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-0754d2-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-0754d2-R1_A23YTGFLT4_1.md.bam --METRICS_FILE aih-tih-sc-0754d2-R1_A23YTGFLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:32:50.699 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 07:32:50 GMT 2026] MarkDuplicates --INPUT aih-tih-sc-0754d2-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-0754d2-R1_A23YTGFLT4_1.md.bam --METRICS_FILE aih-tih-sc-0754d2-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 07:32:50 GMT 2026] Executing as ?@nf-f4583b60dcf03b39033845f143ce7283-1e713-6rmrx 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 07:32:50 MarkDuplicates Start of doWork freeMemory: 105494352; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:32:50 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:32:50 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:32:57 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:18,916,969
INFO 2026-06-08 07:32:57 MarkDuplicates Tracking 1735 as yet unmatched pairs. 30 records in RAM.
INFO 2026-06-08 07:32:59 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: chr1:35,192,740
INFO 2026-06-08 07:32:59 MarkDuplicates Tracking 3418 as yet unmatched pairs. 33 records in RAM.
INFO 2026-06-08 07:33:02 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 3s. Last read position: chr1:58,577,046
INFO 2026-06-08 07:33:02 MarkDuplicates Tracking 6142 as yet unmatched pairs. 739 records in RAM.
INFO 2026-06-08 07:33:05 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 2s. Last read position: chr1:149,842,639
INFO 2026-06-08 07:33:05 MarkDuplicates Tracking 6752 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 07:33:08 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 3s. Last read position: chr1:161,072,695
INFO 2026-06-08 07:33:08 MarkDuplicates Tracking 8289 as yet unmatched pairs. 49 records in RAM.
INFO 2026-06-08 07:33:11 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 2s. Last read position: chr1:222,844,852
INFO 2026-06-08 07:33:11 MarkDuplicates Tracking 9900 as yet unmatched pairs. 0 records in RAM.
INFO 2026-06-08 07:33:14 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 2s. Last read position: chr2:28,778,918
INFO 2026-06-08 07:33:14 MarkDuplicates Tracking 11798 as yet unmatched pairs. 11755 records in RAM.
INFO 2026-06-08 07:33:17 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 3s. Last read position: chr2:74,482,441
INFO 2026-06-08 07:33:17 MarkDuplicates Tracking 103027 as yet unmatched pairs. 2972 records in RAM.
INFO 2026-06-08 07:33:20 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 2s. Last read position: chr2:177,212,771
INFO 2026-06-08 07:33:20 MarkDuplicates Tracking 101493 as yet unmatched pairs. 1437 records in RAM.
INFO 2026-06-08 07:33:23 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 2s. Last read position: chr3:12,600,178
INFO 2026-06-08 07:33:23 MarkDuplicates Tracking 99737 as yet unmatched pairs. 6108 records in RAM.
INFO 2026-06-08 07:33:26 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 2s. Last read position: chr3:52,492,122
INFO 2026-06-08 07:33:26 MarkDuplicates Tracking 97881 as yet unmatched pairs. 4251 records in RAM.
INFO 2026-06-08 07:33:29 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 3s. Last read position: chr3:149,657,225
INFO 2026-06-08 07:33:29 MarkDuplicates Tracking 96348 as yet unmatched pairs. 2718 records in RAM.
INFO 2026-06-08 07:33:33 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 3s. Last read position: chr3:188,866,335
INFO 2026-06-08 07:33:33 MarkDuplicates Tracking 94434 as yet unmatched pairs. 803 records in RAM.
INFO 2026-06-08 07:33:35 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chr4:55,396,195
INFO 2026-06-08 07:33:35 MarkDuplicates Tracking 92925 as yet unmatched pairs. 1110 records in RAM.
INFO 2026-06-08 07:33:39 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 3s. Last read position: chr5:14,358,246
INFO 2026-06-08 07:33:39 MarkDuplicates Tracking 91392 as yet unmatched pairs. 3289 records in RAM.
INFO 2026-06-08 07:33:41 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 2s. Last read position: chr5:140,700,829
INFO 2026-06-08 07:33:41 MarkDuplicates Tracking 89683 as yet unmatched pairs. 1544 records in RAM.
INFO 2026-06-08 07:33:44 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 2s. Last read position: chr6:3,015,538
INFO 2026-06-08 07:33:44 MarkDuplicates Tracking 87863 as yet unmatched pairs. 7012 records in RAM.
INFO 2026-06-08 07:33:47 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 3s. Last read position: chr6:29,829,566
INFO 2026-06-08 07:33:47 MarkDuplicates Tracking 86160 as yet unmatched pairs. 5307 records in RAM.
INFO 2026-06-08 07:33:50 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 2s. Last read position: chr6:31,816,768
INFO 2026-06-08 07:33:50 MarkDuplicates Tracking 85495 as yet unmatched pairs. 4642 records in RAM.
INFO 2026-06-08 07:33:52 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 2s. Last read position: chr6:31,829,132
INFO 2026-06-08 07:33:52 MarkDuplicates Tracking 85386 as yet unmatched pairs. 4533 records in RAM.
INFO 2026-06-08 07:33:55 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 2s. Last read position: chr6:43,770,792
INFO 2026-06-08 07:33:55 MarkDuplicates Tracking 83009 as yet unmatched pairs. 2153 records in RAM.
INFO 2026-06-08 07:33:57 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 2s. Last read position: chr6:158,771,281
INFO 2026-06-08 07:33:57 MarkDuplicates Tracking 81243 as yet unmatched pairs. 379 records in RAM.
INFO 2026-06-08 07:34:01 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 4s. Last read position: chr7:44,884,635
INFO 2026-06-08 07:34:01 MarkDuplicates Tracking 79215 as yet unmatched pairs. 4474 records in RAM.
INFO 2026-06-08 07:34:04 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 2s. Last read position: chr7:76,302,838
INFO 2026-06-08 07:34:04 MarkDuplicates Tracking 79419 as yet unmatched pairs. 4676 records in RAM.
INFO 2026-06-08 07:34:07 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 2s. Last read position: chr7:128,947,818
INFO 2026-06-08 07:34:07 MarkDuplicates Tracking 75427 as yet unmatched pairs. 680 records in RAM.
INFO 2026-06-08 07:34:10 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 2s. Last read position: chr8:60,781,301
INFO 2026-06-08 07:34:10 MarkDuplicates Tracking 73640 as yet unmatched pairs. 6083 records in RAM.
INFO 2026-06-08 07:34:13 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 3s. Last read position: chr8:133,262,118
INFO 2026-06-08 07:34:13 MarkDuplicates Tracking 73279 as yet unmatched pairs. 5719 records in RAM.
INFO 2026-06-08 07:34:16 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 3s. Last read position: chr8:143,859,923
INFO 2026-06-08 07:34:16 MarkDuplicates Tracking 70940 as yet unmatched pairs. 3378 records in RAM.
INFO 2026-06-08 07:34:19 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 3s. Last read position: chr8:143,863,064
INFO 2026-06-08 07:34:19 MarkDuplicates Tracking 70846 as yet unmatched pairs. 3284 records in RAM.
INFO 2026-06-08 07:34:21 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 1s. Last read position: chr8:143,866,317
INFO 2026-06-08 07:34:21 MarkDuplicates Tracking 69916 as yet unmatched pairs. 2352 records in RAM.
INFO 2026-06-08 07:34:24 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 2s. Last read position: chr8:144,095,079
INFO 2026-06-08 07:34:24 MarkDuplicates Tracking 68058 as yet unmatched pairs. 493 records in RAM.
INFO 2026-06-08 07:34:27 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 3s. Last read position: chr9:84,670,440
INFO 2026-06-08 07:34:27 MarkDuplicates Tracking 66409 as yet unmatched pairs. 3744 records in RAM.
INFO 2026-06-08 07:34:30 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 2s. Last read position: chr9:128,166,267
INFO 2026-06-08 07:34:30 MarkDuplicates Tracking 64520 as yet unmatched pairs. 1854 records in RAM.
INFO 2026-06-08 07:34:32 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 2s. Last read position: chr9:137,301,761
INFO 2026-06-08 07:34:32 MarkDuplicates Tracking 62858 as yet unmatched pairs. 190 records in RAM.
INFO 2026-06-08 07:34:35 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 2s. Last read position: chr10:79,296,576
INFO 2026-06-08 07:34:35 MarkDuplicates Tracking 61151 as yet unmatched pairs. 1506 records in RAM.
INFO 2026-06-08 07:34:38 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 2s. Last read position: chr11:561,839
INFO 2026-06-08 07:34:38 MarkDuplicates Tracking 59423 as yet unmatched pairs. 5849 records in RAM.
INFO 2026-06-08 07:34:41 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 3s. Last read position: chr11:46,397,744
INFO 2026-06-08 07:34:41 MarkDuplicates Tracking 57510 as yet unmatched pairs. 3934 records in RAM.
INFO 2026-06-08 07:34:44 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 2s. Last read position: chr11:65,038,798
INFO 2026-06-08 07:34:44 MarkDuplicates Tracking 55790 as yet unmatched pairs. 2202 records in RAM.
INFO 2026-06-08 07:34:46 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 2s. Last read position: chr11:117,392,494
INFO 2026-06-08 07:34:46 MarkDuplicates Tracking 53982 as yet unmatched pairs. 392 records in RAM.
INFO 2026-06-08 07:34:49 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 2s. Last read position: chr12:49,484,613
INFO 2026-06-08 07:34:49 MarkDuplicates Tracking 52473 as yet unmatched pairs. 3870 records in RAM.
INFO 2026-06-08 07:34:51 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 2s. Last read position: chr12:57,156,093
INFO 2026-06-08 07:34:51 MarkDuplicates Tracking 51166 as yet unmatched pairs. 2563 records in RAM.
INFO 2026-06-08 07:34:53 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 2s. Last read position: chr12:122,341,053
INFO 2026-06-08 07:34:53 MarkDuplicates Tracking 49565 as yet unmatched pairs. 960 records in RAM.
INFO 2026-06-08 07:34:56 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 2s. Last read position: chr14:20,343,235
INFO 2026-06-08 07:34:56 MarkDuplicates Tracking 47713 as yet unmatched pairs. 3631 records in RAM.
INFO 2026-06-08 07:34:58 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 2s. Last read position: chr14:76,154,522
INFO 2026-06-08 07:34:58 MarkDuplicates Tracking 46127 as yet unmatched pairs. 2041 records in RAM.
INFO 2026-06-08 07:35:01 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 2s. Last read position: chr14:104,948,580
INFO 2026-06-08 07:35:01 MarkDuplicates Tracking 45359 as yet unmatched pairs. 1267 records in RAM.
INFO 2026-06-08 07:35:04 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 3s. Last read position: chr15:64,681,359
INFO 2026-06-08 07:35:04 MarkDuplicates Tracking 43147 as yet unmatched pairs. 1034 records in RAM.
INFO 2026-06-08 07:35:06 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 2s. Last read position: chr16:2,208,547
INFO 2026-06-08 07:35:06 MarkDuplicates Tracking 41475 as yet unmatched pairs. 4946 records in RAM.
INFO 2026-06-08 07:35:09 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 2s. Last read position: chr16:18,343,617
INFO 2026-06-08 07:35:09 MarkDuplicates Tracking 40092 as yet unmatched pairs. 3563 records in RAM.
INFO 2026-06-08 07:35:11 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 1s. Last read position: chr16:30,225,615
INFO 2026-06-08 07:35:11 MarkDuplicates Tracking 39076 as yet unmatched pairs. 2547 records in RAM.
INFO 2026-06-08 07:35:14 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 2s. Last read position: chr16:81,445,261
INFO 2026-06-08 07:35:14 MarkDuplicates Tracking 37544 as yet unmatched pairs. 1012 records in RAM.
INFO 2026-06-08 07:35:17 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 2s. Last read position: chr17:7,587,190
INFO 2026-06-08 07:35:17 MarkDuplicates Tracking 35716 as yet unmatched pairs. 5880 records in RAM.
INFO 2026-06-08 07:35:19 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 2s. Last read position: chr17:38,850,129
INFO 2026-06-08 07:35:19 MarkDuplicates Tracking 34466 as yet unmatched pairs. 4628 records in RAM.
INFO 2026-06-08 07:35:21 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 2s. Last read position: chr17:47,531,262
INFO 2026-06-08 07:35:21 MarkDuplicates Tracking 33070 as yet unmatched pairs. 3228 records in RAM.
INFO 2026-06-08 07:35:24 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 2s. Last read position: chr17:78,121,032
INFO 2026-06-08 07:35:24 MarkDuplicates Tracking 30937 as yet unmatched pairs. 1095 records in RAM.
INFO 2026-06-08 07:35:26 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 2s. Last read position: chr18:49,992,348
INFO 2026-06-08 07:35:26 MarkDuplicates Tracking 29257 as yet unmatched pairs. 780 records in RAM.
INFO 2026-06-08 07:35:29 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 2s. Last read position: chr19:4,123,802
INFO 2026-06-08 07:35:29 MarkDuplicates Tracking 27230 as yet unmatched pairs. 9108 records in RAM.
INFO 2026-06-08 07:35:32 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 2s. Last read position: chr19:13,993,690
INFO 2026-06-08 07:35:32 MarkDuplicates Tracking 25212 as yet unmatched pairs. 7088 records in RAM.
INFO 2026-06-08 07:35:34 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 2s. Last read position: chr19:34,399,962
INFO 2026-06-08 07:35:34 MarkDuplicates Tracking 23528 as yet unmatched pairs. 5404 records in RAM.
INFO 2026-06-08 07:35:38 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 3s. Last read position: chr19:40,367,709
INFO 2026-06-08 07:35:38 MarkDuplicates Tracking 21599 as yet unmatched pairs. 3474 records in RAM.
INFO 2026-06-08 07:35:41 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 3s. Last read position: chr19:49,090,293
INFO 2026-06-08 07:35:41 MarkDuplicates Tracking 19669 as yet unmatched pairs. 1531 records in RAM.
INFO 2026-06-08 07:35:44 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 3s. Last read position: chr20:17,570,142
INFO 2026-06-08 07:35:44 MarkDuplicates Tracking 17702 as yet unmatched pairs. 2139 records in RAM.
INFO 2026-06-08 07:35:46 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:53s. Time for last 1,000,000: 2s. Last read position: chr20:62,813,465
INFO 2026-06-08 07:35:46 MarkDuplicates Tracking 15920 as yet unmatched pairs. 354 records in RAM.
INFO 2026-06-08 07:35:49 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 2s. Last read position: chr21:8,217,372
INFO 2026-06-08 07:35:49 MarkDuplicates Tracking 14075 as yet unmatched pairs. 3314 records in RAM.
INFO 2026-06-08 07:35:52 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 2s. Last read position: chr21:8,400,314
INFO 2026-06-08 07:35:52 MarkDuplicates Tracking 13208 as yet unmatched pairs. 2444 records in RAM.
INFO 2026-06-08 07:35:54 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 2s. Last read position: chr21:29,327,296
INFO 2026-06-08 07:35:54 MarkDuplicates Tracking 11694 as yet unmatched pairs. 929 records in RAM.
INFO 2026-06-08 07:35:57 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 2s. Last read position: chr22:29,288,659
INFO 2026-06-08 07:35:57 MarkDuplicates Tracking 9996 as yet unmatched pairs. 2950 records in RAM.
INFO 2026-06-08 07:36:00 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 2s. Last read position: chr22:46,263,083
INFO 2026-06-08 07:36:00 MarkDuplicates Tracking 8183 as yet unmatched pairs. 1137 records in RAM.
INFO 2026-06-08 07:36:02 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 2s. Last read position: chrX:53,085,841
INFO 2026-06-08 07:36:02 MarkDuplicates Tracking 6117 as yet unmatched pairs. 1406 records in RAM.
INFO 2026-06-08 07:36:05 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 2s. Last read position: GL000220.1:112,697
INFO 2026-06-08 07:36:05 MarkDuplicates Tracking 4623 as yet unmatched pairs. 1651 records in RAM.
INFO 2026-06-08 07:36:07 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 2s. Last read position: GL000220.1:158,559
INFO 2026-06-08 07:36:07 MarkDuplicates Tracking 3033 as yet unmatched pairs. 61 records in RAM.
INFO 2026-06-08 07:36:10 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 2s. Last read position: KI270733.1:133,598
INFO 2026-06-08 07:36:10 MarkDuplicates Tracking 401 as yet unmatched pairs. 399 records in RAM.
INFO 2026-06-08 07:36:11 MarkDuplicates Read 71844835 records. 0 pairs never matched.
INFO 2026-06-08 07:36:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 23678821944; totalMemory: 33789313024; maxMemory: 63585648640
INFO 2026-06-08 07:36:19 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 07:36:28 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 07:36:50 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 07:36:59 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 07:37:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 34717182336; totalMemory: 50667192320; maxMemory: 63585648640
INFO 2026-06-08 07:37:01 MarkDuplicates Marking 46330714 records as duplicates.
INFO 2026-06-08 07:37:01 MarkDuplicates Found 1131270 optical duplicate clusters.
INFO 2026-06-08 07:37:01 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 07:37:28 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:27s. Time for last 10,000,000: 27s. Last read position: chr3:12,600,178
INFO 2026-06-08 07:37:54 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:53s. Time for last 10,000,000: 25s. Last read position: chr6:31,829,132
INFO 2026-06-08 07:38:20 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:18s. Time for last 10,000,000: 25s. Last read position: chr8:143,866,317
INFO 2026-06-08 07:38:45 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:43s. Time for last 10,000,000: 24s. Last read position: chr12:49,484,613
INFO 2026-06-08 07:39:11 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:02:09s. Time for last 10,000,000: 26s. Last read position: chr16:81,445,261
INFO 2026-06-08 07:39:37 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:35s. Time for last 10,000,000: 26s. Last read position: chr19:49,090,293
INFO 2026-06-08 07:40:04 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:03:02s. Time for last 10,000,000: 26s. Last read position: GL000220.1:158,559
INFO 2026-06-08 07:40:11 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 07:40:11 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 07:40:11 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 07:40:12 MarkDuplicates Before output close freeMemory: 201632528; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 07:40:12 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 07:40:12 MarkDuplicates After output close freeMemory: 104332240; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 07:40:12 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 7.36 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory