Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/fadb7d9f9f7a1a2279e4b732a6186f/aih-tih-sc-284856-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/721bc5acfc288e83e15735b07074d7/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/721bc5acfc288e83e15735b07074d7/.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 aih-tih-sc-284856-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bam --METRICS_FILE aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
08:02:03.958 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 08:02:03 GMT 2026] MarkDuplicates --INPUT aih-tih-sc-284856-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bam --METRICS_FILE aih-tih-sc-284856-R1_A23WJ53LT4_1.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 08:02:03 GMT 2026] Executing as ?@nf-92721bc5acfc288e83e15735b07074d7-9e018-xbpmp 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 08:02:04 MarkDuplicates Start of doWork freeMemory: 105494392; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 08:02:04 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 08:02:04 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 08:02:10 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 4s. Last read position: chr1:8,867,223
INFO 2026-06-08 08:02:10 MarkDuplicates Tracking 2252 as yet unmatched pairs. 194 records in RAM.
INFO 2026-06-08 08:02:13 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 3s. Last read position: chr1:19,657,001
INFO 2026-06-08 08:02:13 MarkDuplicates Tracking 4014 as yet unmatched pairs. 163 records in RAM.
INFO 2026-06-08 08:02:17 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 4s. Last read position: chr1:26,767,883
INFO 2026-06-08 08:02:17 MarkDuplicates Tracking 5702 as yet unmatched pairs. 52 records in RAM.
INFO 2026-06-08 08:02:20 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 3s. Last read position: chr1:35,641,376
INFO 2026-06-08 08:02:20 MarkDuplicates Tracking 7574 as yet unmatched pairs. 23 records in RAM.
INFO 2026-06-08 08:02:24 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 3s. Last read position: chr1:45,566,883
INFO 2026-06-08 08:02:24 MarkDuplicates Tracking 9531 as yet unmatched pairs. 213 records in RAM.
INFO 2026-06-08 08:02:28 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 3s. Last read position: chr1:67,430,028
INFO 2026-06-08 08:02:28 MarkDuplicates Tracking 11223 as yet unmatched pairs. 88 records in RAM.
INFO 2026-06-08 08:02:31 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 3s. Last read position: chr1:110,341,709
INFO 2026-06-08 08:02:31 MarkDuplicates Tracking 12866 as yet unmatched pairs. 114 records in RAM.
INFO 2026-06-08 08:02:35 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 3s. Last read position: chr1:143,975,119
INFO 2026-06-08 08:02:35 MarkDuplicates Tracking 14231 as yet unmatched pairs. 35 records in RAM.
INFO 2026-06-08 08:02:38 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 3s. Last read position: chr1:150,293,876
INFO 2026-06-08 08:02:38 MarkDuplicates Tracking 15184 as yet unmatched pairs. 22 records in RAM.
INFO 2026-06-08 08:02:42 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 3s. Last read position: chr1:153,986,136
INFO 2026-06-08 08:02:42 MarkDuplicates Tracking 16820 as yet unmatched pairs. 52 records in RAM.
INFO 2026-06-08 08:02:45 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 2s. Last read position: chr1:155,868,737
INFO 2026-06-08 08:02:45 MarkDuplicates Tracking 18438 as yet unmatched pairs. 88 records in RAM.
INFO 2026-06-08 08:02:47 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 2s. Last read position: chr1:160,751,380
INFO 2026-06-08 08:02:47 MarkDuplicates Tracking 20241 as yet unmatched pairs. 21 records in RAM.
INFO 2026-06-08 08:02:51 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 3s. Last read position: chr1:182,581,242
INFO 2026-06-08 08:02:51 MarkDuplicates Tracking 21856 as yet unmatched pairs. 29 records in RAM.
INFO 2026-06-08 08:02:54 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 2s. Last read position: chr1:205,618,908
INFO 2026-06-08 08:02:54 MarkDuplicates Tracking 23566 as yet unmatched pairs. 119 records in RAM.
INFO 2026-06-08 08:02:57 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 2s. Last read position: chr1:234,429,162
INFO 2026-06-08 08:02:57 MarkDuplicates Tracking 25267 as yet unmatched pairs. 62 records in RAM.
INFO 2026-06-08 08:03:00 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 3s. Last read position: chr2:25,980,516
INFO 2026-06-08 08:03:00 MarkDuplicates Tracking 26926 as yet unmatched pairs. 26512 records in RAM.
INFO 2026-06-08 08:03:04 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 3s. Last read position: chr2:32,916,406
INFO 2026-06-08 08:03:04 MarkDuplicates Tracking 206672 as yet unmatched pairs. 13521 records in RAM.
INFO 2026-06-08 08:03:08 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 3s. Last read position: chr2:47,834,791
INFO 2026-06-08 08:03:08 MarkDuplicates Tracking 218581 as yet unmatched pairs. 11261 records in RAM.
INFO 2026-06-08 08:03:11 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 3s. Last read position: chr2:74,492,136
INFO 2026-06-08 08:03:11 MarkDuplicates Tracking 216921 as yet unmatched pairs. 9566 records in RAM.
INFO 2026-06-08 08:03:14 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 3s. Last read position: chr2:108,753,941
INFO 2026-06-08 08:03:14 MarkDuplicates Tracking 215678 as yet unmatched pairs. 8304 records in RAM.
INFO 2026-06-08 08:03:17 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 3s. Last read position: chr2:130,108,020
INFO 2026-06-08 08:03:17 MarkDuplicates Tracking 214251 as yet unmatched pairs. 6859 records in RAM.
INFO 2026-06-08 08:03:20 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 3s. Last read position: chr2:178,545,371
INFO 2026-06-08 08:03:20 MarkDuplicates Tracking 212779 as yet unmatched pairs. 5364 records in RAM.
INFO 2026-06-08 08:03:24 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 3s. Last read position: chr2:207,711,999
INFO 2026-06-08 08:03:24 MarkDuplicates Tracking 211204 as yet unmatched pairs. 3772 records in RAM.
INFO 2026-06-08 08:03:27 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 2s. Last read position: chr2:217,848,717
INFO 2026-06-08 08:03:27 MarkDuplicates Tracking 209882 as yet unmatched pairs. 2434 records in RAM.
INFO 2026-06-08 08:03:29 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 2s. Last read position: chr2:240,462,492
INFO 2026-06-08 08:03:29 MarkDuplicates Tracking 208095 as yet unmatched pairs. 612 records in RAM.
INFO 2026-06-08 08:03:33 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 3s. Last read position: chr3:16,409,411
INFO 2026-06-08 08:03:33 MarkDuplicates Tracking 206229 as yet unmatched pairs. 13919 records in RAM.
INFO 2026-06-08 08:03:37 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 4s. Last read position: chr3:43,033,341
INFO 2026-06-08 08:03:37 MarkDuplicates Tracking 204662 as yet unmatched pairs. 12330 records in RAM.
INFO 2026-06-08 08:03:41 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 3s. Last read position: chr3:49,024,616
INFO 2026-06-08 08:03:41 MarkDuplicates Tracking 203072 as yet unmatched pairs. 10726 records in RAM.
INFO 2026-06-08 08:03:44 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 3s. Last read position: chr3:52,504,751
INFO 2026-06-08 08:03:44 MarkDuplicates Tracking 201073 as yet unmatched pairs. 8692 records in RAM.
INFO 2026-06-08 08:03:48 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 3s. Last read position: chr3:101,417,731
INFO 2026-06-08 08:03:48 MarkDuplicates Tracking 199438 as yet unmatched pairs. 7020 records in RAM.
INFO 2026-06-08 08:03:52 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 3s. Last read position: chr3:127,006,078
INFO 2026-06-08 08:03:52 MarkDuplicates Tracking 197937 as yet unmatched pairs. 5477 records in RAM.
INFO 2026-06-08 08:03:55 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 3s. Last read position: chr3:149,371,737
INFO 2026-06-08 08:03:55 MarkDuplicates Tracking 197299 as yet unmatched pairs. 4814 records in RAM.
INFO 2026-06-08 08:03:58 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 2s. Last read position: chr3:184,182,757
INFO 2026-06-08 08:03:58 MarkDuplicates Tracking 194904 as yet unmatched pairs. 2386 records in RAM.
INFO 2026-06-08 08:04:01 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 3s. Last read position: chr3:195,780,973
INFO 2026-06-08 08:04:01 MarkDuplicates Tracking 194702 as yet unmatched pairs. 2143 records in RAM.
INFO 2026-06-08 08:04:04 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 3s. Last read position: chr4:3,206,560
INFO 2026-06-08 08:04:04 MarkDuplicates Tracking 191905 as yet unmatched pairs. 5419 records in RAM.
INFO 2026-06-08 08:04:07 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 2s. Last read position: chr4:48,535,544
INFO 2026-06-08 08:04:07 MarkDuplicates Tracking 190309 as yet unmatched pairs. 3779 records in RAM.
INFO 2026-06-08 08:04:10 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 3s. Last read position: chr4:94,654,505
INFO 2026-06-08 08:04:10 MarkDuplicates Tracking 188940 as yet unmatched pairs. 2388 records in RAM.
INFO 2026-06-08 08:04:15 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 4s. Last read position: chr4:153,781,705
INFO 2026-06-08 08:04:15 MarkDuplicates Tracking 187907 as yet unmatched pairs. 1336 records in RAM.
INFO 2026-06-08 08:04:18 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 3s. Last read position: chr5:32,000,256
INFO 2026-06-08 08:04:18 MarkDuplicates Tracking 185508 as yet unmatched pairs. 13444 records in RAM.
INFO 2026-06-08 08:04:21 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 3s. Last read position: chr5:65,792,579
INFO 2026-06-08 08:04:21 MarkDuplicates Tracking 183958 as yet unmatched pairs. 11870 records in RAM.
INFO 2026-06-08 08:04:24 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 2s. Last read position: chr5:93,740,957
INFO 2026-06-08 08:04:24 MarkDuplicates Tracking 182642 as yet unmatched pairs. 10507 records in RAM.
INFO 2026-06-08 08:04:27 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 2s. Last read position: chr5:137,637,376
INFO 2026-06-08 08:04:27 MarkDuplicates Tracking 181030 as yet unmatched pairs. 8854 records in RAM.
INFO 2026-06-08 08:04:29 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 2s. Last read position: chr5:141,494,824
INFO 2026-06-08 08:04:29 MarkDuplicates Tracking 180015 as yet unmatched pairs. 7824 records in RAM.
INFO 2026-06-08 08:04:32 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 2s. Last read position: chr5:150,403,139
INFO 2026-06-08 08:04:32 MarkDuplicates Tracking 187882 as yet unmatched pairs. 15671 records in RAM.
INFO 2026-06-08 08:04:34 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 2s. Last read position: chr5:151,028,234
INFO 2026-06-08 08:04:34 MarkDuplicates Tracking 175989 as yet unmatched pairs. 3770 records in RAM.
INFO 2026-06-08 08:04:37 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 3s. Last read position: chr5:176,348,007
INFO 2026-06-08 08:04:37 MarkDuplicates Tracking 174302 as yet unmatched pairs. 2064 records in RAM.
INFO 2026-06-08 08:04:40 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 3s. Last read position: chr5:181,059,255
INFO 2026-06-08 08:04:40 MarkDuplicates Tracking 172615 as yet unmatched pairs. 351 records in RAM.
INFO 2026-06-08 08:04:44 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 3s. Last read position: chr6:27,138,658
INFO 2026-06-08 08:04:44 MarkDuplicates Tracking 170909 as yet unmatched pairs. 11369 records in RAM.
INFO 2026-06-08 08:04:47 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 3s. Last read position: chr6:31,888,241
INFO 2026-06-08 08:04:47 MarkDuplicates Tracking 169305 as yet unmatched pairs. 9742 records in RAM.
INFO 2026-06-08 08:04:50 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 3s. Last read position: chr6:32,530,128
INFO 2026-06-08 08:04:50 MarkDuplicates Tracking 168013 as yet unmatched pairs. 8437 records in RAM.
INFO 2026-06-08 08:04:53 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 3s. Last read position: chr6:39,878,577
INFO 2026-06-08 08:04:53 MarkDuplicates Tracking 166055 as yet unmatched pairs. 6454 records in RAM.
INFO 2026-06-08 08:04:57 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 3s. Last read position: chr6:82,364,889
INFO 2026-06-08 08:04:57 MarkDuplicates Tracking 164477 as yet unmatched pairs. 4827 records in RAM.
INFO 2026-06-08 08:04:59 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 2s. Last read position: chr6:129,059,830
INFO 2026-06-08 08:04:59 MarkDuplicates Tracking 162826 as yet unmatched pairs. 3136 records in RAM.
INFO 2026-06-08 08:05:01 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 2s. Last read position: chr6:152,155,965
INFO 2026-06-08 08:05:01 MarkDuplicates Tracking 161208 as yet unmatched pairs. 1493 records in RAM.
INFO 2026-06-08 08:05:04 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 3s. Last read position: chr7:1,498,528
INFO 2026-06-08 08:05:04 MarkDuplicates Tracking 159500 as yet unmatched pairs. 10100 records in RAM.
INFO 2026-06-08 08:05:07 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 3s. Last read position: chr7:27,793,097
INFO 2026-06-08 08:05:07 MarkDuplicates Tracking 157804 as yet unmatched pairs. 8378 records in RAM.
INFO 2026-06-08 08:05:11 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 3s. Last read position: chr7:73,050,410
INFO 2026-06-08 08:05:11 MarkDuplicates Tracking 156111 as yet unmatched pairs. 6659 records in RAM.
INFO 2026-06-08 08:05:14 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 3s. Last read position: chr7:92,095,152
INFO 2026-06-08 08:05:14 MarkDuplicates Tracking 154699 as yet unmatched pairs. 5226 records in RAM.
INFO 2026-06-08 08:05:17 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 2s. Last read position: chr7:101,128,400
INFO 2026-06-08 08:05:17 MarkDuplicates Tracking 153286 as yet unmatched pairs. 3782 records in RAM.
INFO 2026-06-08 08:05:20 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 3s. Last read position: chr7:134,300,180
INFO 2026-06-08 08:05:20 MarkDuplicates Tracking 151280 as yet unmatched pairs. 1750 records in RAM.
INFO 2026-06-08 08:05:23 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 2s. Last read position: chr7:158,760,063
INFO 2026-06-08 08:05:23 MarkDuplicates Tracking 149850 as yet unmatched pairs. 294 records in RAM.
INFO 2026-06-08 08:05:26 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 2s. Last read position: chr8:27,598,172
INFO 2026-06-08 08:05:26 MarkDuplicates Tracking 151340 as yet unmatched pairs. 14022 records in RAM.
INFO 2026-06-08 08:05:28 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 2s. Last read position: chr8:38,413,787
INFO 2026-06-08 08:05:28 MarkDuplicates Tracking 147056 as yet unmatched pairs. 9732 records in RAM.
INFO 2026-06-08 08:05:31 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 3s. Last read position: chr8:70,128,865
INFO 2026-06-08 08:05:31 MarkDuplicates Tracking 145020 as yet unmatched pairs. 7689 records in RAM.
INFO 2026-06-08 08:05:35 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 3s. Last read position: chr8:100,924,945
INFO 2026-06-08 08:05:35 MarkDuplicates Tracking 143741 as yet unmatched pairs. 6387 records in RAM.
INFO 2026-06-08 08:05:38 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 3s. Last read position: chr8:140,846,632
INFO 2026-06-08 08:05:38 MarkDuplicates Tracking 141676 as yet unmatched pairs. 4289 records in RAM.
INFO 2026-06-08 08:05:41 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 2s. Last read position: chr8:143,861,403
INFO 2026-06-08 08:05:41 MarkDuplicates Tracking 140302 as yet unmatched pairs. 2909 records in RAM.
INFO 2026-06-08 08:05:44 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 3s. Last read position: chr8:143,871,054
INFO 2026-06-08 08:05:44 MarkDuplicates Tracking 139801 as yet unmatched pairs. 2402 records in RAM.
INFO 2026-06-08 08:05:48 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 4s. Last read position: chr9:4,286,296
INFO 2026-06-08 08:05:48 MarkDuplicates Tracking 137324 as yet unmatched pairs. 7746 records in RAM.
INFO 2026-06-08 08:05:51 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 3s. Last read position: chr9:65,287,903
INFO 2026-06-08 08:05:51 MarkDuplicates Tracking 135604 as yet unmatched pairs. 5996 records in RAM.
INFO 2026-06-08 08:05:55 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 3s. Last read position: chr9:110,458,526
INFO 2026-06-08 08:05:55 MarkDuplicates Tracking 134069 as yet unmatched pairs. 4446 records in RAM.
INFO 2026-06-08 08:05:57 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 2s. Last read position: chr9:128,617,709
INFO 2026-06-08 08:05:57 MarkDuplicates Tracking 132206 as yet unmatched pairs. 2569 records in RAM.
INFO 2026-06-08 08:05:59 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 2s. Last read position: chr9:136,721,921
INFO 2026-06-08 08:05:59 MarkDuplicates Tracking 130350 as yet unmatched pairs. 690 records in RAM.
INFO 2026-06-08 08:06:02 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 2s. Last read position: chr10:24,546,041
INFO 2026-06-08 08:06:02 MarkDuplicates Tracking 128773 as yet unmatched pairs. 7459 records in RAM.
INFO 2026-06-08 08:06:05 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 2s. Last read position: chr10:49,739,741
INFO 2026-06-08 08:06:05 MarkDuplicates Tracking 127144 as yet unmatched pairs. 5819 records in RAM.
INFO 2026-06-08 08:06:07 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 2s. Last read position: chr10:75,030,694
INFO 2026-06-08 08:06:07 MarkDuplicates Tracking 125503 as yet unmatched pairs. 4160 records in RAM.
INFO 2026-06-08 08:06:10 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 2s. Last read position: chr10:96,750,287
INFO 2026-06-08 08:06:10 MarkDuplicates Tracking 123903 as yet unmatched pairs. 2542 records in RAM.
INFO 2026-06-08 08:06:13 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 3s. Last read position: chr10:120,862,763
INFO 2026-06-08 08:06:13 MarkDuplicates Tracking 122274 as yet unmatched pairs. 893 records in RAM.
INFO 2026-06-08 08:06:17 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 4s. Last read position: chr11:836,061
INFO 2026-06-08 08:06:17 MarkDuplicates Tracking 120589 as yet unmatched pairs. 13920 records in RAM.
INFO 2026-06-08 08:06:21 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 3s. Last read position: chr11:10,496,823
INFO 2026-06-08 08:06:21 MarkDuplicates Tracking 118792 as yet unmatched pairs. 12118 records in RAM.
INFO 2026-06-08 08:06:23 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 2s. Last read position: chr11:47,410,092
INFO 2026-06-08 08:06:23 MarkDuplicates Tracking 117228 as yet unmatched pairs. 10549 records in RAM.
INFO 2026-06-08 08:06:26 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 2s. Last read position: chr11:62,522,841
INFO 2026-06-08 08:06:26 MarkDuplicates Tracking 116735 as yet unmatched pairs. 10050 records in RAM.
INFO 2026-06-08 08:06:28 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 2s. Last read position: chr11:64,799,668
INFO 2026-06-08 08:06:28 MarkDuplicates Tracking 113825 as yet unmatched pairs. 7122 records in RAM.
INFO 2026-06-08 08:06:31 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 2s. Last read position: chr11:67,996,697
INFO 2026-06-08 08:06:31 MarkDuplicates Tracking 111910 as yet unmatched pairs. 5198 records in RAM.
INFO 2026-06-08 08:06:34 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 3s. Last read position: chr11:85,983,867
INFO 2026-06-08 08:06:34 MarkDuplicates Tracking 110128 as yet unmatched pairs. 3395 records in RAM.
INFO 2026-06-08 08:06:36 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 2s. Last read position: chr11:117,437,298
INFO 2026-06-08 08:06:36 MarkDuplicates Tracking 108224 as yet unmatched pairs. 1483 records in RAM.
INFO 2026-06-08 08:06:39 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 2s. Last read position: chr12:908,492
INFO 2026-06-08 08:06:39 MarkDuplicates Tracking 106748 as yet unmatched pairs. 12636 records in RAM.
INFO 2026-06-08 08:06:42 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 3s. Last read position: chr12:9,079,759
INFO 2026-06-08 08:06:42 MarkDuplicates Tracking 105031 as yet unmatched pairs. 10916 records in RAM.
INFO 2026-06-08 08:06:44 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 2s. Last read position: chr12:47,751,481
INFO 2026-06-08 08:06:44 MarkDuplicates Tracking 103430 as yet unmatched pairs. 9298 records in RAM.
INFO 2026-06-08 08:06:47 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 2s. Last read position: chr12:52,519,043
INFO 2026-06-08 08:06:47 MarkDuplicates Tracking 102013 as yet unmatched pairs. 7870 records in RAM.
INFO 2026-06-08 08:06:50 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 3s. Last read position: chr12:56,332,936
INFO 2026-06-08 08:06:50 MarkDuplicates Tracking 100067 as yet unmatched pairs. 5921 records in RAM.
INFO 2026-06-08 08:06:55 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 4s. Last read position: chr12:57,720,426
INFO 2026-06-08 08:06:55 MarkDuplicates Tracking 98467 as yet unmatched pairs. 4317 records in RAM.
INFO 2026-06-08 08:06:58 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 3s. Last read position: chr12:104,265,655
INFO 2026-06-08 08:06:58 MarkDuplicates Tracking 97006 as yet unmatched pairs. 2849 records in RAM.
INFO 2026-06-08 08:07:01 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 3s. Last read position: chr12:122,517,273
INFO 2026-06-08 08:07:01 MarkDuplicates Tracking 95046 as yet unmatched pairs. 869 records in RAM.
INFO 2026-06-08 08:07:04 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 3s. Last read position: chr13:36,335,351
INFO 2026-06-08 08:07:04 MarkDuplicates Tracking 93442 as yet unmatched pairs. 2822 records in RAM.
INFO 2026-06-08 08:07:07 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 3s. Last read position: chr13:100,532,123
INFO 2026-06-08 08:07:07 MarkDuplicates Tracking 91666 as yet unmatched pairs. 1020 records in RAM.
INFO 2026-06-08 08:07:10 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:05:04s. Time for last 1,000,000: 2s. Last read position: chr14:24,189,560
INFO 2026-06-08 08:07:10 MarkDuplicates Tracking 89883 as yet unmatched pairs. 6355 records in RAM.
INFO 2026-06-08 08:07:12 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 2s. Last read position: chr14:64,540,973
INFO 2026-06-08 08:07:12 MarkDuplicates Tracking 88210 as yet unmatched pairs. 4670 records in RAM.
INFO 2026-06-08 08:07:15 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 2s. Last read position: chr14:90,269,522
INFO 2026-06-08 08:07:15 MarkDuplicates Tracking 86436 as yet unmatched pairs. 2876 records in RAM.
INFO 2026-06-08 08:07:17 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 2s. Last read position: chr14:104,944,303
INFO 2026-06-08 08:07:17 MarkDuplicates Tracking 85809 as yet unmatched pairs. 2227 records in RAM.
INFO 2026-06-08 08:07:19 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 2s. Last read position: chr15:32,616,241
INFO 2026-06-08 08:07:19 MarkDuplicates Tracking 83305 as yet unmatched pairs. 5995 records in RAM.
INFO 2026-06-08 08:07:22 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:05:16s. Time for last 1,000,000: 2s. Last read position: chr15:55,376,998
INFO 2026-06-08 08:07:22 MarkDuplicates Tracking 81844 as yet unmatched pairs. 4532 records in RAM.
INFO 2026-06-08 08:07:26 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:05:20s. Time for last 1,000,000: 4s. Last read position: chr15:73,702,853
INFO 2026-06-08 08:07:26 MarkDuplicates Tracking 80203 as yet unmatched pairs. 2881 records in RAM.
INFO 2026-06-08 08:07:29 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 2s. Last read position: chr15:89,670,213
INFO 2026-06-08 08:07:29 MarkDuplicates Tracking 78401 as yet unmatched pairs. 1075 records in RAM.
INFO 2026-06-08 08:07:31 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 2s. Last read position: chr16:1,510,901
INFO 2026-06-08 08:07:31 MarkDuplicates Tracking 76463 as yet unmatched pairs. 8672 records in RAM.
INFO 2026-06-08 08:07:35 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 3s. Last read position: chr16:4,899,293
INFO 2026-06-08 08:07:35 MarkDuplicates Tracking 74644 as yet unmatched pairs. 6846 records in RAM.
INFO 2026-06-08 08:07:37 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 2s. Last read position: chr16:19,267,024
INFO 2026-06-08 08:07:37 MarkDuplicates Tracking 73396 as yet unmatched pairs. 5591 records in RAM.
INFO 2026-06-08 08:07:40 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 2s. Last read position: chr16:29,483,856
INFO 2026-06-08 08:07:40 MarkDuplicates Tracking 72778 as yet unmatched pairs. 4962 records in RAM.
INFO 2026-06-08 08:07:42 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 2s. Last read position: chr16:50,633,257
INFO 2026-06-08 08:07:42 MarkDuplicates Tracking 70891 as yet unmatched pairs. 3072 records in RAM.
INFO 2026-06-08 08:07:44 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 2s. Last read position: chr16:72,889,741
INFO 2026-06-08 08:07:44 MarkDuplicates Tracking 69024 as yet unmatched pairs. 1199 records in RAM.
INFO 2026-06-08 08:07:46 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 2s. Last read position: chr17:2,372,232
INFO 2026-06-08 08:07:46 MarkDuplicates Tracking 67232 as yet unmatched pairs. 17466 records in RAM.
INFO 2026-06-08 08:07:49 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:05:43s. Time for last 1,000,000: 2s. Last read position: chr17:8,377,604
INFO 2026-06-08 08:07:49 MarkDuplicates Tracking 65606 as yet unmatched pairs. 15836 records in RAM.
INFO 2026-06-08 08:07:51 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:05:45s. Time for last 1,000,000: 2s. Last read position: chr17:29,609,164
INFO 2026-06-08 08:07:51 MarkDuplicates Tracking 63765 as yet unmatched pairs. 13989 records in RAM.
INFO 2026-06-08 08:07:54 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 2s. Last read position: chr17:39,723,328
INFO 2026-06-08 08:07:54 MarkDuplicates Tracking 63219 as yet unmatched pairs. 13435 records in RAM.
INFO 2026-06-08 08:07:58 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:05:52s. Time for last 1,000,000: 3s. Last read position: chr17:44,351,388
INFO 2026-06-08 08:07:58 MarkDuplicates Tracking 60396 as yet unmatched pairs. 10600 records in RAM.
INFO 2026-06-08 08:08:00 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 2s. Last read position: chr17:50,188,775
INFO 2026-06-08 08:08:00 MarkDuplicates Tracking 65916 as yet unmatched pairs. 16116 records in RAM.
INFO 2026-06-08 08:08:03 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 2s. Last read position: chr17:50,196,154
INFO 2026-06-08 08:08:03 MarkDuplicates Tracking 62418 as yet unmatched pairs. 12616 records in RAM.
INFO 2026-06-08 08:08:06 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 2s. Last read position: chr17:60,663,455
INFO 2026-06-08 08:08:06 MarkDuplicates Tracking 54724 as yet unmatched pairs. 4915 records in RAM.
INFO 2026-06-08 08:08:10 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 3s. Last read position: chr17:75,614,262
INFO 2026-06-08 08:08:10 MarkDuplicates Tracking 53148 as yet unmatched pairs. 3333 records in RAM.
INFO 2026-06-08 08:08:12 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:06:06s. Time for last 1,000,000: 2s. Last read position: chr17:80,352,946
INFO 2026-06-08 08:08:12 MarkDuplicates Tracking 51216 as yet unmatched pairs. 1395 records in RAM.
INFO 2026-06-08 08:08:14 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 2s. Last read position: chr18:21,363,746
INFO 2026-06-08 08:08:14 MarkDuplicates Tracking 49236 as yet unmatched pairs. 1770 records in RAM.
INFO 2026-06-08 08:08:16 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 2s. Last read position: chr18:74,641,102
INFO 2026-06-08 08:08:16 MarkDuplicates Tracking 47707 as yet unmatched pairs. 240 records in RAM.
INFO 2026-06-08 08:08:20 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 3s. Last read position: chr19:4,839,211
INFO 2026-06-08 08:08:20 MarkDuplicates Tracking 45696 as yet unmatched pairs. 20939 records in RAM.
INFO 2026-06-08 08:08:22 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:06:16s. Time for last 1,000,000: 2s. Last read position: chr19:7,522,646
INFO 2026-06-08 08:08:22 MarkDuplicates Tracking 43809 as yet unmatched pairs. 19046 records in RAM.
INFO 2026-06-08 08:08:25 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 2s. Last read position: chr19:8,957,873
INFO 2026-06-08 08:08:25 MarkDuplicates Tracking 42609 as yet unmatched pairs. 17845 records in RAM.
INFO 2026-06-08 08:08:27 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:06:20s. Time for last 1,000,000: 1s. Last read position: chr19:12,669,766
INFO 2026-06-08 08:08:27 MarkDuplicates Tracking 40684 as yet unmatched pairs. 15916 records in RAM.
INFO 2026-06-08 08:08:29 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 1s. Last read position: chr19:15,254,260
INFO 2026-06-08 08:08:29 MarkDuplicates Tracking 38991 as yet unmatched pairs. 14219 records in RAM.
INFO 2026-06-08 08:08:30 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:06:24s. Time for last 1,000,000: 1s. Last read position: chr19:18,521,926
INFO 2026-06-08 08:08:30 MarkDuplicates Tracking 36769 as yet unmatched pairs. 11993 records in RAM.
INFO 2026-06-08 08:08:33 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:06:27s. Time for last 1,000,000: 2s. Last read position: chr19:35,269,896
INFO 2026-06-08 08:08:33 MarkDuplicates Tracking 35058 as yet unmatched pairs. 10282 records in RAM.
INFO 2026-06-08 08:08:36 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 2s. Last read position: chr19:39,433,320
INFO 2026-06-08 08:08:36 MarkDuplicates Tracking 34624 as yet unmatched pairs. 9848 records in RAM.
INFO 2026-06-08 08:08:39 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:06:33s. Time for last 1,000,000: 3s. Last read position: chr19:42,289,395
INFO 2026-06-08 08:08:39 MarkDuplicates Tracking 31841 as yet unmatched pairs. 7059 records in RAM.
INFO 2026-06-08 08:08:42 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:06:36s. Time for last 1,000,000: 3s. Last read position: chr19:46,756,401
INFO 2026-06-08 08:08:42 MarkDuplicates Tracking 29117 as yet unmatched pairs. 4333 records in RAM.
INFO 2026-06-08 08:08:44 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:06:38s. Time for last 1,000,000: 2s. Last read position: chr19:50,309,797
INFO 2026-06-08 08:08:44 MarkDuplicates Tracking 27094 as yet unmatched pairs. 2306 records in RAM.
INFO 2026-06-08 08:08:46 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:06:40s. Time for last 1,000,000: 1s. Last read position: chr19:57,808,100
INFO 2026-06-08 08:08:46 MarkDuplicates Tracking 25281 as yet unmatched pairs. 486 records in RAM.
INFO 2026-06-08 08:08:49 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:06:43s. Time for last 1,000,000: 2s. Last read position: chr20:13,091,168
INFO 2026-06-08 08:08:49 MarkDuplicates Tracking 23337 as yet unmatched pairs. 8298 records in RAM.
INFO 2026-06-08 08:08:51 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 2s. Last read position: chr20:35,366,556
INFO 2026-06-08 08:08:51 MarkDuplicates Tracking 21707 as yet unmatched pairs. 6662 records in RAM.
INFO 2026-06-08 08:08:53 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:06:47s. Time for last 1,000,000: 2s. Last read position: chr20:45,327,272
INFO 2026-06-08 08:08:53 MarkDuplicates Tracking 21775 as yet unmatched pairs. 6728 records in RAM.
INFO 2026-06-08 08:08:55 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:06:49s. Time for last 1,000,000: 2s. Last read position: chr20:50,891,788
INFO 2026-06-08 08:08:55 MarkDuplicates Tracking 18360 as yet unmatched pairs. 3312 records in RAM.
INFO 2026-06-08 08:08:57 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:06:51s. Time for last 1,000,000: 2s. Last read position: chr20:62,813,353
INFO 2026-06-08 08:08:57 MarkDuplicates Tracking 16148 as yet unmatched pairs. 1100 records in RAM.
INFO 2026-06-08 08:08:59 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:06:53s. Time for last 1,000,000: 1s. Last read position: chr21:26,839,672
INFO 2026-06-08 08:08:59 MarkDuplicates Tracking 14641 as yet unmatched pairs. 2785 records in RAM.
INFO 2026-06-08 08:09:01 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 1s. Last read position: chr21:45,497,606
INFO 2026-06-08 08:09:01 MarkDuplicates Tracking 12747 as yet unmatched pairs. 891 records in RAM.
INFO 2026-06-08 08:09:04 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:06:58s. Time for last 1,000,000: 2s. Last read position: chr22:27,797,290
INFO 2026-06-08 08:09:04 MarkDuplicates Tracking 10715 as yet unmatched pairs. 4279 records in RAM.
INFO 2026-06-08 08:09:07 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:07:01s. Time for last 1,000,000: 3s. Last read position: chr22:38,499,452
INFO 2026-06-08 08:09:07 MarkDuplicates Tracking 8997 as yet unmatched pairs. 2561 records in RAM.
INFO 2026-06-08 08:09:10 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:07:04s. Time for last 1,000,000: 2s. Last read position: chr22:50,290,006
INFO 2026-06-08 08:09:10 MarkDuplicates Tracking 7125 as yet unmatched pairs. 689 records in RAM.
INFO 2026-06-08 08:09:12 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 2s. Last read position: chrX:47,212,843
INFO 2026-06-08 08:09:12 MarkDuplicates Tracking 5253 as yet unmatched pairs. 4629 records in RAM.
INFO 2026-06-08 08:09:14 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:07:08s. Time for last 1,000,000: 2s. Last read position: chrX:75,745,873
INFO 2026-06-08 08:09:14 MarkDuplicates Tracking 3377 as yet unmatched pairs. 2753 records in RAM.
INFO 2026-06-08 08:09:17 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:07:11s. Time for last 1,000,000: 2s. Last read position: chrX:152,959,758
INFO 2026-06-08 08:09:17 MarkDuplicates Tracking 2012 as yet unmatched pairs. 1388 records in RAM.
INFO 2026-06-08 08:09:20 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:07:14s. Time for last 1,000,000: 2s. Last read position: KI270733.1:178,326
INFO 2026-06-08 08:09:20 MarkDuplicates Tracking 6 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 08:09:20 MarkDuplicates Read 148023506 records. 0 pairs never matched.
INFO 2026-06-08 08:09:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 43440808272; totalMemory: 62075699200; maxMemory: 63585648640
INFO 2026-06-08 08:09:31 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 08:09:39 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 08:10:04 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 08:10:24 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 08:10:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300877056; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-08 08:10:27 MarkDuplicates Marking 38954886 records as duplicates.
INFO 2026-06-08 08:10:27 MarkDuplicates Found 4850169 optical duplicate clusters.
INFO 2026-06-08 08:10:27 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 08:10:56 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:28s. Time for last 10,000,000: 28s. Last read position: chr1:153,986,136
INFO 2026-06-08 08:11:21 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:54s. Time for last 10,000,000: 25s. Last read position: chr2:108,753,941
INFO 2026-06-08 08:11:45 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:17s. Time for last 10,000,000: 23s. Last read position: chr3:101,417,731
INFO 2026-06-08 08:12:07 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:39s. Time for last 10,000,000: 21s. Last read position: chr5:65,792,579
INFO 2026-06-08 08:12:30 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:02:02s. Time for last 10,000,000: 23s. Last read position: chr6:32,530,128
INFO 2026-06-08 08:12:53 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:26s. Time for last 10,000,000: 23s. Last read position: chr7:134,300,180
INFO 2026-06-08 08:13:14 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:47s. Time for last 10,000,000: 21s. Last read position: chr9:65,287,903
INFO 2026-06-08 08:13:34 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:03:07s. Time for last 10,000,000: 19s. Last read position: chr11:10,496,823
INFO 2026-06-08 08:13:54 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:03:27s. Time for last 10,000,000: 19s. Last read position: chr12:52,519,043
INFO 2026-06-08 08:14:14 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:03:47s. Time for last 10,000,000: 20s. Last read position: chr14:104,944,303
INFO 2026-06-08 08:14:34 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:04:06s. Time for last 10,000,000: 19s. Last read position: chr16:72,889,741
INFO 2026-06-08 08:14:52 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:04:25s. Time for last 10,000,000: 18s. Last read position: chr17:80,352,946
INFO 2026-06-08 08:15:11 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:04:44s. Time for last 10,000,000: 18s. Last read position: chr19:39,433,320
INFO 2026-06-08 08:15:30 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:05:03s. Time for last 10,000,000: 19s. Last read position: chr21:26,839,672
INFO 2026-06-08 08:15:48 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 08:15:48 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 08:15:48 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 08:15:48 MarkDuplicates Before output close freeMemory: 202093288; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 08:15:48 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 08:15:48 MarkDuplicates After output close freeMemory: 104341432; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 08:15:48 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 13.75 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory