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 BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam --METRICS_FILE BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:29:24.268 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Jun 08 07:29:24 GMT 2026] MarkDuplicates --INPUT BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.md.bam --METRICS_FILE BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_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 07:29:24 GMT 2026] Executing as ?@nf-7df8fd29576e32144814fdce4bb38392-9f32c-rd4f2 on Linux 6.12.88 amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0
INFO 2026-06-08 07:29:24 MarkDuplicates Start of doWork freeMemory: 105828080; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:29:24 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:29:24 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:29:29 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:19,074,799
INFO 2026-06-08 07:29:29 MarkDuplicates Tracking 2356 as yet unmatched pairs. 3 records in RAM.
INFO 2026-06-08 07:29:32 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 3s. Last read position: chr1:41,381,776
INFO 2026-06-08 07:29:32 MarkDuplicates Tracking 4323 as yet unmatched pairs. 3 records in RAM.
INFO 2026-06-08 07:29:35 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 2s. Last read position: chr1:103,617,952
INFO 2026-06-08 07:29:35 MarkDuplicates Tracking 5907 as yet unmatched pairs. 99 records in RAM.
INFO 2026-06-08 07:29:37 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: chr1:103,662,901
INFO 2026-06-08 07:29:37 MarkDuplicates Tracking 6734 as yet unmatched pairs. 348 records in RAM.
INFO 2026-06-08 07:29:39 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: chr1:103,714,755
INFO 2026-06-08 07:29:39 MarkDuplicates Tracking 6983 as yet unmatched pairs. 178 records in RAM.
INFO 2026-06-08 07:29:40 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: chr1:109,171,866
INFO 2026-06-08 07:29:40 MarkDuplicates Tracking 7077 as yet unmatched pairs. 5 records in RAM.
INFO 2026-06-08 07:29:43 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr1:155,187,775
INFO 2026-06-08 07:29:43 MarkDuplicates Tracking 8751 as yet unmatched pairs. 3 records in RAM.
INFO 2026-06-08 07:29:45 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 2s. Last read position: chr1:206,930,285
INFO 2026-06-08 07:29:45 MarkDuplicates Tracking 10814 as yet unmatched pairs. 139 records in RAM.
INFO 2026-06-08 07:29:47 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 2s. Last read position: chr2:10,047,883
INFO 2026-06-08 07:29:47 MarkDuplicates Tracking 12705 as yet unmatched pairs. 12415 records in RAM.
INFO 2026-06-08 07:29:50 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 2s. Last read position: chr2:38,482,724
INFO 2026-06-08 07:29:50 MarkDuplicates Tracking 129747 as yet unmatched pairs. 6518 records in RAM.
INFO 2026-06-08 07:29:52 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 1s. Last read position: chr2:95,276,231
INFO 2026-06-08 07:29:52 MarkDuplicates Tracking 127517 as yet unmatched pairs. 4268 records in RAM.
INFO 2026-06-08 07:29:54 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 2s. Last read position: chr2:178,573,162
INFO 2026-06-08 07:29:54 MarkDuplicates Tracking 125656 as yet unmatched pairs. 2365 records in RAM.
INFO 2026-06-08 07:29:57 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 2s. Last read position: chr2:241,063,676
INFO 2026-06-08 07:29:57 MarkDuplicates Tracking 123754 as yet unmatched pairs. 356 records in RAM.
INFO 2026-06-08 07:29:59 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 2s. Last read position: chr3:48,694,848
INFO 2026-06-08 07:29:59 MarkDuplicates Tracking 121894 as yet unmatched pairs. 3408 records in RAM.
INFO 2026-06-08 07:30:01 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 2s. Last read position: chr3:127,660,820
INFO 2026-06-08 07:30:01 MarkDuplicates Tracking 120565 as yet unmatched pairs. 2052 records in RAM.
INFO 2026-06-08 07:30:03 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 1s. Last read position: chr3:197,026,710
INFO 2026-06-08 07:30:03 MarkDuplicates Tracking 118580 as yet unmatched pairs. 45 records in RAM.
INFO 2026-06-08 07:30:05 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 2s. Last read position: chr4:69,999,670
INFO 2026-06-08 07:30:05 MarkDuplicates Tracking 119365 as yet unmatched pairs. 9880 records in RAM.
INFO 2026-06-08 07:30:07 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 2s. Last read position: chr4:70,384,520
INFO 2026-06-08 07:30:07 MarkDuplicates Tracking 116190 as yet unmatched pairs. 6703 records in RAM.
INFO 2026-06-08 07:30:10 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 2s. Last read position: chr4:70,389,866
INFO 2026-06-08 07:30:10 MarkDuplicates Tracking 115015 as yet unmatched pairs. 5527 records in RAM.
INFO 2026-06-08 07:30:12 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 2s. Last read position: chr4:70,481,286
INFO 2026-06-08 07:30:12 MarkDuplicates Tracking 114078 as yet unmatched pairs. 4589 records in RAM.
INFO 2026-06-08 07:30:15 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 2s. Last read position: chr4:70,481,656
INFO 2026-06-08 07:30:15 MarkDuplicates Tracking 111400 as yet unmatched pairs. 1900 records in RAM.
INFO 2026-06-08 07:30:17 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 2s. Last read position: chr5:443,227
INFO 2026-06-08 07:30:17 MarkDuplicates Tracking 109506 as yet unmatched pairs. 5156 records in RAM.
INFO 2026-06-08 07:30:20 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 2s. Last read position: chr5:132,591,235
INFO 2026-06-08 07:30:20 MarkDuplicates Tracking 107271 as yet unmatched pairs. 2897 records in RAM.
INFO 2026-06-08 07:30:22 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 1s. Last read position: chr5:172,770,753
INFO 2026-06-08 07:30:22 MarkDuplicates Tracking 105618 as yet unmatched pairs. 884 records in RAM.
INFO 2026-06-08 07:30:24 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 1s. Last read position: chr6:30,910,858
INFO 2026-06-08 07:30:24 MarkDuplicates Tracking 103532 as yet unmatched pairs. 3514 records in RAM.
INFO 2026-06-08 07:30:26 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 2s. Last read position: chr6:63,572,572
INFO 2026-06-08 07:30:26 MarkDuplicates Tracking 101850 as yet unmatched pairs. 1820 records in RAM.
INFO 2026-06-08 07:30:28 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 1s. Last read position: chr6:158,783,657
INFO 2026-06-08 07:30:28 MarkDuplicates Tracking 100417 as yet unmatched pairs. 344 records in RAM.
INFO 2026-06-08 07:30:30 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 1s. Last read position: chr7:66,945,138
INFO 2026-06-08 07:30:30 MarkDuplicates Tracking 97961 as yet unmatched pairs. 4607 records in RAM.
INFO 2026-06-08 07:30:32 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 2s. Last read position: chr7:100,694,318
INFO 2026-06-08 07:30:32 MarkDuplicates Tracking 96260 as yet unmatched pairs. 2893 records in RAM.
INFO 2026-06-08 07:30:34 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 1s. Last read position: chr7:144,284,829
INFO 2026-06-08 07:30:34 MarkDuplicates Tracking 93956 as yet unmatched pairs. 549 records in RAM.
INFO 2026-06-08 07:30:36 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 1s. Last read position: chr8:70,148,423
INFO 2026-06-08 07:30:36 MarkDuplicates Tracking 91807 as yet unmatched pairs. 2174 records in RAM.
INFO 2026-06-08 07:30:39 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 2s. Last read position: chr8:143,862,065
INFO 2026-06-08 07:30:39 MarkDuplicates Tracking 90287 as yet unmatched pairs. 604 records in RAM.
INFO 2026-06-08 07:30:41 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 2s. Last read position: chr9:35,398,214
INFO 2026-06-08 07:30:41 MarkDuplicates Tracking 89097 as yet unmatched pairs. 3887 records in RAM.
INFO 2026-06-08 07:30:43 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 2s. Last read position: chr9:121,760,144
INFO 2026-06-08 07:30:43 MarkDuplicates Tracking 87707 as yet unmatched pairs. 2150 records in RAM.
INFO 2026-06-08 07:30:45 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 2s. Last read position: chr10:3,163,756
INFO 2026-06-08 07:30:45 MarkDuplicates Tracking 85500 as yet unmatched pairs. 3925 records in RAM.
INFO 2026-06-08 07:30:47 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 1s. Last read position: chr10:79,277,299
INFO 2026-06-08 07:30:47 MarkDuplicates Tracking 83959 as yet unmatched pairs. 2360 records in RAM.
INFO 2026-06-08 07:30:49 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 2s. Last read position: chr10:122,589,028
INFO 2026-06-08 07:30:49 MarkDuplicates Tracking 82319 as yet unmatched pairs. 661 records in RAM.
INFO 2026-06-08 07:30:51 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 2s. Last read position: chr11:1,242,725
INFO 2026-06-08 07:30:51 MarkDuplicates Tracking 81188 as yet unmatched pairs. 8880 records in RAM.
INFO 2026-06-08 07:30:53 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 1s. Last read position: chr11:1,245,049
INFO 2026-06-08 07:30:53 MarkDuplicates Tracking 80774 as yet unmatched pairs. 8466 records in RAM.
INFO 2026-06-08 07:30:56 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 2s. Last read position: chr11:1,248,038
INFO 2026-06-08 07:30:56 MarkDuplicates Tracking 80246 as yet unmatched pairs. 7938 records in RAM.
INFO 2026-06-08 07:30:57 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 1s. Last read position: chr11:1,250,478
INFO 2026-06-08 07:30:57 MarkDuplicates Tracking 79140 as yet unmatched pairs. 6831 records in RAM.
INFO 2026-06-08 07:31:00 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 2s. Last read position: chr11:45,806,027
INFO 2026-06-08 07:31:00 MarkDuplicates Tracking 77722 as yet unmatched pairs. 5392 records in RAM.
INFO 2026-06-08 07:31:03 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 3s. Last read position: chr11:65,503,409
INFO 2026-06-08 07:31:03 MarkDuplicates Tracking 75705 as yet unmatched pairs. 3351 records in RAM.
INFO 2026-06-08 07:31:05 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 2s. Last read position: chr11:94,869,215
INFO 2026-06-08 07:31:05 MarkDuplicates Tracking 73619 as yet unmatched pairs. 1242 records in RAM.
INFO 2026-06-08 07:31:08 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 2s. Last read position: chr12:7,091,519
INFO 2026-06-08 07:31:08 MarkDuplicates Tracking 71740 as yet unmatched pairs. 8876 records in RAM.
INFO 2026-06-08 07:31:10 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 2s. Last read position: chr12:10,882,383
INFO 2026-06-08 07:31:10 MarkDuplicates Tracking 71343 as yet unmatched pairs. 8479 records in RAM.
INFO 2026-06-08 07:31:13 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 2s. Last read position: chr12:10,929,258
INFO 2026-06-08 07:31:13 MarkDuplicates Tracking 70331 as yet unmatched pairs. 7465 records in RAM.
INFO 2026-06-08 07:31:15 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 2s. Last read position: chr12:10,930,855
INFO 2026-06-08 07:31:15 MarkDuplicates Tracking 69269 as yet unmatched pairs. 6403 records in RAM.
INFO 2026-06-08 07:31:17 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 2s. Last read position: chr12:40,487,305
INFO 2026-06-08 07:31:17 MarkDuplicates Tracking 67577 as yet unmatched pairs. 4706 records in RAM.
INFO 2026-06-08 07:31:20 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 2s. Last read position: chr12:56,642,492
INFO 2026-06-08 07:31:20 MarkDuplicates Tracking 65625 as yet unmatched pairs. 2738 records in RAM.
INFO 2026-06-08 07:31:22 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 2s. Last read position: chr12:110,445,482
INFO 2026-06-08 07:31:22 MarkDuplicates Tracking 64255 as yet unmatched pairs. 1352 records in RAM.
INFO 2026-06-08 07:31:24 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 2s. Last read position: chr13:39,014,375
INFO 2026-06-08 07:31:24 MarkDuplicates Tracking 62682 as yet unmatched pairs. 1347 records in RAM.
INFO 2026-06-08 07:31:26 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 2s. Last read position: chr14:32,545,812
INFO 2026-06-08 07:31:26 MarkDuplicates Tracking 60529 as yet unmatched pairs. 4998 records in RAM.
INFO 2026-06-08 07:31:28 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 1s. Last read position: chr14:92,811,568
INFO 2026-06-08 07:31:28 MarkDuplicates Tracking 58818 as yet unmatched pairs. 3247 records in RAM.
INFO 2026-06-08 07:31:30 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 1s. Last read position: chr14:105,707,164
INFO 2026-06-08 07:31:30 MarkDuplicates Tracking 57877 as yet unmatched pairs. 2253 records in RAM.
INFO 2026-06-08 07:31:32 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 2s. Last read position: chr14:105,931,651
INFO 2026-06-08 07:31:32 MarkDuplicates Tracking 55650 as yet unmatched pairs. 25 records in RAM.
INFO 2026-06-08 07:31:34 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 1s. Last read position: chr15:66,518,855
INFO 2026-06-08 07:31:34 MarkDuplicates Tracking 54390 as yet unmatched pairs. 1291 records in RAM.
INFO 2026-06-08 07:31:37 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 3s. Last read position: chr16:1,459,126
INFO 2026-06-08 07:31:37 MarkDuplicates Tracking 52921 as yet unmatched pairs. 6520 records in RAM.
INFO 2026-06-08 07:31:40 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 2s. Last read position: chr16:4,469,456
INFO 2026-06-08 07:31:40 MarkDuplicates Tracking 50996 as yet unmatched pairs. 4593 records in RAM.
INFO 2026-06-08 07:31:41 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 1s. Last read position: chr16:21,837,207
INFO 2026-06-08 07:31:41 MarkDuplicates Tracking 49854 as yet unmatched pairs. 3445 records in RAM.
INFO 2026-06-08 07:31:43 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 1s. Last read position: chr16:30,711,836
INFO 2026-06-08 07:31:43 MarkDuplicates Tracking 48627 as yet unmatched pairs. 2212 records in RAM.
INFO 2026-06-08 07:31:45 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 1s. Last read position: chr16:88,647,101
INFO 2026-06-08 07:31:45 MarkDuplicates Tracking 46849 as yet unmatched pairs. 372 records in RAM.
INFO 2026-06-08 07:31:47 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 2s. Last read position: chr17:16,382,161
INFO 2026-06-08 07:31:47 MarkDuplicates Tracking 44814 as yet unmatched pairs. 5625 records in RAM.
INFO 2026-06-08 07:31:49 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 2s. Last read position: chr17:42,120,986
INFO 2026-06-08 07:31:49 MarkDuplicates Tracking 43165 as yet unmatched pairs. 3968 records in RAM.
INFO 2026-06-08 07:31:51 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 1s. Last read position: chr17:64,504,244
INFO 2026-06-08 07:31:51 MarkDuplicates Tracking 41369 as yet unmatched pairs. 2167 records in RAM.
INFO 2026-06-08 07:31:54 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 2s. Last read position: chr17:82,587,143
INFO 2026-06-08 07:31:54 MarkDuplicates Tracking 39289 as yet unmatched pairs. 74 records in RAM.
INFO 2026-06-08 07:31:56 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 2s. Last read position: chr19:2,353,114
INFO 2026-06-08 07:31:56 MarkDuplicates Tracking 37549 as yet unmatched pairs. 7936 records in RAM.
INFO 2026-06-08 07:31:59 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 2s. Last read position: chr19:13,137,356
INFO 2026-06-08 07:31:59 MarkDuplicates Tracking 35729 as yet unmatched pairs. 6106 records in RAM.
INFO 2026-06-08 07:32:02 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 2s. Last read position: chr19:39,177,677
INFO 2026-06-08 07:32:02 MarkDuplicates Tracking 33426 as yet unmatched pairs. 3765 records in RAM.
INFO 2026-06-08 07:32:04 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 2s. Last read position: chr19:49,497,270
INFO 2026-06-08 07:32:04 MarkDuplicates Tracking 31035 as yet unmatched pairs. 1353 records in RAM.
INFO 2026-06-08 07:32:06 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 2s. Last read position: chr20:17,658,891
INFO 2026-06-08 07:32:06 MarkDuplicates Tracking 29094 as yet unmatched pairs. 7822 records in RAM.
INFO 2026-06-08 07:32:09 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 3s. Last read position: chr20:23,685,944
INFO 2026-06-08 07:32:09 MarkDuplicates Tracking 27969 as yet unmatched pairs. 6696 records in RAM.
INFO 2026-06-08 07:32:12 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 2s. Last read position: chr20:23,747,843
INFO 2026-06-08 07:32:12 MarkDuplicates Tracking 26383 as yet unmatched pairs. 5110 records in RAM.
INFO 2026-06-08 07:32:14 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 2s. Last read position: chr20:33,169,190
INFO 2026-06-08 07:32:14 MarkDuplicates Tracking 24492 as yet unmatched pairs. 3217 records in RAM.
INFO 2026-06-08 07:32:16 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 2s. Last read position: chr20:51,622,072
INFO 2026-06-08 07:32:16 MarkDuplicates Tracking 22608 as yet unmatched pairs. 1324 records in RAM.
INFO 2026-06-08 07:32:18 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 2s. Last read position: chr21:8,214,783
INFO 2026-06-08 07:32:18 MarkDuplicates Tracking 21176 as yet unmatched pairs. 7565 records in RAM.
INFO 2026-06-08 07:32:20 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 1s. Last read position: chr21:8,254,558
INFO 2026-06-08 07:32:20 MarkDuplicates Tracking 19106 as yet unmatched pairs. 5481 records in RAM.
INFO 2026-06-08 07:32:21 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 1s. Last read position: chr21:8,397,776
INFO 2026-06-08 07:32:21 MarkDuplicates Tracking 18895 as yet unmatched pairs. 5270 records in RAM.
INFO 2026-06-08 07:32:23 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 1s. Last read position: chr21:8,400,997
INFO 2026-06-08 07:32:23 MarkDuplicates Tracking 16024 as yet unmatched pairs. 2382 records in RAM.
INFO 2026-06-08 07:32:25 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,105
INFO 2026-06-08 07:32:25 MarkDuplicates Tracking 14911 as yet unmatched pairs. 1263 records in RAM.
INFO 2026-06-08 07:32:26 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 1s. Last read position: chr21:45,992,208
INFO 2026-06-08 07:32:26 MarkDuplicates Tracking 13852 as yet unmatched pairs. 202 records in RAM.
INFO 2026-06-08 07:32:28 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 1s. Last read position: chr22:37,630,934
INFO 2026-06-08 07:32:28 MarkDuplicates Tracking 11084 as yet unmatched pairs. 1631 records in RAM.
INFO 2026-06-08 07:32:30 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 2s. Last read position: chrX:40,073,338
INFO 2026-06-08 07:32:30 MarkDuplicates Tracking 9100 as yet unmatched pairs. 2096 records in RAM.
INFO 2026-06-08 07:32:32 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 1s. Last read position: chrX:153,694,863
INFO 2026-06-08 07:32:32 MarkDuplicates Tracking 7682 as yet unmatched pairs. 657 records in RAM.
INFO 2026-06-08 07:32:34 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 2s. Last read position: GL000220.1:114,254
INFO 2026-06-08 07:32:34 MarkDuplicates Tracking 6804 as yet unmatched pairs. 2482 records in RAM.
INFO 2026-06-08 07:32:36 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 1s. Last read position: GL000220.1:157,231
INFO 2026-06-08 07:32:36 MarkDuplicates Tracking 4476 as yet unmatched pairs. 153 records in RAM.
INFO 2026-06-08 07:32:37 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 1s. Last read position: GL000220.1:160,308
INFO 2026-06-08 07:32:37 MarkDuplicates Tracking 4341 as yet unmatched pairs. 18 records in RAM.
INFO 2026-06-08 07:32:39 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 1s. Last read position: KI270733.1:131,108
INFO 2026-06-08 07:32:39 MarkDuplicates Tracking 2111 as yet unmatched pairs. 2110 records in RAM.
INFO 2026-06-08 07:32:41 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 2s. Last read position: KI270733.1:175,044
INFO 2026-06-08 07:32:41 MarkDuplicates Tracking 139 as yet unmatched pairs. 138 records in RAM.
INFO 2026-06-08 07:32:43 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 1s. Last read position: KI270733.1:178,276
INFO 2026-06-08 07:32:43 MarkDuplicates Tracking 28 as yet unmatched pairs. 27 records in RAM.
INFO 2026-06-08 07:32:44 MarkDuplicates Read 90356035 records. 0 pairs never matched.
INFO 2026-06-08 07:32:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 25257326160; totalMemory: 36037459968; maxMemory: 63585648640
INFO 2026-06-08 07:32:50 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 07:32:57 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 07:33:01 OpticalDuplicateFinder Large duplicate set. size = 1213
INFO 2026-06-08 07:33:01 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,284
INFO 2026-06-08 07:33:01 OpticalDuplicateFinder Large duplicate set. size = 1297
INFO 2026-06-08 07:33:01 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,952
INFO 2026-06-08 07:33:03 OpticalDuplicateFinder Large duplicate set. size = 1187
INFO 2026-06-08 07:33:03 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,654
INFO 2026-06-08 07:33:03 OpticalDuplicateFinder Large duplicate set. size = 1308
INFO 2026-06-08 07:33:03 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:10,441
INFO 2026-06-08 07:33:03 OpticalDuplicateFinder Large duplicate set. size = 1154
INFO 2026-06-08 07:33:03 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,252
INFO 2026-06-08 07:33:03 OpticalDuplicateFinder Large duplicate set. size = 1569
INFO 2026-06-08 07:33:03 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,103
INFO 2026-06-08 07:33:04 OpticalDuplicateFinder Large duplicate set. size = 1201
INFO 2026-06-08 07:33:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:17,261
INFO 2026-06-08 07:33:04 OpticalDuplicateFinder Large duplicate set. size = 1583
INFO 2026-06-08 07:33:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,520
INFO 2026-06-08 07:33:04 OpticalDuplicateFinder Large duplicate set. size = 1416
INFO 2026-06-08 07:33:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:25,319
INFO 2026-06-08 07:33:04 OpticalDuplicateFinder Large duplicate set. size = 1145
INFO 2026-06-08 07:33:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,417
INFO 2026-06-08 07:33:04 OpticalDuplicateFinder Large duplicate set. size = 1876
INFO 2026-06-08 07:33:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:8,200
INFO 2026-06-08 07:33:04 OpticalDuplicateFinder Large duplicate set. size = 1144
INFO 2026-06-08 07:33:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,725
INFO 2026-06-08 07:33:04 OpticalDuplicateFinder Large duplicate set. size = 1721
INFO 2026-06-08 07:33:04 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,413
INFO 2026-06-08 07:33:10 OpticalDuplicateFinder Large duplicate set. size = 1060
INFO 2026-06-08 07:33:10 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,730
INFO 2026-06-08 07:33:10 OpticalDuplicateFinder Large duplicate set. size = 1076
INFO 2026-06-08 07:33:10 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,824
INFO 2026-06-08 07:33:12 OpticalDuplicateFinder Large duplicate set. size = 1397
INFO 2026-06-08 07:33:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,924
INFO 2026-06-08 07:33:15 OpticalDuplicateFinder Large duplicate set. size = 1060
INFO 2026-06-08 07:33:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,933
INFO 2026-06-08 07:33:15 OpticalDuplicateFinder Large duplicate set. size = 1059
INFO 2026-06-08 07:33:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,811
INFO 2026-06-08 07:33:15 OpticalDuplicateFinder Large duplicate set. size = 1353
INFO 2026-06-08 07:33:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,545
INFO 2026-06-08 07:33:15 OpticalDuplicateFinder Large duplicate set. size = 1120
INFO 2026-06-08 07:33:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,021
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder Large duplicate set. size = 1040
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,035
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder Large duplicate set. size = 1280
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:25,399
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder Large duplicate set. size = 1561
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,520
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder Large duplicate set. size = 1019
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,089
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder Large duplicate set. size = 1137
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,752
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder Large duplicate set. size = 2279
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:1,688
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:23,466
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder Large duplicate set. size = 1433
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,131
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder Large duplicate set. size = 1763
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,463
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder Large duplicate set. size = 1302
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:26,103
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder Large duplicate set. size = 1589
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,035
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder Large duplicate set. size = 1659
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,184
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder Large duplicate set. size = 1644
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,081
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder Large duplicate set. size = 2747
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,776
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,197
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder Large duplicate set. size = 2040
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-22,330
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-22,444
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder Large duplicate set. size = 1159
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-14,572
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder Large duplicate set. size = 1422
INFO 2026-06-08 07:33:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,746
INFO 2026-06-08 07:33:17 OpticalDuplicateFinder Large duplicate set. size = 1148
INFO 2026-06-08 07:33:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:2,594
INFO 2026-06-08 07:33:17 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 07:33:23 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 07:33:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 20087330904; totalMemory: 36037459968; maxMemory: 63585648640
INFO 2026-06-08 07:33:26 MarkDuplicates Marking 59188479 records as duplicates.
INFO 2026-06-08 07:33:26 MarkDuplicates Found 1201115 optical duplicate clusters.
INFO 2026-06-08 07:33:26 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 07:33:49 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:23s. Time for last 10,000,000: 23s. Last read position: chr2:38,482,724
INFO 2026-06-08 07:34:12 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:45s. Time for last 10,000,000: 22s. Last read position: chr4:70,481,286
INFO 2026-06-08 07:34:33 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:07s. Time for last 10,000,000: 21s. Last read position: chr7:144,284,829
INFO 2026-06-08 07:34:54 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:27s. Time for last 10,000,000: 20s. Last read position: chr11:1,248,038
INFO 2026-06-08 07:35:15 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:48s. Time for last 10,000,000: 20s. Last read position: chr12:56,642,492
INFO 2026-06-08 07:35:36 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:09s. Time for last 10,000,000: 20s. Last read position: chr16:21,837,207
INFO 2026-06-08 07:35:56 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:30s. Time for last 10,000,000: 20s. Last read position: chr19:49,497,270
INFO 2026-06-08 07:36:17 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:50s. Time for last 10,000,000: 20s. Last read position: chr21:8,444,105
INFO 2026-06-08 07:36:36 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:03:10s. Time for last 10,000,000: 19s. Last read position: KI270733.1:178,276
INFO 2026-06-08 07:36:40 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 07:36:40 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 07:36:40 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 07:36:40 MarkDuplicates Before output close freeMemory: 201977816; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 07:36:40 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 07:36:40 MarkDuplicates After output close freeMemory: 104222944; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 07:36:40 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 7.27 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory