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/ea/526e7053483629727faa830f5f0499/.command.sh
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/526e7053483629727faa830f5f0499/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/92f6ef93675c9b42488875316588fa/dna_s743.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)
Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT dna_s743.Aligned.sortedByCoord.out.bam --OUTPUT dna_s743.md.bam --METRICS_FILE dna_s743.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:23:24.031 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Jun 08 07:23:24 GMT 2026] MarkDuplicates --INPUT dna_s743.Aligned.sortedByCoord.out.bam --OUTPUT dna_s743.md.bam --METRICS_FILE dna_s743.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 07:23:24 GMT 2026] Executing as ?@nf-ea526e7053483629727faa830f5f0499-2bf00-vdksx on Linux 6.12.88 amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0
INFO 2026-06-08 07:23:24 MarkDuplicates Start of doWork freeMemory: 105829624; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:23:24 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:23:24 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:23:30 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:16,948,433
INFO 2026-06-08 07:23:30 MarkDuplicates Tracking 291 as yet unmatched pairs. 56 records in RAM.
INFO 2026-06-08 07:23:33 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 3s. Last read position: chr1:40,495,348
INFO 2026-06-08 07:23:33 MarkDuplicates Tracking 480 as yet unmatched pairs. 40 records in RAM.
INFO 2026-06-08 07:23:38 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 5s. Last read position: chr1:74,464,479
INFO 2026-06-08 07:23:38 MarkDuplicates Tracking 805 as yet unmatched pairs. 34 records in RAM.
INFO 2026-06-08 07:23:41 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 2s. Last read position: chr1:113,886,421
INFO 2026-06-08 07:23:41 MarkDuplicates Tracking 1173 as yet unmatched pairs. 58 records in RAM.
INFO 2026-06-08 07:23:44 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 2s. Last read position: chr1:150,286,838
INFO 2026-06-08 07:23:44 MarkDuplicates Tracking 1357 as yet unmatched pairs. 37 records in RAM.
INFO 2026-06-08 07:23:47 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 3s. Last read position: chr1:165,544,407
INFO 2026-06-08 07:23:47 MarkDuplicates Tracking 1597 as yet unmatched pairs. 43 records in RAM.
INFO 2026-06-08 07:23:49 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 2s. Last read position: chr1:203,831,815
INFO 2026-06-08 07:23:49 MarkDuplicates Tracking 1936 as yet unmatched pairs. 22 records in RAM.
INFO 2026-06-08 07:23:52 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 3s. Last read position: chr1:232,807,620
INFO 2026-06-08 07:23:52 MarkDuplicates Tracking 2245 as yet unmatched pairs. 43 records in RAM.
INFO 2026-06-08 07:23:55 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 3s. Last read position: chr2:25,741,068
INFO 2026-06-08 07:23:55 MarkDuplicates Tracking 2680 as yet unmatched pairs. 1701 records in RAM.
INFO 2026-06-08 07:23:59 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 3s. Last read position: chr2:55,243,557
INFO 2026-06-08 07:23:59 MarkDuplicates Tracking 14567 as yet unmatched pairs. 985 records in RAM.
INFO 2026-06-08 07:24:01 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 2s. Last read position: chr2:91,974,874
INFO 2026-06-08 07:24:01 MarkDuplicates Tracking 14577 as yet unmatched pairs. 845 records in RAM.
INFO 2026-06-08 07:24:04 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 2s. Last read position: chr2:112,388,559
INFO 2026-06-08 07:24:04 MarkDuplicates Tracking 14561 as yet unmatched pairs. 764 records in RAM.
INFO 2026-06-08 07:24:06 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 2s. Last read position: chr2:151,585,502
INFO 2026-06-08 07:24:06 MarkDuplicates Tracking 14531 as yet unmatched pairs. 566 records in RAM.
INFO 2026-06-08 07:24:09 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 3s. Last read position: chr2:181,525,199
INFO 2026-06-08 07:24:09 MarkDuplicates Tracking 14469 as yet unmatched pairs. 375 records in RAM.
INFO 2026-06-08 07:24:12 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: chr2:218,646,128
INFO 2026-06-08 07:24:12 MarkDuplicates Tracking 14458 as yet unmatched pairs. 182 records in RAM.
INFO 2026-06-08 07:24:15 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 2s. Last read position: chr3:7,578,407
INFO 2026-06-08 07:24:15 MarkDuplicates Tracking 14386 as yet unmatched pairs. 1207 records in RAM.
INFO 2026-06-08 07:24:17 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 2s. Last read position: chr3:30,800,813
INFO 2026-06-08 07:24:17 MarkDuplicates Tracking 14218 as yet unmatched pairs. 953 records in RAM.
INFO 2026-06-08 07:24:21 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 3s. Last read position: chr3:52,503,795
INFO 2026-06-08 07:24:21 MarkDuplicates Tracking 14074 as yet unmatched pairs. 728 records in RAM.
INFO 2026-06-08 07:24:24 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 3s. Last read position: chr3:103,225,333
INFO 2026-06-08 07:24:24 MarkDuplicates Tracking 14025 as yet unmatched pairs. 518 records in RAM.
INFO 2026-06-08 07:24:26 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 2s. Last read position: chr3:138,707,103
INFO 2026-06-08 07:24:26 MarkDuplicates Tracking 14031 as yet unmatched pairs. 382 records in RAM.
INFO 2026-06-08 07:24:29 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 2s. Last read position: chr3:184,303,666
INFO 2026-06-08 07:24:29 MarkDuplicates Tracking 13923 as yet unmatched pairs. 123 records in RAM.
INFO 2026-06-08 07:24:31 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 2s. Last read position: chr4:9,230,970
INFO 2026-06-08 07:24:31 MarkDuplicates Tracking 13932 as yet unmatched pairs. 958 records in RAM.
INFO 2026-06-08 07:24:33 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 2s. Last read position: chr4:54,740,001
INFO 2026-06-08 07:24:33 MarkDuplicates Tracking 13974 as yet unmatched pairs. 867 records in RAM.
INFO 2026-06-08 07:24:36 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 2s. Last read position: chr4:100,465,239
INFO 2026-06-08 07:24:36 MarkDuplicates Tracking 13687 as yet unmatched pairs. 375 records in RAM.
INFO 2026-06-08 07:24:38 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 2s. Last read position: chr4:153,588,903
INFO 2026-06-08 07:24:38 MarkDuplicates Tracking 13711 as yet unmatched pairs. 172 records in RAM.
INFO 2026-06-08 07:24:41 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 2s. Last read position: chr5:30,027,927
INFO 2026-06-08 07:24:41 MarkDuplicates Tracking 13621 as yet unmatched pairs. 938 records in RAM.
INFO 2026-06-08 07:24:44 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 2s. Last read position: chr5:71,502,579
INFO 2026-06-08 07:24:44 MarkDuplicates Tracking 13562 as yet unmatched pairs. 698 records in RAM.
INFO 2026-06-08 07:24:46 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 2s. Last read position: chr5:126,473,347
INFO 2026-06-08 07:24:46 MarkDuplicates Tracking 13428 as yet unmatched pairs. 369 records in RAM.
INFO 2026-06-08 07:24:49 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 2s. Last read position: chr5:151,133,153
INFO 2026-06-08 07:24:49 MarkDuplicates Tracking 13282 as yet unmatched pairs. 152 records in RAM.
INFO 2026-06-08 07:24:51 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 2s. Last read position: chr6:12,123,087
INFO 2026-06-08 07:24:51 MarkDuplicates Tracking 13221 as yet unmatched pairs. 1120 records in RAM.
INFO 2026-06-08 07:24:53 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 2s. Last read position: chr6:33,294,885
INFO 2026-06-08 07:24:53 MarkDuplicates Tracking 13064 as yet unmatched pairs. 925 records in RAM.
INFO 2026-06-08 07:24:55 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 2s. Last read position: chr6:73,409,240
INFO 2026-06-08 07:24:55 MarkDuplicates Tracking 13000 as yet unmatched pairs. 740 records in RAM.
INFO 2026-06-08 07:24:58 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 2s. Last read position: chr6:117,323,340
INFO 2026-06-08 07:24:58 MarkDuplicates Tracking 12976 as yet unmatched pairs. 577 records in RAM.
INFO 2026-06-08 07:25:01 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 2s. Last read position: chr6:150,768,685
INFO 2026-06-08 07:25:01 MarkDuplicates Tracking 12688 as yet unmatched pairs. 179 records in RAM.
INFO 2026-06-08 07:25:04 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 2s. Last read position: chr7:12,369,855
INFO 2026-06-08 07:25:04 MarkDuplicates Tracking 12514 as yet unmatched pairs. 1074 records in RAM.
INFO 2026-06-08 07:25:06 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 2s. Last read position: chr7:48,101,927
INFO 2026-06-08 07:25:06 MarkDuplicates Tracking 12361 as yet unmatched pairs. 839 records in RAM.
INFO 2026-06-08 07:25:08 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 2s. Last read position: chr7:77,932,594
INFO 2026-06-08 07:25:08 MarkDuplicates Tracking 12240 as yet unmatched pairs. 621 records in RAM.
INFO 2026-06-08 07:25:11 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 2s. Last read position: chr7:102,640,269
INFO 2026-06-08 07:25:11 MarkDuplicates Tracking 12151 as yet unmatched pairs. 458 records in RAM.
INFO 2026-06-08 07:25:13 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 2s. Last read position: chr7:140,587,764
INFO 2026-06-08 07:25:13 MarkDuplicates Tracking 11966 as yet unmatched pairs. 173 records in RAM.
INFO 2026-06-08 07:25:15 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 2s. Last read position: chr8:7,509,163
INFO 2026-06-08 07:25:15 MarkDuplicates Tracking 11809 as yet unmatched pairs. 913 records in RAM.
INFO 2026-06-08 07:25:18 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 2s. Last read position: chr8:32,673,930
INFO 2026-06-08 07:25:18 MarkDuplicates Tracking 11799 as yet unmatched pairs. 849 records in RAM.
INFO 2026-06-08 07:25:20 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 2s. Last read position: chr8:47,862,432
INFO 2026-06-08 07:25:20 MarkDuplicates Tracking 11591 as yet unmatched pairs. 603 records in RAM.
INFO 2026-06-08 07:25:23 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 2s. Last read position: chr8:101,608,603
INFO 2026-06-08 07:25:23 MarkDuplicates Tracking 11363 as yet unmatched pairs. 232 records in RAM.
INFO 2026-06-08 07:25:25 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 2s. Last read position: chr9:2,043,522
INFO 2026-06-08 07:25:25 MarkDuplicates Tracking 11365 as yet unmatched pairs. 1184 records in RAM.
INFO 2026-06-08 07:25:27 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 2s. Last read position: chr9:36,837,879
INFO 2026-06-08 07:25:27 MarkDuplicates Tracking 11110 as yet unmatched pairs. 821 records in RAM.
INFO 2026-06-08 07:25:29 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 1s. Last read position: chr9:77,719,828
INFO 2026-06-08 07:25:29 MarkDuplicates Tracking 11070 as yet unmatched pairs. 723 records in RAM.
INFO 2026-06-08 07:25:31 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 2s. Last read position: chr9:95,505,772
INFO 2026-06-08 07:25:31 MarkDuplicates Tracking 10776 as yet unmatched pairs. 394 records in RAM.
INFO 2026-06-08 07:25:33 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 1s. Last read position: chr9:131,075,911
INFO 2026-06-08 07:25:33 MarkDuplicates Tracking 10560 as yet unmatched pairs. 108 records in RAM.
INFO 2026-06-08 07:25:35 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 2s. Last read position: chr10:27,093,596
INFO 2026-06-08 07:25:35 MarkDuplicates Tracking 10378 as yet unmatched pairs. 708 records in RAM.
INFO 2026-06-08 07:25:37 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 1s. Last read position: chr10:68,121,670
INFO 2026-06-08 07:25:37 MarkDuplicates Tracking 10216 as yet unmatched pairs. 454 records in RAM.
INFO 2026-06-08 07:25:40 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 2s. Last read position: chr10:104,123,823
INFO 2026-06-08 07:25:40 MarkDuplicates Tracking 10020 as yet unmatched pairs. 199 records in RAM.
INFO 2026-06-08 07:25:42 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 2s. Last read position: chr11:1,853,108
INFO 2026-06-08 07:25:42 MarkDuplicates Tracking 9843 as yet unmatched pairs. 1170 records in RAM.
INFO 2026-06-08 07:25:44 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 2s. Last read position: chr11:43,677,469
INFO 2026-06-08 07:25:44 MarkDuplicates Tracking 9642 as yet unmatched pairs. 894 records in RAM.
INFO 2026-06-08 07:25:47 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 2s. Last read position: chr11:67,507,358
INFO 2026-06-08 07:25:47 MarkDuplicates Tracking 9401 as yet unmatched pairs. 609 records in RAM.
INFO 2026-06-08 07:25:49 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr11:102,842,636
INFO 2026-06-08 07:25:49 MarkDuplicates Tracking 9176 as yet unmatched pairs. 331 records in RAM.
INFO 2026-06-08 07:25:50 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 1s. Last read position: chr11:129,910,491
INFO 2026-06-08 07:25:50 MarkDuplicates Tracking 8934 as yet unmatched pairs. 54 records in RAM.
INFO 2026-06-08 07:25:52 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 2s. Last read position: chr12:11,794,384
INFO 2026-06-08 07:25:52 MarkDuplicates Tracking 9094 as yet unmatched pairs. 1611 records in RAM.
INFO 2026-06-08 07:25:55 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 2s. Last read position: chr12:29,433,708
INFO 2026-06-08 07:25:55 MarkDuplicates Tracking 8475 as yet unmatched pairs. 969 records in RAM.
INFO 2026-06-08 07:25:57 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 2s. Last read position: chr12:53,543,420
INFO 2026-06-08 07:25:57 MarkDuplicates Tracking 8274 as yet unmatched pairs. 727 records in RAM.
INFO 2026-06-08 07:25:59 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 2s. Last read position: chr12:81,358,089
INFO 2026-06-08 07:25:59 MarkDuplicates Tracking 8078 as yet unmatched pairs. 480 records in RAM.
INFO 2026-06-08 07:26:01 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 1s. Last read position: chr12:116,650,999
INFO 2026-06-08 07:26:01 MarkDuplicates Tracking 7800 as yet unmatched pairs. 142 records in RAM.
INFO 2026-06-08 07:26:03 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 2s. Last read position: chr13:28,456,524
INFO 2026-06-08 07:26:03 MarkDuplicates Tracking 7651 as yet unmatched pairs. 515 records in RAM.
INFO 2026-06-08 07:26:06 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 2s. Last read position: chr13:92,283,424
INFO 2026-06-08 07:26:06 MarkDuplicates Tracking 7354 as yet unmatched pairs. 141 records in RAM.
INFO 2026-06-08 07:26:08 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 2s. Last read position: chr14:34,762,036
INFO 2026-06-08 07:26:08 MarkDuplicates Tracking 7167 as yet unmatched pairs. 556 records in RAM.
INFO 2026-06-08 07:26:11 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 2s. Last read position: chr14:77,887,091
INFO 2026-06-08 07:26:11 MarkDuplicates Tracking 6870 as yet unmatched pairs. 197 records in RAM.
INFO 2026-06-08 07:26:13 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 2s. Last read position: chr15:28,356,144
INFO 2026-06-08 07:26:13 MarkDuplicates Tracking 6618 as yet unmatched pairs. 831 records in RAM.
INFO 2026-06-08 07:26:16 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 2s. Last read position: chr15:52,246,839
INFO 2026-06-08 07:26:16 MarkDuplicates Tracking 6426 as yet unmatched pairs. 615 records in RAM.
INFO 2026-06-08 07:26:17 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 1s. Last read position: chr15:87,861,800
INFO 2026-06-08 07:26:17 MarkDuplicates Tracking 6393 as yet unmatched pairs. 566 records in RAM.
INFO 2026-06-08 07:26:19 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 1s. Last read position: chr15:88,141,825
INFO 2026-06-08 07:26:19 MarkDuplicates Tracking 6106 as yet unmatched pairs. 272 records in RAM.
INFO 2026-06-08 07:26:21 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 2s. Last read position: chr16:4,507,076
INFO 2026-06-08 07:26:21 MarkDuplicates Tracking 5780 as yet unmatched pairs. 649 records in RAM.
INFO 2026-06-08 07:26:23 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 1s. Last read position: chr16:28,625,710
INFO 2026-06-08 07:26:23 MarkDuplicates Tracking 5627 as yet unmatched pairs. 489 records in RAM.
INFO 2026-06-08 07:26:24 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 1s. Last read position: chr16:67,140,430
INFO 2026-06-08 07:26:24 MarkDuplicates Tracking 5388 as yet unmatched pairs. 216 records in RAM.
INFO 2026-06-08 07:26:26 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 2s. Last read position: chr16:90,102,240
INFO 2026-06-08 07:26:26 MarkDuplicates Tracking 5213 as yet unmatched pairs. 24 records in RAM.
INFO 2026-06-08 07:26:29 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 2s. Last read position: chr17:17,383,793
INFO 2026-06-08 07:26:29 MarkDuplicates Tracking 5000 as yet unmatched pairs. 946 records in RAM.
INFO 2026-06-08 07:26:31 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 2s. Last read position: chr17:39,709,787
INFO 2026-06-08 07:26:31 MarkDuplicates Tracking 4798 as yet unmatched pairs. 735 records in RAM.
INFO 2026-06-08 07:26:34 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 2s. Last read position: chr17:46,331,282
INFO 2026-06-08 07:26:34 MarkDuplicates Tracking 4549 as yet unmatched pairs. 485 records in RAM.
INFO 2026-06-08 07:26:36 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 2s. Last read position: chr17:68,401,246
INFO 2026-06-08 07:26:36 MarkDuplicates Tracking 4296 as yet unmatched pairs. 229 records in RAM.
INFO 2026-06-08 07:26:38 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 2s. Last read position: chr18:21,505,772
INFO 2026-06-08 07:26:38 MarkDuplicates Tracking 4000 as yet unmatched pairs. 451 records in RAM.
INFO 2026-06-08 07:26:40 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 2s. Last read position: chr18:63,317,804
INFO 2026-06-08 07:26:40 MarkDuplicates Tracking 3864 as yet unmatched pairs. 286 records in RAM.
INFO 2026-06-08 07:26:42 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 1s. Last read position: chr19:9,828,274
INFO 2026-06-08 07:26:42 MarkDuplicates Tracking 3408 as yet unmatched pairs. 613 records in RAM.
INFO 2026-06-08 07:26:44 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 1s. Last read position: chr19:35,510,224
INFO 2026-06-08 07:26:44 MarkDuplicates Tracking 3148 as yet unmatched pairs. 346 records in RAM.
INFO 2026-06-08 07:26:45 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 1s. Last read position: chr19:49,932,813
INFO 2026-06-08 07:26:45 MarkDuplicates Tracking 2940 as yet unmatched pairs. 130 records in RAM.
INFO 2026-06-08 07:26:47 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 1s. Last read position: chr20:20,520,950
INFO 2026-06-08 07:26:47 MarkDuplicates Tracking 2676 as yet unmatched pairs. 498 records in RAM.
INFO 2026-06-08 07:26:49 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: chr20:46,610,547
INFO 2026-06-08 07:26:49 MarkDuplicates Tracking 2371 as yet unmatched pairs. 180 records in RAM.
INFO 2026-06-08 07:26:51 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 2s. Last read position: chr21:15,451,782
INFO 2026-06-08 07:26:51 MarkDuplicates Tracking 2110 as yet unmatched pairs. 251 records in RAM.
INFO 2026-06-08 07:26:52 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 1s. Last read position: chr22:16,687,971
INFO 2026-06-08 07:26:52 MarkDuplicates Tracking 1824 as yet unmatched pairs. 417 records in RAM.
INFO 2026-06-08 07:26:54 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 1s. Last read position: chr22:28,725,323
INFO 2026-06-08 07:26:54 MarkDuplicates Tracking 1691 as yet unmatched pairs. 278 records in RAM.
INFO 2026-06-08 07:26:56 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 2s. Last read position: chrX:3,033,040
INFO 2026-06-08 07:26:56 MarkDuplicates Tracking 1419 as yet unmatched pairs. 1080 records in RAM.
INFO 2026-06-08 07:26:58 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 1s. Last read position: chrX:57,910,289
INFO 2026-06-08 07:26:58 MarkDuplicates Tracking 1072 as yet unmatched pairs. 731 records in RAM.
INFO 2026-06-08 07:27:01 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 2s. Last read position: chrX:120,447,794
INFO 2026-06-08 07:27:01 MarkDuplicates Tracking 603 as yet unmatched pairs. 260 records in RAM.
INFO 2026-06-08 07:27:03 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 1s. Last read position: chrY:21,536,855
INFO 2026-06-08 07:27:03 MarkDuplicates Tracking 240 as yet unmatched pairs. 42 records in RAM.
INFO 2026-06-08 07:27:04 MarkDuplicates Read 91881850 records. 0 pairs never matched.
INFO 2026-06-08 07:27:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 29085032816; totalMemory: 41506832384; maxMemory: 63585648640
INFO 2026-06-08 07:27:11 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 07:27:18 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 07:27:29 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 07:27:34 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 07:27:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 33207265896; totalMemory: 49157242880; maxMemory: 63585648640
INFO 2026-06-08 07:27:36 MarkDuplicates Marking 34663317 records as duplicates.
INFO 2026-06-08 07:27:36 MarkDuplicates Found 1425530 optical duplicate clusters.
INFO 2026-06-08 07:27:36 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 07:28:02 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:26s. Time for last 10,000,000: 26s. Last read position: chr2:55,243,557
INFO 2026-06-08 07:28:27 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:51s. Time for last 10,000,000: 25s. Last read position: chr3:138,707,103
INFO 2026-06-08 07:28:51 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:15s. Time for last 10,000,000: 24s. Last read position: chr6:12,123,087
INFO 2026-06-08 07:29:16 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:40s. Time for last 10,000,000: 24s. Last read position: chr8:7,509,163
INFO 2026-06-08 07:29:40 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:02:04s. Time for last 10,000,000: 23s. Last read position: chr10:68,121,670
INFO 2026-06-08 07:30:04 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:28s. Time for last 10,000,000: 24s. Last read position: chr12:81,358,089
INFO 2026-06-08 07:30:29 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:53s. Time for last 10,000,000: 25s. Last read position: chr16:4,507,076
INFO 2026-06-08 07:30:56 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:03:20s. Time for last 10,000,000: 26s. Last read position: chr19:9,828,274
INFO 2026-06-08 07:31:23 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:03:46s. Time for last 10,000,000: 26s. Last read position: chrX:120,447,794
INFO 2026-06-08 07:31:32 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 07:31:32 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 07:31:32 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 07:31:32 MarkDuplicates Before output close freeMemory: 202442168; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 07:31:32 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 07:31:32 MarkDuplicates After output close freeMemory: 104385408; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 07:31:32 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 8.14 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory