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_00584_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00584_B23MVV7LT4_1.md.bam --METRICS_FILE tih_rna_sample_00584_B23MVV7LT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:35:00.099 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 07:35:00 GMT 2026] MarkDuplicates --INPUT tih_rna_sample_00584_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00584_B23MVV7LT4_1.md.bam --METRICS_FILE tih_rna_sample_00584_B23MVV7LT4_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 07:35:00 GMT 2026] Executing as ?@nf-730ad11a5986b7874699d98dd39842f9-d772d-r7sjl 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 07:35:00 MarkDuplicates Start of doWork freeMemory: 105494312; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:35:00 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:35:00 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:35:06 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 4s. Last read position: chr1:16,628,602
INFO 2026-06-08 07:35:06 MarkDuplicates Tracking 2398 as yet unmatched pairs. 12 records in RAM.
INFO 2026-06-08 07:35:09 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 3s. Last read position: chr1:31,586,943
INFO 2026-06-08 07:35:09 MarkDuplicates Tracking 4691 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 07:35:13 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 3s. Last read position: chr1:48,436,794
INFO 2026-06-08 07:35:13 MarkDuplicates Tracking 6749 as yet unmatched pairs. 10 records in RAM.
INFO 2026-06-08 07:35:16 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 3s. Last read position: chr1:120,557,169
INFO 2026-06-08 07:35:16 MarkDuplicates Tracking 8970 as yet unmatched pairs. 87 records in RAM.
INFO 2026-06-08 07:35:19 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 3s. Last read position: chr1:154,947,665
INFO 2026-06-08 07:35:19 MarkDuplicates Tracking 10573 as yet unmatched pairs. 35 records in RAM.
INFO 2026-06-08 07:35:22 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 2s. Last read position: chr1:171,636,651
INFO 2026-06-08 07:35:22 MarkDuplicates Tracking 12698 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 07:35:25 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 2s. Last read position: chr1:225,921,825
INFO 2026-06-08 07:35:25 MarkDuplicates Tracking 15020 as yet unmatched pairs. 21 records in RAM.
INFO 2026-06-08 07:35:29 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 3s. Last read position: chr2:32,916,263
INFO 2026-06-08 07:35:29 MarkDuplicates Tracking 23198 as yet unmatched pairs. 16725 records in RAM.
INFO 2026-06-08 07:35:31 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 2s. Last read position: chr2:55,050,001
INFO 2026-06-08 07:35:31 MarkDuplicates Tracking 154798 as yet unmatched pairs. 7740 records in RAM.
INFO 2026-06-08 07:35:35 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 3s. Last read position: chr2:110,536,457
INFO 2026-06-08 07:35:35 MarkDuplicates Tracking 152535 as yet unmatched pairs. 5473 records in RAM.
INFO 2026-06-08 07:35:38 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 3s. Last read position: chr2:189,726,396
INFO 2026-06-08 07:35:38 MarkDuplicates Tracking 150617 as yet unmatched pairs. 3550 records in RAM.
INFO 2026-06-08 07:35:41 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 2s. Last read position: chr2:219,555,991
INFO 2026-06-08 07:35:41 MarkDuplicates Tracking 148492 as yet unmatched pairs. 1421 records in RAM.
INFO 2026-06-08 07:35:43 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 2s. Last read position: chr3:15,679,318
INFO 2026-06-08 07:35:43 MarkDuplicates Tracking 146194 as yet unmatched pairs. 7123 records in RAM.
INFO 2026-06-08 07:35:46 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 2s. Last read position: chr3:50,358,635
INFO 2026-06-08 07:35:46 MarkDuplicates Tracking 144010 as yet unmatched pairs. 4938 records in RAM.
INFO 2026-06-08 07:35:48 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 2s. Last read position: chr3:125,233,576
INFO 2026-06-08 07:35:48 MarkDuplicates Tracking 141745 as yet unmatched pairs. 2667 records in RAM.
INFO 2026-06-08 07:35:52 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 4s. Last read position: chr3:191,389,509
INFO 2026-06-08 07:35:52 MarkDuplicates Tracking 139464 as yet unmatched pairs. 377 records in RAM.
INFO 2026-06-08 07:35:55 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 2s. Last read position: chr4:67,544,173
INFO 2026-06-08 07:35:55 MarkDuplicates Tracking 137162 as yet unmatched pairs. 2207 records in RAM.
INFO 2026-06-08 07:35:58 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 2s. Last read position: chr4:186,603,915
INFO 2026-06-08 07:35:58 MarkDuplicates Tracking 135026 as yet unmatched pairs. 65 records in RAM.
INFO 2026-06-08 07:36:01 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 2s. Last read position: chr5:87,349,231
INFO 2026-06-08 07:36:01 MarkDuplicates Tracking 132832 as yet unmatched pairs. 4629 records in RAM.
INFO 2026-06-08 07:36:04 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 2s. Last read position: chr5:150,402,033
INFO 2026-06-08 07:36:04 MarkDuplicates Tracking 130742 as yet unmatched pairs. 2482 records in RAM.
INFO 2026-06-08 07:36:06 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 2s. Last read position: chr5:179,836,446
INFO 2026-06-08 07:36:06 MarkDuplicates Tracking 128864 as yet unmatched pairs. 602 records in RAM.
INFO 2026-06-08 07:36:09 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 2s. Last read position: chr6:31,817,220
INFO 2026-06-08 07:36:09 MarkDuplicates Tracking 126447 as yet unmatched pairs. 6176 records in RAM.
INFO 2026-06-08 07:36:11 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 2s. Last read position: chr6:42,966,285
INFO 2026-06-08 07:36:11 MarkDuplicates Tracking 124130 as yet unmatched pairs. 3858 records in RAM.
INFO 2026-06-08 07:36:15 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 3s. Last read position: chr6:138,431,714
INFO 2026-06-08 07:36:15 MarkDuplicates Tracking 121940 as yet unmatched pairs. 1662 records in RAM.
INFO 2026-06-08 07:36:19 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 3s. Last read position: chr7:5,325,116
INFO 2026-06-08 07:36:19 MarkDuplicates Tracking 119561 as yet unmatched pairs. 8571 records in RAM.
INFO 2026-06-08 07:36:21 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 2s. Last read position: chr7:66,995,309
INFO 2026-06-08 07:36:21 MarkDuplicates Tracking 117215 as yet unmatched pairs. 6223 records in RAM.
INFO 2026-06-08 07:36:24 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 2s. Last read position: chr7:94,430,247
INFO 2026-06-08 07:36:24 MarkDuplicates Tracking 115401 as yet unmatched pairs. 4409 records in RAM.
INFO 2026-06-08 07:36:27 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 2s. Last read position: chr7:123,709,088
INFO 2026-06-08 07:36:27 MarkDuplicates Tracking 113460 as yet unmatched pairs. 2466 records in RAM.
INFO 2026-06-08 07:36:30 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 3s. Last read position: chr7:155,737,593
INFO 2026-06-08 07:36:30 MarkDuplicates Tracking 111182 as yet unmatched pairs. 186 records in RAM.
INFO 2026-06-08 07:36:34 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 4s. Last read position: chr8:56,073,142
INFO 2026-06-08 07:36:34 MarkDuplicates Tracking 108969 as yet unmatched pairs. 3770 records in RAM.
INFO 2026-06-08 07:36:36 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 2s. Last read position: chr8:143,860,148
INFO 2026-06-08 07:36:36 MarkDuplicates Tracking 106968 as yet unmatched pairs. 1761 records in RAM.
INFO 2026-06-08 07:36:39 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 2s. Last read position: chr8:144,547,619
INFO 2026-06-08 07:36:39 MarkDuplicates Tracking 105279 as yet unmatched pairs. 72 records in RAM.
INFO 2026-06-08 07:36:42 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 3s. Last read position: chr9:86,323,031
INFO 2026-06-08 07:36:42 MarkDuplicates Tracking 103198 as yet unmatched pairs. 5143 records in RAM.
INFO 2026-06-08 07:36:45 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 3s. Last read position: chr9:128,421,134
INFO 2026-06-08 07:36:45 MarkDuplicates Tracking 100902 as yet unmatched pairs. 2846 records in RAM.
INFO 2026-06-08 07:36:48 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 2s. Last read position: chr9:137,168,807
INFO 2026-06-08 07:36:48 MarkDuplicates Tracking 98455 as yet unmatched pairs. 399 records in RAM.
INFO 2026-06-08 07:36:52 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 3s. Last read position: chr10:46,337,100
INFO 2026-06-08 07:36:52 MarkDuplicates Tracking 96170 as yet unmatched pairs. 3912 records in RAM.
INFO 2026-06-08 07:36:55 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 2s. Last read position: chr10:100,987,862
INFO 2026-06-08 07:36:55 MarkDuplicates Tracking 93911 as yet unmatched pairs. 1653 records in RAM.
INFO 2026-06-08 07:36:58 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 3s. Last read position: chr11:836,025
INFO 2026-06-08 07:36:58 MarkDuplicates Tracking 91417 as yet unmatched pairs. 10660 records in RAM.
INFO 2026-06-08 07:37:01 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 3s. Last read position: chr11:57,308,749
INFO 2026-06-08 07:37:01 MarkDuplicates Tracking 89130 as yet unmatched pairs. 8369 records in RAM.
INFO 2026-06-08 07:37:03 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 2s. Last read position: chr11:64,345,024
INFO 2026-06-08 07:37:03 MarkDuplicates Tracking 86812 as yet unmatched pairs. 6034 records in RAM.
INFO 2026-06-08 07:37:06 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 2s. Last read position: chr11:72,013,146
INFO 2026-06-08 07:37:06 MarkDuplicates Tracking 84455 as yet unmatched pairs. 3674 records in RAM.
INFO 2026-06-08 07:37:09 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 3s. Last read position: chr11:118,339,691
INFO 2026-06-08 07:37:09 MarkDuplicates Tracking 82110 as yet unmatched pairs. 1327 records in RAM.
INFO 2026-06-08 07:37:12 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:02:10s. Time for last 1,000,000: 2s. Last read position: chr12:6,652,741
INFO 2026-06-08 07:37:12 MarkDuplicates Tracking 79907 as yet unmatched pairs. 8495 records in RAM.
INFO 2026-06-08 07:37:15 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 2s. Last read position: chr12:50,105,604
INFO 2026-06-08 07:37:15 MarkDuplicates Tracking 77832 as yet unmatched pairs. 6419 records in RAM.
INFO 2026-06-08 07:37:18 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 3s. Last read position: chr12:57,180,697
INFO 2026-06-08 07:37:18 MarkDuplicates Tracking 75479 as yet unmatched pairs. 4066 records in RAM.
INFO 2026-06-08 07:37:21 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 2s. Last read position: chr12:113,185,887
INFO 2026-06-08 07:37:21 MarkDuplicates Tracking 73310 as yet unmatched pairs. 1896 records in RAM.
INFO 2026-06-08 07:37:24 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 3s. Last read position: chr13:39,012,966
INFO 2026-06-08 07:37:24 MarkDuplicates Tracking 71089 as yet unmatched pairs. 1630 records in RAM.
INFO 2026-06-08 07:37:27 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 2s. Last read position: chr14:23,524,681
INFO 2026-06-08 07:37:27 MarkDuplicates Tracking 68801 as yet unmatched pairs. 4417 records in RAM.
INFO 2026-06-08 07:37:30 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 3s. Last read position: chr14:76,762,901
INFO 2026-06-08 07:37:30 MarkDuplicates Tracking 66544 as yet unmatched pairs. 2156 records in RAM.
INFO 2026-06-08 07:37:33 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 2s. Last read position: chr15:28,702,621
INFO 2026-06-08 07:37:33 MarkDuplicates Tracking 64249 as yet unmatched pairs. 4272 records in RAM.
INFO 2026-06-08 07:37:36 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 3s. Last read position: chr15:69,455,182
INFO 2026-06-08 07:37:36 MarkDuplicates Tracking 62146 as yet unmatched pairs. 2168 records in RAM.
INFO 2026-06-08 07:37:40 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 3s. Last read position: chr15:99,131,603
INFO 2026-06-08 07:37:40 MarkDuplicates Tracking 60086 as yet unmatched pairs. 103 records in RAM.
INFO 2026-06-08 07:37:43 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 3s. Last read position: chr16:3,728,073
INFO 2026-06-08 07:37:43 MarkDuplicates Tracking 57678 as yet unmatched pairs. 7129 records in RAM.
INFO 2026-06-08 07:37:46 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 2s. Last read position: chr16:18,379,503
INFO 2026-06-08 07:37:46 MarkDuplicates Tracking 56383 as yet unmatched pairs. 5833 records in RAM.
INFO 2026-06-08 07:37:48 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 2s. Last read position: chr16:28,734,539
INFO 2026-06-08 07:37:48 MarkDuplicates Tracking 55300 as yet unmatched pairs. 4750 records in RAM.
INFO 2026-06-08 07:37:51 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 2s. Last read position: chr16:31,981,985
INFO 2026-06-08 07:37:51 MarkDuplicates Tracking 53448 as yet unmatched pairs. 2894 records in RAM.
INFO 2026-06-08 07:37:54 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 2s. Last read position: chr16:88,430,346
INFO 2026-06-08 07:37:54 MarkDuplicates Tracking 51231 as yet unmatched pairs. 671 records in RAM.
INFO 2026-06-08 07:37:57 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 3s. Last read position: chr17:7,513,218
INFO 2026-06-08 07:37:57 MarkDuplicates Tracking 48964 as yet unmatched pairs. 11267 records in RAM.
INFO 2026-06-08 07:37:59 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 2s. Last read position: chr17:37,978,558
INFO 2026-06-08 07:37:59 MarkDuplicates Tracking 46849 as yet unmatched pairs. 9152 records in RAM.
INFO 2026-06-08 07:38:02 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 2s. Last read position: chr17:48,059,096
INFO 2026-06-08 07:38:02 MarkDuplicates Tracking 44729 as yet unmatched pairs. 7031 records in RAM.
INFO 2026-06-08 07:38:05 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 2s. Last read position: chr17:50,196,655
INFO 2026-06-08 07:38:05 MarkDuplicates Tracking 43216 as yet unmatched pairs. 5518 records in RAM.
INFO 2026-06-08 07:38:09 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 3s. Last read position: chr17:75,616,626
INFO 2026-06-08 07:38:09 MarkDuplicates Tracking 39980 as yet unmatched pairs. 2275 records in RAM.
INFO 2026-06-08 07:38:11 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 2s. Last read position: chr18:9,257,606
INFO 2026-06-08 07:38:11 MarkDuplicates Tracking 37506 as yet unmatched pairs. 1400 records in RAM.
INFO 2026-06-08 07:38:15 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 3s. Last read position: chr19:1,417,499
INFO 2026-06-08 07:38:15 MarkDuplicates Tracking 34974 as yet unmatched pairs. 14650 records in RAM.
INFO 2026-06-08 07:38:17 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 2s. Last read position: chr19:5,131,328
INFO 2026-06-08 07:38:17 MarkDuplicates Tracking 32647 as yet unmatched pairs. 12316 records in RAM.
INFO 2026-06-08 07:38:20 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 2s. Last read position: chr19:12,943,931
INFO 2026-06-08 07:38:20 MarkDuplicates Tracking 30197 as yet unmatched pairs. 9865 records in RAM.
INFO 2026-06-08 07:38:23 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 2s. Last read position: chr19:19,496,194
INFO 2026-06-08 07:38:23 MarkDuplicates Tracking 27748 as yet unmatched pairs. 7413 records in RAM.
INFO 2026-06-08 07:38:27 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 4s. Last read position: chr19:42,086,443
INFO 2026-06-08 07:38:27 MarkDuplicates Tracking 25076 as yet unmatched pairs. 4739 records in RAM.
INFO 2026-06-08 07:38:31 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 3s. Last read position: chr19:49,104,714
INFO 2026-06-08 07:38:31 MarkDuplicates Tracking 22777 as yet unmatched pairs. 2439 records in RAM.
INFO 2026-06-08 07:38:33 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 2s. Last read position: chr19:58,550,492
INFO 2026-06-08 07:38:33 MarkDuplicates Tracking 20459 as yet unmatched pairs. 120 records in RAM.
INFO 2026-06-08 07:38:36 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 2s. Last read position: chr20:43,460,540
INFO 2026-06-08 07:38:36 MarkDuplicates Tracking 18034 as yet unmatched pairs. 2414 records in RAM.
INFO 2026-06-08 07:38:39 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 3s. Last read position: chr21:8,214,680
INFO 2026-06-08 07:38:39 MarkDuplicates Tracking 15558 as yet unmatched pairs. 3600 records in RAM.
INFO 2026-06-08 07:38:41 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 1s. Last read position: chr21:8,443,379
INFO 2026-06-08 07:38:41 MarkDuplicates Tracking 14228 as yet unmatched pairs. 2263 records in RAM.
INFO 2026-06-08 07:38:44 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 2s. Last read position: chr21:46,119,066
INFO 2026-06-08 07:38:44 MarkDuplicates Tracking 12327 as yet unmatched pairs. 362 records in RAM.
INFO 2026-06-08 07:38:48 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 3s. Last read position: chr22:31,712,879
INFO 2026-06-08 07:38:48 MarkDuplicates Tracking 10008 as yet unmatched pairs. 3199 records in RAM.
INFO 2026-06-08 07:38:50 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:03:48s. Time for last 1,000,000: 2s. Last read position: chr22:46,677,162
INFO 2026-06-08 07:38:50 MarkDuplicates Tracking 7790 as yet unmatched pairs. 981 records in RAM.
INFO 2026-06-08 07:38:54 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 3s. Last read position: chrX:53,234,201
INFO 2026-06-08 07:38:54 MarkDuplicates Tracking 5463 as yet unmatched pairs. 2423 records in RAM.
INFO 2026-06-08 07:38:57 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 3s. Last read position: chrX:154,366,751
INFO 2026-06-08 07:38:57 MarkDuplicates Tracking 3398 as yet unmatched pairs. 353 records in RAM.
INFO 2026-06-08 07:38:59 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 2s. Last read position: KI270733.1:131,005
INFO 2026-06-08 07:38:59 MarkDuplicates Tracking 1289 as yet unmatched pairs. 1288 records in RAM.
INFO 2026-06-08 07:39:01 MarkDuplicates Read 79642900 records. 0 pairs never matched.
INFO 2026-06-08 07:39:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 26440903128; totalMemory: 37715181568; maxMemory: 63585648640
INFO 2026-06-08 07:39:07 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 07:39:16 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 07:39:41 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 07:39:50 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 07:39:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 32703928864; totalMemory: 48653926400; maxMemory: 63585648640
INFO 2026-06-08 07:39:53 MarkDuplicates Marking 54350676 records as duplicates.
INFO 2026-06-08 07:39:53 MarkDuplicates Found 1625110 optical duplicate clusters.
INFO 2026-06-08 07:39:53 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 07:40:25 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:32s. Time for last 10,000,000: 32s. Last read position: chr2:110,536,457
INFO 2026-06-08 07:40:55 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:01:01s. Time for last 10,000,000: 29s. Last read position: chr5:150,402,033
INFO 2026-06-08 07:41:23 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:30s. Time for last 10,000,000: 28s. Last read position: chr8:56,073,142
INFO 2026-06-08 07:41:52 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:59s. Time for last 10,000,000: 28s. Last read position: chr11:64,345,024
INFO 2026-06-08 07:42:21 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:02:28s. Time for last 10,000,000: 29s. Last read position: chr15:28,702,621
INFO 2026-06-08 07:42:53 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:03:00s. Time for last 10,000,000: 31s. Last read position: chr17:48,059,096
INFO 2026-06-08 07:43:23 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:03:30s. Time for last 10,000,000: 29s. Last read position: chr19:58,550,492
INFO 2026-06-08 07:43:51 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:03:58s. Time for last 10,000,000: 28s. Last read position: */*
INFO 2026-06-08 07:43:53 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 07:43:53 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 07:43:53 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 07:43:53 MarkDuplicates Before output close freeMemory: 16746995536; totalMemory: 48653926400; maxMemory: 63585648640
INFO 2026-06-08 07:43:53 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 07:43:53 MarkDuplicates After output close freeMemory: 104352712; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 07:43:53 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 8.89 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory