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-2482ef-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bam --METRICS_FILE aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:52:46.514 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 07:52:46 GMT 2026] MarkDuplicates --INPUT aih-tih-sc-2482ef-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-2482ef-R1_A23WJ53LT4_1.md.bam --METRICS_FILE aih-tih-sc-2482ef-R1_A23WJ53LT4_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 07:52:46 GMT 2026] Executing as ?@nf-39d4f81af345da6d261f0499fb254177-9468d-ndbbh 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 07:52:46 MarkDuplicates Start of doWork freeMemory: 105828528; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:52:46 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:52:46 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:52:53 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 4s. Last read position: chr1:21,824,130
INFO 2026-06-08 07:52:53 MarkDuplicates Tracking 2216 as yet unmatched pairs. 51 records in RAM.
INFO 2026-06-08 07:52:57 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 3s. Last read position: chr1:41,510,934
INFO 2026-06-08 07:52:57 MarkDuplicates Tracking 4240 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 07:53:00 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 3s. Last read position: chr1:120,491,865
INFO 2026-06-08 07:53:00 MarkDuplicates Tracking 6208 as yet unmatched pairs. 4 records in RAM.
INFO 2026-06-08 07:53:03 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 2s. Last read position: chr1:154,232,181
INFO 2026-06-08 07:53:03 MarkDuplicates Tracking 7386 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 07:53:06 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 3s. Last read position: chr1:183,023,875
INFO 2026-06-08 07:53:06 MarkDuplicates Tracking 9290 as yet unmatched pairs. 99 records in RAM.
INFO 2026-06-08 07:53:09 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 3s. Last read position: chr1:243,573,004
INFO 2026-06-08 07:53:09 MarkDuplicates Tracking 11197 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 07:53:11 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 2s. Last read position: chr2:42,303,426
INFO 2026-06-08 07:53:11 MarkDuplicates Tracking 119435 as yet unmatched pairs. 6335 records in RAM.
INFO 2026-06-08 07:53:13 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: chr2:109,836,818
INFO 2026-06-08 07:53:13 MarkDuplicates Tracking 117603 as yet unmatched pairs. 4501 records in RAM.
INFO 2026-06-08 07:53:16 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 3s. Last read position: chr2:190,921,184
INFO 2026-06-08 07:53:16 MarkDuplicates Tracking 115760 as yet unmatched pairs. 2657 records in RAM.
INFO 2026-06-08 07:53:19 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 2s. Last read position: chr2:237,366,837
INFO 2026-06-08 07:53:19 MarkDuplicates Tracking 113854 as yet unmatched pairs. 745 records in RAM.
INFO 2026-06-08 07:53:21 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 2s. Last read position: chr3:47,406,502
INFO 2026-06-08 07:53:21 MarkDuplicates Tracking 111556 as yet unmatched pairs. 4159 records in RAM.
INFO 2026-06-08 07:53:24 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 2s. Last read position: chr3:112,638,967
INFO 2026-06-08 07:53:24 MarkDuplicates Tracking 109625 as yet unmatched pairs. 2225 records in RAM.
INFO 2026-06-08 07:53:26 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 2s. Last read position: chr3:195,867,750
INFO 2026-06-08 07:53:26 MarkDuplicates Tracking 107678 as yet unmatched pairs. 263 records in RAM.
INFO 2026-06-08 07:53:28 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 1s. Last read position: chr4:99,314,008
INFO 2026-06-08 07:53:28 MarkDuplicates Tracking 105582 as yet unmatched pairs. 1023 records in RAM.
INFO 2026-06-08 07:53:31 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 2s. Last read position: chr5:57,251,115
INFO 2026-06-08 07:53:31 MarkDuplicates Tracking 103642 as yet unmatched pairs. 3528 records in RAM.
INFO 2026-06-08 07:53:33 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 2s. Last read position: chr5:150,115,925
INFO 2026-06-08 07:53:33 MarkDuplicates Tracking 102368 as yet unmatched pairs. 2247 records in RAM.
INFO 2026-06-08 07:53:35 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 2s. Last read position: chr6:497,394
INFO 2026-06-08 07:53:35 MarkDuplicates Tracking 100121 as yet unmatched pairs. 5842 records in RAM.
INFO 2026-06-08 07:53:38 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 3s. Last read position: chr6:32,079,326
INFO 2026-06-08 07:53:38 MarkDuplicates Tracking 98606 as yet unmatched pairs. 4326 records in RAM.
INFO 2026-06-08 07:53:40 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 2s. Last read position: chr6:85,593,593
INFO 2026-06-08 07:53:40 MarkDuplicates Tracking 96594 as yet unmatched pairs. 2314 records in RAM.
INFO 2026-06-08 07:53:43 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 2s. Last read position: chr6:169,248,560
INFO 2026-06-08 07:53:43 MarkDuplicates Tracking 94382 as yet unmatched pairs. 100 records in RAM.
INFO 2026-06-08 07:53:46 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 2s. Last read position: chr7:67,076,935
INFO 2026-06-08 07:53:46 MarkDuplicates Tracking 92334 as yet unmatched pairs. 3861 records in RAM.
INFO 2026-06-08 07:53:49 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 3s. Last read position: chr7:100,603,453
INFO 2026-06-08 07:53:49 MarkDuplicates Tracking 90630 as yet unmatched pairs. 2156 records in RAM.
INFO 2026-06-08 07:53:52 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 2s. Last read position: chr7:150,628,092
INFO 2026-06-08 07:53:52 MarkDuplicates Tracking 88926 as yet unmatched pairs. 450 records in RAM.
INFO 2026-06-08 07:53:54 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 2s. Last read position: chr8:61,578,181
INFO 2026-06-08 07:53:54 MarkDuplicates Tracking 86722 as yet unmatched pairs. 2756 records in RAM.
INFO 2026-06-08 07:53:56 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 2s. Last read position: chr8:143,916,357
INFO 2026-06-08 07:53:56 MarkDuplicates Tracking 85317 as yet unmatched pairs. 1347 records in RAM.
INFO 2026-06-08 07:53:59 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 2s. Last read position: chr9:69,431,385
INFO 2026-06-08 07:53:59 MarkDuplicates Tracking 82944 as yet unmatched pairs. 3953 records in RAM.
INFO 2026-06-08 07:54:02 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 3s. Last read position: chr9:128,907,667
INFO 2026-06-08 07:54:02 MarkDuplicates Tracking 80988 as yet unmatched pairs. 1995 records in RAM.
INFO 2026-06-08 07:54:04 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 2s. Last read position: chr10:7,799,060
INFO 2026-06-08 07:54:04 MarkDuplicates Tracking 78765 as yet unmatched pairs. 3344 records in RAM.
INFO 2026-06-08 07:54:06 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 2s. Last read position: chr10:80,167,226
INFO 2026-06-08 07:54:06 MarkDuplicates Tracking 77092 as yet unmatched pairs. 1670 records in RAM.
INFO 2026-06-08 07:54:08 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 1s. Last read position: chr11:801,975
INFO 2026-06-08 07:54:08 MarkDuplicates Tracking 75022 as yet unmatched pairs. 6904 records in RAM.
INFO 2026-06-08 07:54:11 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 2s. Last read position: chr11:61,404,692
INFO 2026-06-08 07:54:11 MarkDuplicates Tracking 73054 as yet unmatched pairs. 4934 records in RAM.
INFO 2026-06-08 07:54:14 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 2s. Last read position: chr11:67,611,020
INFO 2026-06-08 07:54:14 MarkDuplicates Tracking 71131 as yet unmatched pairs. 3010 records in RAM.
INFO 2026-06-08 07:54:16 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 2s. Last read position: chr11:118,896,976
INFO 2026-06-08 07:54:16 MarkDuplicates Tracking 68757 as yet unmatched pairs. 636 records in RAM.
INFO 2026-06-08 07:54:18 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 1s. Last read position: chr12:32,294,025
INFO 2026-06-08 07:54:18 MarkDuplicates Tracking 66663 as yet unmatched pairs. 4680 records in RAM.
INFO 2026-06-08 07:54:19 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 1s. Last read position: chr12:57,158,529
INFO 2026-06-08 07:54:19 MarkDuplicates Tracking 64972 as yet unmatched pairs. 2989 records in RAM.
INFO 2026-06-08 07:54:21 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 1s. Last read position: chr12:121,814,445
INFO 2026-06-08 07:54:21 MarkDuplicates Tracking 62961 as yet unmatched pairs. 977 records in RAM.
INFO 2026-06-08 07:54:24 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 2s. Last read position: chr13:110,503,427
INFO 2026-06-08 07:54:24 MarkDuplicates Tracking 60514 as yet unmatched pairs. 294 records in RAM.
INFO 2026-06-08 07:54:25 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 1s. Last read position: chr14:72,997,853
INFO 2026-06-08 07:54:25 MarkDuplicates Tracking 58340 as yet unmatched pairs. 1732 records in RAM.
INFO 2026-06-08 07:54:27 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 1s. Last read position: chr15:28,270,786
INFO 2026-06-08 07:54:27 MarkDuplicates Tracking 56468 as yet unmatched pairs. 3241 records in RAM.
INFO 2026-06-08 07:54:29 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 1s. Last read position: chr15:66,387,404
INFO 2026-06-08 07:54:29 MarkDuplicates Tracking 54818 as yet unmatched pairs. 1591 records in RAM.
INFO 2026-06-08 07:54:31 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 2s. Last read position: chr16:520,563
INFO 2026-06-08 07:54:31 MarkDuplicates Tracking 53091 as yet unmatched pairs. 7288 records in RAM.
INFO 2026-06-08 07:54:33 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 2s. Last read position: chr16:14,234,186
INFO 2026-06-08 07:54:33 MarkDuplicates Tracking 51115 as yet unmatched pairs. 5312 records in RAM.
INFO 2026-06-08 07:54:36 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 2s. Last read position: chr16:21,402,519
INFO 2026-06-08 07:54:36 MarkDuplicates Tracking 50118 as yet unmatched pairs. 4315 records in RAM.
INFO 2026-06-08 07:54:38 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 1s. Last read position: chr16:29,485,424
INFO 2026-06-08 07:54:38 MarkDuplicates Tracking 49344 as yet unmatched pairs. 3541 records in RAM.
INFO 2026-06-08 07:54:40 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 2s. Last read position: chr16:67,668,189
INFO 2026-06-08 07:54:40 MarkDuplicates Tracking 47538 as yet unmatched pairs. 1733 records in RAM.
INFO 2026-06-08 07:54:42 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 2s. Last read position: chr17:2,395,220
INFO 2026-06-08 07:54:42 MarkDuplicates Tracking 45303 as yet unmatched pairs. 19280 records in RAM.
INFO 2026-06-08 07:54:44 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 2s. Last read position: chr17:28,697,998
INFO 2026-06-08 07:54:44 MarkDuplicates Tracking 43302 as yet unmatched pairs. 17277 records in RAM.
INFO 2026-06-08 07:54:48 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 3s. Last read position: chr17:45,241,905
INFO 2026-06-08 07:54:48 MarkDuplicates Tracking 41398 as yet unmatched pairs. 15373 records in RAM.
INFO 2026-06-08 07:54:50 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 2s. Last read position: chr17:50,188,111
INFO 2026-06-08 07:54:50 MarkDuplicates Tracking 47045 as yet unmatched pairs. 21019 records in RAM.
INFO 2026-06-08 07:54:52 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 2s. Last read position: chr17:50,190,004
INFO 2026-06-08 07:54:52 MarkDuplicates Tracking 40899 as yet unmatched pairs. 14873 records in RAM.
INFO 2026-06-08 07:54:55 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 2s. Last read position: chr17:50,192,821
INFO 2026-06-08 07:54:55 MarkDuplicates Tracking 41467 as yet unmatched pairs. 15440 records in RAM.
INFO 2026-06-08 07:54:57 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 2s. Last read position: chr17:50,195,264
INFO 2026-06-08 07:54:57 MarkDuplicates Tracking 38697 as yet unmatched pairs. 12670 records in RAM.
INFO 2026-06-08 07:54:59 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 2s. Last read position: chr17:50,196,644
INFO 2026-06-08 07:54:59 MarkDuplicates Tracking 38981 as yet unmatched pairs. 12954 records in RAM.
INFO 2026-06-08 07:55:02 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 2s. Last read position: chr17:57,106,065
INFO 2026-06-08 07:55:02 MarkDuplicates Tracking 29260 as yet unmatched pairs. 3233 records in RAM.
INFO 2026-06-08 07:55:05 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 3s. Last read position: chr17:80,295,640
INFO 2026-06-08 07:55:05 MarkDuplicates Tracking 27157 as yet unmatched pairs. 1129 records in RAM.
INFO 2026-06-08 07:55:08 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 2s. Last read position: chr18:79,486,609
INFO 2026-06-08 07:55:08 MarkDuplicates Tracking 24935 as yet unmatched pairs. 58 records in RAM.
INFO 2026-06-08 07:55:10 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 2s. Last read position: chr19:8,334,772
INFO 2026-06-08 07:55:10 MarkDuplicates Tracking 22493 as yet unmatched pairs. 8485 records in RAM.
INFO 2026-06-08 07:55:13 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 2s. Last read position: chr19:17,511,803
INFO 2026-06-08 07:55:13 MarkDuplicates Tracking 20257 as yet unmatched pairs. 6249 records in RAM.
INFO 2026-06-08 07:55:15 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 2s. Last read position: chr19:41,905,183
INFO 2026-06-08 07:55:15 MarkDuplicates Tracking 18104 as yet unmatched pairs. 4095 records in RAM.
INFO 2026-06-08 07:55:17 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 1s. Last read position: chr19:49,601,523
INFO 2026-06-08 07:55:17 MarkDuplicates Tracking 15574 as yet unmatched pairs. 1564 records in RAM.
INFO 2026-06-08 07:55:19 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 1s. Last read position: chr20:10,658,472
INFO 2026-06-08 07:55:19 MarkDuplicates Tracking 13384 as yet unmatched pairs. 2398 records in RAM.
INFO 2026-06-08 07:55:21 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 2s. Last read position: chr20:62,335,040
INFO 2026-06-08 07:55:21 MarkDuplicates Tracking 11747 as yet unmatched pairs. 761 records in RAM.
INFO 2026-06-08 07:55:23 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 2s. Last read position: chr21:26,965,305
INFO 2026-06-08 07:55:23 MarkDuplicates Tracking 10033 as yet unmatched pairs. 2141 records in RAM.
INFO 2026-06-08 07:55:25 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 1s. Last read position: chr21:46,265,424
INFO 2026-06-08 07:55:25 MarkDuplicates Tracking 8099 as yet unmatched pairs. 207 records in RAM.
INFO 2026-06-08 07:55:28 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 2s. Last read position: chr22:37,771,721
INFO 2026-06-08 07:55:28 MarkDuplicates Tracking 6092 as yet unmatched pairs. 1888 records in RAM.
INFO 2026-06-08 07:55:31 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 3s. Last read position: chrX:20,234,805
INFO 2026-06-08 07:55:31 MarkDuplicates Tracking 3920 as yet unmatched pairs. 2196 records in RAM.
INFO 2026-06-08 07:55:35 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 3s. Last read position: chrX:154,349,807
INFO 2026-06-08 07:55:35 MarkDuplicates Tracking 2096 as yet unmatched pairs. 371 records in RAM.
INFO 2026-06-08 07:55:37 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 2s. Last read position: KI270733.1:177,391
INFO 2026-06-08 07:55:37 MarkDuplicates Tracking 7 as yet unmatched pairs. 7 records in RAM.
INFO 2026-06-08 07:55:37 MarkDuplicates Read 68066449 records. 0 pairs never matched.
INFO 2026-06-08 07:55:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 24062552304; totalMemory: 34359738368; maxMemory: 63585648640
INFO 2026-06-08 07:55:44 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 07:55:54 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 07:56:08 OpticalDuplicateFinder Large duplicate set. size = 1269
INFO 2026-06-08 07:56:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,822
INFO 2026-06-08 07:56:10 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 07:56:17 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 07:56:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 36193535240; totalMemory: 52143587328; maxMemory: 63585648640
INFO 2026-06-08 07:56:20 MarkDuplicates Marking 50621237 records as duplicates.
INFO 2026-06-08 07:56:20 MarkDuplicates Found 1244297 optical duplicate clusters.
INFO 2026-06-08 07:56:20 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 07:56:47 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:27s. Time for last 10,000,000: 27s. Last read position: chr2:237,366,837
INFO 2026-06-08 07:57:13 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:53s. Time for last 10,000,000: 26s. Last read position: chr6:169,248,560
INFO 2026-06-08 07:57:40 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:19s. Time for last 10,000,000: 26s. Last read position: chr11:801,975
INFO 2026-06-08 07:58:07 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:47s. Time for last 10,000,000: 27s. Last read position: chr15:66,387,404
INFO 2026-06-08 07:58:34 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:02:14s. Time for last 10,000,000: 27s. Last read position: chr17:50,190,004
INFO 2026-06-08 07:59:05 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:44s. Time for last 10,000,000: 30s. Last read position: chr19:49,601,523
INFO 2026-06-08 07:59:30 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 07:59:30 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 07:59:30 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 07:59:30 MarkDuplicates Before output close freeMemory: 201631696; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 07:59:30 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 07:59:30 MarkDuplicates After output close freeMemory: 104281808; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 07:59:30 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 6.74 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory