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/f4/24493b9ba52eb30a771ad1f7c37624/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/24493b9ba52eb30a771ad1f7c37624/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/5d298b7528f78dc4019c240b840ae9/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)
Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bam --METRICS_FILE 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:33:54.451 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 07:33:54 GMT 2026] MarkDuplicates --INPUT 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.md.bam --METRICS_FILE 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_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 07:33:54 GMT 2026] Executing as ?@nf-f424493b9ba52eb30a771ad1f7c37624-b2b7c-dgrhf 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 07:33:54 MarkDuplicates Start of doWork freeMemory: 105492480; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:33:54 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:33:54 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:33:59 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:19,117,884
INFO 2026-06-08 07:33:59 MarkDuplicates Tracking 2679 as yet unmatched pairs. 11 records in RAM.
INFO 2026-06-08 07:34:02 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: chr1:36,287,116
INFO 2026-06-08 07:34:02 MarkDuplicates Tracking 5287 as yet unmatched pairs. 24 records in RAM.
INFO 2026-06-08 07:34:05 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 2s. Last read position: chr1:84,662,301
INFO 2026-06-08 07:34:05 MarkDuplicates Tracking 7795 as yet unmatched pairs. 7 records in RAM.
INFO 2026-06-08 07:34:07 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 2s. Last read position: chr1:146,977,479
INFO 2026-06-08 07:34:07 MarkDuplicates Tracking 9887 as yet unmatched pairs. 11 records in RAM.
INFO 2026-06-08 07:34:10 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: chr1:155,613,748
INFO 2026-06-08 07:34:10 MarkDuplicates Tracking 11686 as yet unmatched pairs. 5 records in RAM.
INFO 2026-06-08 07:34:13 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 2s. Last read position: chr1:186,444,059
INFO 2026-06-08 07:34:13 MarkDuplicates Tracking 14182 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 07:34:16 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 2s. Last read position: chr1:234,318,793
INFO 2026-06-08 07:34:16 MarkDuplicates Tracking 16667 as yet unmatched pairs. 4 records in RAM.
INFO 2026-06-08 07:34:19 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 3s. Last read position: chr2:32,916,264
INFO 2026-06-08 07:34:19 MarkDuplicates Tracking 90654 as yet unmatched pairs. 13446 records in RAM.
INFO 2026-06-08 07:34:21 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 2s. Last read position: chr2:73,489,765
INFO 2026-06-08 07:34:21 MarkDuplicates Tracking 154907 as yet unmatched pairs. 7285 records in RAM.
INFO 2026-06-08 07:34:23 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 2s. Last read position: chr2:130,172,387
INFO 2026-06-08 07:34:23 MarkDuplicates Tracking 152931 as yet unmatched pairs. 5301 records in RAM.
INFO 2026-06-08 07:34:27 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 3s. Last read position: chr2:206,307,561
INFO 2026-06-08 07:34:27 MarkDuplicates Tracking 150658 as yet unmatched pairs. 3022 records in RAM.
INFO 2026-06-08 07:34:29 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 2s. Last read position: chr2:233,469,481
INFO 2026-06-08 07:34:29 MarkDuplicates Tracking 148287 as yet unmatched pairs. 635 records in RAM.
INFO 2026-06-08 07:34:32 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 2s. Last read position: chr3:47,000,243
INFO 2026-06-08 07:34:32 MarkDuplicates Tracking 145823 as yet unmatched pairs. 7281 records in RAM.
INFO 2026-06-08 07:34:35 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 2s. Last read position: chr3:52,693,489
INFO 2026-06-08 07:34:35 MarkDuplicates Tracking 143080 as yet unmatched pairs. 4534 records in RAM.
INFO 2026-06-08 07:34:37 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 2s. Last read position: chr3:139,539,544
INFO 2026-06-08 07:34:37 MarkDuplicates Tracking 140704 as yet unmatched pairs. 2154 records in RAM.
INFO 2026-06-08 07:34:39 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 2s. Last read position: chr4:1,024,077
INFO 2026-06-08 07:34:39 MarkDuplicates Tracking 138394 as yet unmatched pairs. 4068 records in RAM.
INFO 2026-06-08 07:34:42 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: chr4:105,234,948
INFO 2026-06-08 07:34:42 MarkDuplicates Tracking 135999 as yet unmatched pairs. 1662 records in RAM.
INFO 2026-06-08 07:34:45 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 2s. Last read position: chr5:14,487,574
INFO 2026-06-08 07:34:45 MarkDuplicates Tracking 133738 as yet unmatched pairs. 6266 records in RAM.
INFO 2026-06-08 07:34:47 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 2s. Last read position: chr5:129,028,361
INFO 2026-06-08 07:34:47 MarkDuplicates Tracking 131579 as yet unmatched pairs. 4103 records in RAM.
INFO 2026-06-08 07:34:50 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 2s. Last read position: chr5:151,567,377
INFO 2026-06-08 07:34:50 MarkDuplicates Tracking 129160 as yet unmatched pairs. 1650 records in RAM.
INFO 2026-06-08 07:34:52 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 2s. Last read position: chr6:7,583,053
INFO 2026-06-08 07:34:52 MarkDuplicates Tracking 126703 as yet unmatched pairs. 8268 records in RAM.
INFO 2026-06-08 07:34:54 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 2s. Last read position: chr6:31,829,591
INFO 2026-06-08 07:34:54 MarkDuplicates Tracking 124552 as yet unmatched pairs. 6113 records in RAM.
INFO 2026-06-08 07:34:57 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 2s. Last read position: chr6:70,280,811
INFO 2026-06-08 07:34:57 MarkDuplicates Tracking 122023 as yet unmatched pairs. 3580 records in RAM.
INFO 2026-06-08 07:34:59 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 2s. Last read position: chr6:150,809,429
INFO 2026-06-08 07:34:59 MarkDuplicates Tracking 119519 as yet unmatched pairs. 1074 records in RAM.
INFO 2026-06-08 07:35:01 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 2s. Last read position: chr7:30,598,843
INFO 2026-06-08 07:35:01 MarkDuplicates Tracking 116876 as yet unmatched pairs. 7216 records in RAM.
INFO 2026-06-08 07:35:04 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 2s. Last read position: chr7:75,422,358
INFO 2026-06-08 07:35:04 MarkDuplicates Tracking 114986 as yet unmatched pairs. 5323 records in RAM.
INFO 2026-06-08 07:35:06 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 2s. Last read position: chr7:102,554,344
INFO 2026-06-08 07:35:06 MarkDuplicates Tracking 112500 as yet unmatched pairs. 2833 records in RAM.
INFO 2026-06-08 07:35:09 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 2s. Last read position: chr7:144,365,558
INFO 2026-06-08 07:35:09 MarkDuplicates Tracking 110381 as yet unmatched pairs. 700 records in RAM.
INFO 2026-06-08 07:35:11 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 2s. Last read position: chr8:42,181,999
INFO 2026-06-08 07:35:11 MarkDuplicates Tracking 107917 as yet unmatched pairs. 4050 records in RAM.
INFO 2026-06-08 07:35:13 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 2s. Last read position: chr8:143,858,200
INFO 2026-06-08 07:35:13 MarkDuplicates Tracking 105502 as yet unmatched pairs. 1622 records in RAM.
INFO 2026-06-08 07:35:15 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 1s. Last read position: chr9:8,507,301
INFO 2026-06-08 07:35:15 MarkDuplicates Tracking 103393 as yet unmatched pairs. 6904 records in RAM.
INFO 2026-06-08 07:35:17 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 1s. Last read position: chr9:106,928,579
INFO 2026-06-08 07:35:17 MarkDuplicates Tracking 101099 as yet unmatched pairs. 4590 records in RAM.
INFO 2026-06-08 07:35:19 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 2s. Last read position: chr9:131,455,074
INFO 2026-06-08 07:35:19 MarkDuplicates Tracking 98594 as yet unmatched pairs. 2082 records in RAM.
INFO 2026-06-08 07:35:22 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 2s. Last read position: chr10:21,651,720
INFO 2026-06-08 07:35:22 MarkDuplicates Tracking 95785 as yet unmatched pairs. 5266 records in RAM.
INFO 2026-06-08 07:35:25 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 2s. Last read position: chr10:74,082,535
INFO 2026-06-08 07:35:25 MarkDuplicates Tracking 93771 as yet unmatched pairs. 3245 records in RAM.
INFO 2026-06-08 07:35:27 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 2s. Last read position: chr10:110,894,058
INFO 2026-06-08 07:35:27 MarkDuplicates Tracking 91461 as yet unmatched pairs. 931 records in RAM.
INFO 2026-06-08 07:35:29 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 2s. Last read position: chr11:11,964,436
INFO 2026-06-08 07:35:29 MarkDuplicates Tracking 88953 as yet unmatched pairs. 8149 records in RAM.
INFO 2026-06-08 07:35:31 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 2s. Last read position: chr11:62,525,049
INFO 2026-06-08 07:35:31 MarkDuplicates Tracking 86681 as yet unmatched pairs. 5866 records in RAM.
INFO 2026-06-08 07:35:34 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 2s. Last read position: chr11:70,409,908
INFO 2026-06-08 07:35:34 MarkDuplicates Tracking 84056 as yet unmatched pairs. 3238 records in RAM.
INFO 2026-06-08 07:35:36 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 2s. Last read position: chr11:119,335,608
INFO 2026-06-08 07:35:36 MarkDuplicates Tracking 81626 as yet unmatched pairs. 806 records in RAM.
INFO 2026-06-08 07:35:39 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 2s. Last read position: chr12:26,122,905
INFO 2026-06-08 07:35:39 MarkDuplicates Tracking 79159 as yet unmatched pairs. 7452 records in RAM.
INFO 2026-06-08 07:35:41 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 2s. Last read position: chr12:52,517,943
INFO 2026-06-08 07:35:41 MarkDuplicates Tracking 77072 as yet unmatched pairs. 5364 records in RAM.
INFO 2026-06-08 07:35:43 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 2s. Last read position: chr12:79,788,684
INFO 2026-06-08 07:35:43 MarkDuplicates Tracking 74689 as yet unmatched pairs. 2979 records in RAM.
INFO 2026-06-08 07:35:46 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 3s. Last read position: chr12:124,912,389
INFO 2026-06-08 07:35:46 MarkDuplicates Tracking 72256 as yet unmatched pairs. 543 records in RAM.
INFO 2026-06-08 07:35:49 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 2s. Last read position: chr13:110,449,678
INFO 2026-06-08 07:35:49 MarkDuplicates Tracking 69728 as yet unmatched pairs. 613 records in RAM.
INFO 2026-06-08 07:35:51 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 2s. Last read position: chr14:64,487,539
INFO 2026-06-08 07:35:51 MarkDuplicates Tracking 67246 as yet unmatched pairs. 3141 records in RAM.
INFO 2026-06-08 07:35:54 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 2s. Last read position: chr14:104,157,880
INFO 2026-06-08 07:35:54 MarkDuplicates Tracking 64739 as yet unmatched pairs. 617 records in RAM.
INFO 2026-06-08 07:35:56 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 2s. Last read position: chr15:48,962,755
INFO 2026-06-08 07:35:56 MarkDuplicates Tracking 62551 as yet unmatched pairs. 3256 records in RAM.
INFO 2026-06-08 07:35:58 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 2s. Last read position: chr15:88,032,905
INFO 2026-06-08 07:35:58 MarkDuplicates Tracking 60319 as yet unmatched pairs. 1020 records in RAM.
INFO 2026-06-08 07:36:01 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 2s. Last read position: chr16:3,850,887
INFO 2026-06-08 07:36:01 MarkDuplicates Tracking 57564 as yet unmatched pairs. 6786 records in RAM.
INFO 2026-06-08 07:36:03 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 2s. Last read position: chr16:21,400,984
INFO 2026-06-08 07:36:03 MarkDuplicates Tracking 56145 as yet unmatched pairs. 5365 records in RAM.
INFO 2026-06-08 07:36:05 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 1s. Last read position: chr16:29,986,411
INFO 2026-06-08 07:36:05 MarkDuplicates Tracking 54974 as yet unmatched pairs. 4191 records in RAM.
INFO 2026-06-08 07:36:07 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 2s. Last read position: chr16:69,693,569
INFO 2026-06-08 07:36:07 MarkDuplicates Tracking 52650 as yet unmatched pairs. 1861 records in RAM.
INFO 2026-06-08 07:36:09 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 2s. Last read position: chr17:4,672,517
INFO 2026-06-08 07:36:09 MarkDuplicates Tracking 50006 as yet unmatched pairs. 15500 records in RAM.
INFO 2026-06-08 07:36:11 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 1s. Last read position: chr17:27,597,339
INFO 2026-06-08 07:36:11 MarkDuplicates Tracking 47717 as yet unmatched pairs. 13209 records in RAM.
INFO 2026-06-08 07:36:13 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 2s. Last read position: chr17:41,582,322
INFO 2026-06-08 07:36:13 MarkDuplicates Tracking 45613 as yet unmatched pairs. 11102 records in RAM.
INFO 2026-06-08 07:36:15 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 1s. Last read position: chr17:42,114,901
INFO 2026-06-08 07:36:15 MarkDuplicates Tracking 42723 as yet unmatched pairs. 8212 records in RAM.
INFO 2026-06-08 07:36:17 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 2s. Last read position: chr17:50,192,796
INFO 2026-06-08 07:36:17 MarkDuplicates Tracking 40499 as yet unmatched pairs. 5986 records in RAM.
INFO 2026-06-08 07:36:20 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 2s. Last read position: chr17:68,148,032
INFO 2026-06-08 07:36:20 MarkDuplicates Tracking 37587 as yet unmatched pairs. 3074 records in RAM.
INFO 2026-06-08 07:36:23 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 2s. Last read position: chr17:81,868,506
INFO 2026-06-08 07:36:23 MarkDuplicates Tracking 34853 as yet unmatched pairs. 337 records in RAM.
INFO 2026-06-08 07:36:26 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 3s. Last read position: chr19:618,740
INFO 2026-06-08 07:36:26 MarkDuplicates Tracking 32276 as yet unmatched pairs. 14013 records in RAM.
INFO 2026-06-08 07:36:28 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 2s. Last read position: chr19:10,317,497
INFO 2026-06-08 07:36:28 MarkDuplicates Tracking 29354 as yet unmatched pairs. 11090 records in RAM.
INFO 2026-06-08 07:36:31 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 2s. Last read position: chr19:15,244,570
INFO 2026-06-08 07:36:31 MarkDuplicates Tracking 26669 as yet unmatched pairs. 8404 records in RAM.
INFO 2026-06-08 07:36:33 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 2s. Last read position: chr19:38,728,001
INFO 2026-06-08 07:36:33 MarkDuplicates Tracking 23970 as yet unmatched pairs. 5702 records in RAM.
INFO 2026-06-08 07:36:36 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 2s. Last read position: chr19:45,472,903
INFO 2026-06-08 07:36:36 MarkDuplicates Tracking 21324 as yet unmatched pairs. 3053 records in RAM.
INFO 2026-06-08 07:36:38 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 2s. Last read position: chr19:57,284,654
INFO 2026-06-08 07:36:38 MarkDuplicates Tracking 18611 as yet unmatched pairs. 339 records in RAM.
INFO 2026-06-08 07:36:40 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 2s. Last read position: chr20:45,947,372
INFO 2026-06-08 07:36:40 MarkDuplicates Tracking 16105 as yet unmatched pairs. 1781 records in RAM.
INFO 2026-06-08 07:36:43 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 2s. Last read position: chr21:8,397,772
INFO 2026-06-08 07:36:43 MarkDuplicates Tracking 14034 as yet unmatched pairs. 2254 records in RAM.
INFO 2026-06-08 07:36:45 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 2s. Last read position: chr21:46,228,447
INFO 2026-06-08 07:36:45 MarkDuplicates Tracking 11899 as yet unmatched pairs. 115 records in RAM.
INFO 2026-06-08 07:36:47 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 2s. Last read position: chr22:37,374,856
INFO 2026-06-08 07:36:47 MarkDuplicates Tracking 9256 as yet unmatched pairs. 3713 records in RAM.
INFO 2026-06-08 07:36:49 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 2s. Last read position: chr22:42,693,437
INFO 2026-06-08 07:36:49 MarkDuplicates Tracking 6807 as yet unmatched pairs. 1264 records in RAM.
INFO 2026-06-08 07:36:52 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 2s. Last read position: chrX:53,234,612
INFO 2026-06-08 07:36:52 MarkDuplicates Tracking 4068 as yet unmatched pairs. 2453 records in RAM.
INFO 2026-06-08 07:36:54 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 2s. Last read position: chrX:154,465,721
INFO 2026-06-08 07:36:54 MarkDuplicates Tracking 1687 as yet unmatched pairs. 71 records in RAM.
INFO 2026-06-08 07:36:56 MarkDuplicates Read 73785272 records. 0 pairs never matched.
INFO 2026-06-08 07:37:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 25362889960; totalMemory: 36238786560; maxMemory: 63585648640
INFO 2026-06-08 07:37:02 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 07:37:09 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 07:37:18 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 07:37:24 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 07:37:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 30321561704; totalMemory: 46271561728; maxMemory: 63585648640
INFO 2026-06-08 07:37:25 MarkDuplicates Marking 17514885 records as duplicates.
INFO 2026-06-08 07:37:25 MarkDuplicates Found 714194 optical duplicate clusters.
INFO 2026-06-08 07:37:25 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 07:37:51 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:25s. Time for last 10,000,000: 25s. Last read position: chr2:130,172,387
INFO 2026-06-08 07:38:17 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:52s. Time for last 10,000,000: 26s. Last read position: chr5:151,567,377
INFO 2026-06-08 07:38:43 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:18s. Time for last 10,000,000: 25s. Last read position: chr8:143,858,200
INFO 2026-06-08 07:39:08 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:42s. Time for last 10,000,000: 24s. Last read position: chr11:119,335,608
INFO 2026-06-08 07:39:32 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:02:06s. Time for last 10,000,000: 24s. Last read position: chr16:3,850,887
INFO 2026-06-08 07:39:55 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:30s. Time for last 10,000,000: 23s. Last read position: chr17:81,868,506
INFO 2026-06-08 07:40:20 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:55s. Time for last 10,000,000: 24s. Last read position: chr22:37,374,856
INFO 2026-06-08 07:40:31 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 07:40:31 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 07:40:31 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 07:40:31 MarkDuplicates Before output close freeMemory: 204007592; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 07:40:31 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 07:40:31 MarkDuplicates After output close freeMemory: 104346272; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 07:40:31 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 6.62 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory