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/15/1583358bf761ffb33374f0a0b1e427/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/ac5fa0604f5965c14eced2773443f2/659_bMa-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/1583358bf761ffb33374f0a0b1e427/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai
==> STAGING COMPLETE (5 inputs)
Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT 659_bMa-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bam --METRICS_FILE 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
08:02:23.534 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Jun 08 08:02:23 GMT 2026] MarkDuplicates --INPUT 659_bMa-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bam --METRICS_FILE 659_bMa-T1-TRNA-1_B23MHV2LT4_1.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 08:02:23 GMT 2026] Executing as ?@nf-151583358bf761ffb33374f0a0b1e427-6ba85-8thsw on Linux 6.12.88 amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0
INFO 2026-06-08 08:02:23 MarkDuplicates Start of doWork freeMemory: 105830320; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 08:02:23 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 08:02:23 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 08:02:29 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:1,623,911
INFO 2026-06-08 08:02:29 MarkDuplicates Tracking 1719 as yet unmatched pairs. 5 records in RAM.
INFO 2026-06-08 08:02:32 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: chr1:6,593,470
INFO 2026-06-08 08:02:32 MarkDuplicates Tracking 3675 as yet unmatched pairs. 19 records in RAM.
INFO 2026-06-08 08:02:35 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 3s. Last read position: chr1:11,676,099
INFO 2026-06-08 08:02:35 MarkDuplicates Tracking 5533 as yet unmatched pairs. 28 records in RAM.
INFO 2026-06-08 08:02:38 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 2s. Last read position: chr1:16,930,332
INFO 2026-06-08 08:02:38 MarkDuplicates Tracking 7492 as yet unmatched pairs. 15 records in RAM.
INFO 2026-06-08 08:02:42 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 3s. Last read position: chr1:21,598,053
INFO 2026-06-08 08:02:42 MarkDuplicates Tracking 9363 as yet unmatched pairs. 3 records in RAM.
INFO 2026-06-08 08:02:45 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 2s. Last read position: chr1:23,751,484
INFO 2026-06-08 08:02:45 MarkDuplicates Tracking 11018 as yet unmatched pairs. 31 records in RAM.
INFO 2026-06-08 08:02:49 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 3s. Last read position: chr1:26,946,130
INFO 2026-06-08 08:02:49 MarkDuplicates Tracking 12610 as yet unmatched pairs. 35 records in RAM.
INFO 2026-06-08 08:02:52 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 3s. Last read position: chr1:31,585,159
INFO 2026-06-08 08:02:52 MarkDuplicates Tracking 14468 as yet unmatched pairs. 110 records in RAM.
INFO 2026-06-08 08:02:56 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 3s. Last read position: chr1:35,192,517
INFO 2026-06-08 08:02:56 MarkDuplicates Tracking 16282 as yet unmatched pairs. 97 records in RAM.
INFO 2026-06-08 08:02:59 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 3s. Last read position: chr1:39,388,509
INFO 2026-06-08 08:02:59 MarkDuplicates Tracking 17986 as yet unmatched pairs. 5 records in RAM.
INFO 2026-06-08 08:03:02 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 2s. Last read position: chr1:43,447,026
INFO 2026-06-08 08:03:02 MarkDuplicates Tracking 19927 as yet unmatched pairs. 5 records in RAM.
INFO 2026-06-08 08:03:05 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 3s. Last read position: chr1:47,333,933
INFO 2026-06-08 08:03:05 MarkDuplicates Tracking 22089 as yet unmatched pairs. 170 records in RAM.
INFO 2026-06-08 08:03:08 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chr1:62,578,831
INFO 2026-06-08 08:03:08 MarkDuplicates Tracking 23802 as yet unmatched pairs. 5 records in RAM.
INFO 2026-06-08 08:03:11 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: chr1:93,154,781
INFO 2026-06-08 08:03:11 MarkDuplicates Tracking 25438 as yet unmatched pairs. 28 records in RAM.
INFO 2026-06-08 08:03:12 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 1s. Last read position: chr1:111,704,397
INFO 2026-06-08 08:03:12 MarkDuplicates Tracking 27056 as yet unmatched pairs. 58 records in RAM.
INFO 2026-06-08 08:03:16 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 3s. Last read position: chr1:119,915,941
INFO 2026-06-08 08:03:16 MarkDuplicates Tracking 28921 as yet unmatched pairs. 88 records in RAM.
INFO 2026-06-08 08:03:18 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 2s. Last read position: chr1:147,622,308
INFO 2026-06-08 08:03:18 MarkDuplicates Tracking 29963 as yet unmatched pairs. 5 records in RAM.
INFO 2026-06-08 08:03:21 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 2s. Last read position: chr1:150,554,527
INFO 2026-06-08 08:03:21 MarkDuplicates Tracking 31331 as yet unmatched pairs. 109 records in RAM.
INFO 2026-06-08 08:03:24 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 2s. Last read position: chr1:153,607,532
INFO 2026-06-08 08:03:24 MarkDuplicates Tracking 33008 as yet unmatched pairs. 62 records in RAM.
INFO 2026-06-08 08:03:26 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 2s. Last read position: chr1:154,176,162
INFO 2026-06-08 08:03:26 MarkDuplicates Tracking 35505 as yet unmatched pairs. 841 records in RAM.
INFO 2026-06-08 08:03:28 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 1s. Last read position: chr1:155,190,775
INFO 2026-06-08 08:03:28 MarkDuplicates Tracking 36202 as yet unmatched pairs. 44 records in RAM.
INFO 2026-06-08 08:03:30 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 2s. Last read position: chr1:156,135,185
INFO 2026-06-08 08:03:30 MarkDuplicates Tracking 38372 as yet unmatched pairs. 621 records in RAM.
INFO 2026-06-08 08:03:33 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 2s. Last read position: chr1:160,541,888
INFO 2026-06-08 08:03:33 MarkDuplicates Tracking 39714 as yet unmatched pairs. 4 records in RAM.
INFO 2026-06-08 08:03:35 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 2s. Last read position: chr1:169,130,016
INFO 2026-06-08 08:03:35 MarkDuplicates Tracking 42109 as yet unmatched pairs. 604 records in RAM.
INFO 2026-06-08 08:03:38 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 2s. Last read position: chr1:180,935,353
INFO 2026-06-08 08:03:38 MarkDuplicates Tracking 42967 as yet unmatched pairs. 25 records in RAM.
INFO 2026-06-08 08:03:40 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 2s. Last read position: chr1:192,809,150
INFO 2026-06-08 08:03:40 MarkDuplicates Tracking 44754 as yet unmatched pairs. 63 records in RAM.
INFO 2026-06-08 08:03:42 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 2s. Last read position: chr1:203,848,331
INFO 2026-06-08 08:03:42 MarkDuplicates Tracking 46379 as yet unmatched pairs. 89 records in RAM.
INFO 2026-06-08 08:03:44 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 2s. Last read position: chr1:207,783,297
INFO 2026-06-08 08:03:44 MarkDuplicates Tracking 48053 as yet unmatched pairs. 213 records in RAM.
INFO 2026-06-08 08:03:47 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 2s. Last read position: chr1:224,433,838
INFO 2026-06-08 08:03:47 MarkDuplicates Tracking 49917 as yet unmatched pairs. 238 records in RAM.
INFO 2026-06-08 08:03:49 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 1s. Last read position: chr1:232,514,079
INFO 2026-06-08 08:03:49 MarkDuplicates Tracking 51555 as yet unmatched pairs. 24 records in RAM.
INFO 2026-06-08 08:03:51 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 1s. Last read position: chr1:247,100,564
INFO 2026-06-08 08:03:51 MarkDuplicates Tracking 53437 as yet unmatched pairs. 12 records in RAM.
INFO 2026-06-08 08:03:53 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 2s. Last read position: chr2:17,666,438
INFO 2026-06-08 08:03:53 MarkDuplicates Tracking 55203 as yet unmatched pairs. 55114 records in RAM.
INFO 2026-06-08 08:03:55 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 2s. Last read position: chr2:27,201,743
INFO 2026-06-08 08:03:55 MarkDuplicates Tracking 57206 as yet unmatched pairs. 57115 records in RAM.
INFO 2026-06-08 08:03:57 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,261
INFO 2026-06-08 08:03:57 MarkDuplicates Tracking 78142 as yet unmatched pairs. 57522 records in RAM.
INFO 2026-06-08 08:04:00 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,406
INFO 2026-06-08 08:04:00 MarkDuplicates Tracking 519057 as yet unmatched pairs. 42730 records in RAM.
INFO 2026-06-08 08:04:02 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 1s. Last read position: chr2:39,024,128
INFO 2026-06-08 08:04:02 MarkDuplicates Tracking 545135 as yet unmatched pairs. 41218 records in RAM.
INFO 2026-06-08 08:04:04 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 1s. Last read position: chr2:47,373,890
INFO 2026-06-08 08:04:04 MarkDuplicates Tracking 543240 as yet unmatched pairs. 39322 records in RAM.
INFO 2026-06-08 08:04:08 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 3s. Last read position: chr2:55,601,445
INFO 2026-06-08 08:04:08 MarkDuplicates Tracking 541104 as yet unmatched pairs. 37185 records in RAM.
INFO 2026-06-08 08:04:10 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 2s. Last read position: chr2:70,281,654
INFO 2026-06-08 08:04:10 MarkDuplicates Tracking 539359 as yet unmatched pairs. 35437 records in RAM.
INFO 2026-06-08 08:04:13 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 2s. Last read position: chr2:84,821,952
INFO 2026-06-08 08:04:13 MarkDuplicates Tracking 537647 as yet unmatched pairs. 33724 records in RAM.
INFO 2026-06-08 08:04:15 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 2s. Last read position: chr2:96,144,352
INFO 2026-06-08 08:04:15 MarkDuplicates Tracking 535837 as yet unmatched pairs. 31912 records in RAM.
INFO 2026-06-08 08:04:18 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 3s. Last read position: chr2:102,024,504
INFO 2026-06-08 08:04:18 MarkDuplicates Tracking 534143 as yet unmatched pairs. 30218 records in RAM.
INFO 2026-06-08 08:04:21 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 2s. Last read position: chr2:110,115,719
INFO 2026-06-08 08:04:21 MarkDuplicates Tracking 532781 as yet unmatched pairs. 28854 records in RAM.
INFO 2026-06-08 08:04:23 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 2s. Last read position: chr2:119,370,753
INFO 2026-06-08 08:04:23 MarkDuplicates Tracking 531448 as yet unmatched pairs. 27521 records in RAM.
INFO 2026-06-08 08:04:26 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 2s. Last read position: chr2:148,469,713
INFO 2026-06-08 08:04:26 MarkDuplicates Tracking 529933 as yet unmatched pairs. 25996 records in RAM.
INFO 2026-06-08 08:04:29 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 2s. Last read position: chr2:171,867,415
INFO 2026-06-08 08:04:29 MarkDuplicates Tracking 528275 as yet unmatched pairs. 24332 records in RAM.
INFO 2026-06-08 08:04:31 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 2s. Last read position: chr2:186,507,433
INFO 2026-06-08 08:04:31 MarkDuplicates Tracking 526350 as yet unmatched pairs. 22407 records in RAM.
INFO 2026-06-08 08:04:33 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 2s. Last read position: chr2:189,001,543
INFO 2026-06-08 08:04:33 MarkDuplicates Tracking 526097 as yet unmatched pairs. 22154 records in RAM.
INFO 2026-06-08 08:04:36 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 2s. Last read position: chr2:190,497,468
INFO 2026-06-08 08:04:36 MarkDuplicates Tracking 522443 as yet unmatched pairs. 18498 records in RAM.
INFO 2026-06-08 08:04:39 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 3s. Last read position: chr2:203,396,865
INFO 2026-06-08 08:04:39 MarkDuplicates Tracking 520860 as yet unmatched pairs. 16914 records in RAM.
INFO 2026-06-08 08:04:41 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 2s. Last read position: chr2:215,367,983
INFO 2026-06-08 08:04:41 MarkDuplicates Tracking 520027 as yet unmatched pairs. 16081 records in RAM.
INFO 2026-06-08 08:04:44 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 2s. Last read position: chr2:215,376,625
INFO 2026-06-08 08:04:44 MarkDuplicates Tracking 519321 as yet unmatched pairs. 15375 records in RAM.
INFO 2026-06-08 08:04:46 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 2s. Last read position: chr2:215,394,707
INFO 2026-06-08 08:04:46 MarkDuplicates Tracking 518025 as yet unmatched pairs. 14078 records in RAM.
INFO 2026-06-08 08:04:48 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr2:215,414,837
INFO 2026-06-08 08:04:48 MarkDuplicates Tracking 514933 as yet unmatched pairs. 10986 records in RAM.
INFO 2026-06-08 08:04:50 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 1s. Last read position: chr2:215,433,348
INFO 2026-06-08 08:04:50 MarkDuplicates Tracking 515425 as yet unmatched pairs. 11476 records in RAM.
INFO 2026-06-08 08:04:53 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 3s. Last read position: chr2:218,644,321
INFO 2026-06-08 08:04:53 MarkDuplicates Tracking 510867 as yet unmatched pairs. 6916 records in RAM.
INFO 2026-06-08 08:04:56 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 2s. Last read position: chr2:230,442,944
INFO 2026-06-08 08:04:56 MarkDuplicates Tracking 508929 as yet unmatched pairs. 4950 records in RAM.
INFO 2026-06-08 08:04:58 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 2s. Last read position: chr2:232,790,746
INFO 2026-06-08 08:04:58 MarkDuplicates Tracking 507083 as yet unmatched pairs. 3103 records in RAM.
INFO 2026-06-08 08:05:01 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 2s. Last read position: chr2:238,035,888
INFO 2026-06-08 08:05:01 MarkDuplicates Tracking 505340 as yet unmatched pairs. 1343 records in RAM.
INFO 2026-06-08 08:05:04 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 3s. Last read position: chr3:9,429,865
INFO 2026-06-08 08:05:04 MarkDuplicates Tracking 503680 as yet unmatched pairs. 27219 records in RAM.
INFO 2026-06-08 08:05:07 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 2s. Last read position: chr3:22,382,171
INFO 2026-06-08 08:05:07 MarkDuplicates Tracking 502191 as yet unmatched pairs. 25726 records in RAM.
INFO 2026-06-08 08:05:09 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 2s. Last read position: chr3:39,411,943
INFO 2026-06-08 08:05:09 MarkDuplicates Tracking 501293 as yet unmatched pairs. 24825 records in RAM.
INFO 2026-06-08 08:05:12 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 3s. Last read position: chr3:47,009,223
INFO 2026-06-08 08:05:12 MarkDuplicates Tracking 498584 as yet unmatched pairs. 22115 records in RAM.
INFO 2026-06-08 08:05:15 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 2s. Last read position: chr3:48,591,684
INFO 2026-06-08 08:05:15 MarkDuplicates Tracking 496936 as yet unmatched pairs. 20465 records in RAM.
INFO 2026-06-08 08:05:17 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 2s. Last read position: chr3:49,903,277
INFO 2026-06-08 08:05:17 MarkDuplicates Tracking 494968 as yet unmatched pairs. 18495 records in RAM.
INFO 2026-06-08 08:05:20 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 2s. Last read position: chr3:52,523,550
INFO 2026-06-08 08:05:20 MarkDuplicates Tracking 492957 as yet unmatched pairs. 16483 records in RAM.
INFO 2026-06-08 08:05:22 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 2s. Last read position: chr3:68,951,275
INFO 2026-06-08 08:05:22 MarkDuplicates Tracking 491297 as yet unmatched pairs. 14822 records in RAM.
INFO 2026-06-08 08:05:25 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 2s. Last read position: chr3:108,047,245
INFO 2026-06-08 08:05:25 MarkDuplicates Tracking 489939 as yet unmatched pairs. 13461 records in RAM.
INFO 2026-06-08 08:05:28 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 2s. Last read position: chr3:124,413,423
INFO 2026-06-08 08:05:28 MarkDuplicates Tracking 487909 as yet unmatched pairs. 11430 records in RAM.
INFO 2026-06-08 08:05:30 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 2s. Last read position: chr3:132,474,984
INFO 2026-06-08 08:05:30 MarkDuplicates Tracking 486017 as yet unmatched pairs. 9536 records in RAM.
INFO 2026-06-08 08:05:32 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 2s. Last read position: chr3:156,543,228
INFO 2026-06-08 08:05:32 MarkDuplicates Tracking 484364 as yet unmatched pairs. 7879 records in RAM.
INFO 2026-06-08 08:05:35 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 3s. Last read position: chr3:184,117,477
INFO 2026-06-08 08:05:35 MarkDuplicates Tracking 482670 as yet unmatched pairs. 6184 records in RAM.
INFO 2026-06-08 08:05:37 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 2s. Last read position: chr3:188,609,242
INFO 2026-06-08 08:05:37 MarkDuplicates Tracking 481389 as yet unmatched pairs. 4900 records in RAM.
INFO 2026-06-08 08:05:40 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 2s. Last read position: chr3:195,779,502
INFO 2026-06-08 08:05:40 MarkDuplicates Tracking 481235 as yet unmatched pairs. 4745 records in RAM.
INFO 2026-06-08 08:05:43 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 2s. Last read position: chr3:195,781,767
INFO 2026-06-08 08:05:43 MarkDuplicates Tracking 481120 as yet unmatched pairs. 4622 records in RAM.
INFO 2026-06-08 08:05:45 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 2s. Last read position: chr3:195,784,338
INFO 2026-06-08 08:05:45 MarkDuplicates Tracking 480581 as yet unmatched pairs. 4083 records in RAM.
INFO 2026-06-08 08:05:48 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 2s. Last read position: chr3:195,786,957
INFO 2026-06-08 08:05:48 MarkDuplicates Tracking 478479 as yet unmatched pairs. 1980 records in RAM.
INFO 2026-06-08 08:05:51 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 2s. Last read position: chr4:769,054
INFO 2026-06-08 08:05:51 MarkDuplicates Tracking 476622 as yet unmatched pairs. 11643 records in RAM.
INFO 2026-06-08 08:05:53 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 2s. Last read position: chr4:6,861,475
INFO 2026-06-08 08:05:53 MarkDuplicates Tracking 474878 as yet unmatched pairs. 9896 records in RAM.
INFO 2026-06-08 08:05:56 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 3s. Last read position: chr4:40,502,545
INFO 2026-06-08 08:05:56 MarkDuplicates Tracking 473173 as yet unmatched pairs. 8188 records in RAM.
INFO 2026-06-08 08:06:00 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 3s. Last read position: chr4:73,741,606
INFO 2026-06-08 08:06:00 MarkDuplicates Tracking 476244 as yet unmatched pairs. 11252 records in RAM.
INFO 2026-06-08 08:06:03 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 2s. Last read position: chr4:87,108,161
INFO 2026-06-08 08:06:03 MarkDuplicates Tracking 469633 as yet unmatched pairs. 4640 records in RAM.
INFO 2026-06-08 08:06:05 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 2s. Last read position: chr4:119,031,206
INFO 2026-06-08 08:06:05 MarkDuplicates Tracking 467775 as yet unmatched pairs. 2774 records in RAM.
INFO 2026-06-08 08:06:08 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 2s. Last read position: chr4:153,788,803
INFO 2026-06-08 08:06:08 MarkDuplicates Tracking 466465 as yet unmatched pairs. 1458 records in RAM.
INFO 2026-06-08 08:06:11 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 3s. Last read position: chr5:491,861
INFO 2026-06-08 08:06:11 MarkDuplicates Tracking 464718 as yet unmatched pairs. 25544 records in RAM.
INFO 2026-06-08 08:06:14 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 3s. Last read position: chr5:14,488,158
INFO 2026-06-08 08:06:14 MarkDuplicates Tracking 462408 as yet unmatched pairs. 23230 records in RAM.
INFO 2026-06-08 08:06:17 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 2s. Last read position: chr5:43,527,317
INFO 2026-06-08 08:06:17 MarkDuplicates Tracking 460697 as yet unmatched pairs. 21517 records in RAM.
INFO 2026-06-08 08:06:20 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 2s. Last read position: chr5:76,173,757
INFO 2026-06-08 08:06:20 MarkDuplicates Tracking 459129 as yet unmatched pairs. 19946 records in RAM.
INFO 2026-06-08 08:06:23 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 2s. Last read position: chr5:96,881,391
INFO 2026-06-08 08:06:23 MarkDuplicates Tracking 457609 as yet unmatched pairs. 18421 records in RAM.
INFO 2026-06-08 08:06:26 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 2s. Last read position: chr5:131,429,107
INFO 2026-06-08 08:06:26 MarkDuplicates Tracking 455911 as yet unmatched pairs. 16721 records in RAM.
INFO 2026-06-08 08:06:29 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 3s. Last read position: chr5:138,386,068
INFO 2026-06-08 08:06:29 MarkDuplicates Tracking 454287 as yet unmatched pairs. 15096 records in RAM.
INFO 2026-06-08 08:06:32 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 3s. Last read position: chr5:140,877,405
INFO 2026-06-08 08:06:32 MarkDuplicates Tracking 452659 as yet unmatched pairs. 13352 records in RAM.
INFO 2026-06-08 08:06:34 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 2s. Last read position: chr5:149,242,440
INFO 2026-06-08 08:06:34 MarkDuplicates Tracking 451036 as yet unmatched pairs. 11729 records in RAM.
INFO 2026-06-08 08:06:37 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 3s. Last read position: chr5:150,406,263
INFO 2026-06-08 08:06:37 MarkDuplicates Tracking 450839 as yet unmatched pairs. 11532 records in RAM.
INFO 2026-06-08 08:06:40 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 2s. Last read position: chr5:154,793,928
INFO 2026-06-08 08:06:40 MarkDuplicates Tracking 447352 as yet unmatched pairs. 8044 records in RAM.
INFO 2026-06-08 08:06:42 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 2s. Last read position: chr5:171,391,724
INFO 2026-06-08 08:06:42 MarkDuplicates Tracking 448021 as yet unmatched pairs. 8710 records in RAM.
INFO 2026-06-08 08:06:45 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 2s. Last read position: chr5:172,770,845
INFO 2026-06-08 08:06:45 MarkDuplicates Tracking 444111 as yet unmatched pairs. 4800 records in RAM.
INFO 2026-06-08 08:06:47 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 2s. Last read position: chr5:178,120,407
INFO 2026-06-08 08:06:47 MarkDuplicates Tracking 442203 as yet unmatched pairs. 2892 records in RAM.
INFO 2026-06-08 08:06:49 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:04:23s. Time for last 1,000,000: 2s. Last read position: chr5:179,836,448
INFO 2026-06-08 08:06:49 MarkDuplicates Tracking 442000 as yet unmatched pairs. 2688 records in RAM.
INFO 2026-06-08 08:06:51 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 2s. Last read position: chr6:7,229,232
INFO 2026-06-08 08:06:51 MarkDuplicates Tracking 438636 as yet unmatched pairs. 25810 records in RAM.
INFO 2026-06-08 08:06:54 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 2s. Last read position: chr6:18,258,403
INFO 2026-06-08 08:06:54 MarkDuplicates Tracking 437093 as yet unmatched pairs. 24260 records in RAM.
INFO 2026-06-08 08:06:57 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 2s. Last read position: chr6:29,889,375
INFO 2026-06-08 08:06:57 MarkDuplicates Tracking 435530 as yet unmatched pairs. 22694 records in RAM.
INFO 2026-06-08 08:06:59 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 2s. Last read position: chr6:30,744,109
INFO 2026-06-08 08:06:59 MarkDuplicates Tracking 434736 as yet unmatched pairs. 21900 records in RAM.
INFO 2026-06-08 08:07:02 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 2s. Last read position: chr6:31,649,232
INFO 2026-06-08 08:07:02 MarkDuplicates Tracking 432085 as yet unmatched pairs. 19249 records in RAM.
INFO 2026-06-08 08:07:04 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 2s. Last read position: chr6:31,993,794
INFO 2026-06-08 08:07:04 MarkDuplicates Tracking 430413 as yet unmatched pairs. 17575 records in RAM.
INFO 2026-06-08 08:07:07 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 3s. Last read position: chr6:33,313,238
INFO 2026-06-08 08:07:07 MarkDuplicates Tracking 428951 as yet unmatched pairs. 16113 records in RAM.
INFO 2026-06-08 08:07:10 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 2s. Last read position: chr6:36,899,480
INFO 2026-06-08 08:07:10 MarkDuplicates Tracking 426789 as yet unmatched pairs. 13950 records in RAM.
INFO 2026-06-08 08:07:13 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 3s. Last read position: chr6:43,512,257
INFO 2026-06-08 08:07:13 MarkDuplicates Tracking 425183 as yet unmatched pairs. 12341 records in RAM.
INFO 2026-06-08 08:07:16 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 3s. Last read position: chr6:56,569,856
INFO 2026-06-08 08:07:16 MarkDuplicates Tracking 423250 as yet unmatched pairs. 10406 records in RAM.
INFO 2026-06-08 08:07:19 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 2s. Last read position: chr6:87,501,270
INFO 2026-06-08 08:07:19 MarkDuplicates Tracking 421779 as yet unmatched pairs. 8933 records in RAM.
INFO 2026-06-08 08:07:22 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 2s. Last read position: chr6:111,020,593
INFO 2026-06-08 08:07:22 MarkDuplicates Tracking 420373 as yet unmatched pairs. 7518 records in RAM.
INFO 2026-06-08 08:07:24 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 2s. Last read position: chr6:135,037,034
INFO 2026-06-08 08:07:24 MarkDuplicates Tracking 418640 as yet unmatched pairs. 5781 records in RAM.
INFO 2026-06-08 08:07:26 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 1s. Last read position: chr6:149,683,585
INFO 2026-06-08 08:07:26 MarkDuplicates Tracking 416726 as yet unmatched pairs. 3867 records in RAM.
INFO 2026-06-08 08:07:28 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:05:02s. Time for last 1,000,000: 1s. Last read position: chr6:158,783,557
INFO 2026-06-08 08:07:28 MarkDuplicates Tracking 416723 as yet unmatched pairs. 3862 records in RAM.
INFO 2026-06-08 08:07:30 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 1s. Last read position: chr6:169,234,872
INFO 2026-06-08 08:07:30 MarkDuplicates Tracking 413311 as yet unmatched pairs. 450 records in RAM.
INFO 2026-06-08 08:07:32 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 1s. Last read position: chr7:2,731,361
INFO 2026-06-08 08:07:32 MarkDuplicates Tracking 411200 as yet unmatched pairs. 31304 records in RAM.
INFO 2026-06-08 08:07:34 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 2s. Last read position: chr7:5,528,528
INFO 2026-06-08 08:07:34 MarkDuplicates Tracking 411055 as yet unmatched pairs. 31157 records in RAM.
INFO 2026-06-08 08:07:37 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 2s. Last read position: chr7:20,003,014
INFO 2026-06-08 08:07:37 MarkDuplicates Tracking 407185 as yet unmatched pairs. 27286 records in RAM.
INFO 2026-06-08 08:07:39 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 1s. Last read position: chr7:39,833,861
INFO 2026-06-08 08:07:39 MarkDuplicates Tracking 405859 as yet unmatched pairs. 25942 records in RAM.
INFO 2026-06-08 08:07:41 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 2s. Last read position: chr7:47,368,889
INFO 2026-06-08 08:07:41 MarkDuplicates Tracking 404432 as yet unmatched pairs. 24514 records in RAM.
INFO 2026-06-08 08:07:44 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 2s. Last read position: chr7:73,027,811
INFO 2026-06-08 08:07:44 MarkDuplicates Tracking 402945 as yet unmatched pairs. 23023 records in RAM.
INFO 2026-06-08 08:07:46 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 2s. Last read position: chr7:75,286,815
INFO 2026-06-08 08:07:46 MarkDuplicates Tracking 401886 as yet unmatched pairs. 21963 records in RAM.
INFO 2026-06-08 08:07:50 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 3s. Last read position: chr7:76,626,166
INFO 2026-06-08 08:07:50 MarkDuplicates Tracking 400440 as yet unmatched pairs. 20517 records in RAM.
INFO 2026-06-08 08:07:52 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 1s. Last read position: chr7:94,401,605
INFO 2026-06-08 08:07:52 MarkDuplicates Tracking 401511 as yet unmatched pairs. 21587 records in RAM.
INFO 2026-06-08 08:07:55 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 2s. Last read position: chr7:96,191,131
INFO 2026-06-08 08:07:55 MarkDuplicates Tracking 396983 as yet unmatched pairs. 17055 records in RAM.
INFO 2026-06-08 08:07:56 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 1s. Last read position: chr7:100,433,029
INFO 2026-06-08 08:07:56 MarkDuplicates Tracking 395115 as yet unmatched pairs. 15186 records in RAM.
INFO 2026-06-08 08:07:58 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 1s. Last read position: chr7:100,992,605
INFO 2026-06-08 08:07:58 MarkDuplicates Tracking 393703 as yet unmatched pairs. 13772 records in RAM.
INFO 2026-06-08 08:08:00 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 1s. Last read position: chr7:100,996,006
INFO 2026-06-08 08:08:00 MarkDuplicates Tracking 393190 as yet unmatched pairs. 13259 records in RAM.
INFO 2026-06-08 08:08:02 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 2s. Last read position: chr7:100,997,636
INFO 2026-06-08 08:08:02 MarkDuplicates Tracking 392185 as yet unmatched pairs. 12254 records in RAM.
INFO 2026-06-08 08:08:04 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 1s. Last read position: chr7:100,999,596
INFO 2026-06-08 08:08:04 MarkDuplicates Tracking 392856 as yet unmatched pairs. 12925 records in RAM.
INFO 2026-06-08 08:08:05 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 1s. Last read position: chr7:101,001,575
INFO 2026-06-08 08:08:05 MarkDuplicates Tracking 391222 as yet unmatched pairs. 11291 records in RAM.
INFO 2026-06-08 08:08:07 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 2s. Last read position: chr7:101,128,473
INFO 2026-06-08 08:08:07 MarkDuplicates Tracking 390907 as yet unmatched pairs. 10976 records in RAM.
INFO 2026-06-08 08:08:09 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:05:43s. Time for last 1,000,000: 1s. Last read position: chr7:105,055,199
INFO 2026-06-08 08:08:09 MarkDuplicates Tracking 389407 as yet unmatched pairs. 9476 records in RAM.
INFO 2026-06-08 08:08:11 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 2s. Last read position: chr7:123,692,719
INFO 2026-06-08 08:08:11 MarkDuplicates Tracking 387769 as yet unmatched pairs. 7834 records in RAM.
INFO 2026-06-08 08:08:13 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 1s. Last read position: chr7:134,933,291
INFO 2026-06-08 08:08:13 MarkDuplicates Tracking 385719 as yet unmatched pairs. 5782 records in RAM.
INFO 2026-06-08 08:08:16 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 2s. Last read position: chr7:143,381,704
INFO 2026-06-08 08:08:16 MarkDuplicates Tracking 384330 as yet unmatched pairs. 4390 records in RAM.
INFO 2026-06-08 08:08:18 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 2s. Last read position: chr7:149,266,882
INFO 2026-06-08 08:08:18 MarkDuplicates Tracking 383044 as yet unmatched pairs. 3104 records in RAM.
INFO 2026-06-08 08:08:20 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 2s. Last read position: chr7:152,205,132
INFO 2026-06-08 08:08:20 MarkDuplicates Tracking 381006 as yet unmatched pairs. 1065 records in RAM.
INFO 2026-06-08 08:08:22 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 2s. Last read position: chr8:20,197,447
INFO 2026-06-08 08:08:22 MarkDuplicates Tracking 378859 as yet unmatched pairs. 23096 records in RAM.
INFO 2026-06-08 08:08:25 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 3s. Last read position: chr8:37,697,492
INFO 2026-06-08 08:08:25 MarkDuplicates Tracking 377555 as yet unmatched pairs. 21791 records in RAM.
INFO 2026-06-08 08:08:28 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 2s. Last read position: chr8:41,941,157
INFO 2026-06-08 08:08:28 MarkDuplicates Tracking 375668 as yet unmatched pairs. 19901 records in RAM.
INFO 2026-06-08 08:08:30 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 2s. Last read position: chr8:67,172,945
INFO 2026-06-08 08:08:30 MarkDuplicates Tracking 374042 as yet unmatched pairs. 18263 records in RAM.
INFO 2026-06-08 08:08:32 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 1s. Last read position: chr8:96,231,912
INFO 2026-06-08 08:08:32 MarkDuplicates Tracking 372275 as yet unmatched pairs. 16493 records in RAM.
INFO 2026-06-08 08:08:34 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 1s. Last read position: chr8:102,651,460
INFO 2026-06-08 08:08:34 MarkDuplicates Tracking 370672 as yet unmatched pairs. 14889 records in RAM.
INFO 2026-06-08 08:08:36 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 1s. Last read position: chr8:127,738,807
INFO 2026-06-08 08:08:36 MarkDuplicates Tracking 368897 as yet unmatched pairs. 13113 records in RAM.
INFO 2026-06-08 08:08:38 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 2s. Last read position: chr8:143,576,811
INFO 2026-06-08 08:08:38 MarkDuplicates Tracking 367412 as yet unmatched pairs. 11623 records in RAM.
INFO 2026-06-08 08:08:40 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 1s. Last read position: chr8:143,858,536
INFO 2026-06-08 08:08:40 MarkDuplicates Tracking 366378 as yet unmatched pairs. 10589 records in RAM.
INFO 2026-06-08 08:08:41 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 1s. Last read position: chr8:143,859,923
INFO 2026-06-08 08:08:41 MarkDuplicates Tracking 365827 as yet unmatched pairs. 10038 records in RAM.
INFO 2026-06-08 08:08:43 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:06:17s. Time for last 1,000,000: 2s. Last read position: chr8:143,861,228
INFO 2026-06-08 08:08:43 MarkDuplicates Tracking 364623 as yet unmatched pairs. 8833 records in RAM.
INFO 2026-06-08 08:08:45 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:06:19s. Time for last 1,000,000: 1s. Last read position: chr8:143,862,228
INFO 2026-06-08 08:08:45 MarkDuplicates Tracking 364240 as yet unmatched pairs. 8449 records in RAM.
INFO 2026-06-08 08:08:46 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:06:21s. Time for last 1,000,000: 1s. Last read position: chr8:143,863,585
INFO 2026-06-08 08:08:46 MarkDuplicates Tracking 363838 as yet unmatched pairs. 8047 records in RAM.
INFO 2026-06-08 08:08:48 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 1s. Last read position: chr8:143,864,839
INFO 2026-06-08 08:08:48 MarkDuplicates Tracking 363238 as yet unmatched pairs. 7446 records in RAM.
INFO 2026-06-08 08:08:49 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:06:23s. Time for last 1,000,000: 1s. Last read position: chr8:143,866,192
INFO 2026-06-08 08:08:49 MarkDuplicates Tracking 361796 as yet unmatched pairs. 6003 records in RAM.
INFO 2026-06-08 08:08:50 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 1s. Last read position: chr8:143,919,564
INFO 2026-06-08 08:08:50 MarkDuplicates Tracking 360883 as yet unmatched pairs. 5090 records in RAM.
INFO 2026-06-08 08:08:52 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:06:26s. Time for last 1,000,000: 1s. Last read position: chr8:143,985,064
INFO 2026-06-08 08:08:52 MarkDuplicates Tracking 358412 as yet unmatched pairs. 2619 records in RAM.
INFO 2026-06-08 08:08:54 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:06:28s. Time for last 1,000,000: 2s. Last read position: chr8:144,509,820
INFO 2026-06-08 08:08:54 MarkDuplicates Tracking 356143 as yet unmatched pairs. 349 records in RAM.
INFO 2026-06-08 08:08:57 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:06:31s. Time for last 1,000,000: 2s. Last read position: chr9:19,376,337
INFO 2026-06-08 08:08:57 MarkDuplicates Tracking 354693 as yet unmatched pairs. 20458 records in RAM.
INFO 2026-06-08 08:08:59 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:06:33s. Time for last 1,000,000: 1s. Last read position: chr9:35,684,531
INFO 2026-06-08 08:08:59 MarkDuplicates Tracking 352946 as yet unmatched pairs. 18711 records in RAM.
INFO 2026-06-08 08:09:01 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:06:35s. Time for last 1,000,000: 1s. Last read position: chr9:73,163,515
INFO 2026-06-08 08:09:01 MarkDuplicates Tracking 351212 as yet unmatched pairs. 16926 records in RAM.
INFO 2026-06-08 08:09:03 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 1s. Last read position: chr9:93,253,034
INFO 2026-06-08 08:09:03 MarkDuplicates Tracking 349736 as yet unmatched pairs. 15448 records in RAM.
INFO 2026-06-08 08:09:04 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 1s. Last read position: chr9:104,786,891
INFO 2026-06-08 08:09:04 MarkDuplicates Tracking 347890 as yet unmatched pairs. 13598 records in RAM.
INFO 2026-06-08 08:09:06 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 1s. Last read position: chr9:114,406,410
INFO 2026-06-08 08:09:06 MarkDuplicates Tracking 346005 as yet unmatched pairs. 11713 records in RAM.
INFO 2026-06-08 08:09:08 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:06:42s. Time for last 1,000,000: 1s. Last read position: chr9:125,672,397
INFO 2026-06-08 08:09:08 MarkDuplicates Tracking 344304 as yet unmatched pairs. 10010 records in RAM.
INFO 2026-06-08 08:09:10 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:06:44s. Time for last 1,000,000: 1s. Last read position: chr9:128,615,702
INFO 2026-06-08 08:09:10 MarkDuplicates Tracking 342573 as yet unmatched pairs. 8279 records in RAM.
INFO 2026-06-08 08:09:11 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:06:46s. Time for last 1,000,000: 1s. Last read position: chr9:131,476,345
INFO 2026-06-08 08:09:11 MarkDuplicates Tracking 340883 as yet unmatched pairs. 6572 records in RAM.
INFO 2026-06-08 08:09:14 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 2s. Last read position: chr9:134,768,361
INFO 2026-06-08 08:09:14 MarkDuplicates Tracking 339461 as yet unmatched pairs. 5148 records in RAM.
INFO 2026-06-08 08:09:15 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:06:50s. Time for last 1,000,000: 1s. Last read position: chr9:136,823,555
INFO 2026-06-08 08:09:15 MarkDuplicates Tracking 337044 as yet unmatched pairs. 2730 records in RAM.
INFO 2026-06-08 08:09:17 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 2s. Last read position: chr9:137,555,476
INFO 2026-06-08 08:09:17 MarkDuplicates Tracking 334622 as yet unmatched pairs. 306 records in RAM.
INFO 2026-06-08 08:09:19 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 1s. Last read position: chr10:13,118,972
INFO 2026-06-08 08:09:19 MarkDuplicates Tracking 332961 as yet unmatched pairs. 18867 records in RAM.
INFO 2026-06-08 08:09:21 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 1s. Last read position: chr10:30,349,195
INFO 2026-06-08 08:09:21 MarkDuplicates Tracking 331475 as yet unmatched pairs. 17376 records in RAM.
INFO 2026-06-08 08:09:23 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:06:57s. Time for last 1,000,000: 1s. Last read position: chr10:43,387,512
INFO 2026-06-08 08:09:23 MarkDuplicates Tracking 329839 as yet unmatched pairs. 15738 records in RAM.
INFO 2026-06-08 08:09:25 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 1s. Last read position: chr10:59,852,678
INFO 2026-06-08 08:09:25 MarkDuplicates Tracking 329002 as yet unmatched pairs. 14900 records in RAM.
INFO 2026-06-08 08:09:27 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 1s. Last read position: chr10:72,375,858
INFO 2026-06-08 08:09:27 MarkDuplicates Tracking 327046 as yet unmatched pairs. 12942 records in RAM.
INFO 2026-06-08 08:09:28 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:07:02s. Time for last 1,000,000: 1s. Last read position: chr10:79,347,498
INFO 2026-06-08 08:09:28 MarkDuplicates Tracking 326104 as yet unmatched pairs. 12000 records in RAM.
INFO 2026-06-08 08:09:30 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:07:05s. Time for last 1,000,000: 2s. Last read position: chr10:95,238,028
INFO 2026-06-08 08:09:30 MarkDuplicates Tracking 323419 as yet unmatched pairs. 9312 records in RAM.
INFO 2026-06-08 08:09:32 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 1s. Last read position: chr10:102,141,020
INFO 2026-06-08 08:09:32 MarkDuplicates Tracking 321739 as yet unmatched pairs. 7629 records in RAM.
INFO 2026-06-08 08:09:35 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:07:09s. Time for last 1,000,000: 2s. Last read position: chr10:112,426,385
INFO 2026-06-08 08:09:35 MarkDuplicates Tracking 320289 as yet unmatched pairs. 6176 records in RAM.
INFO 2026-06-08 08:09:37 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:07:11s. Time for last 1,000,000: 2s. Last read position: chr10:121,479,908
INFO 2026-06-08 08:09:37 MarkDuplicates Tracking 318531 as yet unmatched pairs. 4414 records in RAM.
INFO 2026-06-08 08:09:39 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 2s. Last read position: chr10:122,595,515
INFO 2026-06-08 08:09:39 MarkDuplicates Tracking 317963 as yet unmatched pairs. 3846 records in RAM.
INFO 2026-06-08 08:09:41 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:07:15s. Time for last 1,000,000: 1s. Last read position: chr10:122,621,111
INFO 2026-06-08 08:09:41 MarkDuplicates Tracking 317518 as yet unmatched pairs. 3401 records in RAM.
INFO 2026-06-08 08:09:42 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:07:17s. Time for last 1,000,000: 1s. Last read position: chr10:132,351,648
INFO 2026-06-08 08:09:42 MarkDuplicates Tracking 314821 as yet unmatched pairs. 697 records in RAM.
INFO 2026-06-08 08:09:45 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:07:19s. Time for last 1,000,000: 2s. Last read position: chr11:319,961
INFO 2026-06-08 08:09:45 MarkDuplicates Tracking 314824 as yet unmatched pairs. 34679 records in RAM.
INFO 2026-06-08 08:09:47 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:07:21s. Time for last 1,000,000: 1s. Last read position: chr11:834,576
INFO 2026-06-08 08:09:47 MarkDuplicates Tracking 311221 as yet unmatched pairs. 31075 records in RAM.
INFO 2026-06-08 08:09:49 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:07:23s. Time for last 1,000,000: 1s. Last read position: chr11:1,242,852
INFO 2026-06-08 08:09:49 MarkDuplicates Tracking 310008 as yet unmatched pairs. 29861 records in RAM.
INFO 2026-06-08 08:09:50 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:07:24s. Time for last 1,000,000: 1s. Last read position: chr11:1,246,750
INFO 2026-06-08 08:09:50 MarkDuplicates Tracking 309255 as yet unmatched pairs. 29108 records in RAM.
INFO 2026-06-08 08:09:51 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:07:26s. Time for last 1,000,000: 1s. Last read position: chr11:1,250,920
INFO 2026-06-08 08:09:51 MarkDuplicates Tracking 308401 as yet unmatched pairs. 28253 records in RAM.
INFO 2026-06-08 08:09:54 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:07:28s. Time for last 1,000,000: 2s. Last read position: chr11:6,217,621
INFO 2026-06-08 08:09:54 MarkDuplicates Tracking 306623 as yet unmatched pairs. 26472 records in RAM.
INFO 2026-06-08 08:09:56 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:07:30s. Time for last 1,000,000: 1s. Last read position: chr11:12,220,409
INFO 2026-06-08 08:09:56 MarkDuplicates Tracking 304569 as yet unmatched pairs. 24416 records in RAM.
INFO 2026-06-08 08:09:57 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:07:31s. Time for last 1,000,000: 1s. Last read position: chr11:34,079,665
INFO 2026-06-08 08:09:57 MarkDuplicates Tracking 303211 as yet unmatched pairs. 23057 records in RAM.
INFO 2026-06-08 08:09:59 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:07:33s. Time for last 1,000,000: 1s. Last read position: chr11:46,808,112
INFO 2026-06-08 08:09:59 MarkDuplicates Tracking 301534 as yet unmatched pairs. 21379 records in RAM.
INFO 2026-06-08 08:10:01 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:07:35s. Time for last 1,000,000: 2s. Last read position: chr11:59,576,828
INFO 2026-06-08 08:10:01 MarkDuplicates Tracking 299685 as yet unmatched pairs. 19530 records in RAM.
INFO 2026-06-08 08:10:03 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:07:38s. Time for last 1,000,000: 2s. Last read position: chr11:62,525,656
INFO 2026-06-08 08:10:03 MarkDuplicates Tracking 298211 as yet unmatched pairs. 18039 records in RAM.
INFO 2026-06-08 08:10:06 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:07:40s. Time for last 1,000,000: 2s. Last read position: chr11:64,230,825
INFO 2026-06-08 08:10:06 MarkDuplicates Tracking 296116 as yet unmatched pairs. 15942 records in RAM.
INFO 2026-06-08 08:10:08 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:07:42s. Time for last 1,000,000: 1s. Last read position: chr11:65,182,751
INFO 2026-06-08 08:10:08 MarkDuplicates Tracking 294376 as yet unmatched pairs. 14200 records in RAM.
INFO 2026-06-08 08:10:10 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:07:44s. Time for last 1,000,000: 1s. Last read position: chr11:65,861,425
INFO 2026-06-08 08:10:10 MarkDuplicates Tracking 292343 as yet unmatched pairs. 12165 records in RAM.
INFO 2026-06-08 08:10:11 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:07:46s. Time for last 1,000,000: 1s. Last read position: chr11:67,285,295
INFO 2026-06-08 08:10:11 MarkDuplicates Tracking 290909 as yet unmatched pairs. 10731 records in RAM.
INFO 2026-06-08 08:10:13 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:07:47s. Time for last 1,000,000: 1s. Last read position: chr11:68,936,882
INFO 2026-06-08 08:10:13 MarkDuplicates Tracking 288841 as yet unmatched pairs. 8663 records in RAM.
INFO 2026-06-08 08:10:15 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:07:49s. Time for last 1,000,000: 1s. Last read position: chr11:73,310,430
INFO 2026-06-08 08:10:15 MarkDuplicates Tracking 287089 as yet unmatched pairs. 6909 records in RAM.
INFO 2026-06-08 08:10:17 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:07:51s. Time for last 1,000,000: 1s. Last read position: chr11:85,958,967
INFO 2026-06-08 08:10:17 MarkDuplicates Tracking 285311 as yet unmatched pairs. 5131 records in RAM.
INFO 2026-06-08 08:10:19 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:07:53s. Time for last 1,000,000: 1s. Last read position: chr11:117,091,159
INFO 2026-06-08 08:10:19 MarkDuplicates Tracking 283702 as yet unmatched pairs. 3521 records in RAM.
INFO 2026-06-08 08:10:20 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:07:55s. Time for last 1,000,000: 1s. Last read position: chr11:121,558,633
INFO 2026-06-08 08:10:20 MarkDuplicates Tracking 281907 as yet unmatched pairs. 1726 records in RAM.
INFO 2026-06-08 08:10:22 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:07:57s. Time for last 1,000,000: 1s. Last read position: chr12:753,613
INFO 2026-06-08 08:10:22 MarkDuplicates Tracking 280431 as yet unmatched pairs. 31988 records in RAM.
INFO 2026-06-08 08:10:24 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:07:58s. Time for last 1,000,000: 1s. Last read position: chr12:6,769,939
INFO 2026-06-08 08:10:24 MarkDuplicates Tracking 278707 as yet unmatched pairs. 30263 records in RAM.
INFO 2026-06-08 08:10:26 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:08:00s. Time for last 1,000,000: 1s. Last read position: chr12:10,702,091
INFO 2026-06-08 08:10:26 MarkDuplicates Tracking 276596 as yet unmatched pairs. 28150 records in RAM.
INFO 2026-06-08 08:10:28 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:08:02s. Time for last 1,000,000: 1s. Last read position: chr12:32,576,288
INFO 2026-06-08 08:10:28 MarkDuplicates Tracking 275020 as yet unmatched pairs. 26573 records in RAM.
INFO 2026-06-08 08:10:30 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:08:04s. Time for last 1,000,000: 2s. Last read position: chr12:49,040,911
INFO 2026-06-08 08:10:30 MarkDuplicates Tracking 273440 as yet unmatched pairs. 24990 records in RAM.
INFO 2026-06-08 08:10:32 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:08:06s. Time for last 1,000,000: 2s. Last read position: chr12:49,741,590
INFO 2026-06-08 08:10:32 MarkDuplicates Tracking 271946 as yet unmatched pairs. 23496 records in RAM.
INFO 2026-06-08 08:10:35 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:08:09s. Time for last 1,000,000: 2s. Last read position: chr12:52,949,213
INFO 2026-06-08 08:10:35 MarkDuplicates Tracking 270967 as yet unmatched pairs. 22516 records in RAM.
INFO 2026-06-08 08:10:37 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:08:11s. Time for last 1,000,000: 1s. Last read position: chr12:54,281,871
INFO 2026-06-08 08:10:37 MarkDuplicates Tracking 269234 as yet unmatched pairs. 20781 records in RAM.
INFO 2026-06-08 08:10:38 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:08:13s. Time for last 1,000,000: 1s. Last read position: chr12:56,231,408
INFO 2026-06-08 08:10:38 MarkDuplicates Tracking 266898 as yet unmatched pairs. 18445 records in RAM.
INFO 2026-06-08 08:10:40 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:08:14s. Time for last 1,000,000: 1s. Last read position: chr12:57,175,946
INFO 2026-06-08 08:10:40 MarkDuplicates Tracking 265241 as yet unmatched pairs. 16788 records in RAM.
INFO 2026-06-08 08:10:42 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:08:16s. Time for last 1,000,000: 1s. Last read position: chr12:68,553,441
INFO 2026-06-08 08:10:42 MarkDuplicates Tracking 263432 as yet unmatched pairs. 14978 records in RAM.
INFO 2026-06-08 08:10:44 MarkDuplicates Read 213,000,000 records. Elapsed time: 00:08:18s. Time for last 1,000,000: 1s. Last read position: chr12:95,474,209
INFO 2026-06-08 08:10:44 MarkDuplicates Tracking 261732 as yet unmatched pairs. 13274 records in RAM.
INFO 2026-06-08 08:10:46 MarkDuplicates Read 214,000,000 records. Elapsed time: 00:08:20s. Time for last 1,000,000: 1s. Last read position: chr12:108,623,639
INFO 2026-06-08 08:10:46 MarkDuplicates Tracking 260010 as yet unmatched pairs. 11552 records in RAM.
INFO 2026-06-08 08:10:47 MarkDuplicates Read 215,000,000 records. Elapsed time: 00:08:22s. Time for last 1,000,000: 1s. Last read position: chr12:112,314,527
INFO 2026-06-08 08:10:47 MarkDuplicates Tracking 258298 as yet unmatched pairs. 9839 records in RAM.
INFO 2026-06-08 08:10:49 MarkDuplicates Read 216,000,000 records. Elapsed time: 00:08:23s. Time for last 1,000,000: 1s. Last read position: chr12:118,052,348
INFO 2026-06-08 08:10:49 MarkDuplicates Tracking 256432 as yet unmatched pairs. 7972 records in RAM.
INFO 2026-06-08 08:10:51 MarkDuplicates Read 217,000,000 records. Elapsed time: 00:08:25s. Time for last 1,000,000: 1s. Last read position: chr12:121,004,146
INFO 2026-06-08 08:10:51 MarkDuplicates Tracking 254629 as yet unmatched pairs. 6169 records in RAM.
INFO 2026-06-08 08:10:54 MarkDuplicates Read 218,000,000 records. Elapsed time: 00:08:28s. Time for last 1,000,000: 2s. Last read position: chr12:122,702,459
INFO 2026-06-08 08:10:54 MarkDuplicates Tracking 253536 as yet unmatched pairs. 5074 records in RAM.
INFO 2026-06-08 08:10:56 MarkDuplicates Read 219,000,000 records. Elapsed time: 00:08:30s. Time for last 1,000,000: 2s. Last read position: chr12:124,346,635
INFO 2026-06-08 08:10:56 MarkDuplicates Tracking 251362 as yet unmatched pairs. 2900 records in RAM.
INFO 2026-06-08 08:10:58 MarkDuplicates Read 220,000,000 records. Elapsed time: 00:08:32s. Time for last 1,000,000: 2s. Last read position: chr12:132,571,441
INFO 2026-06-08 08:10:58 MarkDuplicates Tracking 249299 as yet unmatched pairs. 835 records in RAM.
INFO 2026-06-08 08:11:01 MarkDuplicates Read 221,000,000 records. Elapsed time: 00:08:35s. Time for last 1,000,000: 2s. Last read position: chr13:27,256,446
INFO 2026-06-08 08:11:01 MarkDuplicates Tracking 247424 as yet unmatched pairs. 8827 records in RAM.
INFO 2026-06-08 08:11:03 MarkDuplicates Read 222,000,000 records. Elapsed time: 00:08:37s. Time for last 1,000,000: 2s. Last read position: chr13:39,013,652
INFO 2026-06-08 08:11:03 MarkDuplicates Tracking 245775 as yet unmatched pairs. 7176 records in RAM.
INFO 2026-06-08 08:11:06 MarkDuplicates Read 223,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 2s. Last read position: chr13:48,045,666
INFO 2026-06-08 08:11:06 MarkDuplicates Tracking 243715 as yet unmatched pairs. 5113 records in RAM.
INFO 2026-06-08 08:11:08 MarkDuplicates Read 224,000,000 records. Elapsed time: 00:08:43s. Time for last 1,000,000: 2s. Last read position: chr13:75,359,837
INFO 2026-06-08 08:11:08 MarkDuplicates Tracking 242175 as yet unmatched pairs. 3572 records in RAM.
INFO 2026-06-08 08:11:11 MarkDuplicates Read 225,000,000 records. Elapsed time: 00:08:45s. Time for last 1,000,000: 2s. Last read position: chr13:110,174,492
INFO 2026-06-08 08:11:11 MarkDuplicates Tracking 240731 as yet unmatched pairs. 2122 records in RAM.
INFO 2026-06-08 08:11:13 MarkDuplicates Read 226,000,000 records. Elapsed time: 00:08:48s. Time for last 1,000,000: 2s. Last read position: chr14:20,408,320
INFO 2026-06-08 08:11:13 MarkDuplicates Tracking 238506 as yet unmatched pairs. 14106 records in RAM.
INFO 2026-06-08 08:11:16 MarkDuplicates Read 227,000,000 records. Elapsed time: 00:08:50s. Time for last 1,000,000: 2s. Last read position: chr14:23,323,447
INFO 2026-06-08 08:11:16 MarkDuplicates Tracking 236744 as yet unmatched pairs. 12342 records in RAM.
INFO 2026-06-08 08:11:18 MarkDuplicates Read 228,000,000 records. Elapsed time: 00:08:52s. Time for last 1,000,000: 1s. Last read position: chr14:35,401,997
INFO 2026-06-08 08:11:18 MarkDuplicates Tracking 234773 as yet unmatched pairs. 10371 records in RAM.
INFO 2026-06-08 08:11:20 MarkDuplicates Read 229,000,000 records. Elapsed time: 00:08:54s. Time for last 1,000,000: 1s. Last read position: chr14:57,246,786
INFO 2026-06-08 08:11:20 MarkDuplicates Tracking 233129 as yet unmatched pairs. 8724 records in RAM.
INFO 2026-06-08 08:11:22 MarkDuplicates Read 230,000,000 records. Elapsed time: 00:08:56s. Time for last 1,000,000: 1s. Last read position: chr14:69,053,851
INFO 2026-06-08 08:11:22 MarkDuplicates Tracking 231434 as yet unmatched pairs. 7029 records in RAM.
INFO 2026-06-08 08:11:24 MarkDuplicates Read 231,000,000 records. Elapsed time: 00:08:58s. Time for last 1,000,000: 2s. Last read position: chr14:76,763,001
INFO 2026-06-08 08:11:24 MarkDuplicates Tracking 229610 as yet unmatched pairs. 5203 records in RAM.
INFO 2026-06-08 08:11:27 MarkDuplicates Read 232,000,000 records. Elapsed time: 00:09:01s. Time for last 1,000,000: 3s. Last read position: chr14:99,517,108
INFO 2026-06-08 08:11:27 MarkDuplicates Tracking 228330 as yet unmatched pairs. 3880 records in RAM.
INFO 2026-06-08 08:11:29 MarkDuplicates Read 233,000,000 records. Elapsed time: 00:09:03s. Time for last 1,000,000: 2s. Last read position: chr14:104,770,777
INFO 2026-06-08 08:11:29 MarkDuplicates Tracking 226672 as yet unmatched pairs. 2221 records in RAM.
INFO 2026-06-08 08:11:31 MarkDuplicates Read 234,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 1s. Last read position: chr14:105,708,067
INFO 2026-06-08 08:11:31 MarkDuplicates Tracking 225040 as yet unmatched pairs. 587 records in RAM.
INFO 2026-06-08 08:11:33 MarkDuplicates Read 235,000,000 records. Elapsed time: 00:09:07s. Time for last 1,000,000: 1s. Last read position: chr15:32,732,141
INFO 2026-06-08 08:11:33 MarkDuplicates Tracking 224704 as yet unmatched pairs. 12926 records in RAM.
INFO 2026-06-08 08:11:35 MarkDuplicates Read 236,000,000 records. Elapsed time: 00:09:09s. Time for last 1,000,000: 1s. Last read position: chr15:40,844,754
INFO 2026-06-08 08:11:35 MarkDuplicates Tracking 222172 as yet unmatched pairs. 10392 records in RAM.
INFO 2026-06-08 08:11:37 MarkDuplicates Read 237,000,000 records. Elapsed time: 00:09:11s. Time for last 1,000,000: 2s. Last read position: chr15:44,651,712
INFO 2026-06-08 08:11:37 MarkDuplicates Tracking 220319 as yet unmatched pairs. 8537 records in RAM.
INFO 2026-06-08 08:11:39 MarkDuplicates Read 238,000,000 records. Elapsed time: 00:09:13s. Time for last 1,000,000: 1s. Last read position: chr15:59,769,077
INFO 2026-06-08 08:11:39 MarkDuplicates Tracking 218727 as yet unmatched pairs. 6943 records in RAM.
INFO 2026-06-08 08:11:40 MarkDuplicates Read 239,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 1s. Last read position: chr15:69,360,017
INFO 2026-06-08 08:11:40 MarkDuplicates Tracking 217014 as yet unmatched pairs. 5229 records in RAM.
INFO 2026-06-08 08:11:42 MarkDuplicates Read 240,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 1s. Last read position: chr15:75,206,055
INFO 2026-06-08 08:11:42 MarkDuplicates Tracking 215494 as yet unmatched pairs. 3706 records in RAM.
INFO 2026-06-08 08:11:44 MarkDuplicates Read 241,000,000 records. Elapsed time: 00:09:18s. Time for last 1,000,000: 1s. Last read position: chr15:84,669,996
INFO 2026-06-08 08:11:44 MarkDuplicates Tracking 214419 as yet unmatched pairs. 2629 records in RAM.
INFO 2026-06-08 08:11:46 MarkDuplicates Read 242,000,000 records. Elapsed time: 00:09:20s. Time for last 1,000,000: 1s. Last read position: chr15:92,162,963
INFO 2026-06-08 08:11:46 MarkDuplicates Tracking 212264 as yet unmatched pairs. 474 records in RAM.
INFO 2026-06-08 08:11:48 MarkDuplicates Read 243,000,000 records. Elapsed time: 00:09:22s. Time for last 1,000,000: 2s. Last read position: chr16:666,518
INFO 2026-06-08 08:11:48 MarkDuplicates Tracking 210784 as yet unmatched pairs. 29087 records in RAM.
INFO 2026-06-08 08:11:50 MarkDuplicates Read 244,000,000 records. Elapsed time: 00:09:24s. Time for last 1,000,000: 2s. Last read position: chr16:2,009,575
INFO 2026-06-08 08:11:50 MarkDuplicates Tracking 208625 as yet unmatched pairs. 26927 records in RAM.
INFO 2026-06-08 08:11:52 MarkDuplicates Read 245,000,000 records. Elapsed time: 00:09:26s. Time for last 1,000,000: 1s. Last read position: chr16:2,763,002
INFO 2026-06-08 08:11:52 MarkDuplicates Tracking 206870 as yet unmatched pairs. 25172 records in RAM.
INFO 2026-06-08 08:11:54 MarkDuplicates Read 246,000,000 records. Elapsed time: 00:09:28s. Time for last 1,000,000: 1s. Last read position: chr16:3,549,191
INFO 2026-06-08 08:11:54 MarkDuplicates Tracking 205014 as yet unmatched pairs. 23316 records in RAM.
INFO 2026-06-08 08:11:56 MarkDuplicates Read 247,000,000 records. Elapsed time: 00:09:30s. Time for last 1,000,000: 1s. Last read position: chr16:11,387,221
INFO 2026-06-08 08:11:56 MarkDuplicates Tracking 203232 as yet unmatched pairs. 21533 records in RAM.
INFO 2026-06-08 08:11:57 MarkDuplicates Read 248,000,000 records. Elapsed time: 00:09:31s. Time for last 1,000,000: 1s. Last read position: chr16:15,130,285
INFO 2026-06-08 08:11:57 MarkDuplicates Tracking 202127 as yet unmatched pairs. 20428 records in RAM.
INFO 2026-06-08 08:11:59 MarkDuplicates Read 249,000,000 records. Elapsed time: 00:09:33s. Time for last 1,000,000: 1s. Last read position: chr16:16,393,625
INFO 2026-06-08 08:11:59 MarkDuplicates Tracking 201569 as yet unmatched pairs. 19870 records in RAM.
INFO 2026-06-08 08:12:00 MarkDuplicates Read 250,000,000 records. Elapsed time: 00:09:35s. Time for last 1,000,000: 1s. Last read position: chr16:18,890,877
INFO 2026-06-08 08:12:00 MarkDuplicates Tracking 200481 as yet unmatched pairs. 18782 records in RAM.
INFO 2026-06-08 08:12:02 MarkDuplicates Read 251,000,000 records. Elapsed time: 00:09:37s. Time for last 1,000,000: 2s. Last read position: chr16:21,448,574
INFO 2026-06-08 08:12:02 MarkDuplicates Tracking 199718 as yet unmatched pairs. 18018 records in RAM.
INFO 2026-06-08 08:12:04 MarkDuplicates Read 252,000,000 records. Elapsed time: 00:09:39s. Time for last 1,000,000: 2s. Last read position: chr16:22,429,840
INFO 2026-06-08 08:12:04 MarkDuplicates Tracking 199011 as yet unmatched pairs. 17311 records in RAM.
INFO 2026-06-08 08:12:06 MarkDuplicates Read 253,000,000 records. Elapsed time: 00:09:40s. Time for last 1,000,000: 1s. Last read position: chr16:23,105,449
INFO 2026-06-08 08:12:06 MarkDuplicates Tracking 198700 as yet unmatched pairs. 17000 records in RAM.
INFO 2026-06-08 08:12:08 MarkDuplicates Read 254,000,000 records. Elapsed time: 00:09:43s. Time for last 1,000,000: 2s. Last read position: chr16:28,826,377
INFO 2026-06-08 08:12:08 MarkDuplicates Tracking 197193 as yet unmatched pairs. 15493 records in RAM.
INFO 2026-06-08 08:12:10 MarkDuplicates Read 255,000,000 records. Elapsed time: 00:09:44s. Time for last 1,000,000: 1s. Last read position: chr16:29,483,897
INFO 2026-06-08 08:12:10 MarkDuplicates Tracking 196646 as yet unmatched pairs. 14945 records in RAM.
INFO 2026-06-08 08:12:12 MarkDuplicates Read 256,000,000 records. Elapsed time: 00:09:46s. Time for last 1,000,000: 1s. Last read position: chr16:29,990,949
INFO 2026-06-08 08:12:12 MarkDuplicates Tracking 194995 as yet unmatched pairs. 13294 records in RAM.
INFO 2026-06-08 08:12:14 MarkDuplicates Read 257,000,000 records. Elapsed time: 00:09:48s. Time for last 1,000,000: 1s. Last read position: chr16:30,262,071
INFO 2026-06-08 08:12:14 MarkDuplicates Tracking 193743 as yet unmatched pairs. 12041 records in RAM.
INFO 2026-06-08 08:12:16 MarkDuplicates Read 258,000,000 records. Elapsed time: 00:09:50s. Time for last 1,000,000: 2s. Last read position: chr16:31,078,783
INFO 2026-06-08 08:12:16 MarkDuplicates Tracking 192022 as yet unmatched pairs. 10306 records in RAM.
INFO 2026-06-08 08:12:18 MarkDuplicates Read 259,000,000 records. Elapsed time: 00:09:52s. Time for last 1,000,000: 2s. Last read position: chr16:50,749,579
INFO 2026-06-08 08:12:18 MarkDuplicates Tracking 190508 as yet unmatched pairs. 8783 records in RAM.
INFO 2026-06-08 08:12:20 MarkDuplicates Read 260,000,000 records. Elapsed time: 00:09:54s. Time for last 1,000,000: 1s. Last read position: chr16:58,197,678
INFO 2026-06-08 08:12:20 MarkDuplicates Tracking 188886 as yet unmatched pairs. 7160 records in RAM.
INFO 2026-06-08 08:12:22 MarkDuplicates Read 261,000,000 records. Elapsed time: 00:09:56s. Time for last 1,000,000: 1s. Last read position: chr16:69,566,269
INFO 2026-06-08 08:12:22 MarkDuplicates Tracking 186913 as yet unmatched pairs. 5185 records in RAM.
INFO 2026-06-08 08:12:24 MarkDuplicates Read 262,000,000 records. Elapsed time: 00:09:58s. Time for last 1,000,000: 1s. Last read position: chr16:81,724,502
INFO 2026-06-08 08:12:24 MarkDuplicates Tracking 185059 as yet unmatched pairs. 3327 records in RAM.
INFO 2026-06-08 08:12:26 MarkDuplicates Read 263,000,000 records. Elapsed time: 00:10:00s. Time for last 1,000,000: 1s. Last read position: chr16:88,735,202
INFO 2026-06-08 08:12:26 MarkDuplicates Tracking 183012 as yet unmatched pairs. 1278 records in RAM.
INFO 2026-06-08 08:13:43 MarkDuplicates Read 264,000,000 records. Elapsed time: 00:11:17s. Time for last 1,000,000: 77s. Last read position: chr17:1,422,895
INFO 2026-06-08 08:13:43 MarkDuplicates Tracking 181352 as yet unmatched pairs. 64474 records in RAM.
INFO 2026-06-08 08:13:45 MarkDuplicates Read 265,000,000 records. Elapsed time: 00:11:19s. Time for last 1,000,000: 2s. Last read position: chr17:4,789,526
INFO 2026-06-08 08:13:45 MarkDuplicates Tracking 179368 as yet unmatched pairs. 62490 records in RAM.
INFO 2026-06-08 08:13:46 MarkDuplicates Read 266,000,000 records. Elapsed time: 00:11:21s. Time for last 1,000,000: 1s. Last read position: chr17:7,343,400
INFO 2026-06-08 08:13:46 MarkDuplicates Tracking 177715 as yet unmatched pairs. 60834 records in RAM.
INFO 2026-06-08 08:13:48 MarkDuplicates Read 267,000,000 records. Elapsed time: 00:11:22s. Time for last 1,000,000: 1s. Last read position: chr17:7,848,344
INFO 2026-06-08 08:13:48 MarkDuplicates Tracking 176367 as yet unmatched pairs. 59486 records in RAM.
INFO 2026-06-08 08:13:50 MarkDuplicates Read 268,000,000 records. Elapsed time: 00:11:24s. Time for last 1,000,000: 1s. Last read position: chr17:16,382,366
INFO 2026-06-08 08:13:50 MarkDuplicates Tracking 174645 as yet unmatched pairs. 57763 records in RAM.
INFO 2026-06-08 08:13:52 MarkDuplicates Read 269,000,000 records. Elapsed time: 00:11:26s. Time for last 1,000,000: 1s. Last read position: chr17:28,043,011
INFO 2026-06-08 08:13:52 MarkDuplicates Tracking 173006 as yet unmatched pairs. 56123 records in RAM.
INFO 2026-06-08 08:13:53 MarkDuplicates Read 270,000,000 records. Elapsed time: 00:11:28s. Time for last 1,000,000: 1s. Last read position: chr17:31,488,215
INFO 2026-06-08 08:13:53 MarkDuplicates Tracking 171235 as yet unmatched pairs. 54351 records in RAM.
INFO 2026-06-08 08:13:55 MarkDuplicates Read 271,000,000 records. Elapsed time: 00:11:30s. Time for last 1,000,000: 2s. Last read position: chr17:38,122,829
INFO 2026-06-08 08:13:55 MarkDuplicates Tracking 169487 as yet unmatched pairs. 52601 records in RAM.
INFO 2026-06-08 08:13:58 MarkDuplicates Read 272,000,000 records. Elapsed time: 00:11:32s. Time for last 1,000,000: 2s. Last read position: chr17:39,711,937
INFO 2026-06-08 08:13:58 MarkDuplicates Tracking 168049 as yet unmatched pairs. 51162 records in RAM.
INFO 2026-06-08 08:14:00 MarkDuplicates Read 273,000,000 records. Elapsed time: 00:11:34s. Time for last 1,000,000: 2s. Last read position: chr17:40,630,714
INFO 2026-06-08 08:14:00 MarkDuplicates Tracking 166112 as yet unmatched pairs. 49225 records in RAM.
INFO 2026-06-08 08:14:01 MarkDuplicates Read 274,000,000 records. Elapsed time: 00:11:35s. Time for last 1,000,000: 1s. Last read position: chr17:42,795,151
INFO 2026-06-08 08:14:01 MarkDuplicates Tracking 164561 as yet unmatched pairs. 47673 records in RAM.
INFO 2026-06-08 08:14:03 MarkDuplicates Read 275,000,000 records. Elapsed time: 00:11:37s. Time for last 1,000,000: 1s. Last read position: chr17:45,453,558
INFO 2026-06-08 08:14:03 MarkDuplicates Tracking 162582 as yet unmatched pairs. 45694 records in RAM.
INFO 2026-06-08 08:14:05 MarkDuplicates Read 276,000,000 records. Elapsed time: 00:11:39s. Time for last 1,000,000: 1s. Last read position: chr17:50,140,146
INFO 2026-06-08 08:14:05 MarkDuplicates Tracking 160889 as yet unmatched pairs. 43999 records in RAM.
INFO 2026-06-08 08:14:07 MarkDuplicates Read 277,000,000 records. Elapsed time: 00:11:41s. Time for last 1,000,000: 2s. Last read position: chr17:50,186,699
INFO 2026-06-08 08:14:07 MarkDuplicates Tracking 162876 as yet unmatched pairs. 45986 records in RAM.
INFO 2026-06-08 08:14:09 MarkDuplicates Read 278,000,000 records. Elapsed time: 00:11:43s. Time for last 1,000,000: 1s. Last read position: chr17:50,187,483
INFO 2026-06-08 08:14:09 MarkDuplicates Tracking 166819 as yet unmatched pairs. 49929 records in RAM.
INFO 2026-06-08 08:14:11 MarkDuplicates Read 279,000,000 records. Elapsed time: 00:11:45s. Time for last 1,000,000: 1s. Last read position: chr17:50,188,542
INFO 2026-06-08 08:14:11 MarkDuplicates Tracking 163395 as yet unmatched pairs. 46505 records in RAM.
INFO 2026-06-08 08:14:13 MarkDuplicates Read 280,000,000 records. Elapsed time: 00:11:47s. Time for last 1,000,000: 1s. Last read position: chr17:50,188,980
INFO 2026-06-08 08:14:13 MarkDuplicates Tracking 160818 as yet unmatched pairs. 43927 records in RAM.
INFO 2026-06-08 08:14:15 MarkDuplicates Read 281,000,000 records. Elapsed time: 00:11:49s. Time for last 1,000,000: 1s. Last read position: chr17:50,189,496
INFO 2026-06-08 08:14:15 MarkDuplicates Tracking 160267 as yet unmatched pairs. 43374 records in RAM.
INFO 2026-06-08 08:14:16 MarkDuplicates Read 282,000,000 records. Elapsed time: 00:11:51s. Time for last 1,000,000: 1s. Last read position: chr17:50,190,007
INFO 2026-06-08 08:14:16 MarkDuplicates Tracking 157484 as yet unmatched pairs. 40591 records in RAM.
INFO 2026-06-08 08:14:18 MarkDuplicates Read 283,000,000 records. Elapsed time: 00:11:53s. Time for last 1,000,000: 1s. Last read position: chr17:50,190,445
INFO 2026-06-08 08:14:18 MarkDuplicates Tracking 155835 as yet unmatched pairs. 38942 records in RAM.
INFO 2026-06-08 08:14:20 MarkDuplicates Read 284,000,000 records. Elapsed time: 00:11:55s. Time for last 1,000,000: 1s. Last read position: chr17:50,192,004
INFO 2026-06-08 08:14:20 MarkDuplicates Tracking 158247 as yet unmatched pairs. 41354 records in RAM.
INFO 2026-06-08 08:14:22 MarkDuplicates Read 285,000,000 records. Elapsed time: 00:11:57s. Time for last 1,000,000: 1s. Last read position: chr17:50,193,942
INFO 2026-06-08 08:14:22 MarkDuplicates Tracking 151031 as yet unmatched pairs. 34138 records in RAM.
INFO 2026-06-08 08:14:24 MarkDuplicates Read 286,000,000 records. Elapsed time: 00:11:59s. Time for last 1,000,000: 2s. Last read position: chr17:50,194,415
INFO 2026-06-08 08:14:24 MarkDuplicates Tracking 152327 as yet unmatched pairs. 35434 records in RAM.
INFO 2026-06-08 08:14:27 MarkDuplicates Read 287,000,000 records. Elapsed time: 00:12:01s. Time for last 1,000,000: 2s. Last read position: chr17:50,195,268
INFO 2026-06-08 08:14:27 MarkDuplicates Tracking 147406 as yet unmatched pairs. 30513 records in RAM.
INFO 2026-06-08 08:14:29 MarkDuplicates Read 288,000,000 records. Elapsed time: 00:12:03s. Time for last 1,000,000: 2s. Last read position: chr17:50,195,961
INFO 2026-06-08 08:14:29 MarkDuplicates Tracking 152128 as yet unmatched pairs. 35235 records in RAM.
INFO 2026-06-08 08:14:31 MarkDuplicates Read 289,000,000 records. Elapsed time: 00:12:05s. Time for last 1,000,000: 1s. Last read position: chr17:50,196,334
INFO 2026-06-08 08:14:31 MarkDuplicates Tracking 150983 as yet unmatched pairs. 34090 records in RAM.
INFO 2026-06-08 08:14:33 MarkDuplicates Read 290,000,000 records. Elapsed time: 00:12:07s. Time for last 1,000,000: 1s. Last read position: chr17:50,197,215
INFO 2026-06-08 08:14:33 MarkDuplicates Tracking 146993 as yet unmatched pairs. 30100 records in RAM.
INFO 2026-06-08 08:14:35 MarkDuplicates Read 291,000,000 records. Elapsed time: 00:12:09s. Time for last 1,000,000: 1s. Last read position: chr17:50,199,259
INFO 2026-06-08 08:14:35 MarkDuplicates Tracking 135928 as yet unmatched pairs. 19035 records in RAM.
INFO 2026-06-08 08:14:37 MarkDuplicates Read 292,000,000 records. Elapsed time: 00:12:11s. Time for last 1,000,000: 1s. Last read position: chr17:50,385,160
INFO 2026-06-08 08:14:37 MarkDuplicates Tracking 130656 as yet unmatched pairs. 13763 records in RAM.
INFO 2026-06-08 08:14:39 MarkDuplicates Read 293,000,000 records. Elapsed time: 00:12:13s. Time for last 1,000,000: 1s. Last read position: chr17:59,647,401
INFO 2026-06-08 08:14:39 MarkDuplicates Tracking 129154 as yet unmatched pairs. 12260 records in RAM.
INFO 2026-06-08 08:14:40 MarkDuplicates Read 294,000,000 records. Elapsed time: 00:12:14s. Time for last 1,000,000: 1s. Last read position: chr17:64,506,104
INFO 2026-06-08 08:14:40 MarkDuplicates Tracking 126834 as yet unmatched pairs. 9940 records in RAM.
INFO 2026-06-08 08:14:42 MarkDuplicates Read 295,000,000 records. Elapsed time: 00:12:16s. Time for last 1,000,000: 1s. Last read position: chr17:75,238,122
INFO 2026-06-08 08:14:42 MarkDuplicates Tracking 125358 as yet unmatched pairs. 8454 records in RAM.
INFO 2026-06-08 08:14:44 MarkDuplicates Read 296,000,000 records. Elapsed time: 00:12:18s. Time for last 1,000,000: 1s. Last read position: chr17:76,280,345
INFO 2026-06-08 08:14:44 MarkDuplicates Tracking 123625 as yet unmatched pairs. 6721 records in RAM.
INFO 2026-06-08 08:14:45 MarkDuplicates Read 297,000,000 records. Elapsed time: 00:12:20s. Time for last 1,000,000: 1s. Last read position: chr17:80,073,808
INFO 2026-06-08 08:14:45 MarkDuplicates Tracking 121765 as yet unmatched pairs. 4860 records in RAM.
INFO 2026-06-08 08:14:48 MarkDuplicates Read 298,000,000 records. Elapsed time: 00:12:22s. Time for last 1,000,000: 2s. Last read position: chr17:81,512,275
INFO 2026-06-08 08:14:48 MarkDuplicates Tracking 119693 as yet unmatched pairs. 2782 records in RAM.
INFO 2026-06-08 08:14:49 MarkDuplicates Read 299,000,000 records. Elapsed time: 00:12:24s. Time for last 1,000,000: 1s. Last read position: chr17:82,322,162
INFO 2026-06-08 08:14:49 MarkDuplicates Tracking 117518 as yet unmatched pairs. 607 records in RAM.
INFO 2026-06-08 08:14:51 MarkDuplicates Read 300,000,000 records. Elapsed time: 00:12:25s. Time for last 1,000,000: 1s. Last read position: chr18:13,030,447
INFO 2026-06-08 08:14:51 MarkDuplicates Tracking 115860 as yet unmatched pairs. 3632 records in RAM.
INFO 2026-06-08 08:14:53 MarkDuplicates Read 301,000,000 records. Elapsed time: 00:12:27s. Time for last 1,000,000: 1s. Last read position: chr18:49,488,544
INFO 2026-06-08 08:14:53 MarkDuplicates Tracking 114446 as yet unmatched pairs. 2215 records in RAM.
INFO 2026-06-08 08:14:55 MarkDuplicates Read 302,000,000 records. Elapsed time: 00:12:29s. Time for last 1,000,000: 2s. Last read position: chr19:66,245
INFO 2026-06-08 08:14:55 MarkDuplicates Tracking 112230 as yet unmatched pairs. 51534 records in RAM.
INFO 2026-06-08 08:14:57 MarkDuplicates Read 303,000,000 records. Elapsed time: 00:12:31s. Time for last 1,000,000: 1s. Last read position: chr19:1,113,537
INFO 2026-06-08 08:14:57 MarkDuplicates Tracking 110070 as yet unmatched pairs. 49372 records in RAM.
INFO 2026-06-08 08:14:59 MarkDuplicates Read 304,000,000 records. Elapsed time: 00:12:33s. Time for last 1,000,000: 1s. Last read position: chr19:1,854,567
INFO 2026-06-08 08:14:59 MarkDuplicates Tracking 108496 as yet unmatched pairs. 47798 records in RAM.
INFO 2026-06-08 08:15:00 MarkDuplicates Read 305,000,000 records. Elapsed time: 00:12:35s. Time for last 1,000,000: 1s. Last read position: chr19:3,449,094
INFO 2026-06-08 08:15:00 MarkDuplicates Tracking 106374 as yet unmatched pairs. 45676 records in RAM.
INFO 2026-06-08 08:15:02 MarkDuplicates Read 306,000,000 records. Elapsed time: 00:12:36s. Time for last 1,000,000: 1s. Last read position: chr19:5,119,660
INFO 2026-06-08 08:15:02 MarkDuplicates Tracking 104563 as yet unmatched pairs. 43862 records in RAM.
INFO 2026-06-08 08:15:04 MarkDuplicates Read 307,000,000 records. Elapsed time: 00:12:38s. Time for last 1,000,000: 1s. Last read position: chr19:6,751,237
INFO 2026-06-08 08:15:04 MarkDuplicates Tracking 102942 as yet unmatched pairs. 42241 records in RAM.
INFO 2026-06-08 08:15:06 MarkDuplicates Read 308,000,000 records. Elapsed time: 00:12:40s. Time for last 1,000,000: 1s. Last read position: chr19:9,969,893
INFO 2026-06-08 08:15:06 MarkDuplicates Tracking 100621 as yet unmatched pairs. 39919 records in RAM.
INFO 2026-06-08 08:15:08 MarkDuplicates Read 309,000,000 records. Elapsed time: 00:12:42s. Time for last 1,000,000: 1s. Last read position: chr19:11,030,871
INFO 2026-06-08 08:15:08 MarkDuplicates Tracking 98947 as yet unmatched pairs. 38245 records in RAM.
INFO 2026-06-08 08:15:09 MarkDuplicates Read 310,000,000 records. Elapsed time: 00:12:44s. Time for last 1,000,000: 1s. Last read position: chr19:12,943,844
INFO 2026-06-08 08:15:09 MarkDuplicates Tracking 97573 as yet unmatched pairs. 36871 records in RAM.
INFO 2026-06-08 08:15:11 MarkDuplicates Read 311,000,000 records. Elapsed time: 00:12:46s. Time for last 1,000,000: 2s. Last read position: chr19:14,516,796
INFO 2026-06-08 08:15:11 MarkDuplicates Tracking 96442 as yet unmatched pairs. 35739 records in RAM.
INFO 2026-06-08 08:15:14 MarkDuplicates Read 312,000,000 records. Elapsed time: 00:12:48s. Time for last 1,000,000: 2s. Last read position: chr19:15,272,978
INFO 2026-06-08 08:15:14 MarkDuplicates Tracking 94146 as yet unmatched pairs. 33443 records in RAM.
INFO 2026-06-08 08:15:15 MarkDuplicates Read 313,000,000 records. Elapsed time: 00:12:49s. Time for last 1,000,000: 1s. Last read position: chr19:17,520,958
INFO 2026-06-08 08:15:15 MarkDuplicates Tracking 91827 as yet unmatched pairs. 31122 records in RAM.
INFO 2026-06-08 08:15:17 MarkDuplicates Read 314,000,000 records. Elapsed time: 00:12:51s. Time for last 1,000,000: 1s. Last read position: chr19:18,856,036
INFO 2026-06-08 08:15:17 MarkDuplicates Tracking 90171 as yet unmatched pairs. 29453 records in RAM.
INFO 2026-06-08 08:15:19 MarkDuplicates Read 315,000,000 records. Elapsed time: 00:12:53s. Time for last 1,000,000: 1s. Last read position: chr19:35,011,466
INFO 2026-06-08 08:15:19 MarkDuplicates Tracking 88346 as yet unmatched pairs. 27627 records in RAM.
INFO 2026-06-08 08:15:20 MarkDuplicates Read 316,000,000 records. Elapsed time: 00:12:54s. Time for last 1,000,000: 1s. Last read position: chr19:38,082,913
INFO 2026-06-08 08:15:20 MarkDuplicates Tracking 85982 as yet unmatched pairs. 25262 records in RAM.
INFO 2026-06-08 08:15:22 MarkDuplicates Read 317,000,000 records. Elapsed time: 00:12:56s. Time for last 1,000,000: 1s. Last read position: chr19:39,407,894
INFO 2026-06-08 08:15:22 MarkDuplicates Tracking 84754 as yet unmatched pairs. 24034 records in RAM.
INFO 2026-06-08 08:15:24 MarkDuplicates Read 318,000,000 records. Elapsed time: 00:12:58s. Time for last 1,000,000: 1s. Last read position: chr19:39,877,918
INFO 2026-06-08 08:15:24 MarkDuplicates Tracking 82353 as yet unmatched pairs. 21633 records in RAM.
INFO 2026-06-08 08:15:25 MarkDuplicates Read 319,000,000 records. Elapsed time: 00:12:59s. Time for last 1,000,000: 1s. Last read position: chr19:39,943,532
INFO 2026-06-08 08:15:25 MarkDuplicates Tracking 80550 as yet unmatched pairs. 19830 records in RAM.
INFO 2026-06-08 08:15:27 MarkDuplicates Read 320,000,000 records. Elapsed time: 00:13:01s. Time for last 1,000,000: 1s. Last read position: chr19:41,715,109
INFO 2026-06-08 08:15:27 MarkDuplicates Tracking 79251 as yet unmatched pairs. 18531 records in RAM.
INFO 2026-06-08 08:15:29 MarkDuplicates Read 321,000,000 records. Elapsed time: 00:13:03s. Time for last 1,000,000: 1s. Last read position: chr19:42,272,927
INFO 2026-06-08 08:15:29 MarkDuplicates Tracking 77117 as yet unmatched pairs. 16397 records in RAM.
INFO 2026-06-08 08:15:30 MarkDuplicates Read 322,000,000 records. Elapsed time: 00:13:04s. Time for last 1,000,000: 1s. Last read position: chr19:44,759,464
INFO 2026-06-08 08:15:30 MarkDuplicates Tracking 75336 as yet unmatched pairs. 14604 records in RAM.
INFO 2026-06-08 08:15:33 MarkDuplicates Read 323,000,000 records. Elapsed time: 00:13:07s. Time for last 1,000,000: 2s. Last read position: chr19:45,825,219
INFO 2026-06-08 08:15:33 MarkDuplicates Tracking 73096 as yet unmatched pairs. 12360 records in RAM.
INFO 2026-06-08 08:15:35 MarkDuplicates Read 324,000,000 records. Elapsed time: 00:13:09s. Time for last 1,000,000: 2s. Last read position: chr19:48,470,606
INFO 2026-06-08 08:15:35 MarkDuplicates Tracking 71049 as yet unmatched pairs. 10312 records in RAM.
INFO 2026-06-08 08:15:36 MarkDuplicates Read 325,000,000 records. Elapsed time: 00:13:11s. Time for last 1,000,000: 1s. Last read position: chr19:49,459,827
INFO 2026-06-08 08:15:36 MarkDuplicates Tracking 69074 as yet unmatched pairs. 8337 records in RAM.
INFO 2026-06-08 08:15:38 MarkDuplicates Read 326,000,000 records. Elapsed time: 00:13:12s. Time for last 1,000,000: 1s. Last read position: chr19:49,861,804
INFO 2026-06-08 08:15:38 MarkDuplicates Tracking 67420 as yet unmatched pairs. 6682 records in RAM.
INFO 2026-06-08 08:15:40 MarkDuplicates Read 327,000,000 records. Elapsed time: 00:13:14s. Time for last 1,000,000: 1s. Last read position: chr19:52,212,749
INFO 2026-06-08 08:15:40 MarkDuplicates Tracking 65353 as yet unmatched pairs. 4615 records in RAM.
INFO 2026-06-08 08:15:42 MarkDuplicates Read 328,000,000 records. Elapsed time: 00:13:16s. Time for last 1,000,000: 1s. Last read position: chr19:54,666,298
INFO 2026-06-08 08:15:42 MarkDuplicates Tracking 63650 as yet unmatched pairs. 2911 records in RAM.
INFO 2026-06-08 08:15:43 MarkDuplicates Read 329,000,000 records. Elapsed time: 00:13:17s. Time for last 1,000,000: 1s. Last read position: chr19:56,087,962
INFO 2026-06-08 08:15:43 MarkDuplicates Tracking 61813 as yet unmatched pairs. 1073 records in RAM.
INFO 2026-06-08 08:15:45 MarkDuplicates Read 330,000,000 records. Elapsed time: 00:13:19s. Time for last 1,000,000: 1s. Last read position: chr20:2,838,365
INFO 2026-06-08 08:15:45 MarkDuplicates Tracking 60024 as yet unmatched pairs. 14136 records in RAM.
INFO 2026-06-08 08:15:47 MarkDuplicates Read 331,000,000 records. Elapsed time: 00:13:21s. Time for last 1,000,000: 1s. Last read position: chr20:17,641,856
INFO 2026-06-08 08:15:47 MarkDuplicates Tracking 58300 as yet unmatched pairs. 12411 records in RAM.
INFO 2026-06-08 08:15:48 MarkDuplicates Read 332,000,000 records. Elapsed time: 00:13:23s. Time for last 1,000,000: 1s. Last read position: chr20:31,547,940
INFO 2026-06-08 08:15:48 MarkDuplicates Tracking 56699 as yet unmatched pairs. 10808 records in RAM.
INFO 2026-06-08 08:15:50 MarkDuplicates Read 333,000,000 records. Elapsed time: 00:13:24s. Time for last 1,000,000: 1s. Last read position: chr20:35,714,221
INFO 2026-06-08 08:15:50 MarkDuplicates Tracking 55147 as yet unmatched pairs. 9255 records in RAM.
INFO 2026-06-08 08:15:52 MarkDuplicates Read 334,000,000 records. Elapsed time: 00:13:26s. Time for last 1,000,000: 1s. Last read position: chr20:44,746,256
INFO 2026-06-08 08:15:52 MarkDuplicates Tracking 53117 as yet unmatched pairs. 7224 records in RAM.
INFO 2026-06-08 08:15:54 MarkDuplicates Read 335,000,000 records. Elapsed time: 00:13:28s. Time for last 1,000,000: 1s. Last read position: chr20:50,096,720
INFO 2026-06-08 08:15:54 MarkDuplicates Tracking 51248 as yet unmatched pairs. 5353 records in RAM.
INFO 2026-06-08 08:15:56 MarkDuplicates Read 336,000,000 records. Elapsed time: 00:13:30s. Time for last 1,000,000: 2s. Last read position: chr20:62,139,679
INFO 2026-06-08 08:15:56 MarkDuplicates Tracking 49128 as yet unmatched pairs. 3230 records in RAM.
INFO 2026-06-08 08:15:58 MarkDuplicates Read 337,000,000 records. Elapsed time: 00:13:32s. Time for last 1,000,000: 1s. Last read position: chr20:63,563,936
INFO 2026-06-08 08:15:58 MarkDuplicates Tracking 47329 as yet unmatched pairs. 1429 records in RAM.
INFO 2026-06-08 08:16:00 MarkDuplicates Read 338,000,000 records. Elapsed time: 00:13:34s. Time for last 1,000,000: 1s. Last read position: chr21:8,214,506
INFO 2026-06-08 08:16:00 MarkDuplicates Tracking 45744 as yet unmatched pairs. 11540 records in RAM.
INFO 2026-06-08 08:16:01 MarkDuplicates Read 339,000,000 records. Elapsed time: 00:13:35s. Time for last 1,000,000: 1s. Last read position: chr21:8,217,192
INFO 2026-06-08 08:16:01 MarkDuplicates Tracking 44556 as yet unmatched pairs. 10333 records in RAM.
INFO 2026-06-08 08:16:02 MarkDuplicates Read 340,000,000 records. Elapsed time: 00:13:36s. Time for last 1,000,000: 1s. Last read position: chr21:8,258,974
INFO 2026-06-08 08:16:02 MarkDuplicates Tracking 44295 as yet unmatched pairs. 10071 records in RAM.
INFO 2026-06-08 08:16:04 MarkDuplicates Read 341,000,000 records. Elapsed time: 00:13:38s. Time for last 1,000,000: 1s. Last read position: chr21:8,399,091
INFO 2026-06-08 08:16:04 MarkDuplicates Tracking 44561 as yet unmatched pairs. 10335 records in RAM.
INFO 2026-06-08 08:16:05 MarkDuplicates Read 342,000,000 records. Elapsed time: 00:13:39s. Time for last 1,000,000: 1s. Last read position: chr21:8,441,961
INFO 2026-06-08 08:16:05 MarkDuplicates Tracking 43664 as yet unmatched pairs. 9430 records in RAM.
INFO 2026-06-08 08:16:06 MarkDuplicates Read 343,000,000 records. Elapsed time: 00:13:40s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,595
INFO 2026-06-08 08:16:06 MarkDuplicates Tracking 41477 as yet unmatched pairs. 7242 records in RAM.
INFO 2026-06-08 08:16:08 MarkDuplicates Read 344,000,000 records. Elapsed time: 00:13:42s. Time for last 1,000,000: 1s. Last read position: chr21:33,557,206
INFO 2026-06-08 08:16:08 MarkDuplicates Tracking 39869 as yet unmatched pairs. 5634 records in RAM.
INFO 2026-06-08 08:16:09 MarkDuplicates Read 345,000,000 records. Elapsed time: 00:13:43s. Time for last 1,000,000: 1s. Last read position: chr21:41,942,144
INFO 2026-06-08 08:16:09 MarkDuplicates Tracking 37782 as yet unmatched pairs. 3547 records in RAM.
INFO 2026-06-08 08:16:11 MarkDuplicates Read 346,000,000 records. Elapsed time: 00:13:45s. Time for last 1,000,000: 1s. Last read position: chr21:45,512,208
INFO 2026-06-08 08:16:11 MarkDuplicates Tracking 36304 as yet unmatched pairs. 2068 records in RAM.
INFO 2026-06-08 08:16:13 MarkDuplicates Read 347,000,000 records. Elapsed time: 00:13:47s. Time for last 1,000,000: 1s. Last read position: chr22:17,582,690
INFO 2026-06-08 08:16:13 MarkDuplicates Tracking 34175 as yet unmatched pairs. 12018 records in RAM.
INFO 2026-06-08 08:16:15 MarkDuplicates Read 348,000,000 records. Elapsed time: 00:13:49s. Time for last 1,000,000: 1s. Last read position: chr22:23,767,536
INFO 2026-06-08 08:16:15 MarkDuplicates Tracking 32630 as yet unmatched pairs. 10473 records in RAM.
INFO 2026-06-08 08:16:16 MarkDuplicates Read 349,000,000 records. Elapsed time: 00:13:50s. Time for last 1,000,000: 1s. Last read position: chr22:29,419,167
INFO 2026-06-08 08:16:16 MarkDuplicates Tracking 30384 as yet unmatched pairs. 8227 records in RAM.
INFO 2026-06-08 08:16:19 MarkDuplicates Read 350,000,000 records. Elapsed time: 00:13:53s. Time for last 1,000,000: 2s. Last read position: chr22:36,289,224
INFO 2026-06-08 08:16:19 MarkDuplicates Tracking 28761 as yet unmatched pairs. 6604 records in RAM.
INFO 2026-06-08 08:16:21 MarkDuplicates Read 351,000,000 records. Elapsed time: 00:13:55s. Time for last 1,000,000: 2s. Last read position: chr22:38,486,409
INFO 2026-06-08 08:16:21 MarkDuplicates Tracking 26768 as yet unmatched pairs. 4611 records in RAM.
INFO 2026-06-08 08:16:22 MarkDuplicates Read 352,000,000 records. Elapsed time: 00:13:56s. Time for last 1,000,000: 1s. Last read position: chr22:42,384,545
INFO 2026-06-08 08:16:22 MarkDuplicates Tracking 24997 as yet unmatched pairs. 2840 records in RAM.
INFO 2026-06-08 08:16:24 MarkDuplicates Read 353,000,000 records. Elapsed time: 00:13:58s. Time for last 1,000,000: 1s. Last read position: chr22:50,468,406
INFO 2026-06-08 08:16:24 MarkDuplicates Tracking 23103 as yet unmatched pairs. 946 records in RAM.
INFO 2026-06-08 08:16:26 MarkDuplicates Read 354,000,000 records. Elapsed time: 00:14:00s. Time for last 1,000,000: 1s. Last read position: chrX:16,595,472
INFO 2026-06-08 08:16:26 MarkDuplicates Tracking 20859 as yet unmatched pairs. 12056 records in RAM.
INFO 2026-06-08 08:16:27 MarkDuplicates Read 355,000,000 records. Elapsed time: 00:14:01s. Time for last 1,000,000: 1s. Last read position: chrX:41,923,000
INFO 2026-06-08 08:16:27 MarkDuplicates Tracking 19324 as yet unmatched pairs. 10506 records in RAM.
INFO 2026-06-08 08:16:29 MarkDuplicates Read 356,000,000 records. Elapsed time: 00:14:03s. Time for last 1,000,000: 1s. Last read position: chrX:49,174,392
INFO 2026-06-08 08:16:29 MarkDuplicates Tracking 17759 as yet unmatched pairs. 8936 records in RAM.
INFO 2026-06-08 08:16:31 MarkDuplicates Read 357,000,000 records. Elapsed time: 00:14:05s. Time for last 1,000,000: 1s. Last read position: chrX:68,600,230
INFO 2026-06-08 08:16:31 MarkDuplicates Tracking 15838 as yet unmatched pairs. 7015 records in RAM.
INFO 2026-06-08 08:16:32 MarkDuplicates Read 358,000,000 records. Elapsed time: 00:14:06s. Time for last 1,000,000: 1s. Last read position: chrX:95,131,958
INFO 2026-06-08 08:16:32 MarkDuplicates Tracking 14263 as yet unmatched pairs. 5439 records in RAM.
INFO 2026-06-08 08:16:34 MarkDuplicates Read 359,000,000 records. Elapsed time: 00:14:08s. Time for last 1,000,000: 1s. Last read position: chrX:129,925,945
INFO 2026-06-08 08:16:34 MarkDuplicates Tracking 12635 as yet unmatched pairs. 3811 records in RAM.
INFO 2026-06-08 08:16:36 MarkDuplicates Read 360,000,000 records. Elapsed time: 00:14:10s. Time for last 1,000,000: 1s. Last read position: chrX:153,955,278
INFO 2026-06-08 08:16:36 MarkDuplicates Tracking 10893 as yet unmatched pairs. 2067 records in RAM.
INFO 2026-06-08 08:16:37 MarkDuplicates Read 361,000,000 records. Elapsed time: 00:14:12s. Time for last 1,000,000: 1s. Last read position: chrX:154,645,841
INFO 2026-06-08 08:16:37 MarkDuplicates Tracking 9018 as yet unmatched pairs. 192 records in RAM.
INFO 2026-06-08 08:16:39 MarkDuplicates Read 362,000,000 records. Elapsed time: 00:14:14s. Time for last 1,000,000: 1s. Last read position: GL000220.1:114,206
INFO 2026-06-08 08:16:39 MarkDuplicates Tracking 8604 as yet unmatched pairs. 3767 records in RAM.
INFO 2026-06-08 08:16:41 MarkDuplicates Read 363,000,000 records. Elapsed time: 00:14:15s. Time for last 1,000,000: 1s. Last read position: GL000220.1:157,836
INFO 2026-06-08 08:16:41 MarkDuplicates Tracking 5075 as yet unmatched pairs. 237 records in RAM.
INFO 2026-06-08 08:16:42 MarkDuplicates Read 364,000,000 records. Elapsed time: 00:14:16s. Time for last 1,000,000: 1s. Last read position: GL000220.1:160,314
INFO 2026-06-08 08:16:42 MarkDuplicates Tracking 4843 as yet unmatched pairs. 5 records in RAM.
INFO 2026-06-08 08:16:43 MarkDuplicates Read 365,000,000 records. Elapsed time: 00:14:17s. Time for last 1,000,000: 1s. Last read position: KI270733.1:131,060
INFO 2026-06-08 08:16:43 MarkDuplicates Tracking 2214 as yet unmatched pairs. 2212 records in RAM.
INFO 2026-06-08 08:16:45 MarkDuplicates Read 366,000,000 records. Elapsed time: 00:14:19s. Time for last 1,000,000: 1s. Last read position: KI270733.1:176,047
INFO 2026-06-08 08:16:45 MarkDuplicates Tracking 93 as yet unmatched pairs. 91 records in RAM.
INFO 2026-06-08 08:16:46 MarkDuplicates Read 367,000,000 records. Elapsed time: 00:14:20s. Time for last 1,000,000: 1s. Last read position: KI270733.1:178,689
INFO 2026-06-08 08:16:46 MarkDuplicates Tracking 6 as yet unmatched pairs. 4 records in RAM.
INFO 2026-06-08 08:16:46 MarkDuplicates Read 367248533 records. 0 pairs never matched.
INFO 2026-06-08 08:17:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 31342070840; totalMemory: 44761612288; maxMemory: 63585648640
INFO 2026-06-08 08:17:20 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:17:29 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:17:43 OpticalDuplicateFinder Large duplicate set. size = 1083
INFO 2026-06-08 08:17:43 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,660
INFO 2026-06-08 08:17:46 OpticalDuplicateFinder Large duplicate set. size = 1652
INFO 2026-06-08 08:17:46 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,280
INFO 2026-06-08 08:17:46 OpticalDuplicateFinder Large duplicate set. size = 1682
INFO 2026-06-08 08:17:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,419
INFO 2026-06-08 08:17:47 OpticalDuplicateFinder Large duplicate set. size = 1017
INFO 2026-06-08 08:17:47 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,930
INFO 2026-06-08 08:17:52 OpticalDuplicateFinder Large duplicate set. size = 1137
INFO 2026-06-08 08:17:52 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,995
INFO 2026-06-08 08:18:11 OpticalDuplicateFinder Large duplicate set. size = 1088
INFO 2026-06-08 08:18:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-19,143
INFO 2026-06-08 08:18:11 OpticalDuplicateFinder Large duplicate set. size = 1253
INFO 2026-06-08 08:18:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,378
INFO 2026-06-08 08:18:11 OpticalDuplicateFinder Large duplicate set. size = 1222
INFO 2026-06-08 08:18:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,717
INFO 2026-06-08 08:18:11 OpticalDuplicateFinder Large duplicate set. size = 1058
INFO 2026-06-08 08:18:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,350
INFO 2026-06-08 08:18:11 OpticalDuplicateFinder Large duplicate set. size = 1689
INFO 2026-06-08 08:18:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,686
INFO 2026-06-08 08:18:11 OpticalDuplicateFinder Large duplicate set. size = 1115
INFO 2026-06-08 08:18:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,745
INFO 2026-06-08 08:18:11 OpticalDuplicateFinder Large duplicate set. size = 1268
INFO 2026-06-08 08:18:11 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 08:18:11 OpticalDuplicateFinder Large duplicate set. size = 1395
INFO 2026-06-08 08:18:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,816
INFO 2026-06-08 08:18:11 OpticalDuplicateFinder Large duplicate set. size = 1041
INFO 2026-06-08 08:18:11 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,496
INFO 2026-06-08 08:18:12 OpticalDuplicateFinder Large duplicate set. size = 1382
INFO 2026-06-08 08:18:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:24,137
INFO 2026-06-08 08:18:12 OpticalDuplicateFinder Large duplicate set. size = 1450
INFO 2026-06-08 08:18:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,556
INFO 2026-06-08 08:18:12 OpticalDuplicateFinder Large duplicate set. size = 1637
INFO 2026-06-08 08:18:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,531
INFO 2026-06-08 08:18:12 OpticalDuplicateFinder Large duplicate set. size = 1109
INFO 2026-06-08 08:18:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,015
INFO 2026-06-08 08:18:12 OpticalDuplicateFinder Large duplicate set. size = 1017
INFO 2026-06-08 08:18:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:7,367
INFO 2026-06-08 08:18:12 OpticalDuplicateFinder Large duplicate set. size = 1216
INFO 2026-06-08 08:18:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:17,746
INFO 2026-06-08 08:18:12 OpticalDuplicateFinder Large duplicate set. size = 1023
INFO 2026-06-08 08:18:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,873
INFO 2026-06-08 08:18:12 OpticalDuplicateFinder Large duplicate set. size = 1016
INFO 2026-06-08 08:18:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:8,702
INFO 2026-06-08 08:18:12 OpticalDuplicateFinder Large duplicate set. size = 1032
INFO 2026-06-08 08:18:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,952
INFO 2026-06-08 08:18:12 OpticalDuplicateFinder Large duplicate set. size = 1482
INFO 2026-06-08 08:18:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,515
INFO 2026-06-08 08:18:12 OpticalDuplicateFinder Large duplicate set. size = 1282
INFO 2026-06-08 08:18:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-22,897
INFO 2026-06-08 08:18:12 OpticalDuplicateFinder Large duplicate set. size = 1390
INFO 2026-06-08 08:18:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,341
INFO 2026-06-08 08:18:12 OpticalDuplicateFinder Large duplicate set. size = 1431
INFO 2026-06-08 08:18:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,771
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder Large duplicate set. size = 1214
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:5,805
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder Large duplicate set. size = 1026
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:31,240
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder Large duplicate set. size = 1562
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:8,912
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder Large duplicate set. size = 1004
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,011
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder Large duplicate set. size = 1521
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,286
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder Large duplicate set. size = 1389
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,223
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder Large duplicate set. size = 1337
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,325
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder Large duplicate set. size = 1156
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,227
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder Large duplicate set. size = 1070
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:7,723
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder Large duplicate set. size = 1224
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:14,397
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder Large duplicate set. size = 1514
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:2,125
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder Large duplicate set. size = 1202
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,772
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder Large duplicate set. size = 1153
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,414
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder Large duplicate set. size = 1087
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,195
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder Large duplicate set. size = 1136
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,103
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder Large duplicate set. size = 1768
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,153
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder Large duplicate set. size = 1139
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:1,445
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder Large duplicate set. size = 1257
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,580
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder Large duplicate set. size = 1290
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,390
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder Large duplicate set. size = 1095
INFO 2026-06-08 08:18:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,636
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 2478
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,058
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,279
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1083
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:21,460
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 4223
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:24,963
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:6,550
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 3,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,492
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 4,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:8,896
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1005
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,978
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1064
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,181
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1089
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-22,970
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1353
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-21,918
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1147
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:24,129
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1025
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,466
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1394
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,161
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1064
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:26,306
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1282
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,147
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1448
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,219
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1065
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:8,985
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1805
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,427
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1584
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,276
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1565
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,535
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1933
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,114
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 2361
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,713
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,093
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 2298
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:2,828
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,685
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1022
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,609
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1784
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,201
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 2649
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,867
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:5,199
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1064
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:25,925
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1088
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,942
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1367
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,080
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1422
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:5,716
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1650
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:8,483
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1624
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,822
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1121
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,237
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1031
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,365
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1125
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,334
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1201
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-14,289
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1174
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,026
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1411
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:7,035
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1184
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-25,162
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1226
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,228
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1622
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,631
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1114
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:26,484
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1099
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:15,214
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1019
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,959
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1624
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,168
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1936
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-13,512
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1228
INFO 2026-06-08 08:18:14 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 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1474
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,506
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1265
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:2,214
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1053
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,755
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1157
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,163
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 2550
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,358
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,834
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1589
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:15,449
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1579
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,155
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1147
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-13,982
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder Large duplicate set. size = 1198
INFO 2026-06-08 08:18:14 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,491
INFO 2026-06-08 08:18:15 OpticalDuplicateFinder Large duplicate set. size = 1417
INFO 2026-06-08 08:18:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-18,908
INFO 2026-06-08 08:18:15 OpticalDuplicateFinder Large duplicate set. size = 1052
INFO 2026-06-08 08:18:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,494
INFO 2026-06-08 08:18:15 OpticalDuplicateFinder Large duplicate set. size = 1509
INFO 2026-06-08 08:18:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,737
INFO 2026-06-08 08:18:15 OpticalDuplicateFinder Large duplicate set. size = 1346
INFO 2026-06-08 08:18:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,402
INFO 2026-06-08 08:18:15 OpticalDuplicateFinder Large duplicate set. size = 1102
INFO 2026-06-08 08:18:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,306
INFO 2026-06-08 08:18:15 OpticalDuplicateFinder Large duplicate set. size = 1103
INFO 2026-06-08 08:18:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,013
INFO 2026-06-08 08:18:15 OpticalDuplicateFinder Large duplicate set. size = 1014
INFO 2026-06-08 08:18:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,737
INFO 2026-06-08 08:18:15 OpticalDuplicateFinder Large duplicate set. size = 1785
INFO 2026-06-08 08:18:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-13,569
INFO 2026-06-08 08:18:46 MarkDuplicates Traversing fragment information and detecting duplicates.
WARNING 2026-06-08 08:18:47 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
INFO 2026-06-08 08:19:35 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:19:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 203904776; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:19:36 MarkDuplicates Marking 282041987 records as duplicates.
INFO 2026-06-08 08:19:36 MarkDuplicates Found 3737777 optical duplicate clusters.
INFO 2026-06-08 08:19:36 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 08:19:52 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:16s. Time for last 10,000,000: 16s. Last read position: chr1:39,388,509
INFO 2026-06-08 08:20:11 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:35s. Time for last 10,000,000: 18s. Last read position: chr1:154,176,162
INFO 2026-06-08 08:20:30 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:54s. Time for last 10,000,000: 18s. Last read position: chr1:232,514,079
INFO 2026-06-08 08:20:48 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:12s. Time for last 10,000,000: 18s. Last read position: chr2:84,821,952
INFO 2026-06-08 08:21:04 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:28s. Time for last 10,000,000: 15s. Last read position: chr2:203,396,865
INFO 2026-06-08 08:21:22 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:46s. Time for last 10,000,000: 18s. Last read position: chr3:9,429,865
INFO 2026-06-08 08:21:39 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:03s. Time for last 10,000,000: 17s. Last read position: chr3:132,474,984
INFO 2026-06-08 08:21:55 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:19s. Time for last 10,000,000: 16s. Last read position: chr4:40,502,545
INFO 2026-06-08 08:22:11 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:35s. Time for last 10,000,000: 15s. Last read position: chr5:131,429,107
INFO 2026-06-08 08:22:29 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:02:53s. Time for last 10,000,000: 17s. Last read position: chr6:7,229,232
INFO 2026-06-08 08:22:47 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:03:11s. Time for last 10,000,000: 17s. Last read position: chr6:87,501,270
INFO 2026-06-08 08:23:05 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:29s. Time for last 10,000,000: 18s. Last read position: chr7:47,368,889
INFO 2026-06-08 08:23:22 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:46s. Time for last 10,000,000: 16s. Last read position: chr7:100,999,596
INFO 2026-06-08 08:23:38 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:04:02s. Time for last 10,000,000: 16s. Last read position: chr8:37,697,492
INFO 2026-06-08 08:23:53 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:04:17s. Time for last 10,000,000: 15s. Last read position: chr8:143,862,228
INFO 2026-06-08 08:24:08 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:32s. Time for last 10,000,000: 15s. Last read position: chr9:93,253,034
INFO 2026-06-08 08:24:23 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:04:47s. Time for last 10,000,000: 14s. Last read position: chr10:30,349,195
INFO 2026-06-08 08:24:38 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:05:02s. Time for last 10,000,000: 14s. Last read position: chr10:122,621,111
INFO 2026-06-08 08:24:53 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:05:17s. Time for last 10,000,000: 14s. Last read position: chr11:46,808,112
INFO 2026-06-08 08:25:07 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:05:31s. Time for last 10,000,000: 14s. Last read position: chr11:117,091,159
INFO 2026-06-08 08:25:22 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:05:46s. Time for last 10,000,000: 15s. Last read position: chr12:56,231,408
INFO 2026-06-08 08:25:37 MarkDuplicates Written 220,000,000 records. Elapsed time: 00:06:01s. Time for last 10,000,000: 15s. Last read position: chr12:132,571,441
INFO 2026-06-08 08:25:52 MarkDuplicates Written 230,000,000 records. Elapsed time: 00:06:16s. Time for last 10,000,000: 15s. Last read position: chr14:69,053,851
INFO 2026-06-08 08:26:07 MarkDuplicates Written 240,000,000 records. Elapsed time: 00:06:31s. Time for last 10,000,000: 14s. Last read position: chr15:75,206,055
INFO 2026-06-08 08:26:21 MarkDuplicates Written 250,000,000 records. Elapsed time: 00:06:45s. Time for last 10,000,000: 14s. Last read position: chr16:18,890,877
INFO 2026-06-08 08:26:36 MarkDuplicates Written 260,000,000 records. Elapsed time: 00:07:00s. Time for last 10,000,000: 14s. Last read position: chr16:58,197,678
INFO 2026-06-08 08:26:51 MarkDuplicates Written 270,000,000 records. Elapsed time: 00:07:15s. Time for last 10,000,000: 15s. Last read position: chr17:31,488,215
INFO 2026-06-08 08:27:06 MarkDuplicates Written 280,000,000 records. Elapsed time: 00:07:30s. Time for last 10,000,000: 15s. Last read position: chr17:50,188,980
INFO 2026-06-08 08:27:23 MarkDuplicates Written 290,000,000 records. Elapsed time: 00:07:46s. Time for last 10,000,000: 16s. Last read position: chr17:50,197,215
INFO 2026-06-08 08:27:38 MarkDuplicates Written 300,000,000 records. Elapsed time: 00:08:02s. Time for last 10,000,000: 15s. Last read position: chr18:13,030,447
INFO 2026-06-08 08:27:52 MarkDuplicates Written 310,000,000 records. Elapsed time: 00:08:16s. Time for last 10,000,000: 14s. Last read position: chr19:12,943,844
INFO 2026-06-08 08:28:07 MarkDuplicates Written 320,000,000 records. Elapsed time: 00:08:30s. Time for last 10,000,000: 14s. Last read position: chr19:41,715,109
INFO 2026-06-08 08:28:21 MarkDuplicates Written 330,000,000 records. Elapsed time: 00:08:45s. Time for last 10,000,000: 14s. Last read position: chr20:2,838,365
INFO 2026-06-08 08:28:36 MarkDuplicates Written 340,000,000 records. Elapsed time: 00:09:00s. Time for last 10,000,000: 14s. Last read position: chr21:8,258,974
INFO 2026-06-08 08:28:49 MarkDuplicates Written 350,000,000 records. Elapsed time: 00:09:13s. Time for last 10,000,000: 13s. Last read position: chr22:36,289,224
INFO 2026-06-08 08:29:03 MarkDuplicates Written 360,000,000 records. Elapsed time: 00:09:27s. Time for last 10,000,000: 14s. Last read position: chrX:153,955,278
INFO 2026-06-08 08:29:19 MarkDuplicates Written 370,000,000 records. Elapsed time: 00:09:43s. Time for last 10,000,000: 15s. Last read position: */*
INFO 2026-06-08 08:29:21 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:29:21 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:29:21 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:29:21 MarkDuplicates Before output close freeMemory: 203878800; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:29:21 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:29:21 MarkDuplicates After output close freeMemory: 104117616; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 08:29:21 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 26.96 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory