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 BVT_FFPE_TRNA_bld_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam --OUTPUT BVT_FFPE_TRNA_bld_01_A23WKFTLT4_3.md.bam --METRICS_FILE BVT_FFPE_TRNA_bld_01_A23WKFTLT4_3.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:36:09.877 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 07:36:09 GMT 2026] MarkDuplicates --INPUT BVT_FFPE_TRNA_bld_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam --OUTPUT BVT_FFPE_TRNA_bld_01_A23WKFTLT4_3.md.bam --METRICS_FILE BVT_FFPE_TRNA_bld_01_A23WKFTLT4_3.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 07:36:09 GMT 2026] Executing as ?@nf-4a33785f1567410af5dc74c347b9fd09-d7bbd-ppsgh 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 07:36:09 MarkDuplicates Start of doWork freeMemory: 105495152; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:36:09 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:36:09 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:36:15 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:15,716,755
INFO 2026-06-08 07:36:15 MarkDuplicates Tracking 2513 as yet unmatched pairs. 20 records in RAM.
INFO 2026-06-08 07:36:17 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: chr1:28,526,908
INFO 2026-06-08 07:36:17 MarkDuplicates Tracking 4817 as yet unmatched pairs. 5 records in RAM.
INFO 2026-06-08 07:36:20 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: chr1:45,329,399
INFO 2026-06-08 07:36:20 MarkDuplicates Tracking 7379 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 07:36:23 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 2s. Last read position: chr1:117,062,421
INFO 2026-06-08 07:36:23 MarkDuplicates Tracking 9564 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 07:36:25 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: chr1:152,307,368
INFO 2026-06-08 07:36:25 MarkDuplicates Tracking 11096 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 07:36:28 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr1:160,225,096
INFO 2026-06-08 07:36:28 MarkDuplicates Tracking 13696 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 07:36:30 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 2s. Last read position: chr1:203,847,246
INFO 2026-06-08 07:36:30 MarkDuplicates Tracking 15872 as yet unmatched pairs. 10 records in RAM.
INFO 2026-06-08 07:36:33 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 3s. Last read position: chr1:246,849,932
INFO 2026-06-08 07:36:33 MarkDuplicates Tracking 18054 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 07:36:36 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,264
INFO 2026-06-08 07:36:36 MarkDuplicates Tracking 147101 as yet unmatched pairs. 9723 records in RAM.
INFO 2026-06-08 07:36:38 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 2s. Last read position: chr2:73,774,964
INFO 2026-06-08 07:36:38 MarkDuplicates Tracking 171613 as yet unmatched pairs. 5901 records in RAM.
INFO 2026-06-08 07:36:41 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 2s. Last read position: chr2:149,212,999
INFO 2026-06-08 07:36:41 MarkDuplicates Tracking 169421 as yet unmatched pairs. 3704 records in RAM.
INFO 2026-06-08 07:36:44 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 2s. Last read position: chr2:215,406,388
INFO 2026-06-08 07:36:44 MarkDuplicates Tracking 167686 as yet unmatched pairs. 1966 records in RAM.
INFO 2026-06-08 07:36:46 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 2s. Last read position: chr3:14,132,489
INFO 2026-06-08 07:36:46 MarkDuplicates Tracking 164968 as yet unmatched pairs. 7691 records in RAM.
INFO 2026-06-08 07:36:48 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 2s. Last read position: chr3:49,057,335
INFO 2026-06-08 07:36:48 MarkDuplicates Tracking 162738 as yet unmatched pairs. 5459 records in RAM.
INFO 2026-06-08 07:36:51 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 2s. Last read position: chr3:127,032,491
INFO 2026-06-08 07:36:51 MarkDuplicates Tracking 160445 as yet unmatched pairs. 3160 records in RAM.
INFO 2026-06-08 07:36:53 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chr3:190,312,975
INFO 2026-06-08 07:36:53 MarkDuplicates Tracking 158238 as yet unmatched pairs. 951 records in RAM.
INFO 2026-06-08 07:36:56 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 2s. Last read position: chr4:1,799,777
INFO 2026-06-08 07:36:56 MarkDuplicates Tracking 156771 as yet unmatched pairs. 6162 records in RAM.
INFO 2026-06-08 07:36:58 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 2s. Last read position: chr4:9,226,024
INFO 2026-06-08 07:36:58 MarkDuplicates Tracking 153105 as yet unmatched pairs. 2495 records in RAM.
INFO 2026-06-08 07:37:01 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 2s. Last read position: chr4:143,513,966
INFO 2026-06-08 07:37:01 MarkDuplicates Tracking 151186 as yet unmatched pairs. 574 records in RAM.
INFO 2026-06-08 07:37:03 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 2s. Last read position: chr5:74,685,467
INFO 2026-06-08 07:37:03 MarkDuplicates Tracking 148957 as yet unmatched pairs. 4591 records in RAM.
INFO 2026-06-08 07:37:05 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 2s. Last read position: chr5:147,640,594
INFO 2026-06-08 07:37:05 MarkDuplicates Tracking 147028 as yet unmatched pairs. 2646 records in RAM.
INFO 2026-06-08 07:37:07 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 1s. Last read position: chr5:179,821,001
INFO 2026-06-08 07:37:07 MarkDuplicates Tracking 145420 as yet unmatched pairs. 1034 records in RAM.
INFO 2026-06-08 07:37:10 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 2s. Last read position: chr6:30,490,380
INFO 2026-06-08 07:37:10 MarkDuplicates Tracking 142793 as yet unmatched pairs. 7509 records in RAM.
INFO 2026-06-08 07:37:12 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 2s. Last read position: chr6:34,418,372
INFO 2026-06-08 07:37:12 MarkDuplicates Tracking 140472 as yet unmatched pairs. 5186 records in RAM.
INFO 2026-06-08 07:37:15 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 3s. Last read position: chr6:113,859,899
INFO 2026-06-08 07:37:15 MarkDuplicates Tracking 137912 as yet unmatched pairs. 2617 records in RAM.
INFO 2026-06-08 07:37:18 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 3s. Last read position: chr7:1,477,612
INFO 2026-06-08 07:37:18 MarkDuplicates Tracking 135144 as yet unmatched pairs. 9239 records in RAM.
INFO 2026-06-08 07:37:20 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 2s. Last read position: chr7:44,581,213
INFO 2026-06-08 07:37:20 MarkDuplicates Tracking 132721 as yet unmatched pairs. 6814 records in RAM.
INFO 2026-06-08 07:37:22 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 2s. Last read position: chr7:77,696,500
INFO 2026-06-08 07:37:22 MarkDuplicates Tracking 131000 as yet unmatched pairs. 5089 records in RAM.
INFO 2026-06-08 07:37:24 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 2s. Last read position: chr7:101,088,644
INFO 2026-06-08 07:37:24 MarkDuplicates Tracking 129036 as yet unmatched pairs. 3121 records in RAM.
INFO 2026-06-08 07:37:27 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 2s. Last read position: chr7:142,864,314
INFO 2026-06-08 07:37:27 MarkDuplicates Tracking 127140 as yet unmatched pairs. 1223 records in RAM.
INFO 2026-06-08 07:37:29 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 2s. Last read position: chr8:38,787,690
INFO 2026-06-08 07:37:29 MarkDuplicates Tracking 124642 as yet unmatched pairs. 6207 records in RAM.
INFO 2026-06-08 07:37:31 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 2s. Last read position: chr8:119,758,073
INFO 2026-06-08 07:37:31 MarkDuplicates Tracking 122335 as yet unmatched pairs. 3889 records in RAM.
INFO 2026-06-08 07:37:34 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 2s. Last read position: chr8:143,863,186
INFO 2026-06-08 07:37:34 MarkDuplicates Tracking 120960 as yet unmatched pairs. 2509 records in RAM.
INFO 2026-06-08 07:37:36 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 2s. Last read position: chr9:6,007,713
INFO 2026-06-08 07:37:36 MarkDuplicates Tracking 118346 as yet unmatched pairs. 6367 records in RAM.
INFO 2026-06-08 07:37:39 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 2s. Last read position: chr9:100,126,446
INFO 2026-06-08 07:37:39 MarkDuplicates Tracking 115991 as yet unmatched pairs. 4004 records in RAM.
INFO 2026-06-08 07:37:41 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 2s. Last read position: chr9:133,349,602
INFO 2026-06-08 07:37:41 MarkDuplicates Tracking 113752 as yet unmatched pairs. 1759 records in RAM.
INFO 2026-06-08 07:37:43 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 2s. Last read position: chr10:17,695,016
INFO 2026-06-08 07:37:43 MarkDuplicates Tracking 111094 as yet unmatched pairs. 4057 records in RAM.
INFO 2026-06-08 07:37:45 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 2s. Last read position: chr10:88,938,224
INFO 2026-06-08 07:37:45 MarkDuplicates Tracking 109045 as yet unmatched pairs. 2004 records in RAM.
INFO 2026-06-08 07:37:47 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 2s. Last read position: chr11:319,889
INFO 2026-06-08 07:37:47 MarkDuplicates Tracking 107252 as yet unmatched pairs. 13066 records in RAM.
INFO 2026-06-08 07:37:50 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 3s. Last read position: chr11:11,942,357
INFO 2026-06-08 07:37:50 MarkDuplicates Tracking 104098 as yet unmatched pairs. 9907 records in RAM.
INFO 2026-06-08 07:37:52 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 1s. Last read position: chr11:62,722,671
INFO 2026-06-08 07:37:52 MarkDuplicates Tracking 101760 as yet unmatched pairs. 7565 records in RAM.
INFO 2026-06-08 07:37:55 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 2s. Last read position: chr11:67,286,416
INFO 2026-06-08 07:37:55 MarkDuplicates Tracking 99117 as yet unmatched pairs. 4921 records in RAM.
INFO 2026-06-08 07:37:57 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 2s. Last read position: chr11:73,310,296
INFO 2026-06-08 07:37:57 MarkDuplicates Tracking 96897 as yet unmatched pairs. 2701 records in RAM.
INFO 2026-06-08 07:38:00 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 2s. Last read position: chr11:128,978,739
INFO 2026-06-08 07:38:00 MarkDuplicates Tracking 94469 as yet unmatched pairs. 252 records in RAM.
INFO 2026-06-08 07:38:03 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 2s. Last read position: chr12:46,364,454
INFO 2026-06-08 07:38:03 MarkDuplicates Tracking 92479 as yet unmatched pairs. 7484 records in RAM.
INFO 2026-06-08 07:38:05 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 2s. Last read position: chr12:54,396,249
INFO 2026-06-08 07:38:05 MarkDuplicates Tracking 90278 as yet unmatched pairs. 5279 records in RAM.
INFO 2026-06-08 07:38:08 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 2s. Last read position: chr12:98,599,955
INFO 2026-06-08 07:38:08 MarkDuplicates Tracking 88258 as yet unmatched pairs. 3254 records in RAM.
INFO 2026-06-08 07:38:10 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 2s. Last read position: chr12:123,743,829
INFO 2026-06-08 07:38:10 MarkDuplicates Tracking 85722 as yet unmatched pairs. 717 records in RAM.
INFO 2026-06-08 07:38:12 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 2s. Last read position: chr13:98,482,262
INFO 2026-06-08 07:38:12 MarkDuplicates Tracking 83544 as yet unmatched pairs. 1350 records in RAM.
INFO 2026-06-08 07:38:15 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 2s. Last read position: chr14:24,372,492
INFO 2026-06-08 07:38:15 MarkDuplicates Tracking 80773 as yet unmatched pairs. 3618 records in RAM.
INFO 2026-06-08 07:38:18 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 2s. Last read position: chr14:91,313,616
INFO 2026-06-08 07:38:18 MarkDuplicates Tracking 78775 as yet unmatched pairs. 1617 records in RAM.
INFO 2026-06-08 07:38:20 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 2s. Last read position: chr15:40,441,258
INFO 2026-06-08 07:38:20 MarkDuplicates Tracking 76592 as yet unmatched pairs. 4446 records in RAM.
INFO 2026-06-08 07:38:22 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 2s. Last read position: chr15:74,023,275
INFO 2026-06-08 07:38:22 MarkDuplicates Tracking 74159 as yet unmatched pairs. 2008 records in RAM.
INFO 2026-06-08 07:38:24 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 2s. Last read position: chr16:730,518
INFO 2026-06-08 07:38:24 MarkDuplicates Tracking 71339 as yet unmatched pairs. 10590 records in RAM.
INFO 2026-06-08 07:38:27 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 2s. Last read position: chr16:14,922,543
INFO 2026-06-08 07:38:27 MarkDuplicates Tracking 68950 as yet unmatched pairs. 8200 records in RAM.
INFO 2026-06-08 07:38:29 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 2s. Last read position: chr16:22,533,753
INFO 2026-06-08 07:38:29 MarkDuplicates Tracking 67822 as yet unmatched pairs. 7068 records in RAM.
INFO 2026-06-08 07:38:31 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 1s. Last read position: chr16:30,665,669
INFO 2026-06-08 07:38:31 MarkDuplicates Tracking 66208 as yet unmatched pairs. 5454 records in RAM.
INFO 2026-06-08 07:38:33 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 2s. Last read position: chr16:69,908,817
INFO 2026-06-08 07:38:33 MarkDuplicates Tracking 63060 as yet unmatched pairs. 2306 records in RAM.
INFO 2026-06-08 07:38:36 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 2s. Last read position: chr17:1,483,701
INFO 2026-06-08 07:38:36 MarkDuplicates Tracking 60630 as yet unmatched pairs. 17524 records in RAM.
INFO 2026-06-08 07:38:38 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 2s. Last read position: chr17:28,328,561
INFO 2026-06-08 07:38:38 MarkDuplicates Tracking 58451 as yet unmatched pairs. 15342 records in RAM.
INFO 2026-06-08 07:38:40 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 2s. Last read position: chr17:39,201,211
INFO 2026-06-08 07:38:40 MarkDuplicates Tracking 56297 as yet unmatched pairs. 13188 records in RAM.
INFO 2026-06-08 07:38:43 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 2s. Last read position: chr17:42,130,402
INFO 2026-06-08 07:38:43 MarkDuplicates Tracking 53662 as yet unmatched pairs. 10552 records in RAM.
INFO 2026-06-08 07:38:46 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 2s. Last read position: chr17:50,190,364
INFO 2026-06-08 07:38:46 MarkDuplicates Tracking 52604 as yet unmatched pairs. 9493 records in RAM.
INFO 2026-06-08 07:38:48 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 2s. Last read position: chr17:50,661,023
INFO 2026-06-08 07:38:48 MarkDuplicates Tracking 48123 as yet unmatched pairs. 5010 records in RAM.
INFO 2026-06-08 07:38:50 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 2s. Last read position: chr17:77,402,104
INFO 2026-06-08 07:38:50 MarkDuplicates Tracking 45897 as yet unmatched pairs. 2782 records in RAM.
INFO 2026-06-08 07:38:52 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 2s. Last read position: chr17:83,094,414
INFO 2026-06-08 07:38:52 MarkDuplicates Tracking 43146 as yet unmatched pairs. 31 records in RAM.
INFO 2026-06-08 07:38:55 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 2s. Last read position: chr19:1,254,167
INFO 2026-06-08 07:38:55 MarkDuplicates Tracking 40937 as yet unmatched pairs. 17633 records in RAM.
INFO 2026-06-08 07:38:58 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 2s. Last read position: chr19:7,076,408
INFO 2026-06-08 07:38:58 MarkDuplicates Tracking 38263 as yet unmatched pairs. 14958 records in RAM.
INFO 2026-06-08 07:39:00 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 2s. Last read position: chr19:14,157,422
INFO 2026-06-08 07:39:00 MarkDuplicates Tracking 35532 as yet unmatched pairs. 12227 records in RAM.
INFO 2026-06-08 07:39:02 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 2s. Last read position: chr19:18,532,139
INFO 2026-06-08 07:39:02 MarkDuplicates Tracking 32961 as yet unmatched pairs. 9655 records in RAM.
INFO 2026-06-08 07:39:04 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 1s. Last read position: chr19:38,729,322
INFO 2026-06-08 07:39:04 MarkDuplicates Tracking 30313 as yet unmatched pairs. 7005 records in RAM.
INFO 2026-06-08 07:39:07 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 2s. Last read position: chr19:43,595,151
INFO 2026-06-08 07:39:07 MarkDuplicates Tracking 27534 as yet unmatched pairs. 4224 records in RAM.
INFO 2026-06-08 07:39:09 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 2s. Last read position: chr19:49,860,267
INFO 2026-06-08 07:39:09 MarkDuplicates Tracking 24887 as yet unmatched pairs. 1575 records in RAM.
INFO 2026-06-08 07:39:11 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 2s. Last read position: chr20:10,639,436
INFO 2026-06-08 07:39:11 MarkDuplicates Tracking 22568 as yet unmatched pairs. 4601 records in RAM.
INFO 2026-06-08 07:39:13 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 2s. Last read position: chr20:44,919,195
INFO 2026-06-08 07:39:13 MarkDuplicates Tracking 20186 as yet unmatched pairs. 2218 records in RAM.
INFO 2026-06-08 07:39:16 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 2s. Last read position: chr21:6,112,114
INFO 2026-06-08 07:39:16 MarkDuplicates Tracking 17951 as yet unmatched pairs. 3773 records in RAM.
INFO 2026-06-08 07:39:18 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 1s. Last read position: chr21:26,844,662
INFO 2026-06-08 07:39:18 MarkDuplicates Tracking 16388 as yet unmatched pairs. 2205 records in RAM.
INFO 2026-06-08 07:39:20 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 2s. Last read position: chr22:20,091,618
INFO 2026-06-08 07:39:20 MarkDuplicates Tracking 13666 as yet unmatched pairs. 7021 records in RAM.
INFO 2026-06-08 07:39:23 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 2s. Last read position: chr22:29,297,835
INFO 2026-06-08 07:39:23 MarkDuplicates Tracking 11354 as yet unmatched pairs. 4709 records in RAM.
INFO 2026-06-08 07:39:25 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 2s. Last read position: chr22:37,927,552
INFO 2026-06-08 07:39:25 MarkDuplicates Tracking 8794 as yet unmatched pairs. 2149 records in RAM.
INFO 2026-06-08 07:39:27 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 2s. Last read position: chrX:13,736,543
INFO 2026-06-08 07:39:27 MarkDuplicates Tracking 6166 as yet unmatched pairs. 4369 records in RAM.
INFO 2026-06-08 07:39:30 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 2s. Last read position: chrX:77,654,098
INFO 2026-06-08 07:39:30 MarkDuplicates Tracking 3887 as yet unmatched pairs. 2088 records in RAM.
INFO 2026-06-08 07:39:32 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 2s. Last read position: chrX:154,886,917
INFO 2026-06-08 07:39:32 MarkDuplicates Tracking 1841 as yet unmatched pairs. 42 records in RAM.
INFO 2026-06-08 07:39:34 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: KI270733.1:177,531
INFO 2026-06-08 07:39:34 MarkDuplicates Tracking 9 as yet unmatched pairs. 4 records in RAM.
INFO 2026-06-08 07:39:34 MarkDuplicates Read 84082635 records. 0 pairs never matched.
INFO 2026-06-08 07:39:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 27724527936; totalMemory: 39594229760; maxMemory: 63585648640
INFO 2026-06-08 07:39:39 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 07:39:45 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 07:40:00 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 07:40:08 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 07:40:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 23644225640; totalMemory: 39594229760; maxMemory: 63585648640
INFO 2026-06-08 07:40:11 MarkDuplicates Marking 60326406 records as duplicates.
INFO 2026-06-08 07:40:11 MarkDuplicates Found 1331318 optical duplicate clusters.
INFO 2026-06-08 07:40:11 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 07:40:36 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:25s. Time for last 10,000,000: 25s. Last read position: chr2:73,774,964
INFO 2026-06-08 07:41:00 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:48s. Time for last 10,000,000: 23s. Last read position: chr5:74,685,467
INFO 2026-06-08 07:41:23 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:12s. Time for last 10,000,000: 23s. Last read position: chr7:142,864,314
INFO 2026-06-08 07:41:48 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:37s. Time for last 10,000,000: 24s. Last read position: chr11:11,942,357
INFO 2026-06-08 07:42:10 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:59s. Time for last 10,000,000: 22s. Last read position: chr14:24,372,492
INFO 2026-06-08 07:42:32 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:20s. Time for last 10,000,000: 21s. Last read position: chr17:28,328,561
INFO 2026-06-08 07:42:54 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:42s. Time for last 10,000,000: 22s. Last read position: chr19:18,532,139
INFO 2026-06-08 07:43:13 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:03:01s. Time for last 10,000,000: 18s. Last read position: chr22:37,927,552
INFO 2026-06-08 07:43:23 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 07:43:23 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 07:43:23 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 07:43:23 MarkDuplicates Before output close freeMemory: 201715688; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 07:43:23 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 07:43:23 MarkDuplicates After output close freeMemory: 104344216; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 07:43:23 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 7.23 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory