15 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 2s. Last read position: chr3:162,411,415
INFO 2026-06-08 08:03:15 MarkDuplicates Tracking 301079 as yet unmatched pairs. 2540 records in RAM.
INFO 2026-06-08 08:03:18 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 2s. Last read position: chr3:183,718,585
INFO 2026-06-08 08:03:18 MarkDuplicates Tracking 300529 as yet unmatched pairs. 1985 records in RAM.
INFO 2026-06-08 08:03:20 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 2s. Last read position: chr3:185,731,983
INFO 2026-06-08 08:03:20 MarkDuplicates Tracking 299856 as yet unmatched pairs. 1308 records in RAM.
INFO 2026-06-08 08:03:22 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 1s. Last read position: chr3:195,713,955
INFO 2026-06-08 08:03:22 MarkDuplicates Tracking 299248 as yet unmatched pairs. 687 records in RAM.
INFO 2026-06-08 08:03:25 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 2s. Last read position: chr3:196,965,655
INFO 2026-06-08 08:03:25 MarkDuplicates Tracking 298712 as yet unmatched pairs. 148 records in RAM.
INFO 2026-06-08 08:03:29 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 3s. Last read position: chr4:1,024,933
INFO 2026-06-08 08:03:29 MarkDuplicates Tracking 298429 as yet unmatched pairs. 8502 records in RAM.
INFO 2026-06-08 08:03:31 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 2s. Last read position: chr4:1,984,010
INFO 2026-06-08 08:03:31 MarkDuplicates Tracking 297176 as yet unmatched pairs. 7246 records in RAM.
INFO 2026-06-08 08:03:34 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 2s. Last read position: chr4:6,796,055
INFO 2026-06-08 08:03:34 MarkDuplicates Tracking 296335 as yet unmatched pairs. 6399 records in RAM.
INFO 2026-06-08 08:03:36 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 2s. Last read position: chr4:15,004,166
INFO 2026-06-08 08:03:36 MarkDuplicates Tracking 295643 as yet unmatched pairs. 5699 records in RAM.
INFO 2026-06-08 08:03:38 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 2s. Last read position: chr4:40,123,132
INFO 2026-06-08 08:03:38 MarkDuplicates Tracking 294972 as yet unmatched pairs. 5010 records in RAM.
INFO 2026-06-08 08:03:42 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 3s. Last read position: chr4:57,040,911
INFO 2026-06-08 08:03:42 MarkDuplicates Tracking 294409 as yet unmatched pairs. 4437 records in RAM.
INFO 2026-06-08 08:03:44 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 2s. Last read position: chr4:76,675,558
INFO 2026-06-08 08:03:44 MarkDuplicates Tracking 293467 as yet unmatched pairs. 3482 records in RAM.
INFO 2026-06-08 08:03:47 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 2s. Last read position: chr4:90,838,901
INFO 2026-06-08 08:03:47 MarkDuplicates Tracking 292763 as yet unmatched pairs. 2769 records in RAM.
INFO 2026-06-08 08:03:50 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 2s. Last read position: chr4:119,213,372
INFO 2026-06-08 08:03:50 MarkDuplicates Tracking 292066 as yet unmatched pairs. 2062 records in RAM.
INFO 2026-06-08 08:03:53 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 3s. Last read position: chr4:146,517,055
INFO 2026-06-08 08:03:53 MarkDuplicates Tracking 291485 as yet unmatched pairs. 1473 records in RAM.
INFO 2026-06-08 08:03:56 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 2s. Last read position: chr4:161,572,343
INFO 2026-06-08 08:03:56 MarkDuplicates Tracking 290740 as yet unmatched pairs. 711 records in RAM.
INFO 2026-06-08 08:03:59 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 3s. Last read position: chr5:271,729
INFO 2026-06-08 08:03:59 MarkDuplicates Tracking 290198 as yet unmatched pairs. 14711 records in RAM.
INFO 2026-06-08 08:04:02 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 2s. Last read position: chr5:10,261,594
INFO 2026-06-08 08:04:02 MarkDuplicates Tracking 289213 as yet unmatched pairs. 13721 records in RAM.
INFO 2026-06-08 08:04:05 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 3s. Last read position: chr5:14,504,466
INFO 2026-06-08 08:04:05 MarkDuplicates Tracking 288521 as yet unmatched pairs. 13027 records in RAM.
INFO 2026-06-08 08:04:09 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 3s. Last read position: chr5:39,153,518
INFO 2026-06-08 08:04:09 MarkDuplicates Tracking 287648 as yet unmatched pairs. 12146 records in RAM.
INFO 2026-06-08 08:04:12 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 3s. Last read position: chr5:67,164,212
INFO 2026-06-08 08:04:12 MarkDuplicates Tracking 287045 as yet unmatched pairs. 11536 records in RAM.
INFO 2026-06-08 08:04:14 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 1s. Last read position: chr5:77,693,265
INFO 2026-06-08 08:04:14 MarkDuplicates Tracking 286612 as yet unmatched pairs. 11100 records in RAM.
INFO 2026-06-08 08:04:16 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 2s. Last read position: chr5:96,722,688
INFO 2026-06-08 08:04:16 MarkDuplicates Tracking 286187 as yet unmatched pairs. 10666 records in RAM.
INFO 2026-06-08 08:04:18 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 2s. Last read position: chr5:126,804,794
INFO 2026-06-08 08:04:18 MarkDuplicates Tracking 285326 as yet unmatched pairs. 9791 records in RAM.
INFO 2026-06-08 08:04:21 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 2s. Last read position: chr5:132,826,966
INFO 2026-06-08 08:04:21 MarkDuplicates Tracking 284339 as yet unmatched pairs. 8799 records in RAM.
INFO 2026-06-08 08:04:23 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 2s. Last read position: chr5:138,386,294
INFO 2026-06-08 08:04:23 MarkDuplicates Tracking 283781 as yet unmatched pairs. 8235 records in RAM.
INFO 2026-06-08 08:04:25 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 2s. Last read position: chr5:139,561,694
INFO 2026-06-08 08:04:25 MarkDuplicates Tracking 283203 as yet unmatched pairs. 7656 records in RAM.
INFO 2026-06-08 08:04:28 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 2s. Last read position: chr5:141,189,148
INFO 2026-06-08 08:04:28 MarkDuplicates Tracking 283406 as yet unmatched pairs. 7652 records in RAM.
INFO 2026-06-08 08:04:30 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 2s. Last read position: chr5:141,410,016
INFO 2026-06-08 08:04:30 MarkDuplicates Tracking 282268 as yet unmatched pairs. 6514 records in RAM.
INFO 2026-06-08 08:04:33 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 3s. Last read position: chr5:146,060,079
INFO 2026-06-08 08:04:33 MarkDuplicates Tracking 281325 as yet unmatched pairs. 5566 records in RAM.
INFO 2026-06-08 08:04:37 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 3s. Last read position: chr5:150,357,719
INFO 2026-06-08 08:04:37 MarkDuplicates Tracking 280474 as yet unmatched pairs. 4713 records in RAM.
INFO 2026-06-08 08:04:40 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 2s. Last read position: chr5:150,656,885
INFO 2026-06-08 08:04:40 MarkDuplicates Tracking 279952 as yet unmatched pairs. 4189 records in RAM.
INFO 2026-06-08 08:04:43 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 2s. Last read position: chr5:160,598,869
INFO 2026-06-08 08:04:43 MarkDuplicates Tracking 279215 as yet unmatched pairs. 3444 records in RAM.
INFO 2026-06-08 08:04:45 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 2s. Last read position: chr5:172,641,415
INFO 2026-06-08 08:04:45 MarkDuplicates Tracking 278657 as yet unmatched pairs. 2876 records in RAM.
INFO 2026-06-08 08:04:48 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 2s. Last read position: chr5:177,307,368
INFO 2026-06-08 08:04:48 MarkDuplicates Tracking 277696 as yet unmatched pairs. 1909 records in RAM.
INFO 2026-06-08 08:04:51 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 2s. Last read position: chr5:179,766,172
INFO 2026-06-08 08:04:51 MarkDuplicates Tracking 277090 as yet unmatched pairs. 1303 records in RAM.
INFO 2026-06-08 08:04:54 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 2s. Last read position: chr5:180,313,838
INFO 2026-06-08 08:04:54 MarkDuplicates Tracking 276019 as yet unmatched pairs. 230 records in RAM.
INFO 2026-06-08 08:04:57 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 3s. Last read position: chr6:7,110,489
INFO 2026-06-08 08:04:57 MarkDuplicates Tracking 275080 as yet unmatched pairs. 14148 records in RAM.
INFO 2026-06-08 08:05:00 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 2s. Last read position: chr6:13,711,048
INFO 2026-06-08 08:05:00 MarkDuplicates Tracking 274333 as yet unmatched pairs. 13400 records in RAM.
INFO 2026-06-08 08:05:03 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 3s. Last read position: chr6:26,156,846
INFO 2026-06-08 08:05:03 MarkDuplicates Tracking 273575 as yet unmatched pairs. 12630 records in RAM.
INFO 2026-06-08 08:05:07 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 3s. Last read position: chr6:30,491,250
INFO 2026-06-08 08:05:07 MarkDuplicates Tracking 272938 as yet unmatched pairs. 11989 records in RAM.
INFO 2026-06-08 08:05:10 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 3s. Last read position: chr6:31,271,941
INFO 2026-06-08 08:05:10 MarkDuplicates Tracking 272146 as yet unmatched pairs. 11197 records in RAM.
INFO 2026-06-08 08:05:13 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 2s. Last read position: chr6:31,729,001
INFO 2026-06-08 08:05:13 MarkDuplicates Tracking 271441 as yet unmatched pairs. 10489 records in RAM.
INFO 2026-06-08 08:05:15 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 1s. Last read position: chr6:31,871,536
INFO 2026-06-08 08:05:15 MarkDuplicates Tracking 270976 as yet unmatched pairs. 10024 records in RAM.
INFO 2026-06-08 08:05:16 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 1s. Last read position: chr6:32,948,788
INFO 2026-06-08 08:05:16 MarkDuplicates Tracking 270149 as yet unmatched pairs. 9197 records in RAM.
INFO 2026-06-08 08:05:18 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 1s. Last read position: chr6:33,685,430
INFO 2026-06-08 08:05:18 MarkDuplicates Tracking 269406 as yet unmatched pairs. 8451 records in RAM.
INFO 2026-06-08 08:05:21 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 2s. Last read position: chr6:37,819,934
INFO 2026-06-08 08:05:21 MarkDuplicates Tracking 268801 as yet unmatched pairs. 7840 records in RAM.
INFO 2026-06-08 08:05:23 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 1s. Last read position: chr6:43,146,624
INFO 2026-06-08 08:05:23 MarkDuplicates Tracking 267873 as yet unmatched pairs. 6905 records in RAM.
INFO 2026-06-08 08:05:25 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 1s. Last read position: chr6:46,835,432
INFO 2026-06-08 08:05:25 MarkDuplicates Tracking 266938 as yet unmatched pairs. 5968 records in RAM.
INFO 2026-06-08 08:05:26 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 1s. Last read position: chr6:70,815,579
INFO 2026-06-08 08:05:26 MarkDuplicates Tracking 266408 as yet unmatched pairs. 5432 records in RAM.
INFO 2026-06-08 08:05:29 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 3s. Last read position: chr6:89,338,193
INFO 2026-06-08 08:05:29 MarkDuplicates Tracking 265788 as yet unmatched pairs. 4802 records in RAM.
INFO 2026-06-08 08:05:33 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 3s. Last read position: chr6:108,663,584
INFO 2026-06-08 08:05:33 MarkDuplicates Tracking 265036 as yet unmatched pairs. 4048 records in RAM.
INFO 2026-06-08 08:05:36 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 2s. Last read position: chr6:121,447,888
INFO 2026-06-08 08:05:36 MarkDuplicates Tracking 264435 as yet unmatched pairs. 3427 records in RAM.
INFO 2026-06-08 08:05:39 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 3s. Last read position: chr6:136,792,618
INFO 2026-06-08 08:05:39 MarkDuplicates Tracking 263712 as yet unmatched pairs. 2699 records in RAM.
INFO 2026-06-08 08:05:42 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 2s. Last read position: chr6:149,683,242
INFO 2026-06-08 08:05:42 MarkDuplicates Tracking 262976 as yet unmatched pairs. 1959 records in RAM.
INFO 2026-06-08 08:05:45 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 3s. Last read position: chr6:158,636,780
INFO 2026-06-08 08:05:45 MarkDuplicates Tracking 262342 as yet unmatched pairs. 1318 records in RAM.
INFO 2026-06-08 08:05:48 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 2s. Last read position: chr6:167,004,334
INFO 2026-06-08 08:05:48 MarkDuplicates Tracking 261544 as yet unmatched pairs. 514 records in RAM.
INFO 2026-06-08 08:05:51 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 3s. Last read position: chr7:905,760
INFO 2026-06-08 08:05:51 MarkDuplicates Tracking 260887 as yet unmatched pairs. 17254 records in RAM.
INFO 2026-06-08 08:05:54 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 2s. Last read position: chr7:2,661,686
INFO 2026-06-08 08:05:54 MarkDuplicates Tracking 259815 as yet unmatched pairs. 16174 records in RAM.
INFO 2026-06-08 08:05:56 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:06:32s. Time for last 1,000,000: 2s. Last read position: chr7:5,388,296
INFO 2026-06-08 08:05:56 MarkDuplicates Tracking 259646 as yet unmatched pairs. 16002 records in RAM.
INFO 2026-06-08 08:06:00 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 3s. Last read position: chr7:6,187,092
INFO 2026-06-08 08:06:00 MarkDuplicates Tracking 257989 as yet unmatched pairs. 14340 records in RAM.
INFO 2026-06-08 08:06:03 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:06:39s. Time for last 1,000,000: 3s. Last read position: chr7:27,155,045
INFO 2026-06-08 08:06:03 MarkDuplicates Tracking 257276 as yet unmatched pairs. 13623 records in RAM.
INFO 2026-06-08 08:06:06 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 2s. Last read position: chr7:41,972,381
INFO 2026-06-08 08:06:06 MarkDuplicates Tracking 256482 as yet unmatched pairs. 12827 records in RAM.
INFO 2026-06-08 08:06:09 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 3s. Last read position: chr7:44,884,740
INFO 2026-06-08 08:06:09 MarkDuplicates Tracking 255872 as yet unmatched pairs. 12214 records in RAM.
INFO 2026-06-08 08:06:12 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 2s. Last read position: chr7:65,890,052
INFO 2026-06-08 08:06:12 MarkDuplicates Tracking 255202 as yet unmatched pairs. 11535 records in RAM.
INFO 2026-06-08 08:06:15 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 2s. Last read position: chr7:73,297,242
INFO 2026-06-08 08:06:15 MarkDuplicates Tracking 254748 as yet unmatched pairs. 11073 records in RAM.
INFO 2026-06-08 08:06:18 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 3s. Last read position: chr7:74,601,133
INFO 2026-06-08 08:06:18 MarkDuplicates Tracking 253908 as yet unmatched pairs. 10230 records in RAM.
INFO 2026-06-08 08:06:21 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:06:56s. Time for last 1,000,000: 3s. Last read position: chr7:76,302,953
INFO 2026-06-08 08:06:21 MarkDuplicates Tracking 254013 as yet unmatched pairs. 10334 records in RAM.
INFO 2026-06-08 08:06:24 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 2s. Last read position: chr7:88,210,902
INFO 2026-06-08 08:06:24 MarkDuplicates Tracking 252887 as yet unmatched pairs. 9194 records in RAM.
INFO 2026-06-08 08:06:27 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 2s. Last read position: chr7:94,423,092
INFO 2026-06-08 08:06:27 MarkDuplicates Tracking 252404 as yet unmatched pairs. 8707 records in RAM.
INFO 2026-06-08 08:06:30 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 2s. Last read position: chr7:99,676,188
INFO 2026-06-08 08:06:30 MarkDuplicates Tracking 251541 as yet unmatched pairs. 7828 records in RAM.
INFO 2026-06-08 08:06:32 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 2s. Last read position: chr7:100,686,038
INFO 2026-06-08 08:06:32 MarkDuplicates Tracking 250708 as yet unmatched pairs. 6991 records in RAM.
INFO 2026-06-08 08:06:34 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:07:10s. Time for last 1,000,000: 1s. Last read position: chr7:100,996,441
INFO 2026-06-08 08:06:34 MarkDuplicates Tracking 250872 as yet unmatched pairs. 7150 records in RAM.
INFO 2026-06-08 08:06:37 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:07:12s. Time for last 1,000,000: 2s. Last read position: chr7:101,001,187
INFO 2026-06-08 08:06:37 MarkDuplicates Tracking 250026 as yet unmatched pairs. 6304 records in RAM.
INFO 2026-06-08 08:06:39 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:07:15s. Time for last 1,000,000: 2s. Last read position: chr7:102,348,070
INFO 2026-06-08 08:06:39 MarkDuplicates Tracking 249124 as yet unmatched pairs. 5401 records in RAM.
INFO 2026-06-08 08:06:42 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:07:18s. Time for last 1,000,000: 2s. Last read position: chr7:102,809,606
INFO 2026-06-08 08:06:42 MarkDuplicates Tracking 248829 as yet unmatched pairs. 5106 records in RAM.
INFO 2026-06-08 08:06:45 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:07:21s. Time for last 1,000,000: 3s. Last read position: chr7:118,184,243
INFO 2026-06-08 08:06:45 MarkDuplicates Tracking 248189 as yet unmatched pairs. 4419 records in RAM.
INFO 2026-06-08 08:06:48 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:07:24s. Time for last 1,000,000: 2s. Last read position: chr7:129,948,404
INFO 2026-06-08 08:06:48 MarkDuplicates Tracking 247619 as yet unmatched pairs. 3842 records in RAM.
INFO 2026-06-08 08:06:51 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 2s. Last read position: chr7:139,283,477
INFO 2026-06-08 08:06:51 MarkDuplicates Tracking 246863 as yet unmatched pairs. 3078 records in RAM.
INFO 2026-06-08 08:06:54 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:07:30s. Time for last 1,000,000: 2s. Last read position: chr7:144,267,022
INFO 2026-06-08 08:06:54 MarkDuplicates Tracking 246270 as yet unmatched pairs. 2482 records in RAM.
INFO 2026-06-08 08:06:56 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:07:32s. Time for last 1,000,000: 2s. Last read position: chr7:149,451,543
INFO 2026-06-08 08:06:56 MarkDuplicates Tracking 245790 as yet unmatched pairs. 2000 records in RAM.
INFO 2026-06-08 08:06:59 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:07:35s. Time for last 1,000,000: 2s. Last read position: chr7:151,117,426
INFO 2026-06-08 08:06:59 MarkDuplicates Tracking 244731 as yet unmatched pairs. 940 records in RAM.
INFO 2026-06-08 08:07:02 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:07:38s. Time for last 1,000,000: 2s. Last read position: chr7:158,884,573
INFO 2026-06-08 08:07:02 MarkDuplicates Tracking 243884 as yet unmatched pairs. 87 records in RAM.
INFO 2026-06-08 08:07:05 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:07:41s. Time for last 1,000,000: 3s. Last read position: chr8:13,099,634
INFO 2026-06-08 08:07:05 MarkDuplicates Tracking 243018 as yet unmatched pairs. 14043 records in RAM.
INFO 2026-06-08 08:07:09 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:07:45s. Time for last 1,000,000: 3s. Last read position: chr8:22,607,969
INFO 2026-06-08 08:07:09 MarkDuplicates Tracking 242400 as yet unmatched pairs. 13419 records in RAM.
INFO 2026-06-08 08:07:12 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:07:48s. Time for last 1,000,000: 2s. Last read position: chr8:29,071,956
INFO 2026-06-08 08:07:12 MarkDuplicates Tracking 241604 as yet unmatched pairs. 12615 records in RAM.
INFO 2026-06-08 08:07:15 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:07:51s. Time for last 1,000,000: 2s. Last read position: chr8:37,869,779
INFO 2026-06-08 08:07:15 MarkDuplicates Tracking 240791 as yet unmatched pairs. 11799 records in RAM.
INFO 2026-06-08 08:07:17 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:07:53s. Time for last 1,000,000: 2s. Last read position: chr8:42,528,977
INFO 2026-06-08 08:07:17 MarkDuplicates Tracking 239728 as yet unmatched pairs. 10732 records in RAM.
INFO 2026-06-08 08:07:19 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:07:55s. Time for last 1,000,000: 1s. Last read position: chr8:66,665,858
INFO 2026-06-08 08:07:19 MarkDuplicates Tracking 239107 as yet unmatched pairs. 10098 records in RAM.
INFO 2026-06-08 08:07:21 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:07:57s. Time for last 1,000,000: 1s. Last read position: chr8:93,922,287
INFO 2026-06-08 08:07:21 MarkDuplicates Tracking 238529 as yet unmatched pairs. 9508 records in RAM.
INFO 2026-06-08 08:07:24 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:07:59s. Time for last 1,000,000: 2s. Last read position: chr8:103,068,670
INFO 2026-06-08 08:07:24 MarkDuplicates Tracking 237760 as yet unmatched pairs. 8729 records in RAM.
INFO 2026-06-08 08:07:27 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:08:03s. Time for last 1,000,000: 3s. Last read position: chr8:127,738,265
INFO 2026-06-08 08:07:27 MarkDuplicates Tracking 237993 as yet unmatched pairs. 8956 records in RAM.
INFO 2026-06-08 08:07:30 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:08:06s. Time for last 1,000,000: 2s. Last read position: chr8:141,163,815
INFO 2026-06-08 08:07:30 MarkDuplicates Tracking 236278 as yet unmatched pairs. 7227 records in RAM.
INFO 2026-06-08 08:07:33 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:08:09s. Time for last 1,000,000: 2s. Last read position: chr8:143,795,278
INFO 2026-06-08 08:07:33 MarkDuplicates Tracking 235351 as yet unmatched pairs. 6284 records in RAM.
INFO 2026-06-08 08:07:35 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:08:11s. Time for last 1,000,000: 2s. Last read position: chr8:143,858,997
INFO 2026-06-08 08:07:35 MarkDuplicates Tracking 236609 as yet unmatched pairs. 7542 records in RAM.
INFO 2026-06-08 08:07:38 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:08:13s. Time for last 1,000,000: 2s. Last read position: chr8:143,860,408
INFO 2026-06-08 08:07:38 MarkDuplicates Tracking 234952 as yet unmatched pairs. 5885 records in RAM.
INFO 2026-06-08 08:07:40 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 2s. Last read position: chr8:143,861,610
INFO 2026-06-08 08:07:40 MarkDuplicates Tracking 234104 as yet unmatched pairs. 5037 records in RAM.
INFO 2026-06-08 08:07:42 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:08:17s. Time for last 1,000,000: 1s. Last read position: chr8:143,862,716
INFO 2026-06-08 08:07:42 MarkDuplicates Tracking 234236 as yet unmatched pairs. 5169 records in RAM.
INFO 2026-06-08 08:07:43 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:08:19s. Time for last 1,000,000: 1s. Last read position: chr8:143,863,891
INFO 2026-06-08 08:07:43 MarkDuplicates Tracking 233092 as yet unmatched pairs. 4025 records in RAM.
INFO 2026-06-08 08:07:45 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:08:21s. Time for last 1,000,000: 2s. Last read position: chr8:143,865,409
INFO 2026-06-08 08:07:45 MarkDuplicates Tracking 232670 as yet unmatched pairs. 3603 records in RAM.
INFO 2026-06-08 08:07:47 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 1s. Last read position: chr8:143,867,711
INFO 2026-06-08 08:07:47 MarkDuplicates Tracking 232912 as yet unmatched pairs. 3845 records in RAM.
INFO 2026-06-08 08:07:49 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 2s. Last read position: chr8:143,921,228
INFO 2026-06-08 08:07:49 MarkDuplicates Tracking 231884 as yet unmatched pairs. 2817 records in RAM.
INFO 2026-06-08 08:07:52 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:08:28s. Time for last 1,000,000: 3s. Last read position: chr8:144,086,009
INFO 2026-06-08 08:07:52 MarkDuplicates Tracking 230764 as yet unmatched pairs. 1697 records in RAM.
INFO 2026-06-08 08:07:55 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:08:31s. Time for last 1,000,000: 2s. Last read position: chr8:144,473,153
INFO 2026-06-08 08:07:55 MarkDuplicates Tracking 229821 as yet unmatched pairs. 752 records in RAM.
INFO 2026-06-08 08:07:58 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:08:33s. Time for last 1,000,000: 2s. Last read position: chr9:5,787,506
INFO 2026-06-08 08:07:58 MarkDuplicates Tracking 228710 as yet unmatched pairs. 15349 records in RAM.
INFO 2026-06-08 08:08:00 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:08:36s. Time for last 1,000,000: 2s. Last read position: chr9:16,436,561
INFO 2026-06-08 08:08:00 MarkDuplicates Tracking 228010 as yet unmatched pairs. 14648 records in RAM.
INFO 2026-06-08 08:08:03 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:08:39s. Time for last 1,000,000: 2s. Last read position: chr9:34,635,401
INFO 2026-06-08 08:08:03 MarkDuplicates Tracking 227353 as yet unmatched pairs. 13976 records in RAM.
INFO 2026-06-08 08:08:05 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:08:41s. Time for last 1,000,000: 2s. Last read position: chr9:36,191,183
INFO 2026-06-08 08:08:05 MarkDuplicates Tracking 226666 as yet unmatched pairs. 13288 records in RAM.
INFO 2026-06-08 08:08:07 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:08:43s. Time for last 1,000,000: 2s. Last read position: chr9:72,355,948
INFO 2026-06-08 08:08:07 MarkDuplicates Tracking 225960 as yet unmatched pairs. 12526 records in RAM.
INFO 2026-06-08 08:08:11 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:08:46s. Time for last 1,000,000: 3s. Last read position: chr9:92,087,718
INFO 2026-06-08 08:08:11 MarkDuplicates Tracking 225312 as yet unmatched pairs. 11871 records in RAM.
INFO 2026-06-08 08:08:14 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:08:50s. Time for last 1,000,000: 3s. Last read position: chr9:93,515,672
INFO 2026-06-08 08:08:14 MarkDuplicates Tracking 224672 as yet unmatched pairs. 11228 records in RAM.
INFO 2026-06-08 08:08:17 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:08:53s. Time for last 1,000,000: 2s. Last read position: chr9:99,066,905
INFO 2026-06-08 08:08:17 MarkDuplicates Tracking 223748 as yet unmatched pairs. 10297 records in RAM.
INFO 2026-06-08 08:08:20 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:08:55s. Time for last 1,000,000: 2s. Last read position: chr9:112,127,816
INFO 2026-06-08 08:08:20 MarkDuplicates Tracking 222957 as yet unmatched pairs. 9501 records in RAM.
INFO 2026-06-08 08:08:23 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:08:58s. Time for last 1,000,000: 2s. Last read position: chr9:115,086,450
INFO 2026-06-08 08:08:23 MarkDuplicates Tracking 222352 as yet unmatched pairs. 8891 records in RAM.
INFO 2026-06-08 08:08:25 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:09:01s. Time for last 1,000,000: 2s. Last read position: chr9:125,241,113
INFO 2026-06-08 08:08:25 MarkDuplicates Tracking 221599 as yet unmatched pairs. 8127 records in RAM.
INFO 2026-06-08 08:08:28 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:09:04s. Time for last 1,000,000: 2s. Last read position: chr9:128,166,200
INFO 2026-06-08 08:08:28 MarkDuplicates Tracking 220753 as yet unmatched pairs. 7280 records in RAM.
INFO 2026-06-08 08:08:32 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 3s. Last read position: chr9:129,142,503
INFO 2026-06-08 08:08:32 MarkDuplicates Tracking 220148 as yet unmatched pairs. 6673 records in RAM.
INFO 2026-06-08 08:08:35 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:09:10s. Time for last 1,000,000: 2s. Last read position: chr9:131,444,279
INFO 2026-06-08 08:08:35 MarkDuplicates Tracking 219085 as yet unmatched pairs. 5608 records in RAM.
INFO 2026-06-08 08:08:37 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:09:12s. Time for last 1,000,000: 1s. Last read position: chr9:133,346,602
INFO 2026-06-08 08:08:37 MarkDuplicates Tracking 218404 as yet unmatched pairs. 4920 records in RAM.
INFO 2026-06-08 08:08:38 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 1s. Last read position: chr9:134,814,885
INFO 2026-06-08 08:08:38 MarkDuplicates Tracking 217655 as yet unmatched pairs. 4170 records in RAM.
INFO 2026-06-08 08:08:41 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 2s. Last read position: chr9:136,497,337
INFO 2026-06-08 08:08:41 MarkDuplicates Tracking 216736 as yet unmatched pairs. 3249 records in RAM.
INFO 2026-06-08 08:08:43 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:09:18s. Time for last 1,000,000: 2s. Last read position: chr9:136,845,663
INFO 2026-06-08 08:08:43 MarkDuplicates Tracking 215780 as yet unmatched pairs. 2293 records in RAM.
INFO 2026-06-08 08:08:45 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 1s. Last read position: chr9:137,177,832
INFO 2026-06-08 08:08:45 MarkDuplicates Tracking 214482 as yet unmatched pairs. 995 records in RAM.
INFO 2026-06-08 08:08:46 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 1s. Last read position: chr9:137,779,651
INFO 2026-06-08 08:08:46 MarkDuplicates Tracking 213569 as yet unmatched pairs. 82 records in RAM.
INFO 2026-06-08 08:08:48 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:09:24s. Time for last 1,000,000: 1s. Last read position: chr10:12,387,572
INFO 2026-06-08 08:08:48 MarkDuplicates Tracking 212892 as yet unmatched pairs. 9648 records in RAM.
INFO 2026-06-08 08:08:50 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:09:26s. Time for last 1,000,000: 1s. Last read position: chr10:26,748,588
INFO 2026-06-08 08:08:50 MarkDuplicates Tracking 212237 as yet unmatched pairs. 8989 records in RAM.
INFO 2026-06-08 08:08:52 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:09:28s. Time for last 1,000,000: 1s. Last read position: chr10:32,911,551
INFO 2026-06-08 08:08:52 MarkDuplicates Tracking 211591 as yet unmatched pairs. 8341 records in RAM.
INFO 2026-06-08 08:08:54 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:09:30s. Time for last 1,000,000: 2s. Last read position: chr10:47,523,227
INFO 2026-06-08 08:08:54 MarkDuplicates Tracking 211063 as yet unmatched pairs. 7806 records in RAM.
INFO 2026-06-08 08:08:57 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:09:33s. Time for last 1,000,000: 2s. Last read position: chr10:68,072,941
INFO 2026-06-08 08:08:57 MarkDuplicates Tracking 210454 as yet unmatched pairs. 7196 records in RAM.
INFO 2026-06-08 08:08:59 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 2s. Last read position: chr10:73,471,467
INFO 2026-06-08 08:08:59 MarkDuplicates Tracking 209684 as yet unmatched pairs. 6411 records in RAM.
INFO 2026-06-08 08:09:01 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 1s. Last read position: chr10:77,926,455
INFO 2026-06-08 08:09:01 MarkDuplicates Tracking 208861 as yet unmatched pairs. 5583 records in RAM.
INFO 2026-06-08 08:09:04 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:09:39s. Time for last 1,000,000: 2s. Last read position: chr10:87,072,107
INFO 2026-06-08 08:09:04 MarkDuplicates Tracking 208260 as yet unmatched pairs. 4981 records in RAM.
INFO 2026-06-08 08:09:06 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:09:41s. Time for last 1,000,000: 1s. Last read position: chr10:95,868,256
INFO 2026-06-08 08:09:06 MarkDuplicates Tracking 207631 as yet unmatched pairs. 4348 records in RAM.
INFO 2026-06-08 08:09:07 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:09:43s. Time for last 1,000,000: 1s. Last read position: chr10:101,011,980
INFO 2026-06-08 08:09:07 MarkDuplicates Tracking 206763 as yet unmatched pairs. 3476 records in RAM.
INFO 2026-06-08 08:09:09 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:09:45s. Time for last 1,000,000: 1s. Last read position: chr10:103,602,598
INFO 2026-06-08 08:09:09 MarkDuplicates Tracking 205975 as yet unmatched pairs. 2681 records in RAM.
INFO 2026-06-08 08:09:11 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:09:47s. Time for last 1,000,000: 1s. Last read position: chr10:114,938,508
INFO 2026-06-08 08:09:11 MarkDuplicates Tracking 205320 as yet unmatched pairs. 1988 records in RAM.
INFO 2026-06-08 08:09:14 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:09:49s. Time for last 1,000,000: 2s. Last read position: chr10:122,113,173
INFO 2026-06-08 08:09:14 MarkDuplicates Tracking 204754 as yet unmatched pairs. 1420 records in RAM.
INFO 2026-06-08 08:09:16 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:09:51s. Time for last 1,000,000: 2s. Last read position: chr10:127,916,024
INFO 2026-06-08 08:09:16 MarkDuplicates Tracking 203980 as yet unmatched pairs. 643 records in RAM.
INFO 2026-06-08 08:09:18 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:09:53s. Time for last 1,000,000: 1s. Last read position: chr11:319,886
INFO 2026-06-08 08:09:18 MarkDuplicates Tracking 203759 as yet unmatched pairs. 16405 records in RAM.
INFO 2026-06-08 08:09:20 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:09:55s. Time for last 1,000,000: 1s. Last read position: chr11:691,526
INFO 2026-06-08 08:09:20 MarkDuplicates Tracking 202419 as yet unmatched pairs. 15065 records in RAM.
INFO 2026-06-08 08:09:21 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:09:57s. Time for last 1,000,000: 1s. Last read position: chr11:2,132,010
INFO 2026-06-08 08:09:21 MarkDuplicates Tracking 201409 as yet unmatched pairs. 14053 records in RAM.
INFO 2026-06-08 08:09:24 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:10:00s. Time for last 1,000,000: 2s. Last read position: chr11:2,445,401
INFO 2026-06-08 08:09:24 MarkDuplicates Tracking 200593 as yet unmatched pairs. 13236 records in RAM.
INFO 2026-06-08 08:09:27 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:10:02s. Time for last 1,000,000: 2s. Last read position: chr11:8,729,992
INFO 2026-06-08 08:09:27 MarkDuplicates Tracking 199707 as yet unmatched pairs. 12350 records in RAM.
INFO 2026-06-08 08:09:29 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:10:05s. Time for last 1,000,000: 2s. Last read position: chr11:17,521,356
INFO 2026-06-08 08:09:29 MarkDuplicates Tracking 198946 as yet unmatched pairs. 11586 records in RAM.
INFO 2026-06-08 08:09:31 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:10:07s. Time for last 1,000,000: 2s. Last read position: chr11:43,886,624
INFO 2026-06-08 08:09:31 MarkDuplicates Tracking 198270 as yet unmatched pairs. 10901 records in RAM.
INFO 2026-06-08 08:09:33 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 1s. Last read position: chr11:47,276,026
INFO 2026-06-08 08:09:33 MarkDuplicates Tracking 197646 as yet unmatched pairs. 10275 records in RAM.
INFO 2026-06-08 08:09:35 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:10:11s. Time for last 1,000,000: 1s. Last read position: chr11:60,849,986
INFO 2026-06-08 08:09:35 MarkDuplicates Tracking 196948 as yet unmatched pairs. 9576 records in RAM.
INFO 2026-06-08 08:09:37 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:10:13s. Time for last 1,000,000: 1s. Last read position: chr11:62,649,746
INFO 2026-06-08 08:09:37 MarkDuplicates Tracking 196342 as yet unmatched pairs. 8929 records in RAM.
INFO 2026-06-08 08:09:39 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:10:14s. Time for last 1,000,000: 1s. Last read position: chr11:64,244,704
INFO 2026-06-08 08:09:39 MarkDuplicates Tracking 195701 as yet unmatched pairs. 8267 records in RAM.
INFO 2026-06-08 08:09:41 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:10:17s. Time for last 1,000,000: 2s. Last read position: chr11:64,371,347
INFO 2026-06-08 08:09:41 MarkDuplicates Tracking 194614 as yet unmatched pairs. 7180 records in RAM.
INFO 2026-06-08 08:09:43 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:10:18s. Time for last 1,000,000: 1s. Last read position: chr11:65,442,622
INFO 2026-06-08 08:09:43 MarkDuplicates Tracking 193689 as yet unmatched pairs. 6254 records in RAM.
INFO 2026-06-08 08:09:45 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:10:21s. Time for last 1,000,000: 2s. Last read position: chr11:65,780,024
INFO 2026-06-08 08:09:45 MarkDuplicates Tracking 192714 as yet unmatched pairs. 5277 records in RAM.
INFO 2026-06-08 08:09:47 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:10:23s. Time for last 1,000,000: 2s. Last read position: chr11:67,398,619
INFO 2026-06-08 08:09:47 MarkDuplicates Tracking 191994 as yet unmatched pairs. 4555 records in RAM.
INFO 2026-06-08 08:09:50 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 3s. Last read position: chr11:69,699,258
INFO 2026-06-08 08:09:50 MarkDuplicates Tracking 191187 as yet unmatched pairs. 3747 records in RAM.
INFO 2026-06-08 08:09:53 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:10:29s. Time for last 1,000,000: 2s. Last read position: chr11:73,363,210
INFO 2026-06-08 08:09:53 MarkDuplicates Tracking 190352 as yet unmatched pairs. 2909 records in RAM.
INFO 2026-06-08 08:09:56 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:10:31s. Time for last 1,000,000: 2s. Last read position: chr11:86,878,601
INFO 2026-06-08 08:09:56 MarkDuplicates Tracking 189497 as yet unmatched pairs. 2048 records in RAM.
INFO 2026-06-08 08:09:58 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:10:33s. Time for last 1,000,000: 2s. Last read position: chr11:116,954,067
INFO 2026-06-08 08:09:58 MarkDuplicates Tracking 188872 as yet unmatched pairs. 1411 records in RAM.
INFO 2026-06-08 08:10:00 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:10:35s. Time for last 1,000,000: 2s. Last read position: chr11:119,420,073
INFO 2026-06-08 08:10:00 MarkDuplicates Tracking 188120 as yet unmatched pairs. 658 records in RAM.
INFO 2026-06-08 08:10:01 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:10:37s. Time for last 1,000,000: 1s. Last read position: chr11:134,176,306
INFO 2026-06-08 08:10:01 MarkDuplicates Tracking 187494 as yet unmatched pairs. 24 records in RAM.
INFO 2026-06-08 08:10:03 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:10:39s. Time for last 1,000,000: 2s. Last read position: chr12:4,928,391
INFO 2026-06-08 08:10:03 MarkDuplicates Tracking 186887 as yet unmatched pairs. 16603 records in RAM.
INFO 2026-06-08 08:10:06 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:10:41s. Time for last 1,000,000: 2s. Last read position: chr12:6,768,389
INFO 2026-06-08 08:10:06 MarkDuplicates Tracking 186194 as yet unmatched pairs. 15910 records in RAM.
INFO 2026-06-08 08:10:08 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:10:44s. Time for last 1,000,000: 2s. Last read position: chr12:9,109,928
INFO 2026-06-08 08:10:08 MarkDuplicates Tracking 185393 as yet unmatched pairs. 15104 records in RAM.
INFO 2026-06-08 08:10:10 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:10:46s. Time for last 1,000,000: 2s. Last read position: chr12:14,787,096
INFO 2026-06-08 08:10:10 MarkDuplicates Tracking 184609 as yet unmatched pairs. 14315 records in RAM.
INFO 2026-06-08 08:10:12 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:10:48s. Time for last 1,000,000: 1s. Last read position: chr12:32,337,601
INFO 2026-06-08 08:10:12 MarkDuplicates Tracking 183989 as yet unmatched pairs. 13686 records in RAM.
INFO 2026-06-08 08:10:14 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:10:50s. Time for last 1,000,000: 2s. Last read position: chr12:49,026,970
INFO 2026-06-08 08:10:14 MarkDuplicates Tracking 183536 as yet unmatched pairs. 13229 records in RAM.
INFO 2026-06-08 08:10:16 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:10:52s. Time for last 1,000,000: 2s. Last read position: chr12:49,273,033
INFO 2026-06-08 08:10:16 MarkDuplicates Tracking 182775 as yet unmatched pairs. 12466 records in RAM.
INFO 2026-06-08 08:10:18 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:10:54s. Time for last 1,000,000: 2s. Last read position: chr12:52,054,414
INFO 2026-06-08 08:10:18 MarkDuplicates Tracking 185014 as yet unmatched pairs. 14703 records in RAM.
INFO 2026-06-08 08:10:21 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:10:57s. Time for last 1,000,000: 2s. Last read position: chr12:52,904,769
INFO 2026-06-08 08:10:21 MarkDuplicates Tracking 181500 as yet unmatched pairs. 11189 records in RAM.
INFO 2026-06-08 08:10:24 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:10:59s. Time for last 1,000,000: 2s. Last read position: chr12:53,713,724
INFO 2026-06-08 08:10:24 MarkDuplicates Tracking 180476 as yet unmatched pairs. 10165 records in RAM.
INFO 2026-06-08 08:10:27 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:11:02s. Time for last 1,000,000: 2s. Last read position: chr12:56,159,697
INFO 2026-06-08 08:10:27 MarkDuplicates Tracking 179927 as yet unmatched pairs. 9615 records in RAM.
INFO 2026-06-08 08:10:29 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:11:05s. Time for last 1,000,000: 2s. Last read position: chr12:56,720,836
INFO 2026-06-08 08:10:29 MarkDuplicates Tracking 179131 as yet unmatched pairs. 8818 records in RAM.
INFO 2026-06-08 08:10:32 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:11:07s. Time for last 1,000,000: 2s. Last read position: chr12:57,177,150
INFO 2026-06-08 08:10:32 MarkDuplicates Tracking 178391 as yet unmatched pairs. 8076 records in RAM.
INFO 2026-06-08 08:10:34 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:11:10s. Time for last 1,000,000: 2s. Last read position: chr12:57,615,956
INFO 2026-06-08 08:10:34 MarkDuplicates Tracking 177461 as yet unmatched pairs. 7146 records in RAM.
INFO 2026-06-08 08:10:37 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:11:12s. Time for last 1,000,000: 2s. Last read position: chr12:70,346,243
INFO 2026-06-08 08:10:37 MarkDuplicates Tracking 176824 as yet unmatched pairs. 6507 records in RAM.
INFO 2026-06-08 08:10:39 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:11:15s. Time for last 1,000,000: 2s. Last read position: chr12:93,395,502
INFO 2026-06-08 08:10:39 MarkDuplicates Tracking 176537 as yet unmatched pairs. 6217 records in RAM.
INFO 2026-06-08 08:10:41 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:11:17s. Time for last 1,000,000: 2s. Last read position: chr12:107,739,430
INFO 2026-06-08 08:10:41 MarkDuplicates Tracking 175645 as yet unmatched pairs. 5323 records in RAM.
INFO 2026-06-08 08:10:44 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:11:20s. Time for last 1,000,000: 2s. Last read position: chr12:111,809,543
INFO 2026-06-08 08:10:44 MarkDuplicates Tracking 174853 as yet unmatched pairs. 4529 records in RAM.
INFO 2026-06-08 08:11:55 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:12:31s. Time for last 1,000,000: 70s. Last read position: chr12:116,836,192
INFO 2026-06-08 08:11:55 MarkDuplicates Tracking 174012 as yet unmatched pairs. 3686 records in RAM.
INFO 2026-06-08 08:11:58 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:12:33s. Time for last 1,000,000: 2s. Last read position: chr12:120,971,129
INFO 2026-06-08 08:11:58 MarkDuplicates Tracking 173239 as yet unmatched pairs. 2912 records in RAM.
INFO 2026-06-08 08:12:00 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:12:35s. Time for last 1,000,000: 1s. Last read position: chr12:122,715,557
INFO 2026-06-08 08:12:00 MarkDuplicates Tracking 172597 as yet unmatched pairs. 2269 records in RAM.
INFO 2026-06-08 08:12:02 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:12:37s. Time for last 1,000,000: 1s. Last read position: chr12:124,356,707
INFO 2026-06-08 08:12:02 MarkDuplicates Tracking 172108 as yet unmatched pairs. 1779 records in RAM.
INFO 2026-06-08 08:12:04 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:12:39s. Time for last 1,000,000: 2s. Last read position: chr12:132,120,402
INFO 2026-06-08 08:12:04 MarkDuplicates Tracking 171095 as yet unmatched pairs. 760 records in RAM.
INFO 2026-06-08 08:12:06 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:12:42s. Time for last 1,000,000: 2s. Last read position: chr13:19,993,156
INFO 2026-06-08 08:12:06 MarkDuplicates Tracking 170484 as yet unmatched pairs. 5825 records in RAM.
INFO 2026-06-08 08:12:09 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:12:45s. Time for last 1,000,000: 3s. Last read position: chr13:27,962,342
INFO 2026-06-08 08:12:09 MarkDuplicates Tracking 169713 as yet unmatched pairs. 5043 records in RAM.
INFO 2026-06-08 08:12:12 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:12:47s. Time for last 1,000,000: 2s. Last read position: chr13:39,013,994
INFO 2026-06-08 08:12:12 MarkDuplicates Tracking 168839 as yet unmatched pairs. 4163 records in RAM.
INFO 2026-06-08 08:12:15 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:12:50s. Time for last 1,000,000: 2s. Last read position: chr13:46,691,861
INFO 2026-06-08 08:12:15 MarkDuplicates Tracking 167976 as yet unmatched pairs. 3298 records in RAM.
INFO 2026-06-08 08:12:17 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:12:53s. Time for last 1,000,000: 2s. Last read position: chr13:73,062,139
INFO 2026-06-08 08:12:17 MarkDuplicates Tracking 167443 as yet unmatched pairs. 2756 records in RAM.
INFO 2026-06-08 08:12:20 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:12:56s. Time for last 1,000,000: 2s. Last read position: chr13:98,519,455
INFO 2026-06-08 08:12:20 MarkDuplicates Tracking 166683 as yet unmatched pairs. 1991 records in RAM.
INFO 2026-06-08 08:12:22 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:12:58s. Time for last 1,000,000: 2s. Last read position: chr13:110,434,413
INFO 2026-06-08 08:12:22 MarkDuplicates Tracking 165704 as yet unmatched pairs. 1005 records in RAM.
INFO 2026-06-08 08:12:24 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:13:00s. Time for last 1,000,000: 1s. Last read position: chr13:113,832,690
INFO 2026-06-08 08:12:24 MarkDuplicates Tracking 164917 as yet unmatched pairs. 217 records in RAM.
INFO 2026-06-08 08:12:26 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:13:02s. Time for last 1,000,000: 2s. Last read position: chr14:22,875,588
INFO 2026-06-08 08:12:26 MarkDuplicates Tracking 164157 as yet unmatched pairs. 9142 records in RAM.
INFO 2026-06-08 08:12:28 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:13:04s. Time for last 1,000,000: 1s. Last read position: chr14:24,304,092
INFO 2026-06-08 08:12:28 MarkDuplicates Tracking 163515 as yet unmatched pairs. 8500 records in RAM.
INFO 2026-06-08 08:12:30 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:13:05s. Time for last 1,000,000: 1s. Last read position: chr14:39,177,601
INFO 2026-06-08 08:12:30 MarkDuplicates Tracking 162635 as yet unmatched pairs. 7592 records in RAM.
INFO 2026-06-08 08:12:32 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:13:07s. Time for last 1,000,000: 1s. Last read position: chr14:49,586,738
INFO 2026-06-08 08:12:32 MarkDuplicates Tracking 162295 as yet unmatched pairs. 7252 records in RAM.
INFO 2026-06-08 08:12:33 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:13:09s. Time for last 1,000,000: 1s. Last read position: chr14:49,862,629
INFO 2026-06-08 08:12:33 MarkDuplicates Tracking 165260 as yet unmatched pairs. 10213 records in RAM.
INFO 2026-06-08 08:12:35 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:13:10s. Time for last 1,000,000: 1s. Last read position: chr14:55,619,205
INFO 2026-06-08 08:12:35 MarkDuplicates Tracking 161546 as yet unmatched pairs. 6493 records in RAM.
INFO 2026-06-08 08:12:36 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:13:12s. Time for last 1,000,000: 1s. Last read position: chr14:67,390,735
INFO 2026-06-08 08:12:36 MarkDuplicates Tracking 160659 as yet unmatched pairs. 5604 records in RAM.
INFO 2026-06-08 08:12:38 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:13:14s. Time for last 1,000,000: 2s. Last read position: chr14:73,738,600
INFO 2026-06-08 08:12:38 MarkDuplicates Tracking 159979 as yet unmatched pairs. 4922 records in RAM.
INFO 2026-06-08 08:12:40 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:13:16s. Time for last 1,000,000: 1s. Last read position: chr14:77,469,111
INFO 2026-06-08 08:12:40 MarkDuplicates Tracking 159189 as yet unmatched pairs. 4120 records in RAM.
INFO 2026-06-08 08:12:42 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:13:18s. Time for last 1,000,000: 1s. Last read position: chr14:95,103,383
INFO 2026-06-08 08:12:42 MarkDuplicates Tracking 158679 as yet unmatched pairs. 3599 records in RAM.
INFO 2026-06-08 08:12:44 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:13:19s. Time for last 1,000,000: 1s. Last read position: chr14:102,507,737
INFO 2026-06-08 08:12:44 MarkDuplicates Tracking 158210 as yet unmatched pairs. 3087 records in RAM.
INFO 2026-06-08 08:12:45 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:13:21s. Time for last 1,000,000: 1s. Last read position: chr14:104,792,597
INFO 2026-06-08 08:12:45 MarkDuplicates Tracking 156873 as yet unmatched pairs. 1747 records in RAM.
INFO 2026-06-08 08:12:47 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:13:23s. Time for last 1,000,000: 1s. Last read position: chr14:105,588,086
INFO 2026-06-08 08:12:47 MarkDuplicates Tracking 156594 as yet unmatched pairs. 1463 records in RAM.
INFO 2026-06-08 08:12:49 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:13:25s. Time for last 1,000,000: 1s. Last read position: chr14:105,707,801
INFO 2026-06-08 08:12:49 MarkDuplicates Tracking 156133 as yet unmatched pairs. 1002 records in RAM.
INFO 2026-06-08 08:12:50 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:13:26s. Time for last 1,000,000: 1s. Last read position: chr15:23,646,281
INFO 2026-06-08 08:12:50 MarkDuplicates Tracking 155112 as yet unmatched pairs. 8554 records in RAM.
INFO 2026-06-08 08:12:52 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:13:28s. Time for last 1,000,000: 1s. Last read position: chr15:39,582,196
INFO 2026-06-08 08:12:52 MarkDuplicates Tracking 154568 as yet unmatched pairs. 7995 records in RAM.
INFO 2026-06-08 08:12:54 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:13:30s. Time for last 1,000,000: 2s. Last read position: chr15:42,685,151
INFO 2026-06-08 08:12:54 MarkDuplicates Tracking 153593 as yet unmatched pairs. 7012 records in RAM.
INFO 2026-06-08 08:12:57 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:13:32s. Time for last 1,000,000: 2s. Last read position: chr15:48,487,094
INFO 2026-06-08 08:12:57 MarkDuplicates Tracking 152966 as yet unmatched pairs. 6385 records in RAM.
INFO 2026-06-08 08:12:58 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:13:34s. Time for last 1,000,000: 1s. Last read position: chr15:59,173,746
INFO 2026-06-08 08:12:58 MarkDuplicates Tracking 152488 as yet unmatched pairs. 5903 records in RAM.
INFO 2026-06-08 08:13:00 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:13:35s. Time for last 1,000,000: 1s. Last read position: chr15:64,680,193
INFO 2026-06-08 08:13:00 MarkDuplicates Tracking 151758 as yet unmatched pairs. 5173 records in RAM.
INFO 2026-06-08 08:13:02 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:13:37s. Time for last 1,000,000: 1s. Last read position: chr15:71,771,087
INFO 2026-06-08 08:13:02 MarkDuplicates Tracking 151001 as yet unmatched pairs. 4414 records in RAM.
INFO 2026-06-08 08:13:03 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:13:39s. Time for last 1,000,000: 1s. Last read position: chr15:74,035,928
INFO 2026-06-08 08:13:03 MarkDuplicates Tracking 150574 as yet unmatched pairs. 3987 records in RAM.
INFO 2026-06-08 08:13:05 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:13:41s. Time for last 1,000,000: 1s. Last read position: chr15:75,356,300
INFO 2026-06-08 08:13:05 MarkDuplicates Tracking 149380 as yet unmatched pairs. 2792 records in RAM.
INFO 2026-06-08 08:13:07 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:13:43s. Time for last 1,000,000: 2s. Last read position: chr15:80,936,752
INFO 2026-06-08 08:13:07 MarkDuplicates Tracking 148539 as yet unmatched pairs. 1947 records in RAM.
INFO 2026-06-08 08:13:10 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:13:45s. Time for last 1,000,000: 2s. Last read position: chr15:88,857,785
INFO 2026-06-08 08:13:10 MarkDuplicates Tracking 147810 as yet unmatched pairs. 1191 records in RAM.
INFO 2026-06-08 08:13:12 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:13:47s. Time for last 1,000,000: 2s. Last read position: chr15:92,711,877
INFO 2026-06-08 08:13:12 MarkDuplicates Tracking 147067 as yet unmatched pairs. 448 records in RAM.
INFO 2026-06-08 08:13:14 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:13:49s. Time for last 1,000,000: 1s. Last read position: chr16:372,170
INFO 2026-06-08 08:13:14 MarkDuplicates Tracking 146520 as yet unmatched pairs. 20514 records in RAM.
INFO 2026-06-08 08:13:15 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:13:51s. Time for last 1,000,000: 1s. Last read position: chr16:721,679
INFO 2026-06-08 08:13:15 MarkDuplicates Tracking 145256 as yet unmatched pairs. 19249 records in RAM.
INFO 2026-06-08 08:13:17 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:13:53s. Time for last 1,000,000: 1s. Last read position: chr16:1,819,157
INFO 2026-06-08 08:13:17 MarkDuplicates Tracking 144257 as yet unmatched pairs. 18247 records in RAM.
INFO 2026-06-08 08:13:19 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:13:55s. Time for last 1,000,000: 1s. Last read position: chr16:2,117,852
INFO 2026-06-08 08:13:19 MarkDuplicates Tracking 143239 as yet unmatched pairs. 17229 records in RAM.
INFO 2026-06-08 08:13:21 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:13:57s. Time for last 1,000,000: 1s. Last read position: chr16:2,766,012
INFO 2026-06-08 08:13:21 MarkDuplicates Tracking 142707 as yet unmatched pairs. 16697 records in RAM.
INFO 2026-06-08 08:13:23 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:13:58s. Time for last 1,000,000: 1s. Last read position: chr16:3,235,374
INFO 2026-06-08 08:13:23 MarkDuplicates Tracking 141531 as yet unmatched pairs. 15519 records in RAM.
INFO 2026-06-08 08:13:25 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:14:00s. Time for last 1,000,000: 2s. Last read position: chr16:4,795,751
INFO 2026-06-08 08:13:25 MarkDuplicates Tracking 141151 as yet unmatched pairs. 15137 records in RAM.
INFO 2026-06-08 08:13:26 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:14:02s. Time for last 1,000,000: 1s. Last read position: chr16:14,245,561
INFO 2026-06-08 08:13:26 MarkDuplicates Tracking 140089 as yet unmatched pairs. 14072 records in RAM.
INFO 2026-06-08 08:13:28 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:14:04s. Time for last 1,000,000: 1s. Last read position: chr16:15,133,884
INFO 2026-06-08 08:13:28 MarkDuplicates Tracking 139722 as yet unmatched pairs. 13705 records in RAM.
INFO 2026-06-08 08:13:30 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:14:06s. Time for last 1,000,000: 1s. Last read position: chr16:16,324,892
INFO 2026-06-08 08:13:30 MarkDuplicates Tracking 139313 as yet unmatched pairs. 13296 records in RAM.
INFO 2026-06-08 08:13:31 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:14:07s. Time for last 1,000,000: 1s. Last read position: chr16:18,349,994
INFO 2026-06-08 08:13:31 MarkDuplicates Tracking 139007 as yet unmatched pairs. 12989 records in RAM.
INFO 2026-06-08 08:13:33 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:14:09s. Time for last 1,000,000: 2s. Last read position: chr16:19,115,843
INFO 2026-06-08 08:13:33 MarkDuplicates Tracking 138626 as yet unmatched pairs. 12608 records in RAM.
INFO 2026-06-08 08:13:35 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:14:11s. Time for last 1,000,000: 1s. Last read position: chr16:21,456,286
INFO 2026-06-08 08:13:35 MarkDuplicates Tracking 138201 as yet unmatched pairs. 12183 records in RAM.
INFO 2026-06-08 08:13:37 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:14:13s. Time for last 1,000,000: 1s. Last read position: chr16:22,462,295
INFO 2026-06-08 08:13:37 MarkDuplicates Tracking 137914 as yet unmatched pairs. 11896 records in RAM.
INFO 2026-06-08 08:13:39 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:14:14s. Time for last 1,000,000: 1s. Last read position: chr16:23,557,899
INFO 2026-06-08 08:13:39 MarkDuplicates Tracking 137731 as yet unmatched pairs. 11713 records in RAM.
INFO 2026-06-08 08:13:40 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:14:16s. Time for last 1,000,000: 1s. Last read position: chr16:28,538,809
INFO 2026-06-08 08:13:40 MarkDuplicates Tracking 137043 as yet unmatched pairs. 11025 records in RAM.
INFO 2026-06-08 08:13:42 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:14:18s. Time for last 1,000,000: 1s. Last read position: chr16:29,383,566
INFO 2026-06-08 08:13:42 MarkDuplicates Tracking 136483 as yet unmatched pairs. 10463 records in RAM.
INFO 2026-06-08 08:13:43 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:14:19s. Time for last 1,000,000: 1s. Last read position: chr16:29,804,759
INFO 2026-06-08 08:13:43 MarkDuplicates Tracking 136218 as yet unmatched pairs. 10198 records in RAM.
INFO 2026-06-08 08:13:45 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:14:21s. Time for last 1,000,000: 1s. Last read position: chr16:30,122,399
INFO 2026-06-08 08:13:45 MarkDuplicates Tracking 135437 as yet unmatched pairs. 9416 records in RAM.
INFO 2026-06-08 08:13:47 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:14:22s. Time for last 1,000,000: 1s. Last read position: chr16:30,569,891
INFO 2026-06-08 08:13:47 MarkDuplicates Tracking 135036 as yet unmatched pairs. 9015 records in RAM.
INFO 2026-06-08 08:13:48 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:14:24s. Time for last 1,000,000: 1s. Last read position: chr16:30,946,938
INFO 2026-06-08 08:13:48 MarkDuplicates Tracking 134466 as yet unmatched pairs. 8444 records in RAM.
INFO 2026-06-08 08:13:50 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:14:26s. Time for last 1,000,000: 1s. Last read position: chr16:47,083,369
INFO 2026-06-08 08:13:50 MarkDuplicates Tracking 133507 as yet unmatched pairs. 7483 records in RAM.
INFO 2026-06-08 08:13:52 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:14:28s. Time for last 1,000,000: 1s. Last read position: chr16:57,567,913
INFO 2026-06-08 08:13:52 MarkDuplicates Tracking 132748 as yet unmatched pairs. 6716 records in RAM.
INFO 2026-06-08 08:13:54 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:14:29s. Time for last 1,000,000: 1s. Last read position: chr16:67,284,317
INFO 2026-06-08 08:13:54 MarkDuplicates Tracking 131934 as yet unmatched pairs. 5899 records in RAM.
INFO 2026-06-08 08:13:55 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:14:31s. Time for last 1,000,000: 1s. Last read position: chr16:68,823,395
INFO 2026-06-08 08:13:55 MarkDuplicates Tracking 131126 as yet unmatched pairs. 5088 records in RAM.
INFO 2026-06-08 08:13:58 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:14:33s. Time for last 1,000,000: 2s. Last read position: chr16:70,679,311
INFO 2026-06-08 08:13:58 MarkDuplicates Tracking 130387 as yet unmatched pairs. 4348 records in RAM.
INFO 2026-06-08 08:14:00 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:14:36s. Time for last 1,000,000: 2s. Last read position: chr16:75,264,365
INFO 2026-06-08 08:14:00 MarkDuplicates Tracking 129664 as yet unmatched pairs. 3619 records in RAM.
INFO 2026-06-08 08:14:02 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:14:38s. Time for last 1,000,000: 1s. Last read position: chr16:85,555,648
INFO 2026-06-08 08:14:02 MarkDuplicates Tracking 128799 as yet unmatched pairs. 2736 records in RAM.
INFO 2026-06-08 08:14:04 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:14:40s. Time for last 1,000,000: 2s. Last read position: chr16:88,611,272
INFO 2026-06-08 08:14:04 MarkDuplicates Tracking 128016 as yet unmatched pairs. 1948 records in RAM.
INFO 2026-06-08 08:14:07 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:14:42s. Time for last 1,000,000: 2s. Last read position: chr16:89,561,274
INFO 2026-06-08 08:14:07 MarkDuplicates Tracking 128016 as yet unmatched pairs. 1948 records in RAM.
INFO 2026-06-08 08:14:09 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:14:44s. Time for last 1,000,000: 2s. Last read position: chr16:90,039,522
INFO 2026-06-08 08:14:09 MarkDuplicates Tracking 126093 as yet unmatched pairs. 25 records in RAM.
INFO 2026-06-08 08:14:11 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:14:47s. Time for last 1,000,000: 2s. Last read position: chr17:1,649,687
INFO 2026-06-08 08:14:11 MarkDuplicates Tracking 125448 as yet unmatched pairs. 31081 records in RAM.
INFO 2026-06-08 08:14:13 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:14:48s. Time for last 1,000,000: 1s. Last read position: chr17:3,660,222
INFO 2026-06-08 08:14:13 MarkDuplicates Tracking 124718 as yet unmatched pairs. 30351 records in RAM.
INFO 2026-06-08 08:14:15 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:14:51s. Time for last 1,000,000: 2s. Last read position: chr17:4,891,525
INFO 2026-06-08 08:14:15 MarkDuplicates Tracking 124309 as yet unmatched pairs. 29942 records in RAM.
INFO 2026-06-08 08:14:17 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:14:53s. Time for last 1,000,000: 1s. Last read position: chr17:7,224,234
INFO 2026-06-08 08:14:17 MarkDuplicates Tracking 123277 as yet unmatched pairs. 28907 records in RAM.
INFO 2026-06-08 08:14:19 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:14:55s. Time for last 1,000,000: 1s. Last read position: chr17:7,557,462
INFO 2026-06-08 08:14:19 MarkDuplicates Tracking 122637 as yet unmatched pairs. 28267 records in RAM.
INFO 2026-06-08 08:14:21 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:14:57s. Time for last 1,000,000: 1s. Last read position: chr17:8,160,837
INFO 2026-06-08 08:14:21 MarkDuplicates Tracking 121751 as yet unmatched pairs. 27379 records in RAM.
INFO 2026-06-08 08:14:23 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:14:59s. Time for last 1,000,000: 2s. Last read position: chr17:16,382,268
INFO 2026-06-08 08:14:23 MarkDuplicates Tracking 121318 as yet unmatched pairs. 26944 records in RAM.
INFO 2026-06-08 08:14:26 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:15:02s. Time for last 1,000,000: 2s. Last read position: chr17:18,277,904
INFO 2026-06-08 08:14:26 MarkDuplicates Tracking 120242 as yet unmatched pairs. 25868 records in RAM.
INFO 2026-06-08 08:14:28 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:15:03s. Time for last 1,000,000: 1s. Last read position: chr17:27,643,552
INFO 2026-06-08 08:14:28 MarkDuplicates Tracking 120106 as yet unmatched pairs. 25731 records in RAM.
INFO 2026-06-08 08:14:30 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:15:05s. Time for last 1,000,000: 2s. Last read position: chr17:29,575,629
INFO 2026-06-08 08:14:30 MarkDuplicates Tracking 118972 as yet unmatched pairs. 24595 records in RAM.
INFO 2026-06-08 08:14:32 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:15:07s. Time for last 1,000,000: 1s. Last read position: chr17:35,674,222
INFO 2026-06-08 08:14:32 MarkDuplicates Tracking 118242 as yet unmatched pairs. 23862 records in RAM.
INFO 2026-06-08 08:14:33 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:15:09s. Time for last 1,000,000: 1s. Last read position: chr17:38,562,127
INFO 2026-06-08 08:14:33 MarkDuplicates Tracking 117705 as yet unmatched pairs. 23325 records in RAM.
INFO 2026-06-08 08:14:35 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:15:11s. Time for last 1,000,000: 1s. Last read position: chr17:39,708,337
INFO 2026-06-08 08:14:35 MarkDuplicates Tracking 117051 as yet unmatched pairs. 22671 records in RAM.
INFO 2026-06-08 08:14:37 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:15:13s. Time for last 1,000,000: 1s. Last read position: chr17:40,247,060
INFO 2026-06-08 08:14:37 MarkDuplicates Tracking 116239 as yet unmatched pairs. 21858 records in RAM.
INFO 2026-06-08 08:14:39 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:15:15s. Time for last 1,000,000: 1s. Last read position: chr17:42,324,797
INFO 2026-06-08 08:14:39 MarkDuplicates Tracking 115505 as yet unmatched pairs. 21124 records in RAM.
INFO 2026-06-08 08:14:41 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:15:17s. Time for last 1,000,000: 1s. Last read position: chr17:43,533,832
INFO 2026-06-08 08:14:41 MarkDuplicates Tracking 115955 as yet unmatched pairs. 21573 records in RAM.
INFO 2026-06-08 08:14:43 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:15:18s. Time for last 1,000,000: 1s. Last read position: chr17:45,424,005
INFO 2026-06-08 08:14:43 MarkDuplicates Tracking 113974 as yet unmatched pairs. 19591 records in RAM.
INFO 2026-06-08 08:14:45 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:15:20s. Time for last 1,000,000: 1s. Last read position: chr17:47,916,520
INFO 2026-06-08 08:14:45 MarkDuplicates Tracking 113403 as yet unmatched pairs. 19018 records in RAM.
INFO 2026-06-08 08:14:47 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:15:23s. Time for last 1,000,000: 2s. Last read position: chr17:50,185,841
INFO 2026-06-08 08:14:47 MarkDuplicates Tracking 113905 as yet unmatched pairs. 19518 records in RAM.
INFO 2026-06-08 08:14:49 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:15:25s. Time for last 1,000,000: 2s. Last read position: chr17:50,187,514
INFO 2026-06-08 08:14:49 MarkDuplicates Tracking 116218 as yet unmatched pairs. 21831 records in RAM.
INFO 2026-06-08 08:14:51 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:15:27s. Time for last 1,000,000: 1s. Last read position: chr17:50,188,746
INFO 2026-06-08 08:14:51 MarkDuplicates Tracking 114346 as yet unmatched pairs. 19958 records in RAM.
INFO 2026-06-08 08:14:53 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:15:29s. Time for last 1,000,000: 1s. Last read position: chr17:50,189,517
INFO 2026-06-08 08:14:53 MarkDuplicates Tracking 117256 as yet unmatched pairs. 22868 records in RAM.
INFO 2026-06-08 08:14:55 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:15:31s. Time for last 1,000,000: 2s. Last read position: chr17:50,190,351
INFO 2026-06-08 08:14:55 MarkDuplicates Tracking 116401 as yet unmatched pairs. 22013 records in RAM.
INFO 2026-06-08 08:14:57 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:15:33s. Time for last 1,000,000: 1s. Last read position: chr17:50,192,509
INFO 2026-06-08 08:14:57 MarkDuplicates Tracking 114054 as yet unmatched pairs. 19666 records in RAM.
INFO 2026-06-08 08:14:59 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:15:35s. Time for last 1,000,000: 2s. Last read position: chr17:50,194,129
INFO 2026-06-08 08:14:59 MarkDuplicates Tracking 113910 as yet unmatched pairs. 19522 records in RAM.
INFO 2026-06-08 08:15:01 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:15:37s. Time for last 1,000,000: 2s. Last read position: chr17:50,195,265
INFO 2026-06-08 08:15:01 MarkDuplicates Tracking 112412 as yet unmatched pairs. 18024 records in RAM.
INFO 2026-06-08 08:15:03 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:15:39s. Time for last 1,000,000: 2s. Last read position: chr17:50,196,177
INFO 2026-06-08 08:15:03 MarkDuplicates Tracking 113583 as yet unmatched pairs. 19195 records in RAM.
INFO 2026-06-08 08:15:06 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:15:41s. Time for last 1,000,000: 2s. Last read position: chr17:50,197,731
INFO 2026-06-08 08:15:06 MarkDuplicates Tracking 112338 as yet unmatched pairs. 17950 records in RAM.
INFO 2026-06-08 08:15:08 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:15:44s. Time for last 1,000,000: 2s. Last read position: chr17:50,199,440
INFO 2026-06-08 08:15:08 MarkDuplicates Tracking 106559 as yet unmatched pairs. 12171 records in RAM.
INFO 2026-06-08 08:15:10 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:15:46s. Time for last 1,000,000: 1s. Last read position: chr17:56,913,475
INFO 2026-06-08 08:15:10 MarkDuplicates Tracking 104098 as yet unmatched pairs. 9708 records in RAM.
INFO 2026-06-08 08:15:12 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:15:47s. Time for last 1,000,000: 1s. Last read position: chr17:58,358,134
INFO 2026-06-08 08:15:12 MarkDuplicates Tracking 105016 as yet unmatched pairs. 10626 records in RAM.
INFO 2026-06-08 08:15:14 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:15:49s. Time for last 1,000,000: 1s. Last read position: chr17:60,525,763
INFO 2026-06-08 08:15:14 MarkDuplicates Tracking 102322 as yet unmatched pairs. 7930 records in RAM.
INFO 2026-06-08 08:15:15 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:15:51s. Time for last 1,000,000: 1s. Last read position: chr17:64,896,789
INFO 2026-06-08 08:15:15 MarkDuplicates Tracking 101443 as yet unmatched pairs. 7045 records in RAM.
INFO 2026-06-08 08:15:17 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:15:53s. Time for last 1,000,000: 1s. Last read position: chr17:72,124,043
INFO 2026-06-08 08:15:17 MarkDuplicates Tracking 101010 as yet unmatched pairs. 6611 records in RAM.
INFO 2026-06-08 08:15:19 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:15:54s. Time for last 1,000,000: 1s. Last read position: chr17:75,546,789
INFO 2026-06-08 08:15:19 MarkDuplicates Tracking 100267 as yet unmatched pairs. 5856 records in RAM.
INFO 2026-06-08 08:15:21 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:15:57s. Time for last 1,000,000: 2s. Last read position: chr17:75,778,588
INFO 2026-06-08 08:15:21 MarkDuplicates Tracking 99508 as yet unmatched pairs. 5097 records in RAM.
INFO 2026-06-08 08:15:23 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:15:59s. Time for last 1,000,000: 1s. Last read position: chr17:76,737,080
INFO 2026-06-08 08:15:23 MarkDuplicates Tracking 98316 as yet unmatched pairs. 3905 records in RAM.
INFO 2026-06-08 08:15:25 MarkDuplicates Read 368,000,000 records. Elapsed time: 00:16:00s. Time for last 1,000,000: 1s. Last read position: chr17:79,085,732
INFO 2026-06-08 08:15:25 MarkDuplicates Tracking 97995 as yet unmatched pairs. 3584 records in RAM.
INFO 2026-06-08 08:15:26 MarkDuplicates Read 369,000,000 records. Elapsed time: 00:16:02s. Time for last 1,000,000: 1s. Last read position: chr17:81,229,108
INFO 2026-06-08 08:15:26 MarkDuplicates Tracking 96675 as yet unmatched pairs. 2262 records in RAM.
INFO 2026-06-08 08:15:29 MarkDuplicates Read 370,000,000 records. Elapsed time: 00:16:04s. Time for last 1,000,000: 2s. Last read position: chr17:81,869,363
INFO 2026-06-08 08:15:29 MarkDuplicates Tracking 96073 as yet unmatched pairs. 1659 records in RAM.
INFO 2026-06-08 08:15:31 MarkDuplicates Read 371,000,000 records. Elapsed time: 00:16:06s. Time for last 1,000,000: 2s. Last read position: chr17:82,443,840
INFO 2026-06-08 08:15:31 MarkDuplicates Tracking 94736 as yet unmatched pairs. 319 records in RAM.
INFO 2026-06-08 08:15:33 MarkDuplicates Read 372,000,000 records. Elapsed time: 00:16:08s. Time for last 1,000,000: 1s. Last read position: chr18:13,053,023
INFO 2026-06-08 08:15:33 MarkDuplicates Tracking 93934 as yet unmatched pairs. 1916 records in RAM.
INFO 2026-06-08 08:15:34 MarkDuplicates Read 373,000,000 records. Elapsed time: 00:16:10s. Time for last 1,000,000: 1s. Last read position: chr18:48,950,146
INFO 2026-06-08 08:15:34 MarkDuplicates Tracking 93311 as yet unmatched pairs. 1291 records in RAM.
INFO 2026-06-08 08:15:36 MarkDuplicates Read 374,000,000 records. Elapsed time: 00:16:12s. Time for last 1,000,000: 1s. Last read position: chr18:75,800,995
INFO 2026-06-08 08:15:36 MarkDuplicates Tracking 92241 as yet unmatched pairs. 215 records in RAM.
INFO 2026-06-08 08:15:39 MarkDuplicates Read 375,000,000 records. Elapsed time: 00:16:15s. Time for last 1,000,000: 2s. Last read position: chr19:810,703
INFO 2026-06-08 08:15:39 MarkDuplicates Tracking 91673 as yet unmatched pairs. 33277 records in RAM.
INFO 2026-06-08 08:15:41 MarkDuplicates Read 376,000,000 records. Elapsed time: 00:16:17s. Time for last 1,000,000: 2s. Last read position: chr19:1,254,346
INFO 2026-06-08 08:15:41 MarkDuplicates Tracking 90799 as yet unmatched pairs. 32403 records in RAM.
INFO 2026-06-08 08:15:43 MarkDuplicates Read 377,000,000 records. Elapsed time: 00:16:19s. Time for last 1,000,000: 1s. Last read position: chr19:1,828,092
INFO 2026-06-08 08:15:43 MarkDuplicates Tracking 89359 as yet unmatched pairs. 30960 records in RAM.
INFO 2026-06-08 08:15:45 MarkDuplicates Read 378,000,000 records. Elapsed time: 00:16:21s. Time for last 1,000,000: 1s. Last read position: chr19:2,328,331
INFO 2026-06-08 08:15:45 MarkDuplicates Tracking 88291 as yet unmatched pairs. 29891 records in RAM.
INFO 2026-06-08 08:15:48 MarkDuplicates Read 379,000,000 records. Elapsed time: 00:16:23s. Time for last 1,000,000: 2s. Last read position: chr19:3,751,507
INFO 2026-06-08 08:15:48 MarkDuplicates Tracking 87371 as yet unmatched pairs. 28968 records in RAM.
INFO 2026-06-08 08:15:50 MarkDuplicates Read 380,000,000 records. Elapsed time: 00:16:26s. Time for last 1,000,000: 2s. Last read position: chr19:4,929,219
INFO 2026-06-08 08:15:50 MarkDuplicates Tracking 86565 as yet unmatched pairs. 28158 records in RAM.
INFO 2026-06-08 08:15:53 MarkDuplicates Read 381,000,000 records. Elapsed time: 00:16:29s. Time for last 1,000,000: 3s. Last read position: chr19:5,994,852
INFO 2026-06-08 08:15:53 MarkDuplicates Tracking 85820 as yet unmatched pairs. 27411 records in RAM.
INFO 2026-06-08 08:15:56 MarkDuplicates Read 382,000,000 records. Elapsed time: 00:16:31s. Time for last 1,000,000: 2s. Last read position: chr19:7,611,794
INFO 2026-06-08 08:15:56 MarkDuplicates Tracking 85235 as yet unmatched pairs. 26826 records in RAM.
INFO 2026-06-08 08:15:58 MarkDuplicates Read 383,000,000 records. Elapsed time: 00:16:34s. Time for last 1,000,000: 2s. Last read position: chr19:10,118,881
INFO 2026-06-08 08:15:58 MarkDuplicates Tracking 84221 as yet unmatched pairs. 25811 records in RAM.
INFO 2026-06-08 08:16:00 MarkDuplicates Read 384,000,000 records. Elapsed time: 00:16:36s. Time for last 1,000,000: 2s. Last read position: chr19:10,871,893
INFO 2026-06-08 08:16:00 MarkDuplicates Tracking 83248 as yet unmatched pairs. 24838 records in RAM.
INFO 2026-06-08 08:16:02 MarkDuplicates Read 385,000,000 records. Elapsed time: 00:16:38s. Time for last 1,000,000: 1s. Last read position: chr19:12,179,263
INFO 2026-06-08 08:16:02 MarkDuplicates Tracking 82482 as yet unmatched pairs. 24071 records in RAM.
INFO 2026-06-08 08:16:04 MarkDuplicates Read 386,000,000 records. Elapsed time: 00:16:40s. Time for last 1,000,000: 2s. Last read position: chr19:13,153,339
INFO 2026-06-08 08:16:04 MarkDuplicates Tracking 82213 as yet unmatched pairs. 23802 records in RAM.
INFO 2026-06-08 08:16:06 MarkDuplicates Read 387,000,000 records. Elapsed time: 00:16:42s. Time for last 1,000,000: 2s. Last read position: chr19:14,451,941
INFO 2026-06-08 08:16:06 MarkDuplicates Tracking 80433 as yet unmatched pairs. 22019 records in RAM.
INFO 2026-06-08 08:16:08 MarkDuplicates Read 388,000,000 records. Elapsed time: 00:16:44s. Time for last 1,000,000: 1s. Last read position: chr19:15,243,309
INFO 2026-06-08 08:16:08 MarkDuplicates Tracking 79998 as yet unmatched pairs. 21583 records in RAM.
INFO 2026-06-08 08:16:10 MarkDuplicates Read 389,000,000 records. Elapsed time: 00:16:46s. Time for last 1,000,000: 2s. Last read position: chr19:16,185,672
INFO 2026-06-08 08:16:10 MarkDuplicates Tracking 78908 as yet unmatched pairs. 20492 records in RAM.
INFO 2026-06-08 08:16:12 MarkDuplicates Read 390,000,000 records. Elapsed time: 00:16:48s. Time for last 1,000,000: 2s. Last read position: chr19:17,807,871
INFO 2026-06-08 08:16:12 MarkDuplicates Tracking 78426 as yet unmatched pairs. 20007 records in RAM.
INFO 2026-06-08 08:16:15 MarkDuplicates Read 391,000,000 records. Elapsed time: 00:16:50s. Time for last 1,000,000: 2s. Last read position: chr19:18,450,839
INFO 2026-06-08 08:16:15 MarkDuplicates Tracking 76913 as yet unmatched pairs. 18494 records in RAM.
INFO 2026-06-08 08:16:17 MarkDuplicates Read 392,000,000 records. Elapsed time: 00:16:52s. Time for last 1,000,000: 2s. Last read position: chr19:19,646,271
INFO 2026-06-08 08:16:17 MarkDuplicates Tracking 76063 as yet unmatched pairs. 17643 records in RAM.
INFO 2026-06-08 08:16:19 MarkDuplicates Read 393,000,000 records. Elapsed time: 00:16:54s. Time for last 1,000,000: 1s. Last read position: chr19:35,013,254
INFO 2026-06-08 08:16:19 MarkDuplicates Tracking 75381 as yet unmatched pairs. 16960 records in RAM.
INFO 2026-06-08 08:16:21 MarkDuplicates Read 394,000,000 records. Elapsed time: 00:16:56s. Time for last 1,000,000: 1s. Last read position: chr19:35,787,326
INFO 2026-06-08 08:16:21 MarkDuplicates Tracking 74140 as yet unmatched pairs. 15719 records in RAM.
INFO 2026-06-08 08:16:23 MarkDuplicates Read 395,000,000 records. Elapsed time: 00:16:58s. Time for last 1,000,000: 2s. Last read position: chr19:38,723,957
INFO 2026-06-08 08:16:23 MarkDuplicates Tracking 73085 as yet unmatched pairs. 14662 records in RAM.
INFO 2026-06-08 08:16:25 MarkDuplicates Read 396,000,000 records. Elapsed time: 00:17:01s. Time for last 1,000,000: 2s. Last read position: chr19:39,408,466
INFO 2026-06-08 08:16:25 MarkDuplicates Tracking 72404 as yet unmatched pairs. 13980 records in RAM.
INFO 2026-06-08 08:16:26 MarkDuplicates Read 397,000,000 records. Elapsed time: 00:17:02s. Time for last 1,000,000: 1s. Last read position: chr19:40,192,347
INFO 2026-06-08 08:16:26 MarkDuplicates Tracking 71489 as yet unmatched pairs. 13065 records in RAM.
INFO 2026-06-08 08:16:28 MarkDuplicates Read 398,000,000 records. Elapsed time: 00:17:04s. Time for last 1,000,000: 1s. Last read position: chr19:41,305,805
INFO 2026-06-08 08:16:28 MarkDuplicates Tracking 70828 as yet unmatched pairs. 12403 records in RAM.
INFO 2026-06-08 08:16:30 MarkDuplicates Read 399,000,000 records. Elapsed time: 00:17:06s. Time for last 1,000,000: 1s. Last read position: chr19:41,761,288
INFO 2026-06-08 08:16:30 MarkDuplicates Tracking 70455 as yet unmatched pairs. 12030 records in RAM.
INFO 2026-06-08 08:16:34 MarkDuplicates Read 400,000,000 records. Elapsed time: 00:17:09s. Time for last 1,000,000: 3s. Last read position: chr19:42,286,842
INFO 2026-06-08 08:16:34 MarkDuplicates Tracking 69801 as yet unmatched pairs. 11376 records in RAM.
INFO 2026-06-08 08:16:36 MarkDuplicates Read 401,000,000 records. Elapsed time: 00:17:11s. Time for last 1,000,000: 2s. Last read position: chr19:43,750,622
INFO 2026-06-08 08:16:36 MarkDuplicates Tracking 68282 as yet unmatched pairs. 9820 records in RAM.
INFO 2026-06-08 08:16:38 MarkDuplicates Read 402,000,000 records. Elapsed time: 00:17:13s. Time for last 1,000,000: 1s. Last read position: chr19:45,468,647
INFO 2026-06-08 08:16:38 MarkDuplicates Tracking 67526 as yet unmatched pairs. 9063 records in RAM.
INFO 2026-06-08 08:16:39 MarkDuplicates Read 403,000,000 records. Elapsed time: 00:17:15s. Time for last 1,000,000: 1s. Last read position: chr19:46,605,827
INFO 2026-06-08 08:16:39 MarkDuplicates Tracking 66688 as yet unmatched pairs. 8223 records in RAM.
INFO 2026-06-08 08:16:41 MarkDuplicates Read 404,000,000 records. Elapsed time: 00:17:17s. Time for last 1,000,000: 1s. Last read position: chr19:47,750,986
INFO 2026-06-08 08:16:41 MarkDuplicates Tracking 65555 as yet unmatched pairs. 7084 records in RAM.
INFO 2026-06-08 08:16:43 MarkDuplicates Read 405,000,000 records. Elapsed time: 00:17:19s. Time for last 1,000,000: 1s. Last read position: chr19:48,873,461
INFO 2026-06-08 08:16:43 MarkDuplicates Tracking 64634 as yet unmatched pairs. 6161 records in RAM.
INFO 2026-06-08 08:16:45 MarkDuplicates Read 406,000,000 records. Elapsed time: 00:17:21s. Time for last 1,000,000: 2s. Last read position: chr19:49,514,378
INFO 2026-06-08 08:16:45 MarkDuplicates Tracking 64323 as yet unmatched pairs. 5850 records in RAM.
INFO 2026-06-08 08:16:48 MarkDuplicates Read 407,000,000 records. Elapsed time: 00:17:23s. Time for last 1,000,000: 2s. Last read position: chr19:49,851,455
INFO 2026-06-08 08:16:48 MarkDuplicates Tracking 62993 as yet unmatched pairs. 4520 records in RAM.
INFO 2026-06-08 08:16:50 MarkDuplicates Read 408,000,000 records. Elapsed time: 00:17:25s. Time for last 1,000,000: 2s. Last read position: chr19:50,482,441
INFO 2026-06-08 08:16:50 MarkDuplicates Tracking 62245 as yet unmatched pairs. 3772 records in RAM.
INFO 2026-06-08 08:16:52 MarkDuplicates Read 409,000,000 records. Elapsed time: 00:17:28s. Time for last 1,000,000: 2s. Last read position: chr19:54,220,586
INFO 2026-06-08 08:16:52 MarkDuplicates Tracking 61318 as yet unmatched pairs. 2844 records in RAM.
INFO 2026-06-08 08:16:54 MarkDuplicates Read 410,000,000 records. Elapsed time: 00:17:30s. Time for last 1,000,000: 2s. Last read position: chr19:55,384,035
INFO 2026-06-08 08:16:54 MarkDuplicates Tracking 60478 as yet unmatched pairs. 2003 records in RAM.
INFO 2026-06-08 08:16:57 MarkDuplicates Read 411,000,000 records. Elapsed time: 00:17:32s. Time for last 1,000,000: 2s. Last read position: chr19:57,278,306
INFO 2026-06-08 08:16:57 MarkDuplicates Tracking 59150 as yet unmatched pairs. 675 records in RAM.
INFO 2026-06-08 08:16:59 MarkDuplicates Read 412,000,000 records. Elapsed time: 00:17:35s. Time for last 1,000,000: 2s. Last read position: chr20:483,979
INFO 2026-06-08 08:16:59 MarkDuplicates Tracking 58414 as yet unmatched pairs. 12186 records in RAM.
INFO 2026-06-08 08:17:02 MarkDuplicates Read 413,000,000 records. Elapsed time: 00:17:38s. Time for last 1,000,000: 2s. Last read position: chr20:10,423,274
INFO 2026-06-08 08:17:02 MarkDuplicates Tracking 57511 as yet unmatched pairs. 11282 records in RAM.
INFO 2026-06-08 08:17:04 MarkDuplicates Read 414,000,000 records. Elapsed time: 00:17:40s. Time for last 1,000,000: 2s. Last read position: chr20:22,582,914
INFO 2026-06-08 08:17:04 MarkDuplicates Tracking 56889 as yet unmatched pairs. 10656 records in RAM.
INFO 2026-06-08 08:17:06 MarkDuplicates Read 415,000,000 records. Elapsed time: 00:17:42s. Time for last 1,000,000: 1s. Last read position: chr20:32,310,661
INFO 2026-06-08 08:17:06 MarkDuplicates Tracking 55990 as yet unmatched pairs. 9755 records in RAM.
INFO 2026-06-08 08:17:08 MarkDuplicates Read 416,000,000 records. Elapsed time: 00:17:44s. Time for last 1,000,000: 1s. Last read position: chr20:34,757,557
INFO 2026-06-08 08:17:08 MarkDuplicates Tracking 55516 as yet unmatched pairs. 9275 records in RAM.
INFO 2026-06-08 08:17:10 MarkDuplicates Read 417,000,000 records. Elapsed time: 00:17:46s. Time for last 1,000,000: 1s. Last read position: chr20:35,729,312
INFO 2026-06-08 08:17:10 MarkDuplicates Tracking 54477 as yet unmatched pairs. 8235 records in RAM.
INFO 2026-06-08 08:17:12 MarkDuplicates Read 418,000,000 records. Elapsed time: 00:17:47s. Time for last 1,000,000: 1s. Last read position: chr20:38,500,977
INFO 2026-06-08 08:17:12 MarkDuplicates Tracking 53669 as yet unmatched pairs. 7425 records in RAM.
INFO 2026-06-08 08:17:14 MarkDuplicates Read 419,000,000 records. Elapsed time: 00:17:49s. Time for last 1,000,000: 1s. Last read position: chr20:44,513,965
INFO 2026-06-08 08:17:14 MarkDuplicates Tracking 53160 as yet unmatched pairs. 6912 records in RAM.
INFO 2026-06-08 08:17:16 MarkDuplicates Read 420,000,000 records. Elapsed time: 00:17:51s. Time for last 1,000,000: 1s. Last read position: chr20:46,613,506
INFO 2026-06-08 08:17:16 MarkDuplicates Tracking 52359 as yet unmatched pairs. 6111 records in RAM.
INFO 2026-06-08 08:17:18 MarkDuplicates Read 421,000,000 records. Elapsed time: 00:17:54s. Time for last 1,000,000: 2s. Last read position: chr20:50,191,993
INFO 2026-06-08 08:17:18 MarkDuplicates Tracking 51952 as yet unmatched pairs. 5704 records in RAM.
INFO 2026-06-08 08:17:20 MarkDuplicates Read 422,000,000 records. Elapsed time: 00:17:56s. Time for last 1,000,000: 1s. Last read position: chr20:57,652,563
INFO 2026-06-08 08:17:20 MarkDuplicates Tracking 51015 as yet unmatched pairs. 4766 records in RAM.
INFO 2026-06-08 08:17:22 MarkDuplicates Read 423,000,000 records. Elapsed time: 00:17:58s. Time for last 1,000,000: 1s. Last read position: chr20:62,310,711
INFO 2026-06-08 08:17:22 MarkDuplicates Tracking 50054 as yet unmatched pairs. 3803 records in RAM.
INFO 2026-06-08 08:17:24 MarkDuplicates Read 424,000,000 records. Elapsed time: 00:18:00s. Time for last 1,000,000: 2s. Last read position: chr20:62,813,454
INFO 2026-06-08 08:17:24 MarkDuplicates Tracking 49153 as yet unmatched pairs. 2901 records in RAM.
INFO 2026-06-08 08:17:26 MarkDuplicates Read 425,000,000 records. Elapsed time: 00:18:02s. Time for last 1,000,000: 2s. Last read position: chr20:63,521,846
INFO 2026-06-08 08:17:26 MarkDuplicates Tracking 48340 as yet unmatched pairs. 2088 records in RAM.
INFO 2026-06-08 08:17:28 MarkDuplicates Read 426,000,000 records. Elapsed time: 00:18:04s. Time for last 1,000,000: 2s. Last read position: chr20:63,700,670
INFO 2026-06-08 08:17:28 MarkDuplicates Tracking 47168 as yet unmatched pairs. 916 records in RAM.
INFO 2026-06-08 08:17:30 MarkDuplicates Read 427,000,000 records. Elapsed time: 00:18:06s. Time for last 1,000,000: 1s. Last read position: chr21:6,121,285
INFO 2026-06-08 08:17:30 MarkDuplicates Tracking 46191 as yet unmatched pairs. 15804 records in RAM.
INFO 2026-06-08 08:17:32 MarkDuplicates Read 428,000,000 records. Elapsed time: 00:18:07s. Time for last 1,000,000: 1s. Last read position: chr21:8,213,385
INFO 2026-06-08 08:17:32 MarkDuplicates Tracking 45854 as yet unmatched pairs. 15467 records in RAM.
INFO 2026-06-08 08:17:33 MarkDuplicates Read 429,000,000 records. Elapsed time: 00:18:09s. Time for last 1,000,000: 1s. Last read position: chr21:8,215,994
INFO 2026-06-08 08:17:33 MarkDuplicates Tracking 45639 as yet unmatched pairs. 15252 records in RAM.
INFO 2026-06-08 08:17:34 MarkDuplicates Read 430,000,000 records. Elapsed time: 00:18:10s. Time for last 1,000,000: 1s. Last read position: chr21:8,216,848
INFO 2026-06-08 08:17:34 MarkDuplicates Tracking 43447 as yet unmatched pairs. 13015 records in RAM.
INFO 2026-06-08 08:17:36 MarkDuplicates Read 431,000,000 records. Elapsed time: 00:18:12s. Time for last 1,000,000: 1s. Last read position: chr21:8,218,649
INFO 2026-06-08 08:17:36 MarkDuplicates Tracking 42716 as yet unmatched pairs. 12281 records in RAM.
INFO 2026-06-08 08:17:38 MarkDuplicates Read 432,000,000 records. Elapsed time: 00:18:14s. Time for last 1,000,000: 2s. Last read position: chr21:8,257,864
INFO 2026-06-08 08:17:38 MarkDuplicates Tracking 42193 as yet unmatched pairs. 11756 records in RAM.
INFO 2026-06-08 08:17:40 MarkDuplicates Read 433,000,000 records. Elapsed time: 00:18:15s. Time for last 1,000,000: 1s. Last read position: chr21:8,258,958
INFO 2026-06-08 08:17:40 MarkDuplicates Tracking 42098 as yet unmatched pairs. 11661 records in RAM.
INFO 2026-06-08 08:17:41 MarkDuplicates Read 434,000,000 records. Elapsed time: 00:18:17s. Time for last 1,000,000: 1s. Last read position: chr21:8,260,319
INFO 2026-06-08 08:17:41 MarkDuplicates Tracking 41702 as yet unmatched pairs. 11264 records in RAM.
INFO 2026-06-08 08:17:43 MarkDuplicates Read 435,000,000 records. Elapsed time: 00:18:18s. Time for last 1,000,000: 1s. Last read position: chr21:8,396,720
INFO 2026-06-08 08:17:43 MarkDuplicates Tracking 41136 as yet unmatched pairs. 10698 records in RAM.
INFO 2026-06-08 08:17:44 MarkDuplicates Read 436,000,000 records. Elapsed time: 00:18:20s. Time for last 1,000,000: 1s. Last read position: chr21:8,399,068
INFO 2026-06-08 08:17:44 MarkDuplicates Tracking 41041 as yet unmatched pairs. 10601 records in RAM.
INFO 2026-06-08 08:17:45 MarkDuplicates Read 437,000,000 records. Elapsed time: 00:18:21s. Time for last 1,000,000: 1s. Last read position: chr21:8,399,883
INFO 2026-06-08 08:17:45 MarkDuplicates Tracking 40357 as yet unmatched pairs. 9906 records in RAM.
INFO 2026-06-08 08:17:47 MarkDuplicates Read 438,000,000 records. Elapsed time: 00:18:23s. Time for last 1,000,000: 1s. Last read position: chr21:8,400,328
INFO 2026-06-08 08:17:47 MarkDuplicates Tracking 37822 as yet unmatched pairs. 7369 records in RAM.
INFO 2026-06-08 08:17:48 MarkDuplicates Read 439,000,000 records. Elapsed time: 00:18:24s. Time for last 1,000,000: 1s. Last read position: chr21:8,439,095
INFO 2026-06-08 08:17:48 MarkDuplicates Tracking 37143 as yet unmatched pairs. 6688 records in RAM.
INFO 2026-06-08 08:17:49 MarkDuplicates Read 440,000,000 records. Elapsed time: 00:18:25s. Time for last 1,000,000: 1s. Last read position: chr21:8,441,948
INFO 2026-06-08 08:17:49 MarkDuplicates Tracking 36939 as yet unmatched pairs. 6484 records in RAM.
INFO 2026-06-08 08:17:51 MarkDuplicates Read 441,000,000 records. Elapsed time: 00:18:26s. Time for last 1,000,000: 1s. Last read position: chr21:8,443,258
INFO 2026-06-08 08:17:51 MarkDuplicates Tracking 36590 as yet unmatched pairs. 6135 records in RAM.
INFO 2026-06-08 08:17:52 MarkDuplicates Read 442,000,000 records. Elapsed time: 00:18:28s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,121
INFO 2026-06-08 08:17:52 MarkDuplicates Tracking 34874 as yet unmatched pairs. 4414 records in RAM.
INFO 2026-06-08 08:17:53 MarkDuplicates Read 443,000,000 records. Elapsed time: 00:18:29s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,590
INFO 2026-06-08 08:17:53 MarkDuplicates Tracking 34835 as yet unmatched pairs. 4375 records in RAM.
INFO 2026-06-08 08:17:55 MarkDuplicates Read 444,000,000 records. Elapsed time: 00:18:31s. Time for last 1,000,000: 2s. Last read position: chr21:31,873,692
INFO 2026-06-08 08:17:55 MarkDuplicates Tracking 33744 as yet unmatched pairs. 3282 records in RAM.
INFO 2026-06-08 08:17:58 MarkDuplicates Read 445,000,000 records. Elapsed time: 00:18:34s. Time for last 1,000,000: 2s. Last read position: chr21:39,235,749
INFO 2026-06-08 08:17:58 MarkDuplicates Tracking 32893 as yet unmatched pairs. 2431 records in RAM.
INFO 2026-06-08 08:18:00 MarkDuplicates Read 446,000,000 records. Elapsed time: 00:18:36s. Time for last 1,000,000: 2s. Last read position: chr21:43,060,098
INFO 2026-06-08 08:18:00 MarkDuplicates Tracking 32001 as yet unmatched pairs. 1538 records in RAM.
INFO 2026-06-08 08:18:02 MarkDuplicates Read 447,000,000 records. Elapsed time: 00:18:38s. Time for last 1,000,000: 1s. Last read position: chr21:45,509,544
INFO 2026-06-08 08:18:02 MarkDuplicates Tracking 31419 as yet unmatched pairs. 955 records in RAM.
INFO 2026-06-08 08:18:05 MarkDuplicates Read 448,000,000 records. Elapsed time: 00:18:40s. Time for last 1,000,000: 2s. Last read position: chr22:11,702,159
INFO 2026-06-08 08:18:05 MarkDuplicates Tracking 30465 as yet unmatched pairs. 7457 records in RAM.
INFO 2026-06-08 08:18:06 MarkDuplicates Read 449,000,000 records. Elapsed time: 00:18:42s. Time for last 1,000,000: 1s. Last read position: chr22:20,991,816
INFO 2026-06-08 08:18:06 MarkDuplicates Tracking 29665 as yet unmatched pairs. 6657 records in RAM.
INFO 2026-06-08 08:18:08 MarkDuplicates Read 450,000,000 records. Elapsed time: 00:18:44s. Time for last 1,000,000: 1s. Last read position: chr22:24,611,164
INFO 2026-06-08 08:18:08 MarkDuplicates Tracking 28759 as yet unmatched pairs. 5751 records in RAM.
INFO 2026-06-08 08:18:10 MarkDuplicates Read 451,000,000 records. Elapsed time: 00:18:45s. Time for last 1,000,000: 1s. Last read position: chr22:30,020,812
INFO 2026-06-08 08:18:10 MarkDuplicates Tracking 27944 as yet unmatched pairs. 4936 records in RAM.
INFO 2026-06-08 08:18:12 MarkDuplicates Read 452,000,000 records. Elapsed time: 00:18:47s. Time for last 1,000,000: 1s. Last read position: chr22:36,285,703
INFO 2026-06-08 08:18:12 MarkDuplicates Tracking 27605 as yet unmatched pairs. 4597 records in RAM.
INFO 2026-06-08 08:18:13 MarkDuplicates Read 453,000,000 records. Elapsed time: 00:18:49s. Time for last 1,000,000: 1s. Last read position: chr22:37,805,835
INFO 2026-06-08 08:18:13 MarkDuplicates Tracking 26570 as yet unmatched pairs. 3562 records in RAM.
INFO 2026-06-08 08:18:15 MarkDuplicates Read 454,000,000 records. Elapsed time: 00:18:51s. Time for last 1,000,000: 1s. Last read position: chr22:40,789,153
INFO 2026-06-08 08:18:15 MarkDuplicates Tracking 25493 as yet unmatched pairs. 2485 records in RAM.
INFO 2026-06-08 08:18:17 MarkDuplicates Read 455,000,000 records. Elapsed time: 00:18:53s. Time for last 1,000,000: 1s. Last read position: chr22:44,802,080
INFO 2026-06-08 08:18:17 MarkDuplicates Tracking 24836 as yet unmatched pairs. 1827 records in RAM.
INFO 2026-06-08 08:18:19 MarkDuplicates Read 456,000,000 records. Elapsed time: 00:18:54s. Time for last 1,000,000: 1s. Last read position: chr22:50,318,971
INFO 2026-06-08 08:18:19 MarkDuplicates Tracking 23742 as yet unmatched pairs. 730 records in RAM.
INFO 2026-06-08 08:18:21 MarkDuplicates Read 457,000,000 records. Elapsed time: 00:18:57s. Time for last 1,000,000: 2s. Last read position: chrX:2,407,985
INFO 2026-06-08 08:18:21 MarkDuplicates Tracking 22738 as yet unmatched pairs. 8111 records in RAM.
INFO 2026-06-08 08:18:23 MarkDuplicates Read 458,000,000 records. Elapsed time: 00:18:59s. Time for last 1,000,000: 2s. Last read position: chrX:16,719,868
INFO 2026-06-08 08:18:23 MarkDuplicates Tracking 22007 as yet unmatched pairs. 7379 records in RAM.
INFO 2026-06-08 08:18:25 MarkDuplicates Read 459,000,000 records. Elapsed time: 00:19:01s. Time for last 1,000,000: 1s. Last read position: chrX:40,605,581
INFO 2026-06-08 08:18:25 MarkDuplicates Tracking 21382 as yet unmatched pairs. 6693 records in RAM.
INFO 2026-06-08 08:18:27 MarkDuplicates Read 460,000,000 records. Elapsed time: 00:19:02s. Time for last 1,000,000: 1s. Last read position: chrX:48,528,234
INFO 2026-06-08 08:18:27 MarkDuplicates Tracking 20746 as yet unmatched pairs. 6055 records in RAM.
INFO 2026-06-08 08:18:29 MarkDuplicates Read 461,000,000 records. Elapsed time: 00:19:04s. Time for last 1,000,000: 1s. Last read position: chrX:51,896,582
INFO 2026-06-08 08:18:29 MarkDuplicates Tracking 19946 as yet unmatched pairs. 5255 records in RAM.
INFO 2026-06-08 08:18:30 MarkDuplicates Read 462,000,000 records. Elapsed time: 00:19:06s. Time for last 1,000,000: 1s. Last read position: chrX:55,006,798
INFO 2026-06-08 08:18:30 MarkDuplicates Tracking 19297 as yet unmatched pairs. 4605 records in RAM.
INFO 2026-06-08 08:18:32 MarkDuplicates Read 463,000,000 records. Elapsed time: 00:19:08s. Time for last 1,000,000: 1s. Last read position: chrX:71,377,655
INFO 2026-06-08 08:18:32 MarkDuplicates Tracking 18412 as yet unmatched pairs. 3716 records in RAM.
INFO 2026-06-08 08:18:34 MarkDuplicates Read 464,000,000 records. Elapsed time: 00:19:09s. Time for last 1,000,000: 1s. Last read position: chrX:100,138,839
INFO 2026-06-08 08:18:34 MarkDuplicates Tracking 17846 as yet unmatched pairs. 3149 records in RAM.
INFO 2026-06-08 08:18:36 MarkDuplicates Read 465,000,000 records. Elapsed time: 00:19:11s. Time for last 1,000,000: 1s. Last read position: chrX:119,871,151
INFO 2026-06-08 08:18:36 MarkDuplicates Tracking 17109 as yet unmatched pairs. 2411 records in RAM.
INFO 2026-06-08 08:18:37 MarkDuplicates Read 466,000,000 records. Elapsed time: 00:19:13s. Time for last 1,000,000: 1s. Last read position: chrX:148,052,591
INFO 2026-06-08 08:18:37 MarkDuplicates Tracking 16492 as yet unmatched pairs. 1791 records in RAM.
INFO 2026-06-08 08:18:40 MarkDuplicates Read 467,000,000 records. Elapsed time: 00:19:15s. Time for last 1,000,000: 2s. Last read position: chrX:154,019,199
INFO 2026-06-08 08:18:40 MarkDuplicates Tracking 16154 as yet unmatched pairs. 1452 records in RAM.
INFO 2026-06-08 08:18:42 MarkDuplicates Read 468,000,000 records. Elapsed time: 00:19:17s. Time for last 1,000,000: 1s. Last read position: chrX:154,766,277
INFO 2026-06-08 08:18:42 MarkDuplicates Tracking 15057 as yet unmatched pairs. 354 records in RAM.
INFO 2026-06-08 08:18:43 MarkDuplicates Read 469,000,000 records. Elapsed time: 00:19:19s. Time for last 1,000,000: 1s. Last read position: chrM:5,954
INFO 2026-06-08 08:18:43 MarkDuplicates Tracking 14615 as yet unmatched pairs. 571 records in RAM.
INFO 2026-06-08 08:18:45 MarkDuplicates Read 470,000,000 records. Elapsed time: 00:19:21s. Time for last 1,000,000: 1s. Last read position: GL000220.1:107,598
INFO 2026-06-08 08:18:45 MarkDuplicates Tracking 14026 as yet unmatched pairs. 3585 records in RAM.
INFO 2026-06-08 08:18:46 MarkDuplicates Read 471,000,000 records. Elapsed time: 00:19:22s. Time for last 1,000,000: 1s. Last read position: GL000220.1:113,505
INFO 2026-06-08 08:18:46 MarkDuplicates Tracking 13583 as yet unmatched pairs. 3142 records in RAM.
INFO 2026-06-08 08:18:48 MarkDuplicates Read 472,000,000 records. Elapsed time: 00:19:23s. Time for last 1,000,000: 1s. Last read position: GL000220.1:114,199
INFO 2026-06-08 08:18:48 MarkDuplicates Tracking 13612 as yet unmatched pairs. 3171 records in RAM.
INFO 2026-06-08 08:18:49 MarkDuplicates Read 473,000,000 records. Elapsed time: 00:19:25s. Time for last 1,000,000: 1s. Last read position: GL000220.1:116,303
INFO 2026-06-08 08:18:49 MarkDuplicates Tracking 10687 as yet unmatched pairs. 245 records in RAM.
INFO 2026-06-08 08:18:50 MarkDuplicates Read 474,000,000 records. Elapsed time: 00:19:26s. Time for last 1,000,000: 1s. Last read position: GL000220.1:116,527
INFO 2026-06-08 08:18:50 MarkDuplicates Tracking 10702 as yet unmatched pairs. 260 records in RAM.
INFO 2026-06-08 08:18:52 MarkDuplicates Read 475,000,000 records. Elapsed time: 00:19:27s. Time for last 1,000,000: 1s. Last read position: GL000220.1:152,047
INFO 2026-06-08 08:18:52 MarkDuplicates Tracking 10718 as yet unmatched pairs. 276 records in RAM.
INFO 2026-06-08 08:18:53 MarkDuplicates Read 476,000,000 records. Elapsed time: 00:19:29s. Time for last 1,000,000: 1s. Last read position: GL000220.1:157,872
INFO 2026-06-08 08:18:53 MarkDuplicates Tracking 10710 as yet unmatched pairs. 268 records in RAM.
INFO 2026-06-08 08:18:55 MarkDuplicates Read 477,000,000 records. Elapsed time: 00:19:30s. Time for last 1,000,000: 1s. Last read position: GL000220.1:158,191
INFO 2026-06-08 08:18:55 MarkDuplicates Tracking 10678 as yet unmatched pairs. 236 records in RAM.
INFO 2026-06-08 08:18:56 MarkDuplicates Read 478,000,000 records. Elapsed time: 00:19:32s. Time for last 1,000,000: 1s. Last read position: GL000220.1:160,283
INFO 2026-06-08 08:18:56 MarkDuplicates Tracking 10488 as yet unmatched pairs. 46 records in RAM.
INFO 2026-06-08 08:18:57 MarkDuplicates Read 479,000,000 records. Elapsed time: 00:19:33s. Time for last 1,000,000: 1s. Last read position: GL000220.1:160,624
INFO 2026-06-08 08:18:57 MarkDuplicates Tracking 10460 as yet unmatched pairs. 18 records in RAM.
INFO 2026-06-08 08:18:59 MarkDuplicates Read 480,000,000 records. Elapsed time: 00:19:35s. Time for last 1,000,000: 1s. Last read position: KI270733.1:124,883
INFO 2026-06-08 08:18:59 MarkDuplicates Tracking 10336 as yet unmatched pairs. 10330 records in RAM.
INFO 2026-06-08 08:19:01 MarkDuplicates Read 481,000,000 records. Elapsed time: 00:19:36s. Time for last 1,000,000: 1s. Last read position: KI270733.1:129,916
INFO 2026-06-08 08:19:01 MarkDuplicates Tracking 10690 as yet unmatched pairs. 10684 records in RAM.
INFO 2026-06-08 08:19:03 MarkDuplicates Read 482,000,000 records. Elapsed time: 00:19:38s. Time for last 1,000,000: 1s. Last read position: KI270733.1:131,038
INFO 2026-06-08 08:19:03 MarkDuplicates Tracking 6509 as yet unmatched pairs. 6503 records in RAM.
INFO 2026-06-08 08:19:05 MarkDuplicates Read 483,000,000 records. Elapsed time: 00:19:40s. Time for last 1,000,000: 1s. Last read position: KI270733.1:132,535
INFO 2026-06-08 08:19:05 MarkDuplicates Tracking 4168 as yet unmatched pairs. 4162 records in RAM.
INFO 2026-06-08 08:19:06 MarkDuplicates Read 484,000,000 records. Elapsed time: 00:19:42s. Time for last 1,000,000: 1s. Last read position: KI270733.1:133,632
INFO 2026-06-08 08:19:06 MarkDuplicates Tracking 3550 as yet unmatched pairs. 3544 records in RAM.
INFO 2026-06-08 08:19:08 MarkDuplicates Read 485,000,000 records. Elapsed time: 00:19:43s. Time for last 1,000,000: 1s. Last read position: KI270733.1:173,231
INFO 2026-06-08 08:19:08 MarkDuplicates Tracking 2410 as yet unmatched pairs. 2404 records in RAM.
INFO 2026-06-08 08:19:09 MarkDuplicates Read 486,000,000 records. Elapsed time: 00:19:45s. Time for last 1,000,000: 1s. Last read position: KI270733.1:176,062
INFO 2026-06-08 08:19:09 MarkDuplicates Tracking 147 as yet unmatched pairs. 141 records in RAM.
INFO 2026-06-08 08:19:10 MarkDuplicates Read 487,000,000 records. Elapsed time: 00:19:46s. Time for last 1,000,000: 1s. Last read position: KI270733.1:176,403
INFO 2026-06-08 08:19:10 MarkDuplicates Tracking 111 as yet unmatched pairs. 105 records in RAM.
INFO 2026-06-08 08:19:12 MarkDuplicates Read 488,000,000 records. Elapsed time: 00:19:47s. Time for last 1,000,000: 1s. Last read position: KI270733.1:178,262
INFO 2026-06-08 08:19:12 MarkDuplicates Tracking 39 as yet unmatched pairs. 33 records in RAM.
INFO 2026-06-08 08:19:13 MarkDuplicates Read 488943062 records. 0 pairs never matched.
INFO 2026-06-08 08:20:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 38877299656; totalMemory: 55499030528; maxMemory: 63585648640
INFO 2026-06-08 08:20:20 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:20:26 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:20:44 OpticalDuplicateFinder Large duplicate set. size = 1305
INFO 2026-06-08 08:20:44 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-22,508
INFO 2026-06-08 08:20:44 OpticalDuplicateFinder Large duplicate set. size = 1561
INFO 2026-06-08 08:20:44 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:14,502
INFO 2026-06-08 08:21:01 OpticalDuplicateFinder Large duplicate set. size = 1066
INFO 2026-06-08 08:21:01 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,040
INFO 2026-06-08 08:21:01 OpticalDuplicateFinder Large duplicate set. size = 1152
INFO 2026-06-08 08:21:01 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:10,215
INFO 2026-06-08 08:21:01 OpticalDuplicateFinder Large duplicate set. size = 1010
INFO 2026-06-08 08:21:01 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,524
INFO 2026-06-08 08:21:01 OpticalDuplicateFinder Large duplicate set. size = 1018
INFO 2026-06-08 08:21:01 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,624
INFO 2026-06-08 08:21:10 OpticalDuplicateFinder Large duplicate set. size = 1098
INFO 2026-06-08 08:21:10 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,576
INFO 2026-06-08 08:21:10 OpticalDuplicateFinder Large duplicate set. size = 1027
INFO 2026-06-08 08:21:10 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,767
INFO 2026-06-08 08:21:17 OpticalDuplicateFinder Large duplicate set. size = 1049
INFO 2026-06-08 08:21:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,295
INFO 2026-06-08 08:21:18 OpticalDuplicateFinder Large duplicate set. size = 1144
INFO 2026-06-08 08:21:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,499
INFO 2026-06-08 08:21:18 OpticalDuplicateFinder Large duplicate set. size = 1501
INFO 2026-06-08 08:21:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:2,011
INFO 2026-06-08 08:21:18 OpticalDuplicateFinder Large duplicate set. size = 1926
INFO 2026-06-08 08:21:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-22,484
INFO 2026-06-08 08:21:18 OpticalDuplicateFinder Large duplicate set. size = 1145
INFO 2026-06-08 08:21:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:14,640
INFO 2026-06-08 08:21:18 OpticalDuplicateFinder Large duplicate set. size = 1035
INFO 2026-06-08 08:21:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,426
INFO 2026-06-08 08:21:18 OpticalDuplicateFinder Large duplicate set. size = 1053
INFO 2026-06-08 08:21:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:7,432
INFO 2026-06-08 08:21:18 OpticalDuplicateFinder Large duplicate set. size = 1426
INFO 2026-06-08 08:21:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:10,562
INFO 2026-06-08 08:21:19 OpticalDuplicateFinder Large duplicate set. size = 1499
INFO 2026-06-08 08:21:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:1,922
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder Large duplicate set. size = 1002
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-21,602
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder Large duplicate set. size = 1286
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-18,269
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder Large duplicate set. size = 1244
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,406
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder Large duplicate set. size = 1067
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:10,546
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder Large duplicate set. size = 1096
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,013
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder Large duplicate set. size = 1201
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,012
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder Large duplicate set. size = 1167
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-22,622
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder Large duplicate set. size = 1129
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:14,988
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder Large duplicate set. size = 1081
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,730
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder Large duplicate set. size = 1272
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-18,002
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder Large duplicate set. size = 1156
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,852
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder Large duplicate set. size = 1148
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,835
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder Large duplicate set. size = 1706
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,308
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder Large duplicate set. size = 1165
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,148
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder Large duplicate set. size = 1223
INFO 2026-06-08 08:21:44 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,275
INFO 2026-06-08 08:21:48 MarkDuplicates Traversing fragment information and detecting duplicates.
WARNING 2026-06-08 08:21:48 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
INFO 2026-06-08 08:22:44 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:22:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 203941552; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:22:48 MarkDuplicates Marking 318951326 records as duplicates.
INFO 2026-06-08 08:22:48 MarkDuplicates Found 13003498 optical duplicate clusters.
INFO 2026-06-08 08:22:48 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 08:23:11 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:23s. Time for last 10,000,000: 23s. Last read position: chr1:28,529,866
INFO 2026-06-08 08:23:31 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:43s. Time for last 10,000,000: 20s. Last read position: chr1:120,912,275
INFO 2026-06-08 08:23:50 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:01s. Time for last 10,000,000: 18s. Last read position: chr1:180,094,139
INFO 2026-06-08 08:24:08 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:20s. Time for last 10,000,000: 18s. Last read position: chr2:25,239,132
INFO 2026-06-08 08:24:26 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:37s. Time for last 10,000,000: 17s. Last read position: chr2:100,397,619
INFO 2026-06-08 08:24:43 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:55s. Time for last 10,000,000: 17s. Last read position: chr2:215,375,321
INFO 2026-06-08 08:25:04 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:15s. Time for last 10,000,000: 20s. Last read position: chr3:23,977,229
INFO 2026-06-08 08:25:24 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:36s. Time for last 10,000,000: 20s. Last read position: chr3:111,884,738
INFO 2026-06-08 08:25:48 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:03:00s. Time for last 10,000,000: 23s. Last read position: chr4:1,984,010
INFO 2026-06-08 08:26:13 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:03:24s. Time for last 10,000,000: 24s. Last read position: chr5:271,729
INFO 2026-06-08 08:26:36 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:03:48s. Time for last 10,000,000: 23s. Last read position: chr5:139,561,694
INFO 2026-06-08 08:26:58 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:04:10s. Time for last 10,000,000: 21s. Last read position: chr5:180,313,838
INFO 2026-06-08 08:27:22 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:04:33s. Time for last 10,000,000: 23s. Last read position: chr6:37,819,934
INFO 2026-06-08 08:27:43 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:04:55s. Time for last 10,000,000: 21s. Last read position: chr6:167,004,334
INFO 2026-06-08 08:28:08 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:05:20s. Time for last 10,000,000: 24s. Last read position: chr7:74,601,133
INFO 2026-06-08 08:28:35 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:05:47s. Time for last 10,000,000: 27s. Last read position: chr7:118,184,243
INFO 2026-06-08 08:28:58 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:06:10s. Time for last 10,000,000: 23s. Last read position: chr8:37,869,779
INFO 2026-06-08 08:29:21 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:06:33s. Time for last 10,000,000: 22s. Last read position: chr8:143,861,610
INFO 2026-06-08 08:29:45 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:06:56s. Time for last 10,000,000: 23s. Last read position: chr9:34,635,401
INFO 2026-06-08 08:30:07 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:07:19s. Time for last 10,000,000: 22s. Last read position: chr9:129,142,503
INFO 2026-06-08 08:30:31 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:07:43s. Time for last 10,000,000: 24s. Last read position: chr10:32,911,551
INFO 2026-06-08 08:30:56 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:08:08s. Time for last 10,000,000: 25s. Last read position: chr10:122,113,173
INFO 2026-06-08 08:31:23 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:08:35s. Time for last 10,000,000: 26s. Last read position: chr11:60,849,986
INFO 2026-06-08 08:31:48 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:08:59s. Time for last 10,000,000: 24s. Last read position: chr11:116,954,067
INFO 2026-06-08 08:32:09 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:09:21s. Time for last 10,000,000: 21s. Last read position: chr12:52,054,414
INFO 2026-06-08 08:32:33 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:09:45s. Time for last 10,000,000: 23s. Last read position: chr12:111,809,543
INFO 2026-06-08 08:33:00 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:10:11s. Time for last 10,000,000: 26s. Last read position: chr13:73,062,139
INFO 2026-06-08 08:33:25 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:10:37s. Time for last 10,000,000: 25s. Last read position: chr14:67,390,735
INFO 2026-06-08 08:33:50 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:11:02s. Time for last 10,000,000: 25s. Last read position: chr15:42,685,151
INFO 2026-06-08 08:34:17 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:11:28s. Time for last 10,000,000: 26s. Last read position: chr16:372,170
INFO 2026-06-08 08:34:42 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:11:54s. Time for last 10,000,000: 25s. Last read position: chr16:18,349,994
INFO 2026-06-08 08:35:09 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:12:20s. Time for last 10,000,000: 26s. Last read position: chr16:30,946,938
INFO 2026-06-08 08:35:35 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:12:46s. Time for last 10,000,000: 26s. Last read position: chr16:90,039,522
INFO 2026-06-08 08:36:00 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:13:12s. Time for last 10,000,000: 25s. Last read position: chr17:29,575,629
INFO 2026-06-08 08:36:24 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:13:36s. Time for last 10,000,000: 24s. Last read position: chr17:50,187,514
INFO 2026-06-08 08:36:51 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:14:03s. Time for last 10,000,000: 27s. Last read position: chr17:56,913,475
INFO 2026-06-08 08:37:18 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:14:30s. Time for last 10,000,000: 26s. Last read position: chr17:81,869,363
INFO 2026-06-08 08:37:44 MarkDuplicates Written 380,000,000 records. Elapsed time: 00:14:55s. Time for last 10,000,000: 25s. Last read position: chr19:4,929,219
INFO 2026-06-08 08:38:09 MarkDuplicates Written 390,000,000 records. Elapsed time: 00:15:21s. Time for last 10,000,000: 25s. Last read position: chr19:17,807,871
INFO 2026-06-08 08:38:35 MarkDuplicates Written 400,000,000 records. Elapsed time: 00:15:46s. Time for last 10,000,000: 25s. Last read position: chr19:42,286,842
INFO 2026-06-08 08:39:04 MarkDuplicates Written 410,000,000 records. Elapsed time: 00:16:16s. Time for last 10,000,000: 29s. Last read position: chr19:55,384,035
INFO 2026-06-08 08:39:35 MarkDuplicates Written 420,000,000 records. Elapsed time: 00:16:46s. Time for last 10,000,000: 30s. Last read position: chr20:46,613,506
INFO 2026-06-08 08:40:03 MarkDuplicates Written 430,000,000 records. Elapsed time: 00:17:15s. Time for last 10,000,000: 28s. Last read position: chr21:8,216,848
INFO 2026-06-08 08:40:28 MarkDuplicates Written 440,000,000 records. Elapsed time: 00:17:40s. Time for last 10,000,000: 25s. Last read position: chr21:8,441,948
INFO 2026-06-08 08:40:58 MarkDuplicates Written 450,000,000 records. Elapsed time: 00:18:10s. Time for last 10,000,000: 30s. Last read position: chr22:24,611,164
INFO 2026-06-08 08:41:28 MarkDuplicates Written 460,000,000 records. Elapsed time: 00:18:40s. Time for last 10,000,000: 30s. Last read position: chrX:48,528,234
INFO 2026-06-08 08:41:56 MarkDuplicates Written 470,000,000 records. Elapsed time: 00:19:08s. Time for last 10,000,000: 27s. Last read position: GL000220.1:107,598
INFO 2026-06-08 08:42:22 MarkDuplicates Written 480,000,000 records. Elapsed time: 00:19:33s. Time for last 10,000,000: 25s. Last read position: KI270733.1:124,883
INFO 2026-06-08 08:42:50 MarkDuplicates Written 490,000,000 records. Elapsed time: 00:20:01s. Time for last 10,000,000: 28s. Last read position: */*
INFO 2026-06-08 08:43:07 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:43:07 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:43:07 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:43:07 MarkDuplicates Before output close freeMemory: 203886856; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:43:07 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:43:07 MarkDuplicates After output close freeMemory: 104143328; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 08:43:07 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 43.76 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory