Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/efedf9c256727b30ecd682c62a130f/aih-tih-sc-24ecfe-R1_A23YTGFLT4_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/0e/e73622620af9fd165283c621bbd739/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/e73622620af9fd165283c621bbd739/.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-24ecfe-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bam --METRICS_FILE aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:34:52.863 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 07:34:52 GMT 2026] MarkDuplicates --INPUT aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.md.bam --METRICS_FILE aih-tih-sc-24ecfe-R1_A23YTGFLT4_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 07:34:52 GMT 2026] Executing as ?@nf-0ee73622620af9fd165283c621bbd739-bd3da-q7mch 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 07:34:52 MarkDuplicates Start of doWork freeMemory: 105853016; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:34:52 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:34:52 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:34:59 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 4s. Last read position: chr1:20,661,311
INFO 2026-06-08 07:34:59 MarkDuplicates Tracking 1816 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 07:35:02 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 3s. Last read position: chr1:35,883,358
INFO 2026-06-08 07:35:02 MarkDuplicates Tracking 3597 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 07:35:05 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 3s. Last read position: chr1:112,525,377
INFO 2026-06-08 07:35:05 MarkDuplicates Tracking 5328 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 07:35:08 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 3s. Last read position: chr1:155,060,725
INFO 2026-06-08 07:35:08 MarkDuplicates Tracking 6600 as yet unmatched pairs. 12 records in RAM.
INFO 2026-06-08 07:35:12 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 3s. Last read position: chr1:201,817,087
INFO 2026-06-08 07:35:12 MarkDuplicates Tracking 8154 as yet unmatched pairs. 0 records in RAM.
INFO 2026-06-08 07:35:15 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 3s. Last read position: chr2:17,931,676
INFO 2026-06-08 07:35:15 MarkDuplicates Tracking 9829 as yet unmatched pairs. 9785 records in RAM.
INFO 2026-06-08 07:35:18 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 2s. Last read position: chr2:47,005,991
INFO 2026-06-08 07:35:18 MarkDuplicates Tracking 103929 as yet unmatched pairs. 5686 records in RAM.
INFO 2026-06-08 07:35:20 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 2s. Last read position: chr2:108,534,554
INFO 2026-06-08 07:35:20 MarkDuplicates Tracking 102471 as yet unmatched pairs. 4225 records in RAM.
INFO 2026-06-08 07:35:22 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 2s. Last read position: chr2:190,999,626
INFO 2026-06-08 07:35:22 MarkDuplicates Tracking 101021 as yet unmatched pairs. 2767 records in RAM.
INFO 2026-06-08 07:35:26 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 3s. Last read position: chr2:219,418,482
INFO 2026-06-08 07:35:26 MarkDuplicates Tracking 99768 as yet unmatched pairs. 1512 records in RAM.
INFO 2026-06-08 07:35:31 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 5s. Last read position: chr3:12,901,128
INFO 2026-06-08 07:35:31 MarkDuplicates Tracking 97977 as yet unmatched pairs. 3975 records in RAM.
INFO 2026-06-08 07:35:33 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 1s. Last read position: chr3:52,516,735
INFO 2026-06-08 07:35:33 MarkDuplicates Tracking 96250 as yet unmatched pairs. 2241 records in RAM.
INFO 2026-06-08 07:35:36 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 2s. Last read position: chr3:170,129,354
INFO 2026-06-08 07:35:36 MarkDuplicates Tracking 94660 as yet unmatched pairs. 636 records in RAM.
INFO 2026-06-08 07:35:40 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 4s. Last read position: chr4:10,098,990
INFO 2026-06-08 07:35:40 MarkDuplicates Tracking 93332 as yet unmatched pairs. 1891 records in RAM.
INFO 2026-06-08 07:35:44 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 3s. Last read position: chr4:154,540,889
INFO 2026-06-08 07:35:44 MarkDuplicates Tracking 91851 as yet unmatched pairs. 401 records in RAM.
INFO 2026-06-08 07:35:47 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 3s. Last read position: chr5:122,775,099
INFO 2026-06-08 07:35:47 MarkDuplicates Tracking 90278 as yet unmatched pairs. 2955 records in RAM.
INFO 2026-06-08 07:35:51 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 3s. Last read position: chr5:150,407,152
INFO 2026-06-08 07:35:51 MarkDuplicates Tracking 89207 as yet unmatched pairs. 1807 records in RAM.
INFO 2026-06-08 07:35:54 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 2s. Last read position: chr6:495,294
INFO 2026-06-08 07:35:54 MarkDuplicates Tracking 87400 as yet unmatched pairs. 5036 records in RAM.
INFO 2026-06-08 07:35:56 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 2s. Last read position: chr6:31,645,003
INFO 2026-06-08 07:35:56 MarkDuplicates Tracking 85948 as yet unmatched pairs. 3579 records in RAM.
INFO 2026-06-08 07:35:59 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 2s. Last read position: chr6:43,051,419
INFO 2026-06-08 07:35:59 MarkDuplicates Tracking 84432 as yet unmatched pairs. 2063 records in RAM.
INFO 2026-06-08 07:36:02 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 2s. Last read position: chr6:152,352,241
INFO 2026-06-08 07:36:02 MarkDuplicates Tracking 82909 as yet unmatched pairs. 532 records in RAM.
INFO 2026-06-08 07:36:05 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 3s. Last read position: chr7:6,501,816
INFO 2026-06-08 07:36:05 MarkDuplicates Tracking 81231 as yet unmatched pairs. 4907 records in RAM.
INFO 2026-06-08 07:36:08 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 2s. Last read position: chr7:76,048,144
INFO 2026-06-08 07:36:08 MarkDuplicates Tracking 80025 as yet unmatched pairs. 3698 records in RAM.
INFO 2026-06-08 07:36:12 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 3s. Last read position: chr7:100,994,326
INFO 2026-06-08 07:36:12 MarkDuplicates Tracking 78469 as yet unmatched pairs. 2139 records in RAM.
INFO 2026-06-08 07:36:14 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 2s. Last read position: chr7:102,642,629
INFO 2026-06-08 07:36:14 MarkDuplicates Tracking 77950 as yet unmatched pairs. 1620 records in RAM.
INFO 2026-06-08 07:36:17 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 3s. Last read position: chr7:151,079,853
INFO 2026-06-08 07:36:17 MarkDuplicates Tracking 76598 as yet unmatched pairs. 257 records in RAM.
INFO 2026-06-08 07:36:21 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 3s. Last read position: chr8:64,580,836
INFO 2026-06-08 07:36:21 MarkDuplicates Tracking 74989 as yet unmatched pairs. 2435 records in RAM.
INFO 2026-06-08 07:36:24 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 3s. Last read position: chr8:143,862,590
INFO 2026-06-08 07:36:24 MarkDuplicates Tracking 73636 as yet unmatched pairs. 1072 records in RAM.
INFO 2026-06-08 07:36:27 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 2s. Last read position: chr9:32,550,876
INFO 2026-06-08 07:36:27 MarkDuplicates Tracking 72250 as yet unmatched pairs. 3446 records in RAM.
INFO 2026-06-08 07:36:31 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 3s. Last read position: chr9:115,086,604
INFO 2026-06-08 07:36:31 MarkDuplicates Tracking 70808 as yet unmatched pairs. 1996 records in RAM.
INFO 2026-06-08 07:36:34 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 2s. Last read position: chr9:136,497,027
INFO 2026-06-08 07:36:34 MarkDuplicates Tracking 69223 as yet unmatched pairs. 407 records in RAM.
INFO 2026-06-08 07:36:37 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 3s. Last read position: chr10:69,415,941
INFO 2026-06-08 07:36:37 MarkDuplicates Tracking 67889 as yet unmatched pairs. 1615 records in RAM.
INFO 2026-06-08 07:36:40 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 3s. Last read position: chr10:119,651,679
INFO 2026-06-08 07:36:40 MarkDuplicates Tracking 66569 as yet unmatched pairs. 287 records in RAM.
INFO 2026-06-08 07:36:43 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 2s. Last read position: chr11:2,928,915
INFO 2026-06-08 07:36:43 MarkDuplicates Tracking 65005 as yet unmatched pairs. 5410 records in RAM.
INFO 2026-06-08 07:36:47 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 3s. Last read position: chr11:62,519,717
INFO 2026-06-08 07:36:47 MarkDuplicates Tracking 63454 as yet unmatched pairs. 3850 records in RAM.
INFO 2026-06-08 07:36:50 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 2s. Last read position: chr11:66,599,243
INFO 2026-06-08 07:36:50 MarkDuplicates Tracking 61799 as yet unmatched pairs. 2194 records in RAM.
INFO 2026-06-08 07:36:52 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 2s. Last read position: chr11:114,254,573
INFO 2026-06-08 07:36:52 MarkDuplicates Tracking 60267 as yet unmatched pairs. 659 records in RAM.
INFO 2026-06-08 07:36:55 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 3s. Last read position: chr12:7,921,550
INFO 2026-06-08 07:36:55 MarkDuplicates Tracking 58830 as yet unmatched pairs. 4235 records in RAM.
INFO 2026-06-08 07:36:59 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 3s. Last read position: chr12:54,283,815
INFO 2026-06-08 07:36:59 MarkDuplicates Tracking 57490 as yet unmatched pairs. 2893 records in RAM.
INFO 2026-06-08 07:37:02 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 2s. Last read position: chr12:108,591,851
INFO 2026-06-08 07:37:02 MarkDuplicates Tracking 56195 as yet unmatched pairs. 1598 records in RAM.
INFO 2026-06-08 07:37:04 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 2s. Last read position: chr13:20,002,894
INFO 2026-06-08 07:37:04 MarkDuplicates Tracking 54569 as yet unmatched pairs. 1349 records in RAM.
INFO 2026-06-08 07:37:07 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 2s. Last read position: chr14:22,998,445
INFO 2026-06-08 07:37:07 MarkDuplicates Tracking 53045 as yet unmatched pairs. 4566 records in RAM.
INFO 2026-06-08 07:37:10 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 2s. Last read position: chr14:77,025,941
INFO 2026-06-08 07:37:10 MarkDuplicates Tracking 51582 as yet unmatched pairs. 3099 records in RAM.
INFO 2026-06-08 07:37:13 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 2s. Last read position: chr14:105,643,216
INFO 2026-06-08 07:37:13 MarkDuplicates Tracking 50220 as yet unmatched pairs. 1726 records in RAM.
INFO 2026-06-08 07:37:16 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 3s. Last read position: chr14:105,742,074
INFO 2026-06-08 07:37:16 MarkDuplicates Tracking 49302 as yet unmatched pairs. 807 records in RAM.
INFO 2026-06-08 07:37:19 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 3s. Last read position: chr15:39,581,196
INFO 2026-06-08 07:37:19 MarkDuplicates Tracking 48135 as yet unmatched pairs. 2607 records in RAM.
INFO 2026-06-08 07:37:23 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 3s. Last read position: chr15:75,208,378
INFO 2026-06-08 07:37:23 MarkDuplicates Tracking 46622 as yet unmatched pairs. 1091 records in RAM.
INFO 2026-06-08 07:37:27 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 3s. Last read position: chr16:1,777,287
INFO 2026-06-08 07:37:27 MarkDuplicates Tracking 44906 as yet unmatched pairs. 6348 records in RAM.
INFO 2026-06-08 07:37:29 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 2s. Last read position: chr16:15,718,349
INFO 2026-06-08 07:37:29 MarkDuplicates Tracking 43353 as yet unmatched pairs. 4792 records in RAM.
INFO 2026-06-08 07:37:32 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 3s. Last read position: chr16:21,834,866
INFO 2026-06-08 07:37:32 MarkDuplicates Tracking 42195 as yet unmatched pairs. 3634 records in RAM.
INFO 2026-06-08 07:37:35 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 3s. Last read position: chr16:30,729,063
INFO 2026-06-08 07:37:35 MarkDuplicates Tracking 41176 as yet unmatched pairs. 2613 records in RAM.
INFO 2026-06-08 07:37:38 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 3s. Last read position: chr16:79,599,116
INFO 2026-06-08 07:37:38 MarkDuplicates Tracking 39513 as yet unmatched pairs. 948 records in RAM.
INFO 2026-06-08 07:37:41 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 3s. Last read position: chr17:7,015,082
INFO 2026-06-08 07:37:41 MarkDuplicates Tracking 37873 as yet unmatched pairs. 11902 records in RAM.
INFO 2026-06-08 07:37:45 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 3s. Last read position: chr17:35,441,773
INFO 2026-06-08 07:37:45 MarkDuplicates Tracking 36580 as yet unmatched pairs. 10605 records in RAM.
INFO 2026-06-08 07:37:49 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 3s. Last read position: chr17:48,058,939
INFO 2026-06-08 07:37:49 MarkDuplicates Tracking 34825 as yet unmatched pairs. 8849 records in RAM.
INFO 2026-06-08 07:37:53 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 4s. Last read position: chr17:50,189,266
INFO 2026-06-08 07:37:53 MarkDuplicates Tracking 33604 as yet unmatched pairs. 7628 records in RAM.
INFO 2026-06-08 07:37:56 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 3s. Last read position: chr17:50,192,796
INFO 2026-06-08 07:37:56 MarkDuplicates Tracking 31725 as yet unmatched pairs. 5749 records in RAM.
INFO 2026-06-08 07:38:00 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 3s. Last read position: chr17:50,196,185
INFO 2026-06-08 07:38:00 MarkDuplicates Tracking 30474 as yet unmatched pairs. 4497 records in RAM.
INFO 2026-06-08 07:38:04 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 3s. Last read position: chr17:63,681,782
INFO 2026-06-08 07:38:04 MarkDuplicates Tracking 28127 as yet unmatched pairs. 2149 records in RAM.
INFO 2026-06-08 07:38:06 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 2s. Last read position: chr17:81,846,475
INFO 2026-06-08 07:38:06 MarkDuplicates Tracking 26446 as yet unmatched pairs. 463 records in RAM.
INFO 2026-06-08 07:38:10 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 3s. Last read position: chr19:1,272,088
INFO 2026-06-08 07:38:10 MarkDuplicates Tracking 24638 as yet unmatched pairs. 8662 records in RAM.
INFO 2026-06-08 07:38:13 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 3s. Last read position: chr19:10,713,167
INFO 2026-06-08 07:38:13 MarkDuplicates Tracking 23032 as yet unmatched pairs. 7056 records in RAM.
INFO 2026-06-08 07:38:17 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 3s. Last read position: chr19:18,427,775
INFO 2026-06-08 07:38:17 MarkDuplicates Tracking 21319 as yet unmatched pairs. 5339 records in RAM.
INFO 2026-06-08 07:38:20 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 3s. Last read position: chr19:39,913,812
INFO 2026-06-08 07:38:20 MarkDuplicates Tracking 19476 as yet unmatched pairs. 3494 records in RAM.
INFO 2026-06-08 07:38:23 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 2s. Last read position: chr19:47,745,724
INFO 2026-06-08 07:38:23 MarkDuplicates Tracking 17856 as yet unmatched pairs. 1857 records in RAM.
INFO 2026-06-08 07:38:27 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 3s. Last read position: chr19:57,280,724
INFO 2026-06-08 07:38:27 MarkDuplicates Tracking 16185 as yet unmatched pairs. 185 records in RAM.
INFO 2026-06-08 07:38:31 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 4s. Last read position: chr20:43,460,774
INFO 2026-06-08 07:38:31 MarkDuplicates Tracking 14513 as yet unmatched pairs. 1652 records in RAM.
INFO 2026-06-08 07:38:34 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 3s. Last read position: chr21:5,163,565
INFO 2026-06-08 07:38:34 MarkDuplicates Tracking 12837 as yet unmatched pairs. 3419 records in RAM.
INFO 2026-06-08 07:38:36 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 2s. Last read position: chr21:8,397,739
INFO 2026-06-08 07:38:36 MarkDuplicates Tracking 12108 as yet unmatched pairs. 2683 records in RAM.
INFO 2026-06-08 07:38:39 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 2s. Last read position: chr21:8,444,618
INFO 2026-06-08 07:38:39 MarkDuplicates Tracking 10900 as yet unmatched pairs. 1469 records in RAM.
INFO 2026-06-08 07:38:43 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 4s. Last read position: chr22:18,517,172
INFO 2026-06-08 07:38:43 MarkDuplicates Tracking 9334 as yet unmatched pairs. 3416 records in RAM.
INFO 2026-06-08 07:38:46 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 3s. Last read position: chr22:37,128,650
INFO 2026-06-08 07:38:46 MarkDuplicates Tracking 7802 as yet unmatched pairs. 1884 records in RAM.
INFO 2026-06-08 07:38:49 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 3s. Last read position: chrX:9,684,079
INFO 2026-06-08 07:38:49 MarkDuplicates Tracking 5755 as yet unmatched pairs. 2735 records in RAM.
INFO 2026-06-08 07:38:52 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 2s. Last read position: chrX:136,207,097
INFO 2026-06-08 07:38:52 MarkDuplicates Tracking 4409 as yet unmatched pairs. 1367 records in RAM.
INFO 2026-06-08 07:38:56 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 3s. Last read position: GL000220.1:114,146
INFO 2026-06-08 07:38:56 MarkDuplicates Tracking 2948 as yet unmatched pairs. 447 records in RAM.
INFO 2026-06-08 07:38:58 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 2s. Last read position: GL000220.1:160,719
INFO 2026-06-08 07:38:58 MarkDuplicates Tracking 2501 as yet unmatched pairs. 0 records in RAM.
INFO 2026-06-08 07:39:01 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 2s. Last read position: KI270733.1:177,463
INFO 2026-06-08 07:39:01 MarkDuplicates Tracking 43 as yet unmatched pairs. 40 records in RAM.
INFO 2026-06-08 07:39:01 MarkDuplicates Read 77300804 records. 0 pairs never matched.
INFO 2026-06-08 07:39:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 25245810736; totalMemory: 36037459968; maxMemory: 63585648640
INFO 2026-06-08 07:39:08 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 07:39:19 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 07:39:46 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 07:39:57 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 07:40:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 34683611624; totalMemory: 50633637888; maxMemory: 63585648640
INFO 2026-06-08 07:40:00 MarkDuplicates Marking 51558360 records as duplicates.
INFO 2026-06-08 07:40:00 MarkDuplicates Found 929911 optical duplicate clusters.
INFO 2026-06-08 07:40:00 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 07:40:33 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:32s. Time for last 10,000,000: 32s. Last read position: chr2:219,418,482
INFO 2026-06-08 07:41:04 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:01:03s. Time for last 10,000,000: 30s. Last read position: chr6:43,051,419
INFO 2026-06-08 07:41:33 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:32s. Time for last 10,000,000: 29s. Last read position: chr9:115,086,604
INFO 2026-06-08 07:42:02 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:02:01s. Time for last 10,000,000: 28s. Last read position: chr12:108,591,851
INFO 2026-06-08 07:42:30 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:02:29s. Time for last 10,000,000: 28s. Last read position: chr16:21,834,866
INFO 2026-06-08 07:42:59 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:58s. Time for last 10,000,000: 28s. Last read position: chr17:81,846,475
INFO 2026-06-08 07:43:26 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:03:26s. Time for last 10,000,000: 27s. Last read position: chr21:8,444,618
INFO 2026-06-08 07:43:51 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 07:43:51 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 07:43:51 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 07:43:51 MarkDuplicates Before output close freeMemory: 202610368; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 07:43:51 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 07:43:51 MarkDuplicates After output close freeMemory: 104321704; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 07:43:51 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 8.98 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory