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/2c/725ca26c9065ea5a9d255d74c336fe/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/725ca26c9065ea5a9d255d74c336fe/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/708828745aa92ea96e9a7231bb51c7/tih_rna_sample_00105_23H5VFLT4_s21.Aligned.sortedByCoord.out.bam
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 tih_rna_sample_00105_23H5VFLT4_s21.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00105_23H5VFLT4_s21.md.bam --METRICS_FILE tih_rna_sample_00105_23H5VFLT4_s21.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:29:00.400 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 07:29:00 GMT 2026] MarkDuplicates --INPUT tih_rna_sample_00105_23H5VFLT4_s21.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00105_23H5VFLT4_s21.md.bam --METRICS_FILE tih_rna_sample_00105_23H5VFLT4_s21.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 07:29:00 GMT 2026] Executing as ?@nf-2c725ca26c9065ea5a9d255d74c336fe-8da3f-bbswl 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 07:29:00 MarkDuplicates Start of doWork freeMemory: 105829416; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:29:00 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:29:00 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:29:05 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:12,308,674
INFO 2026-06-08 07:29:05 MarkDuplicates Tracking 699 as yet unmatched pairs. 8 records in RAM.
INFO 2026-06-08 07:29:08 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 3s. Last read position: chr1:26,731,352
INFO 2026-06-08 07:29:08 MarkDuplicates Tracking 1246 as yet unmatched pairs. 21 records in RAM.
INFO 2026-06-08 07:29:11 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: chr1:41,070,600
INFO 2026-06-08 07:29:11 MarkDuplicates Tracking 1816 as yet unmatched pairs. 14 records in RAM.
INFO 2026-06-08 07:29:13 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 2s. Last read position: chr1:68,205,881
INFO 2026-06-08 07:29:13 MarkDuplicates Tracking 2451 as yet unmatched pairs. 3 records in RAM.
INFO 2026-06-08 07:29:16 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: chr1:114,737,973
INFO 2026-06-08 07:29:16 MarkDuplicates Tracking 3101 as yet unmatched pairs. 14 records in RAM.
INFO 2026-06-08 07:29:19 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr1:148,126,907
INFO 2026-06-08 07:29:19 MarkDuplicates Tracking 3609 as yet unmatched pairs. 5 records in RAM.
INFO 2026-06-08 07:29:21 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 2s. Last read position: chr1:151,428,236
INFO 2026-06-08 07:29:21 MarkDuplicates Tracking 4154 as yet unmatched pairs. 81 records in RAM.
INFO 2026-06-08 07:29:24 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 2s. Last read position: chr1:155,192,027
INFO 2026-06-08 07:29:24 MarkDuplicates Tracking 4873 as yet unmatched pairs. 58 records in RAM.
INFO 2026-06-08 07:29:27 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 3s. Last read position: chr1:161,042,155
INFO 2026-06-08 07:29:27 MarkDuplicates Tracking 5443 as yet unmatched pairs. 4 records in RAM.
INFO 2026-06-08 07:29:30 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 2s. Last read position: chr1:178,799,090
INFO 2026-06-08 07:29:30 MarkDuplicates Tracking 6085 as yet unmatched pairs. 21 records in RAM.
INFO 2026-06-08 07:29:32 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 2s. Last read position: chr1:203,307,369
INFO 2026-06-08 07:29:32 MarkDuplicates Tracking 6641 as yet unmatched pairs. 15 records in RAM.
INFO 2026-06-08 07:29:35 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 2s. Last read position: chr1:223,772,180
INFO 2026-06-08 07:29:35 MarkDuplicates Tracking 7216 as yet unmatched pairs. 23 records in RAM.
INFO 2026-06-08 07:29:37 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 2s. Last read position: chr1:236,898,390
INFO 2026-06-08 07:29:37 MarkDuplicates Tracking 7907 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 07:29:41 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 3s. Last read position: chr2:24,838,456
INFO 2026-06-08 07:29:41 MarkDuplicates Tracking 8492 as yet unmatched pairs. 8286 records in RAM.
INFO 2026-06-08 07:29:44 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 3s. Last read position: chr2:43,943,875
INFO 2026-06-08 07:29:44 MarkDuplicates Tracking 72334 as yet unmatched pairs. 3762 records in RAM.
INFO 2026-06-08 07:29:47 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 2s. Last read position: chr2:84,433,387
INFO 2026-06-08 07:29:47 MarkDuplicates Tracking 71740 as yet unmatched pairs. 3156 records in RAM.
INFO 2026-06-08 07:29:49 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 2s. Last read position: chr2:110,451,872
INFO 2026-06-08 07:29:49 MarkDuplicates Tracking 71307 as yet unmatched pairs. 2707 records in RAM.
INFO 2026-06-08 07:29:52 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 2s. Last read position: chr2:133,280,350
INFO 2026-06-08 07:29:52 MarkDuplicates Tracking 70896 as yet unmatched pairs. 2292 records in RAM.
INFO 2026-06-08 07:29:54 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 2s. Last read position: chr2:181,916,162
INFO 2026-06-08 07:29:54 MarkDuplicates Tracking 70378 as yet unmatched pairs. 1764 records in RAM.
INFO 2026-06-08 07:29:57 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 2s. Last read position: chr2:215,370,409
INFO 2026-06-08 07:29:57 MarkDuplicates Tracking 69940 as yet unmatched pairs. 1317 records in RAM.
INFO 2026-06-08 07:30:00 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 2s. Last read position: chr2:224,775,004
INFO 2026-06-08 07:30:00 MarkDuplicates Tracking 69218 as yet unmatched pairs. 555 records in RAM.
INFO 2026-06-08 07:30:02 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 2s. Last read position: chr3:9,442,178
INFO 2026-06-08 07:30:02 MarkDuplicates Tracking 68569 as yet unmatched pairs. 3558 records in RAM.
INFO 2026-06-08 07:30:05 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 2s. Last read position: chr3:43,691,004
INFO 2026-06-08 07:30:05 MarkDuplicates Tracking 67962 as yet unmatched pairs. 2940 records in RAM.
INFO 2026-06-08 07:30:08 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 2s. Last read position: chr3:52,399,673
INFO 2026-06-08 07:30:08 MarkDuplicates Tracking 67187 as yet unmatched pairs. 2159 records in RAM.
INFO 2026-06-08 07:30:11 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 3s. Last read position: chr3:105,524,388
INFO 2026-06-08 07:30:11 MarkDuplicates Tracking 66625 as yet unmatched pairs. 1570 records in RAM.
INFO 2026-06-08 07:30:14 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 3s. Last read position: chr3:140,007,148
INFO 2026-06-08 07:30:14 MarkDuplicates Tracking 66028 as yet unmatched pairs. 965 records in RAM.
INFO 2026-06-08 07:30:16 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 2s. Last read position: chr3:186,079,937
INFO 2026-06-08 07:30:16 MarkDuplicates Tracking 65390 as yet unmatched pairs. 321 records in RAM.
INFO 2026-06-08 07:30:19 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 2s. Last read position: chr4:8,381,539
INFO 2026-06-08 07:30:19 MarkDuplicates Tracking 64719 as yet unmatched pairs. 1383 records in RAM.
INFO 2026-06-08 07:30:21 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 2s. Last read position: chr4:83,104,938
INFO 2026-06-08 07:30:21 MarkDuplicates Tracking 64160 as yet unmatched pairs. 802 records in RAM.
INFO 2026-06-08 07:30:24 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 2s. Last read position: chr4:150,584,007
INFO 2026-06-08 07:30:24 MarkDuplicates Tracking 63720 as yet unmatched pairs. 351 records in RAM.
INFO 2026-06-08 07:30:26 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 2s. Last read position: chr5:14,369,371
INFO 2026-06-08 07:30:26 MarkDuplicates Tracking 63048 as yet unmatched pairs. 3170 records in RAM.
INFO 2026-06-08 07:30:29 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 2s. Last read position: chr5:65,060,569
INFO 2026-06-08 07:30:29 MarkDuplicates Tracking 62436 as yet unmatched pairs. 2546 records in RAM.
INFO 2026-06-08 07:30:30 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 1s. Last read position: chr5:72,195,176
INFO 2026-06-08 07:30:30 MarkDuplicates Tracking 62180 as yet unmatched pairs. 2288 records in RAM.
INFO 2026-06-08 07:30:33 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 2s. Last read position: chr5:123,595,023
INFO 2026-06-08 07:30:33 MarkDuplicates Tracking 61691 as yet unmatched pairs. 1785 records in RAM.
INFO 2026-06-08 07:30:36 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 3s. Last read position: chr5:141,123,473
INFO 2026-06-08 07:30:36 MarkDuplicates Tracking 61077 as yet unmatched pairs. 1090 records in RAM.
INFO 2026-06-08 07:30:39 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 3s. Last read position: chr5:171,405,313
INFO 2026-06-08 07:30:39 MarkDuplicates Tracking 60462 as yet unmatched pairs. 468 records in RAM.
INFO 2026-06-08 07:30:42 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 2s. Last read position: chr6:7,542,049
INFO 2026-06-08 07:30:42 MarkDuplicates Tracking 59806 as yet unmatched pairs. 3379 records in RAM.
INFO 2026-06-08 07:30:44 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 2s. Last read position: chr6:31,633,469
INFO 2026-06-08 07:30:44 MarkDuplicates Tracking 59209 as yet unmatched pairs. 2773 records in RAM.
INFO 2026-06-08 07:30:47 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 2s. Last read position: chr6:33,415,060
INFO 2026-06-08 07:30:47 MarkDuplicates Tracking 58698 as yet unmatched pairs. 2261 records in RAM.
INFO 2026-06-08 07:30:49 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 2s. Last read position: chr6:56,593,778
INFO 2026-06-08 07:30:49 MarkDuplicates Tracking 57959 as yet unmatched pairs. 1517 records in RAM.
INFO 2026-06-08 07:30:52 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 2s. Last read position: chr6:125,890,717
INFO 2026-06-08 07:30:52 MarkDuplicates Tracking 57411 as yet unmatched pairs. 947 records in RAM.
INFO 2026-06-08 07:30:54 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 2s. Last read position: chr6:158,566,132
INFO 2026-06-08 07:30:54 MarkDuplicates Tracking 56720 as yet unmatched pairs. 252 records in RAM.
INFO 2026-06-08 07:30:57 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 2s. Last read position: chr7:7,801,668
INFO 2026-06-08 07:30:57 MarkDuplicates Tracking 55948 as yet unmatched pairs. 3054 records in RAM.
INFO 2026-06-08 07:30:59 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 2s. Last read position: chr7:56,074,679
INFO 2026-06-08 07:30:59 MarkDuplicates Tracking 55403 as yet unmatched pairs. 2504 records in RAM.
INFO 2026-06-08 07:31:01 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 2s. Last read position: chr7:76,303,834
INFO 2026-06-08 07:31:01 MarkDuplicates Tracking 55098 as yet unmatched pairs. 2194 records in RAM.
INFO 2026-06-08 07:31:05 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 3s. Last read position: chr7:100,071,124
INFO 2026-06-08 07:31:05 MarkDuplicates Tracking 54481 as yet unmatched pairs. 1571 records in RAM.
INFO 2026-06-08 07:31:08 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 2s. Last read position: chr7:118,184,179
INFO 2026-06-08 07:31:08 MarkDuplicates Tracking 53851 as yet unmatched pairs. 900 records in RAM.
INFO 2026-06-08 07:31:10 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 2s. Last read position: chr7:144,365,075
INFO 2026-06-08 07:31:10 MarkDuplicates Tracking 53362 as yet unmatched pairs. 402 records in RAM.
INFO 2026-06-08 07:31:13 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 2s. Last read position: chr8:18,773,702
INFO 2026-06-08 07:31:13 MarkDuplicates Tracking 52748 as yet unmatched pairs. 3015 records in RAM.
INFO 2026-06-08 07:31:15 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 2s. Last read position: chr8:47,396,484
INFO 2026-06-08 07:31:15 MarkDuplicates Tracking 52090 as yet unmatched pairs. 2352 records in RAM.
INFO 2026-06-08 07:31:17 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 2s. Last read position: chr8:99,891,908
INFO 2026-06-08 07:31:17 MarkDuplicates Tracking 51533 as yet unmatched pairs. 1786 records in RAM.
INFO 2026-06-08 07:31:20 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 2s. Last read position: chr8:140,397,675
INFO 2026-06-08 07:31:20 MarkDuplicates Tracking 50894 as yet unmatched pairs. 1138 records in RAM.
INFO 2026-06-08 07:31:22 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 2s. Last read position: chr8:143,863,224
INFO 2026-06-08 07:31:22 MarkDuplicates Tracking 50477 as yet unmatched pairs. 711 records in RAM.
INFO 2026-06-08 07:31:24 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 2s. Last read position: chr9:21,613
INFO 2026-06-08 07:31:24 MarkDuplicates Tracking 49769 as yet unmatched pairs. 2685 records in RAM.
INFO 2026-06-08 07:31:27 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 2s. Last read position: chr9:65,699,684
INFO 2026-06-08 07:31:27 MarkDuplicates Tracking 49249 as yet unmatched pairs. 2148 records in RAM.
INFO 2026-06-08 07:31:29 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 2s. Last read position: chr9:113,390,817
INFO 2026-06-08 07:31:29 MarkDuplicates Tracking 48634 as yet unmatched pairs. 1526 records in RAM.
INFO 2026-06-08 07:31:32 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 2s. Last read position: chr9:131,475,772
INFO 2026-06-08 07:31:32 MarkDuplicates Tracking 47905 as yet unmatched pairs. 792 records in RAM.
INFO 2026-06-08 07:31:35 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 3s. Last read position: chr10:824,971
INFO 2026-06-08 07:31:35 MarkDuplicates Tracking 47089 as yet unmatched pairs. 2985 records in RAM.
INFO 2026-06-08 07:31:38 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 2s. Last read position: chr10:27,038,030
INFO 2026-06-08 07:31:38 MarkDuplicates Tracking 46451 as yet unmatched pairs. 2341 records in RAM.
INFO 2026-06-08 07:31:40 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 2s. Last read position: chr10:37,251,433
INFO 2026-06-08 07:31:40 MarkDuplicates Tracking 46061 as yet unmatched pairs. 1948 records in RAM.
INFO 2026-06-08 07:31:42 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 2s. Last read position: chr10:62,091,317
INFO 2026-06-08 07:31:42 MarkDuplicates Tracking 45557 as yet unmatched pairs. 1441 records in RAM.
INFO 2026-06-08 07:31:44 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 2s. Last read position: chr10:95,625,391
INFO 2026-06-08 07:31:44 MarkDuplicates Tracking 45066 as yet unmatched pairs. 944 records in RAM.
INFO 2026-06-08 07:31:47 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 2s. Last read position: chr10:121,551,420
INFO 2026-06-08 07:31:47 MarkDuplicates Tracking 44440 as yet unmatched pairs. 280 records in RAM.
INFO 2026-06-08 07:31:50 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 2s. Last read position: chr11:1,226,863
INFO 2026-06-08 07:31:50 MarkDuplicates Tracking 43780 as yet unmatched pairs. 5024 records in RAM.
INFO 2026-06-08 07:31:52 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 2s. Last read position: chr11:1,247,550
INFO 2026-06-08 07:31:52 MarkDuplicates Tracking 43534 as yet unmatched pairs. 4777 records in RAM.
INFO 2026-06-08 07:31:54 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 2s. Last read position: chr11:6,456,328
INFO 2026-06-08 07:31:54 MarkDuplicates Tracking 42984 as yet unmatched pairs. 4225 records in RAM.
INFO 2026-06-08 07:31:56 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 2s. Last read position: chr11:36,067,044
INFO 2026-06-08 07:31:56 MarkDuplicates Tracking 42379 as yet unmatched pairs. 3616 records in RAM.
INFO 2026-06-08 07:32:00 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 3s. Last read position: chr11:61,946,662
INFO 2026-06-08 07:32:00 MarkDuplicates Tracking 41725 as yet unmatched pairs. 2936 records in RAM.
INFO 2026-06-08 07:32:03 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 2s. Last read position: chr11:65,437,661
INFO 2026-06-08 07:32:03 MarkDuplicates Tracking 41059 as yet unmatched pairs. 2267 records in RAM.
INFO 2026-06-08 07:32:05 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 2s. Last read position: chr11:66,718,581
INFO 2026-06-08 07:32:05 MarkDuplicates Tracking 40312 as yet unmatched pairs. 1519 records in RAM.
INFO 2026-06-08 07:32:08 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 2s. Last read position: chr11:72,018,930
INFO 2026-06-08 07:32:08 MarkDuplicates Tracking 39721 as yet unmatched pairs. 901 records in RAM.
INFO 2026-06-08 07:32:10 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 2s. Last read position: chr11:110,255,612
INFO 2026-06-08 07:32:10 MarkDuplicates Tracking 39134 as yet unmatched pairs. 302 records in RAM.
INFO 2026-06-08 07:32:13 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 2s. Last read position: chr12:6,770,509
INFO 2026-06-08 07:32:13 MarkDuplicates Tracking 38536 as yet unmatched pairs. 4099 records in RAM.
INFO 2026-06-08 07:32:15 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 2s. Last read position: chr12:40,440,757
INFO 2026-06-08 07:32:15 MarkDuplicates Tracking 37885 as yet unmatched pairs. 3442 records in RAM.
INFO 2026-06-08 07:32:17 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 2s. Last read position: chr12:49,272,572
INFO 2026-06-08 07:32:17 MarkDuplicates Tracking 37204 as yet unmatched pairs. 2755 records in RAM.
INFO 2026-06-08 07:32:20 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 2s. Last read position: chr12:56,314,912
INFO 2026-06-08 07:32:20 MarkDuplicates Tracking 36529 as yet unmatched pairs. 2074 records in RAM.
INFO 2026-06-08 07:32:22 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 2s. Last read position: chr12:79,052,498
INFO 2026-06-08 07:32:22 MarkDuplicates Tracking 35935 as yet unmatched pairs. 1474 records in RAM.
INFO 2026-06-08 07:32:25 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 2s. Last read position: chr12:113,282,666
INFO 2026-06-08 07:32:25 MarkDuplicates Tracking 35303 as yet unmatched pairs. 838 records in RAM.
INFO 2026-06-08 07:32:28 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 2s. Last read position: chr12:132,570,357
INFO 2026-06-08 07:32:28 MarkDuplicates Tracking 34571 as yet unmatched pairs. 99 records in RAM.
INFO 2026-06-08 07:32:30 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 2s. Last read position: chr13:77,189,000
INFO 2026-06-08 07:32:30 MarkDuplicates Tracking 34112 as yet unmatched pairs. 299 records in RAM.
INFO 2026-06-08 07:32:32 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 2s. Last read position: chr14:24,099,046
INFO 2026-06-08 07:32:32 MarkDuplicates Tracking 33478 as yet unmatched pairs. 2744 records in RAM.
INFO 2026-06-08 07:32:34 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 2s. Last read position: chr14:49,618,954
INFO 2026-06-08 07:32:34 MarkDuplicates Tracking 32822 as yet unmatched pairs. 2082 records in RAM.
INFO 2026-06-08 07:32:37 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 2s. Last read position: chr14:68,925,662
INFO 2026-06-08 07:32:37 MarkDuplicates Tracking 32317 as yet unmatched pairs. 1573 records in RAM.
INFO 2026-06-08 07:32:39 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 2s. Last read position: chr14:94,380,980
INFO 2026-06-08 07:32:39 MarkDuplicates Tracking 31677 as yet unmatched pairs. 920 records in RAM.
INFO 2026-06-08 07:32:42 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 2s. Last read position: chr14:104,946,508
INFO 2026-06-08 07:32:42 MarkDuplicates Tracking 31008 as yet unmatched pairs. 222 records in RAM.
INFO 2026-06-08 07:32:44 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 2s. Last read position: chr15:42,350,033
INFO 2026-06-08 07:32:44 MarkDuplicates Tracking 30433 as yet unmatched pairs. 1470 records in RAM.
INFO 2026-06-08 07:32:47 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 2s. Last read position: chr15:66,501,803
INFO 2026-06-08 07:32:47 MarkDuplicates Tracking 29816 as yet unmatched pairs. 851 records in RAM.
INFO 2026-06-08 07:32:49 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 2s. Last read position: chr15:90,221,046
INFO 2026-06-08 07:32:49 MarkDuplicates Tracking 29175 as yet unmatched pairs. 188 records in RAM.
INFO 2026-06-08 07:32:52 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 2s. Last read position: chr16:1,964,449
INFO 2026-06-08 07:32:52 MarkDuplicates Tracking 28405 as yet unmatched pairs. 4441 records in RAM.
INFO 2026-06-08 07:32:54 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 2s. Last read position: chr16:3,850,928
INFO 2026-06-08 07:32:54 MarkDuplicates Tracking 27701 as yet unmatched pairs. 3737 records in RAM.
INFO 2026-06-08 07:32:56 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 2s. Last read position: chr16:15,612,664
INFO 2026-06-08 07:32:56 MarkDuplicates Tracking 27207 as yet unmatched pairs. 3239 records in RAM.
INFO 2026-06-08 07:32:58 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 1s. Last read position: chr16:21,402,515
INFO 2026-06-08 07:32:58 MarkDuplicates Tracking 26850 as yet unmatched pairs. 2881 records in RAM.
INFO 2026-06-08 07:33:00 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 1s. Last read position: chr16:22,485,165
INFO 2026-06-08 07:33:00 MarkDuplicates Tracking 26670 as yet unmatched pairs. 2701 records in RAM.
INFO 2026-06-08 07:33:02 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 2s. Last read position: chr16:28,836,427
INFO 2026-06-08 07:33:02 MarkDuplicates Tracking 26344 as yet unmatched pairs. 2374 records in RAM.
INFO 2026-06-08 07:33:04 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 2s. Last read position: chr16:30,224,625
INFO 2026-06-08 07:33:04 MarkDuplicates Tracking 25898 as yet unmatched pairs. 1928 records in RAM.
INFO 2026-06-08 07:33:06 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 1s. Last read position: chr16:52,448,865
INFO 2026-06-08 07:33:06 MarkDuplicates Tracking 25330 as yet unmatched pairs. 1358 records in RAM.
INFO 2026-06-08 07:33:09 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 2s. Last read position: chr16:74,474,612
INFO 2026-06-08 07:33:09 MarkDuplicates Tracking 24558 as yet unmatched pairs. 582 records in RAM.
INFO 2026-06-08 07:33:11 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 2s. Last read position: chr17:2,329,344
INFO 2026-06-08 07:33:11 MarkDuplicates Tracking 23783 as yet unmatched pairs. 5059 records in RAM.
INFO 2026-06-08 07:33:14 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:04:12s. Time for last 1,000,000: 2s. Last read position: chr17:17,794,521
INFO 2026-06-08 07:33:14 MarkDuplicates Tracking 23089 as yet unmatched pairs. 4361 records in RAM.
INFO 2026-06-08 07:33:16 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 2s. Last read position: chr17:36,378,073
INFO 2026-06-08 07:33:16 MarkDuplicates Tracking 22442 as yet unmatched pairs. 3709 records in RAM.
INFO 2026-06-08 07:33:19 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 2s. Last read position: chr17:43,000,070
INFO 2026-06-08 07:33:19 MarkDuplicates Tracking 21822 as yet unmatched pairs. 3088 records in RAM.
INFO 2026-06-08 07:33:21 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 2s. Last read position: chr17:50,186,879
INFO 2026-06-08 07:33:21 MarkDuplicates Tracking 21399 as yet unmatched pairs. 2665 records in RAM.
INFO 2026-06-08 07:33:24 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 2s. Last read position: chr17:51,006,160
INFO 2026-06-08 07:33:24 MarkDuplicates Tracking 20419 as yet unmatched pairs. 1685 records in RAM.
INFO 2026-06-08 07:33:26 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 2s. Last read position: chr17:73,170,225
INFO 2026-06-08 07:33:26 MarkDuplicates Tracking 19707 as yet unmatched pairs. 970 records in RAM.
INFO 2026-06-08 07:33:29 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 2s. Last read position: chr17:81,511,092
INFO 2026-06-08 07:33:29 MarkDuplicates Tracking 19001 as yet unmatched pairs. 251 records in RAM.
INFO 2026-06-08 07:33:31 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 2s. Last read position: chr18:23,576,067
INFO 2026-06-08 07:33:31 MarkDuplicates Tracking 18406 as yet unmatched pairs. 797 records in RAM.
INFO 2026-06-08 07:33:33 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 2s. Last read position: chr18:75,459,122
INFO 2026-06-08 07:33:33 MarkDuplicates Tracking 17712 as yet unmatched pairs. 96 records in RAM.
INFO 2026-06-08 07:33:36 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 2s. Last read position: chr19:4,486,004
INFO 2026-06-08 07:33:36 MarkDuplicates Tracking 16862 as yet unmatched pairs. 5857 records in RAM.
INFO 2026-06-08 07:33:39 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 3s. Last read position: chr19:10,987,693
INFO 2026-06-08 07:33:39 MarkDuplicates Tracking 16170 as yet unmatched pairs. 5162 records in RAM.
INFO 2026-06-08 07:33:42 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 2s. Last read position: chr19:16,525,488
INFO 2026-06-08 07:33:42 MarkDuplicates Tracking 15388 as yet unmatched pairs. 4378 records in RAM.
INFO 2026-06-08 07:33:44 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 2s. Last read position: chr19:35,000,401
INFO 2026-06-08 07:33:44 MarkDuplicates Tracking 14680 as yet unmatched pairs. 3666 records in RAM.
INFO 2026-06-08 07:33:47 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:04:44s. Time for last 1,000,000: 2s. Last read position: chr19:40,801,717
INFO 2026-06-08 07:33:47 MarkDuplicates Tracking 13924 as yet unmatched pairs. 2909 records in RAM.
INFO 2026-06-08 07:33:49 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 2s. Last read position: chr19:45,626,803
INFO 2026-06-08 07:33:49 MarkDuplicates Tracking 13196 as yet unmatched pairs. 2152 records in RAM.
INFO 2026-06-08 07:33:52 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 2s. Last read position: chr19:49,616,154
INFO 2026-06-08 07:33:52 MarkDuplicates Tracking 12428 as yet unmatched pairs. 1384 records in RAM.
INFO 2026-06-08 07:33:54 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 2s. Last read position: chr19:55,517,221
INFO 2026-06-08 07:33:54 MarkDuplicates Tracking 11709 as yet unmatched pairs. 663 records in RAM.
INFO 2026-06-08 07:33:57 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 2s. Last read position: chr20:2,964,872
INFO 2026-06-08 07:33:57 MarkDuplicates Tracking 10892 as yet unmatched pairs. 2019 records in RAM.
INFO 2026-06-08 07:33:59 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 2s. Last read position: chr20:34,096,777
INFO 2026-06-08 07:33:59 MarkDuplicates Tracking 10287 as yet unmatched pairs. 1409 records in RAM.
INFO 2026-06-08 07:34:02 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 2s. Last read position: chr20:46,733,767
INFO 2026-06-08 07:34:02 MarkDuplicates Tracking 9641 as yet unmatched pairs. 762 records in RAM.
INFO 2026-06-08 07:34:05 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 2s. Last read position: chr20:63,521,311
INFO 2026-06-08 07:34:05 MarkDuplicates Tracking 9110 as yet unmatched pairs. 226 records in RAM.
INFO 2026-06-08 07:34:08 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 2s. Last read position: chr21:8,216,876
INFO 2026-06-08 07:34:08 MarkDuplicates Tracking 8407 as yet unmatched pairs. 2581 records in RAM.
INFO 2026-06-08 07:34:09 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 1s. Last read position: chr21:8,397,566
INFO 2026-06-08 07:34:09 MarkDuplicates Tracking 8025 as yet unmatched pairs. 2199 records in RAM.
INFO 2026-06-08 07:34:11 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr21:8,441,962
INFO 2026-06-08 07:34:11 MarkDuplicates Tracking 6987 as yet unmatched pairs. 1154 records in RAM.
INFO 2026-06-08 07:34:13 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 1s. Last read position: chr21:29,436,172
INFO 2026-06-08 07:34:13 MarkDuplicates Tracking 6664 as yet unmatched pairs. 827 records in RAM.
INFO 2026-06-08 07:34:15 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 1s. Last read position: chr21:46,275,206
INFO 2026-06-08 07:34:15 MarkDuplicates Tracking 5911 as yet unmatched pairs. 72 records in RAM.
INFO 2026-06-08 07:34:17 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 2s. Last read position: chr22:29,558,891
INFO 2026-06-08 07:34:17 MarkDuplicates Tracking 5196 as yet unmatched pairs. 1249 records in RAM.
INFO 2026-06-08 07:34:20 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 2s. Last read position: chr22:42,086,162
INFO 2026-06-08 07:34:20 MarkDuplicates Tracking 4554 as yet unmatched pairs. 606 records in RAM.
INFO 2026-06-08 07:34:21 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 1s. Last read position: chrX:12,975,120
INFO 2026-06-08 07:34:21 MarkDuplicates Tracking 3841 as yet unmatched pairs. 1371 records in RAM.
INFO 2026-06-08 07:34:24 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 2s. Last read position: chrX:69,387,453
INFO 2026-06-08 07:34:24 MarkDuplicates Tracking 3292 as yet unmatched pairs. 801 records in RAM.
INFO 2026-06-08 07:34:26 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 2s. Last read position: chrX:141,178,600
INFO 2026-06-08 07:34:26 MarkDuplicates Tracking 2746 as yet unmatched pairs. 254 records in RAM.
INFO 2026-06-08 07:34:27 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:05:25s. Time for last 1,000,000: 1s. Last read position: GL000220.1:112,749
INFO 2026-06-08 07:34:27 MarkDuplicates Tracking 2263 as yet unmatched pairs. 281 records in RAM.
INFO 2026-06-08 07:34:29 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 1s. Last read position: GL000220.1:155,927
INFO 2026-06-08 07:34:29 MarkDuplicates Tracking 2020 as yet unmatched pairs. 36 records in RAM.
INFO 2026-06-08 07:34:30 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 1s. Last read position: KI270727.1:189,546
INFO 2026-06-08 07:34:30 MarkDuplicates Tracking 1946 as yet unmatched pairs. 0 records in RAM.
INFO 2026-06-08 07:34:32 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 2s. Last read position: KI270733.1:134,305
INFO 2026-06-08 07:34:32 MarkDuplicates Tracking 343 as yet unmatched pairs. 335 records in RAM.
INFO 2026-06-08 07:34:33 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 1s. Last read position: KI270733.1:178,802
INFO 2026-06-08 07:34:33 MarkDuplicates Tracking 9 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 07:34:33 MarkDuplicates Read 134078666 records. 0 pairs never matched.
INFO 2026-06-08 07:34:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 32540364600; totalMemory: 48016392192; maxMemory: 63585648640
INFO 2026-06-08 07:34:38 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 07:34:40 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 07:34:48 OpticalDuplicateFinder Large duplicate set. size = 1281
INFO 2026-06-08 07:34:48 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,806
INFO 2026-06-08 07:34:48 OpticalDuplicateFinder Large duplicate set. size = 1438
INFO 2026-06-08 07:34:48 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:26,694
INFO 2026-06-08 07:35:00 OpticalDuplicateFinder Large duplicate set. size = 2059
INFO 2026-06-08 07:35:00 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,740
INFO 2026-06-08 07:35:00 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:24,817
INFO 2026-06-08 07:35:00 OpticalDuplicateFinder Large duplicate set. size = 1595
INFO 2026-06-08 07:35:00 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-25,874
INFO 2026-06-08 07:35:00 OpticalDuplicateFinder Large duplicate set. size = 1474
INFO 2026-06-08 07:35:00 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,962
INFO 2026-06-08 07:35:00 OpticalDuplicateFinder Large duplicate set. size = 1509
INFO 2026-06-08 07:35:00 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,145
INFO 2026-06-08 07:35:01 OpticalDuplicateFinder Large duplicate set. size = 1492
INFO 2026-06-08 07:35:01 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,923
INFO 2026-06-08 07:35:01 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 07:35:12 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 07:35:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300851512; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-08 07:35:16 MarkDuplicates Marking 71271093 records as duplicates.
INFO 2026-06-08 07:35:16 MarkDuplicates Found 2706736 optical duplicate clusters.
INFO 2026-06-08 07:35:16 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 07:35:42 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:25s. Time for last 10,000,000: 25s. Last read position: chr1:178,799,090
INFO 2026-06-08 07:36:06 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:50s. Time for last 10,000,000: 24s. Last read position: chr2:215,370,409
INFO 2026-06-08 07:36:30 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:14s. Time for last 10,000,000: 24s. Last read position: chr4:150,584,007
INFO 2026-06-08 07:36:55 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:38s. Time for last 10,000,000: 24s. Last read position: chr6:56,593,778
INFO 2026-06-08 07:37:19 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:02:02s. Time for last 10,000,000: 24s. Last read position: chr8:47,396,484
INFO 2026-06-08 07:37:45 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:28s. Time for last 10,000,000: 26s. Last read position: chr10:37,251,433
INFO 2026-06-08 07:38:09 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:53s. Time for last 10,000,000: 24s. Last read position: chr11:66,718,581
INFO 2026-06-08 07:38:34 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:03:17s. Time for last 10,000,000: 24s. Last read position: chr13:77,189,000
INFO 2026-06-08 07:38:58 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:03:42s. Time for last 10,000,000: 24s. Last read position: chr16:3,850,928
INFO 2026-06-08 07:39:24 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:04:07s. Time for last 10,000,000: 25s. Last read position: chr17:36,378,073
INFO 2026-06-08 07:39:48 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:04:31s. Time for last 10,000,000: 24s. Last read position: chr19:16,525,488
INFO 2026-06-08 07:40:12 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:04:55s. Time for last 10,000,000: 24s. Last read position: chr21:8,216,876
INFO 2026-06-08 07:40:35 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:05:19s. Time for last 10,000,000: 23s. Last read position: GL000220.1:112,749
INFO 2026-06-08 07:40:49 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 07:40:49 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 07:40:49 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 07:40:49 MarkDuplicates Before output close freeMemory: 201586024; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 07:40:49 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 07:40:49 MarkDuplicates After output close freeMemory: 104314648; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 07:40:49 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 11.82 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory