Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/b35d930a678a00f304113d70219d61/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/b35d930a678a00f304113d70219d61/.command.run Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/3d69f286743fc925a3e0acd1cf500f/tih_rna_sample_00575_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam ==> STAGING COMPLETE (5 inputs) 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_00575_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00575_B23MVV7LT4_1.md.bam --METRICS_FILE tih_rna_sample_00575_B23MVV7LT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT 07:45:17.363 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 07:45:17 GMT 2026] MarkDuplicates --INPUT tih_rna_sample_00575_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00575_B23MVV7LT4_1.md.bam --METRICS_FILE tih_rna_sample_00575_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 --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 07:45:17 GMT 2026] Executing as ?@nf-01b35d930a678a00f304113d70219d61-edcb1-57qsm 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 07:45:17 MarkDuplicates Start of doWork freeMemory: 105828752; totalMemory: 134217728; maxMemory: 63585648640 INFO 2026-06-08 07:45:17 MarkDuplicates Reading input file and constructing read end information. INFO 2026-06-08 07:45:17 MarkDuplicates Will retain up to 230382784 data points before spilling to disk. INFO 2026-06-08 07:45:21 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:6,469,069 INFO 2026-06-08 07:45:21 MarkDuplicates Tracking 2361 as yet unmatched pairs. 0 records in RAM. INFO 2026-06-08 07:45:23 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 2s. Last read position: chr1:16,939,985 INFO 2026-06-08 07:45:23 MarkDuplicates Tracking 4432 as yet unmatched pairs. 24 records in RAM. INFO 2026-06-08 07:45:25 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: chr1:23,318,495 INFO 2026-06-08 07:45:25 MarkDuplicates Tracking 6738 as yet unmatched pairs. 75 records in RAM. INFO 2026-06-08 07:45:27 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: chr1:31,700,101 INFO 2026-06-08 07:45:27 MarkDuplicates Tracking 8897 as yet unmatched pairs. 148 records in RAM. INFO 2026-06-08 07:45:29 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: chr1:39,388,420 INFO 2026-06-08 07:45:29 MarkDuplicates Tracking 11379 as yet unmatched pairs. 54 records in RAM. INFO 2026-06-08 07:45:31 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: chr1:52,041,563 INFO 2026-06-08 07:45:31 MarkDuplicates Tracking 13510 as yet unmatched pairs. 25 records in RAM. INFO 2026-06-08 07:45:33 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: chr1:102,935,067 INFO 2026-06-08 07:45:33 MarkDuplicates Tracking 15779 as yet unmatched pairs. 217 records in RAM. INFO 2026-06-08 07:45:37 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 3s. Last read position: chr1:116,603,653 INFO 2026-06-08 07:45:37 MarkDuplicates Tracking 17833 as yet unmatched pairs. 13 records in RAM. INFO 2026-06-08 07:45:38 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: chr1:148,589,338 INFO 2026-06-08 07:45:38 MarkDuplicates Tracking 19262 as yet unmatched pairs. 9 records in RAM. INFO 2026-06-08 07:45:41 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 2s. Last read position: chr1:153,618,888 INFO 2026-06-08 07:45:41 MarkDuplicates Tracking 21489 as yet unmatched pairs. 15 records in RAM. INFO 2026-06-08 07:45:43 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 2s. Last read position: chr1:155,634,739 INFO 2026-06-08 07:45:43 MarkDuplicates Tracking 23313 as yet unmatched pairs. 0 records in RAM. INFO 2026-06-08 07:45:45 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 1s. Last read position: chr1:161,525,057 INFO 2026-06-08 07:45:45 MarkDuplicates Tracking 25958 as yet unmatched pairs. 118 records in RAM. INFO 2026-06-08 07:45:47 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 1s. Last read position: chr1:185,309,074 INFO 2026-06-08 07:45:47 MarkDuplicates Tracking 28041 as yet unmatched pairs. 20 records in RAM. INFO 2026-06-08 07:45:49 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 1s. Last read position: chr1:211,667,099 INFO 2026-06-08 07:45:49 MarkDuplicates Tracking 29913 as yet unmatched pairs. 6 records in RAM. INFO 2026-06-08 07:45:51 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 2s. Last read position: chr1:234,608,728 INFO 2026-06-08 07:45:51 MarkDuplicates Tracking 32141 as yet unmatched pairs. 74 records in RAM. INFO 2026-06-08 07:45:53 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 2s. Last read position: chr2:20,202,764 INFO 2026-06-08 07:45:53 MarkDuplicates Tracking 34733 as yet unmatched pairs. 34689 records in RAM. INFO 2026-06-08 07:45:56 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 3s. Last read position: chr2:32,916,264 INFO 2026-06-08 07:45:56 MarkDuplicates Tracking 57043 as yet unmatched pairs. 35634 records in RAM. INFO 2026-06-08 07:45:59 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 2s. Last read position: chr2:39,337,525 INFO 2026-06-08 07:45:59 MarkDuplicates Tracking 324666 as yet unmatched pairs. 25263 records in RAM. INFO 2026-06-08 07:46:00 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 1s. Last read position: chr2:70,211,166 INFO 2026-06-08 07:46:00 MarkDuplicates Tracking 322625 as yet unmatched pairs. 23219 records in RAM. INFO 2026-06-08 07:46:02 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 1s. Last read position: chr2:99,376,425 INFO 2026-06-08 07:46:02 MarkDuplicates Tracking 320533 as yet unmatched pairs. 21118 records in RAM. INFO 2026-06-08 07:46:04 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: chr2:134,954,438 INFO 2026-06-08 07:46:04 MarkDuplicates Tracking 318930 as yet unmatched pairs. 19513 records in RAM. INFO 2026-06-08 07:46:06 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 1s. Last read position: chr2:188,993,400 INFO 2026-06-08 07:46:06 MarkDuplicates Tracking 317201 as yet unmatched pairs. 17781 records in RAM. INFO 2026-06-08 07:46:08 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 2s. Last read position: chr2:189,110,236 INFO 2026-06-08 07:46:08 MarkDuplicates Tracking 314779 as yet unmatched pairs. 15359 records in RAM. INFO 2026-06-08 07:46:11 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 2s. Last read position: chr2:215,365,523 INFO 2026-06-08 07:46:11 MarkDuplicates Tracking 313723 as yet unmatched pairs. 14295 records in RAM. INFO 2026-06-08 07:46:13 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 2s. Last read position: chr2:215,376,633 INFO 2026-06-08 07:46:13 MarkDuplicates Tracking 313009 as yet unmatched pairs. 13581 records in RAM. INFO 2026-06-08 07:46:15 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 1s. Last read position: chr2:215,399,328 INFO 2026-06-08 07:46:15 MarkDuplicates Tracking 309637 as yet unmatched pairs. 10209 records in RAM. INFO 2026-06-08 07:46:18 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 3s. Last read position: chr2:215,422,140 INFO 2026-06-08 07:46:18 MarkDuplicates Tracking 307230 as yet unmatched pairs. 7802 records in RAM. INFO 2026-06-08 07:46:20 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 1s. Last read position: chr2:215,435,709 INFO 2026-06-08 07:46:20 MarkDuplicates Tracking 305459 as yet unmatched pairs. 6031 records in RAM. INFO 2026-06-08 07:46:21 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 1s. Last read position: chr2:231,712,930 INFO 2026-06-08 07:46:21 MarkDuplicates Tracking 302324 as yet unmatched pairs. 2870 records in RAM. INFO 2026-06-08 07:46:23 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 2s. Last read position: chr2:240,590,746 INFO 2026-06-08 07:46:23 MarkDuplicates Tracking 300089 as yet unmatched pairs. 635 records in RAM. INFO 2026-06-08 07:46:26 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 2s. Last read position: chr3:29,434,780 INFO 2026-06-08 07:46:26 MarkDuplicates Tracking 297771 as yet unmatched pairs. 12507 records in RAM. INFO 2026-06-08 07:46:27 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 1s. Last read position: chr3:48,420,196 INFO 2026-06-08 07:46:27 MarkDuplicates Tracking 295731 as yet unmatched pairs. 10465 records in RAM. INFO 2026-06-08 07:46:30 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 3s. Last read position: chr3:51,969,943 INFO 2026-06-08 07:46:30 MarkDuplicates Tracking 293248 as yet unmatched pairs. 7982 records in RAM. INFO 2026-06-08 07:46:33 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 2s. Last read position: chr3:101,681,138 INFO 2026-06-08 07:46:33 MarkDuplicates Tracking 291031 as yet unmatched pairs. 5761 records in RAM. INFO 2026-06-08 07:46:35 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 2s. Last read position: chr3:131,825,883 INFO 2026-06-08 07:46:35 MarkDuplicates Tracking 288717 as yet unmatched pairs. 3445 records in RAM. INFO 2026-06-08 07:46:37 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 1s. Last read position: chr3:184,327,296 INFO 2026-06-08 07:46:37 MarkDuplicates Tracking 286858 as yet unmatched pairs. 1583 records in RAM. INFO 2026-06-08 07:46:39 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 2s. Last read position: chr4:2,067,578 INFO 2026-06-08 07:46:39 MarkDuplicates Tracking 284256 as yet unmatched pairs. 6786 records in RAM. INFO 2026-06-08 07:46:41 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 1s. Last read position: chr4:48,512,543 INFO 2026-06-08 07:46:41 MarkDuplicates Tracking 282187 as yet unmatched pairs. 4709 records in RAM. INFO 2026-06-08 07:46:43 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 2s. Last read position: chr4:108,622,584 INFO 2026-06-08 07:46:43 MarkDuplicates Tracking 279921 as yet unmatched pairs. 2437 records in RAM. INFO 2026-06-08 07:46:45 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 2s. Last read position: chr4:168,903,884 INFO 2026-06-08 07:46:45 MarkDuplicates Tracking 277924 as yet unmatched pairs. 438 records in RAM. INFO 2026-06-08 07:46:47 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 2s. Last read position: chr5:32,088,198 INFO 2026-06-08 07:46:47 MarkDuplicates Tracking 275792 as yet unmatched pairs. 11211 records in RAM. INFO 2026-06-08 07:46:49 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 1s. Last read position: chr5:80,654,722 INFO 2026-06-08 07:46:49 MarkDuplicates Tracking 273985 as yet unmatched pairs. 9401 records in RAM. INFO 2026-06-08 07:46:51 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 1s. Last read position: chr5:135,578,731 INFO 2026-06-08 07:46:51 MarkDuplicates Tracking 272289 as yet unmatched pairs. 7703 records in RAM. INFO 2026-06-08 07:46:53 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 2s. Last read position: chr5:147,405,623 INFO 2026-06-08 07:46:53 MarkDuplicates Tracking 270242 as yet unmatched pairs. 5609 records in RAM. INFO 2026-06-08 07:46:55 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 1s. Last read position: chr5:151,673,192 INFO 2026-06-08 07:46:55 MarkDuplicates Tracking 268471 as yet unmatched pairs. 3838 records in RAM. INFO 2026-06-08 07:46:58 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 2s. Last read position: chr5:179,114,133 INFO 2026-06-08 07:46:58 MarkDuplicates Tracking 265825 as yet unmatched pairs. 1190 records in RAM. INFO 2026-06-08 07:46:59 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 1s. Last read position: chr6:7,910,521 INFO 2026-06-08 07:46:59 MarkDuplicates Tracking 263661 as yet unmatched pairs. 18840 records in RAM. INFO 2026-06-08 07:47:02 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 2s. Last read position: chr6:30,708,301 INFO 2026-06-08 07:47:02 MarkDuplicates Tracking 261469 as yet unmatched pairs. 16639 records in RAM. INFO 2026-06-08 07:47:04 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 1s. Last read position: chr6:31,816,147 INFO 2026-06-08 07:47:04 MarkDuplicates Tracking 259883 as yet unmatched pairs. 15053 records in RAM. INFO 2026-06-08 07:47:05 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:46s. Time for last 1,000,000: 1s. Last read position: chr6:31,817,343 INFO 2026-06-08 07:47:05 MarkDuplicates Tracking 260685 as yet unmatched pairs. 15855 records in RAM. INFO 2026-06-08 07:47:06 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 1s. Last read position: chr6:31,829,088 INFO 2026-06-08 07:47:06 MarkDuplicates Tracking 258861 as yet unmatched pairs. 14031 records in RAM. INFO 2026-06-08 07:47:07 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 1s. Last read position: chr6:31,994,521 INFO 2026-06-08 07:47:07 MarkDuplicates Tracking 255887 as yet unmatched pairs. 11057 records in RAM. INFO 2026-06-08 07:47:09 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 1s. Last read position: chr6:33,416,588 INFO 2026-06-08 07:47:09 MarkDuplicates Tracking 253835 as yet unmatched pairs. 9004 records in RAM. INFO 2026-06-08 07:47:12 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 3s. Last read position: chr6:44,135,069 INFO 2026-06-08 07:47:12 MarkDuplicates Tracking 251449 as yet unmatched pairs. 6618 records in RAM. INFO 2026-06-08 07:47:15 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 3s. Last read position: chr6:85,487,386 INFO 2026-06-08 07:47:15 MarkDuplicates Tracking 249412 as yet unmatched pairs. 4578 records in RAM. INFO 2026-06-08 07:47:18 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 2s. Last read position: chr6:142,753,479 INFO 2026-06-08 07:47:18 MarkDuplicates Tracking 247183 as yet unmatched pairs. 2346 records in RAM. INFO 2026-06-08 07:47:19 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 1s. Last read position: chr6:169,232,714 INFO 2026-06-08 07:47:19 MarkDuplicates Tracking 245418 as yet unmatched pairs. 577 records in RAM. INFO 2026-06-08 07:47:22 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 3s. Last read position: chr7:5,528,566 INFO 2026-06-08 07:47:22 MarkDuplicates Tracking 243157 as yet unmatched pairs. 16494 records in RAM. INFO 2026-06-08 07:47:24 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 2s. Last read position: chr7:44,104,681 INFO 2026-06-08 07:47:24 MarkDuplicates Tracking 240806 as yet unmatched pairs. 14140 records in RAM. INFO 2026-06-08 07:47:26 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 2s. Last read position: chr7:56,104,372 INFO 2026-06-08 07:47:26 MarkDuplicates Tracking 238540 as yet unmatched pairs. 11874 records in RAM. INFO 2026-06-08 07:47:28 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 1s. Last read position: chr7:76,302,901 INFO 2026-06-08 07:47:28 MarkDuplicates Tracking 239013 as yet unmatched pairs. 12345 records in RAM. INFO 2026-06-08 07:47:31 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 2s. Last read position: chr7:94,408,812 INFO 2026-06-08 07:47:31 MarkDuplicates Tracking 235599 as yet unmatched pairs. 8931 records in RAM. INFO 2026-06-08 07:47:34 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 2s. Last read position: chr7:98,962,303 INFO 2026-06-08 07:47:34 MarkDuplicates Tracking 232677 as yet unmatched pairs. 6008 records in RAM. INFO 2026-06-08 07:47:36 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 1s. Last read position: chr7:102,587,633 INFO 2026-06-08 07:47:36 MarkDuplicates Tracking 231036 as yet unmatched pairs. 4367 records in RAM. INFO 2026-06-08 07:47:37 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 1s. Last read position: chr7:137,908,325 INFO 2026-06-08 07:47:37 MarkDuplicates Tracking 229056 as yet unmatched pairs. 2385 records in RAM. INFO 2026-06-08 07:47:39 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 1s. Last read position: chr7:152,181,462 INFO 2026-06-08 07:47:39 MarkDuplicates Tracking 227089 as yet unmatched pairs. 416 records in RAM. INFO 2026-06-08 07:47:42 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 3s. Last read position: chr8:26,383,155 INFO 2026-06-08 07:47:42 MarkDuplicates Tracking 225152 as yet unmatched pairs. 9482 records in RAM. INFO 2026-06-08 07:47:44 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 1s. Last read position: chr8:58,581,713 INFO 2026-06-08 07:47:44 MarkDuplicates Tracking 222588 as yet unmatched pairs. 6917 records in RAM. INFO 2026-06-08 07:47:46 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 1s. Last read position: chr8:115,604,272 INFO 2026-06-08 07:47:46 MarkDuplicates Tracking 220743 as yet unmatched pairs. 5067 records in RAM. INFO 2026-06-08 07:47:47 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 1s. Last read position: chr8:143,860,571 INFO 2026-06-08 07:47:47 MarkDuplicates Tracking 218825 as yet unmatched pairs. 3148 records in RAM. INFO 2026-06-08 07:47:49 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 1s. Last read position: chr8:143,924,380 INFO 2026-06-08 07:47:49 MarkDuplicates Tracking 217557 as yet unmatched pairs. 1880 records in RAM. INFO 2026-06-08 07:47:50 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 1s. Last read position: chr9:20,874,732 INFO 2026-06-08 07:47:50 MarkDuplicates Tracking 214899 as yet unmatched pairs. 12101 records in RAM. INFO 2026-06-08 07:47:53 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:34s. Time for last 1,000,000: 2s. Last read position: chr9:83,707,521 INFO 2026-06-08 07:47:53 MarkDuplicates Tracking 212900 as yet unmatched pairs. 10084 records in RAM. INFO 2026-06-08 07:47:55 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 1s. Last read position: chr9:114,205,771 INFO 2026-06-08 07:47:55 MarkDuplicates Tracking 210792 as yet unmatched pairs. 7975 records in RAM. INFO 2026-06-08 07:47:56 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 1s. Last read position: chr9:128,613,383 INFO 2026-06-08 07:47:56 MarkDuplicates Tracking 208237 as yet unmatched pairs. 5418 records in RAM. INFO 2026-06-08 07:47:58 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 1s. Last read position: chr9:134,753,856 INFO 2026-06-08 07:47:58 MarkDuplicates Tracking 205952 as yet unmatched pairs. 3133 records in RAM. INFO 2026-06-08 07:47:59 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 1s. Last read position: chr9:137,110,703 INFO 2026-06-08 07:47:59 MarkDuplicates Tracking 203524 as yet unmatched pairs. 704 records in RAM. INFO 2026-06-08 07:48:01 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 1s. Last read position: chr10:24,495,182 INFO 2026-06-08 07:48:01 MarkDuplicates Tracking 201193 as yet unmatched pairs. 8528 records in RAM. INFO 2026-06-08 07:48:03 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 1s. Last read position: chr10:49,988,826 INFO 2026-06-08 07:48:03 MarkDuplicates Tracking 199414 as yet unmatched pairs. 6748 records in RAM. INFO 2026-06-08 07:48:04 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 1s. Last read position: chr10:79,709,868 INFO 2026-06-08 07:48:04 MarkDuplicates Tracking 197153 as yet unmatched pairs. 4486 records in RAM. INFO 2026-06-08 07:48:06 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 1s. Last read position: chr10:102,423,796 INFO 2026-06-08 07:48:06 MarkDuplicates Tracking 195066 as yet unmatched pairs. 2398 records in RAM. INFO 2026-06-08 07:48:07 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:48s. Time for last 1,000,000: 1s. Last read position: chr10:132,405,330 INFO 2026-06-08 07:48:07 MarkDuplicates Tracking 192899 as yet unmatched pairs. 229 records in RAM. INFO 2026-06-08 07:48:10 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 2s. Last read position: chr11:1,880,115 INFO 2026-06-08 07:48:10 MarkDuplicates Tracking 190331 as yet unmatched pairs. 16703 records in RAM. INFO 2026-06-08 07:48:12 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 1s. Last read position: chr11:32,100,568 INFO 2026-06-08 07:48:12 MarkDuplicates Tracking 187912 as yet unmatched pairs. 14283 records in RAM. INFO 2026-06-08 07:48:14 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:55s. Time for last 1,000,000: 2s. Last read position: chr11:59,152,946 INFO 2026-06-08 07:48:14 MarkDuplicates Tracking 185746 as yet unmatched pairs. 12117 records in RAM. INFO 2026-06-08 07:48:17 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 2s. Last read position: chr11:62,824,190 INFO 2026-06-08 07:48:17 MarkDuplicates Tracking 183584 as yet unmatched pairs. 9945 records in RAM. INFO 2026-06-08 07:48:19 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 2s. Last read position: chr11:65,849,835 INFO 2026-06-08 07:48:19 MarkDuplicates Tracking 181054 as yet unmatched pairs. 7413 records in RAM. INFO 2026-06-08 07:48:21 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 2s. Last read position: chr11:71,472,489 INFO 2026-06-08 07:48:21 MarkDuplicates Tracking 178847 as yet unmatched pairs. 5205 records in RAM. INFO 2026-06-08 07:48:24 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 2s. Last read position: chr11:90,077,332 INFO 2026-06-08 07:48:24 MarkDuplicates Tracking 176613 as yet unmatched pairs. 2971 records in RAM. INFO 2026-06-08 07:48:26 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:03:07s. Time for last 1,000,000: 2s. Last read position: chr11:119,420,191 INFO 2026-06-08 07:48:26 MarkDuplicates Tracking 174693 as yet unmatched pairs. 1050 records in RAM. INFO 2026-06-08 07:48:29 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 3s. Last read position: chr12:6,587,871 INFO 2026-06-08 07:48:29 MarkDuplicates Tracking 172415 as yet unmatched pairs. 15352 records in RAM. INFO 2026-06-08 07:48:32 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 2s. Last read position: chr12:26,495,243 INFO 2026-06-08 07:48:32 MarkDuplicates Tracking 170391 as yet unmatched pairs. 13327 records in RAM. INFO 2026-06-08 07:48:34 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 2s. Last read position: chr12:51,190,176 INFO 2026-06-08 07:48:34 MarkDuplicates Tracking 168461 as yet unmatched pairs. 11396 records in RAM. INFO 2026-06-08 07:48:36 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 2s. Last read position: chr12:55,728,961 INFO 2026-06-08 07:48:36 MarkDuplicates Tracking 166289 as yet unmatched pairs. 9224 records in RAM. INFO 2026-06-08 07:48:38 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 2s. Last read position: chr12:57,195,891 INFO 2026-06-08 07:48:38 MarkDuplicates Tracking 164212 as yet unmatched pairs. 7147 records in RAM. INFO 2026-06-08 07:48:41 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 2s. Last read position: chr12:95,683,611 INFO 2026-06-08 07:48:41 MarkDuplicates Tracking 162161 as yet unmatched pairs. 5094 records in RAM. INFO 2026-06-08 07:48:43 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 2s. Last read position: chr12:118,246,175 INFO 2026-06-08 07:48:43 MarkDuplicates Tracking 160000 as yet unmatched pairs. 2933 records in RAM. INFO 2026-06-08 07:48:46 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 2s. Last read position: chr12:131,084,592 INFO 2026-06-08 07:48:46 MarkDuplicates Tracking 157994 as yet unmatched pairs. 926 records in RAM. INFO 2026-06-08 07:48:48 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 2s. Last read position: chr13:40,665,716 INFO 2026-06-08 07:48:48 MarkDuplicates Tracking 156057 as yet unmatched pairs. 2997 records in RAM. INFO 2026-06-08 07:48:50 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 2s. Last read position: chr13:110,357,492 INFO 2026-06-08 07:48:50 MarkDuplicates Tracking 154046 as yet unmatched pairs. 984 records in RAM. INFO 2026-06-08 07:48:52 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 2s. Last read position: chr14:23,561,972 INFO 2026-06-08 07:48:52 MarkDuplicates Tracking 151582 as yet unmatched pairs. 7605 records in RAM. INFO 2026-06-08 07:48:55 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 2s. Last read position: chr14:60,719,878 INFO 2026-06-08 07:48:55 MarkDuplicates Tracking 149290 as yet unmatched pairs. 5310 records in RAM. INFO 2026-06-08 07:48:57 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 1s. Last read position: chr14:75,280,621 INFO 2026-06-08 07:48:57 MarkDuplicates Tracking 147350 as yet unmatched pairs. 3368 records in RAM. INFO 2026-06-08 07:48:59 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 2s. Last read position: chr14:102,593,159 INFO 2026-06-08 07:48:59 MarkDuplicates Tracking 145103 as yet unmatched pairs. 1110 records in RAM. INFO 2026-06-08 07:49:01 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 2s. Last read position: chr15:34,038,847 INFO 2026-06-08 07:49:01 MarkDuplicates Tracking 143297 as yet unmatched pairs. 8179 records in RAM. INFO 2026-06-08 07:49:04 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 2s. Last read position: chr15:48,460,246 INFO 2026-06-08 07:49:04 MarkDuplicates Tracking 141320 as yet unmatched pairs. 6201 records in RAM. INFO 2026-06-08 07:49:06 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 2s. Last read position: chr15:68,317,320 INFO 2026-06-08 07:49:06 MarkDuplicates Tracking 139016 as yet unmatched pairs. 3895 records in RAM. INFO 2026-06-08 07:49:09 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 2s. Last read position: chr15:78,892,214 INFO 2026-06-08 07:49:09 MarkDuplicates Tracking 136880 as yet unmatched pairs. 1757 records in RAM. INFO 2026-06-08 07:49:11 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 2s. Last read position: chr16:229,209 INFO 2026-06-08 07:49:11 MarkDuplicates Tracking 134992 as yet unmatched pairs. 16654 records in RAM. INFO 2026-06-08 07:49:13 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 2s. Last read position: chr16:2,277,625 INFO 2026-06-08 07:49:13 MarkDuplicates Tracking 132664 as yet unmatched pairs. 14326 records in RAM. INFO 2026-06-08 07:49:15 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 2s. Last read position: chr16:11,549,640 INFO 2026-06-08 07:49:15 MarkDuplicates Tracking 130736 as yet unmatched pairs. 12397 records in RAM. INFO 2026-06-08 07:49:17 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 1s. Last read position: chr16:16,357,759 INFO 2026-06-08 07:49:17 MarkDuplicates Tracking 129679 as yet unmatched pairs. 11340 records in RAM. INFO 2026-06-08 07:49:19 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 1s. Last read position: chr16:21,403,983 INFO 2026-06-08 07:49:19 MarkDuplicates Tracking 128907 as yet unmatched pairs. 10568 records in RAM. INFO 2026-06-08 07:49:21 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 1s. Last read position: chr16:27,497,687 INFO 2026-06-08 07:49:21 MarkDuplicates Tracking 127843 as yet unmatched pairs. 9503 records in RAM. INFO 2026-06-08 07:49:23 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 2s. Last read position: chr16:30,223,303 INFO 2026-06-08 07:49:23 MarkDuplicates Tracking 126273 as yet unmatched pairs. 7931 records in RAM. INFO 2026-06-08 07:49:25 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 2s. Last read position: chr16:53,454,749 INFO 2026-06-08 07:49:25 MarkDuplicates Tracking 124395 as yet unmatched pairs. 6052 records in RAM. INFO 2026-06-08 07:49:27 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 2s. Last read position: chr16:68,296,732 INFO 2026-06-08 07:49:27 MarkDuplicates Tracking 122164 as yet unmatched pairs. 3820 records in RAM. INFO 2026-06-08 07:49:30 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 3s. Last read position: chr16:87,334,128 INFO 2026-06-08 07:49:30 MarkDuplicates Tracking 120160 as yet unmatched pairs. 1812 records in RAM. INFO 2026-06-08 07:49:33 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:04:14s. Time for last 1,000,000: 2s. Last read position: chr17:1,558,534 INFO 2026-06-08 07:49:33 MarkDuplicates Tracking 117902 as yet unmatched pairs. 51757 records in RAM. INFO 2026-06-08 07:49:35 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 2s. Last read position: chr17:7,557,407 INFO 2026-06-08 07:49:35 MarkDuplicates Tracking 115838 as yet unmatched pairs. 49692 records in RAM. INFO 2026-06-08 07:49:37 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 2s. Last read position: chr17:27,597,328 INFO 2026-06-08 07:49:37 MarkDuplicates Tracking 113801 as yet unmatched pairs. 47654 records in RAM. INFO 2026-06-08 07:49:39 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 2s. Last read position: chr17:38,735,234 INFO 2026-06-08 07:49:39 MarkDuplicates Tracking 112031 as yet unmatched pairs. 45881 records in RAM. INFO 2026-06-08 07:49:41 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 1s. Last read position: chr17:41,771,744 INFO 2026-06-08 07:49:41 MarkDuplicates Tracking 109784 as yet unmatched pairs. 43634 records in RAM. INFO 2026-06-08 07:49:43 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 1s. Last read position: chr17:46,422,544 INFO 2026-06-08 07:49:43 MarkDuplicates Tracking 107690 as yet unmatched pairs. 41539 records in RAM. INFO 2026-06-08 07:49:45 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 2s. Last read position: chr17:50,186,469 INFO 2026-06-08 07:49:45 MarkDuplicates Tracking 106376 as yet unmatched pairs. 40225 records in RAM. INFO 2026-06-08 07:49:47 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr17:50,187,519 INFO 2026-06-08 07:49:47 MarkDuplicates Tracking 111266 as yet unmatched pairs. 45115 records in RAM. INFO 2026-06-08 07:49:50 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:04:31s. Time for last 1,000,000: 2s. Last read position: chr17:50,188,551 INFO 2026-06-08 07:49:50 MarkDuplicates Tracking 106038 as yet unmatched pairs. 39887 records in RAM. INFO 2026-06-08 07:49:52 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 2s. Last read position: chr17:50,189,221 INFO 2026-06-08 07:49:52 MarkDuplicates Tracking 102669 as yet unmatched pairs. 36518 records in RAM. INFO 2026-06-08 07:49:54 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 2s. Last read position: chr17:50,189,860 INFO 2026-06-08 07:49:54 MarkDuplicates Tracking 105825 as yet unmatched pairs. 39674 records in RAM. INFO 2026-06-08 07:49:57 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 2s. Last read position: chr17:50,190,543 INFO 2026-06-08 07:49:57 MarkDuplicates Tracking 98695 as yet unmatched pairs. 32544 records in RAM. INFO 2026-06-08 07:49:59 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 2s. Last read position: chr17:50,192,456 INFO 2026-06-08 07:49:59 MarkDuplicates Tracking 97829 as yet unmatched pairs. 31678 records in RAM. INFO 2026-06-08 07:50:02 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 2s. Last read position: chr17:50,193,019 INFO 2026-06-08 07:50:02 MarkDuplicates Tracking 95965 as yet unmatched pairs. 29813 records in RAM. INFO 2026-06-08 07:50:04 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 2s. Last read position: chr17:50,194,408 INFO 2026-06-08 07:50:04 MarkDuplicates Tracking 97787 as yet unmatched pairs. 31635 records in RAM. INFO 2026-06-08 07:50:06 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 2s. Last read position: chr17:50,195,091 INFO 2026-06-08 07:50:06 MarkDuplicates Tracking 91125 as yet unmatched pairs. 24973 records in RAM. INFO 2026-06-08 07:50:09 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 2s. Last read position: chr17:50,195,945 INFO 2026-06-08 07:50:09 MarkDuplicates Tracking 88189 as yet unmatched pairs. 22037 records in RAM. INFO 2026-06-08 07:50:11 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 2s. Last read position: chr17:50,196,342 INFO 2026-06-08 07:50:11 MarkDuplicates Tracking 88277 as yet unmatched pairs. 22124 records in RAM. INFO 2026-06-08 07:50:13 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 2s. Last read position: chr17:50,197,741 INFO 2026-06-08 07:50:13 MarkDuplicates Tracking 83200 as yet unmatched pairs. 17047 records in RAM. INFO 2026-06-08 07:50:16 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 2s. Last read position: chr17:50,199,288 INFO 2026-06-08 07:50:16 MarkDuplicates Tracking 80777 as yet unmatched pairs. 14624 records in RAM. INFO 2026-06-08 07:50:18 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 2s. Last read position: chr17:58,512,890 INFO 2026-06-08 07:50:18 MarkDuplicates Tracking 73335 as yet unmatched pairs. 7182 records in RAM. INFO 2026-06-08 07:50:20 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 2s. Last read position: chr17:74,958,982 INFO 2026-06-08 07:50:20 MarkDuplicates Tracking 71208 as yet unmatched pairs. 5052 records in RAM. INFO 2026-06-08 07:50:22 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 2s. Last read position: chr17:80,214,652 INFO 2026-06-08 07:50:22 MarkDuplicates Tracking 68886 as yet unmatched pairs. 2729 records in RAM. INFO 2026-06-08 07:50:25 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 2s. Last read position: chr17:82,584,058 INFO 2026-06-08 07:50:25 MarkDuplicates Tracking 66363 as yet unmatched pairs. 206 records in RAM. INFO 2026-06-08 07:50:26 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 1s. Last read position: chr18:58,535,012 INFO 2026-06-08 07:50:26 MarkDuplicates Tracking 64341 as yet unmatched pairs. 1074 records in RAM. INFO 2026-06-08 07:50:28 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr19:1,360,765 INFO 2026-06-08 07:50:28 MarkDuplicates Tracking 61948 as yet unmatched pairs. 27541 records in RAM. INFO 2026-06-08 07:50:30 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 1s. Last read position: chr19:4,513,337 INFO 2026-06-08 07:50:30 MarkDuplicates Tracking 59497 as yet unmatched pairs. 25090 records in RAM. INFO 2026-06-08 07:50:32 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 1s. Last read position: chr19:8,948,668 INFO 2026-06-08 07:50:32 MarkDuplicates Tracking 57220 as yet unmatched pairs. 22813 records in RAM. INFO 2026-06-08 07:50:34 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 2s. Last read position: chr19:12,940,091 INFO 2026-06-08 07:50:34 MarkDuplicates Tracking 55063 as yet unmatched pairs. 20656 records in RAM. INFO 2026-06-08 07:50:37 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:05:18s. Time for last 1,000,000: 2s. Last read position: chr19:15,180,772 INFO 2026-06-08 07:50:37 MarkDuplicates Tracking 52823 as yet unmatched pairs. 18414 records in RAM. INFO 2026-06-08 07:50:40 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:05:21s. Time for last 1,000,000: 2s. Last read position: chr19:18,281,143 INFO 2026-06-08 07:50:40 MarkDuplicates Tracking 50632 as yet unmatched pairs. 16222 records in RAM. INFO 2026-06-08 07:50:41 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 1s. Last read position: chr19:35,725,570 INFO 2026-06-08 07:50:41 MarkDuplicates Tracking 47786 as yet unmatched pairs. 13374 records in RAM. INFO 2026-06-08 07:50:43 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 1s. Last read position: chr19:40,367,820 INFO 2026-06-08 07:50:43 MarkDuplicates Tracking 45819 as yet unmatched pairs. 11407 records in RAM. INFO 2026-06-08 07:50:45 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 2s. Last read position: chr19:44,748,762 INFO 2026-06-08 07:50:45 MarkDuplicates Tracking 43272 as yet unmatched pairs. 8858 records in RAM. INFO 2026-06-08 07:50:47 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 2s. Last read position: chr19:47,678,435 INFO 2026-06-08 07:50:47 MarkDuplicates Tracking 40683 as yet unmatched pairs. 6265 records in RAM. INFO 2026-06-08 07:50:50 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 2s. Last read position: chr19:49,594,459 INFO 2026-06-08 07:50:50 MarkDuplicates Tracking 38154 as yet unmatched pairs. 3735 records in RAM. INFO 2026-06-08 07:50:53 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:05:34s. Time for last 1,000,000: 3s. Last read position: chr19:54,665,874 INFO 2026-06-08 07:50:53 MarkDuplicates Tracking 36069 as yet unmatched pairs. 1649 records in RAM. INFO 2026-06-08 07:50:55 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 2s. Last read position: chr20:3,381,488 INFO 2026-06-08 07:50:55 MarkDuplicates Tracking 33910 as yet unmatched pairs. 7016 records in RAM. INFO 2026-06-08 07:50:57 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 2s. Last read position: chr20:35,699,635 INFO 2026-06-08 07:50:57 MarkDuplicates Tracking 31690 as yet unmatched pairs. 4796 records in RAM. INFO 2026-06-08 07:50:59 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 2s. Last read position: chr20:51,628,980 INFO 2026-06-08 07:50:59 MarkDuplicates Tracking 29492 as yet unmatched pairs. 2598 records in RAM. INFO 2026-06-08 07:51:02 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 2s. Last read position: chr20:63,944,544 INFO 2026-06-08 07:51:02 MarkDuplicates Tracking 27098 as yet unmatched pairs. 203 records in RAM. INFO 2026-06-08 07:51:03 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 1s. Last read position: chr21:8,397,804 INFO 2026-06-08 07:51:03 MarkDuplicates Tracking 26294 as yet unmatched pairs. 7125 records in RAM. INFO 2026-06-08 07:51:05 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 1s. Last read position: chr21:25,975,070 INFO 2026-06-08 07:51:05 MarkDuplicates Tracking 25158 as yet unmatched pairs. 5987 records in RAM. INFO 2026-06-08 07:51:07 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 1s. Last read position: chr21:45,468,437 INFO 2026-06-08 07:51:07 MarkDuplicates Tracking 22982 as yet unmatched pairs. 3810 records in RAM. INFO 2026-06-08 07:51:10 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 3s. Last read position: chr21:46,116,029 INFO 2026-06-08 07:51:10 MarkDuplicates Tracking 20502 as yet unmatched pairs. 1330 records in RAM. INFO 2026-06-08 07:51:12 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 2s. Last read position: chr22:23,781,221 INFO 2026-06-08 07:51:12 MarkDuplicates Tracking 17866 as yet unmatched pairs. 6989 records in RAM. INFO 2026-06-08 07:51:14 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 2s. Last read position: chr22:36,285,879 INFO 2026-06-08 07:51:14 MarkDuplicates Tracking 15579 as yet unmatched pairs. 4702 records in RAM. INFO 2026-06-08 07:51:16 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 2s. Last read position: chr22:41,436,785 INFO 2026-06-08 07:51:16 MarkDuplicates Tracking 13252 as yet unmatched pairs. 2375 records in RAM. INFO 2026-06-08 07:51:19 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:05:59s. Time for last 1,000,000: 2s. Last read position: chrX:2,691,418 INFO 2026-06-08 07:51:19 MarkDuplicates Tracking 11073 as yet unmatched pairs. 7945 records in RAM. INFO 2026-06-08 07:51:21 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:06:02s. Time for last 1,000,000: 2s. Last read position: chrX:48,604,862 INFO 2026-06-08 07:51:21 MarkDuplicates Tracking 8615 as yet unmatched pairs. 5471 records in RAM. INFO 2026-06-08 07:51:24 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 2s. Last read position: chrX:76,177,696 INFO 2026-06-08 07:51:24 MarkDuplicates Tracking 6602 as yet unmatched pairs. 3458 records in RAM. INFO 2026-06-08 07:51:26 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:06:07s. Time for last 1,000,000: 1s. Last read position: chrX:153,954,664 INFO 2026-06-08 07:51:26 MarkDuplicates Tracking 4781 as yet unmatched pairs. 1635 records in RAM. INFO 2026-06-08 07:51:28 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:06:09s. Time for last 1,000,000: 1s. Last read position: GL000220.1:114,202 INFO 2026-06-08 07:51:28 MarkDuplicates Tracking 3118 as yet unmatched pairs. 984 records in RAM. INFO 2026-06-08 07:51:29 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 1s. Last read position: KI270733.1:130,975 INFO 2026-06-08 07:51:29 MarkDuplicates Tracking 2091 as yet unmatched pairs. 2084 records in RAM. INFO 2026-06-08 07:51:31 MarkDuplicates Read 172995388 records. 0 pairs never matched. INFO 2026-06-08 07:51:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 43350748712; totalMemory: 63552094208; maxMemory: 63585648640 INFO 2026-06-08 07:51:44 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk. INFO 2026-06-08 07:51:52 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2026-06-08 07:52:24 OpticalDuplicateFinder Large duplicate set. size = 1121 INFO 2026-06-08 07:52:24 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:26,540 INFO 2026-06-08 07:52:24 OpticalDuplicateFinder Large duplicate set. size = 1083 INFO 2026-06-08 07:52:24 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,899 INFO 2026-06-08 07:52:24 OpticalDuplicateFinder Large duplicate set. size = 1594 INFO 2026-06-08 07:52:24 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,986 INFO 2026-06-08 07:52:24 OpticalDuplicateFinder Large duplicate set. size = 1401 INFO 2026-06-08 07:52:24 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:2,197 INFO 2026-06-08 07:52:24 OpticalDuplicateFinder Large duplicate set. size = 1083 INFO 2026-06-08 07:52:24 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,173 INFO 2026-06-08 07:52:24 OpticalDuplicateFinder Large duplicate set. size = 2005 INFO 2026-06-08 07:52:24 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,265 INFO 2026-06-08 07:52:24 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,537 INFO 2026-06-08 07:52:24 OpticalDuplicateFinder Large duplicate set. size = 1112 INFO 2026-06-08 07:52:24 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,616 INFO 2026-06-08 07:52:24 OpticalDuplicateFinder Large duplicate set. size = 1046 INFO 2026-06-08 07:52:24 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:17,714 INFO 2026-06-08 07:52:24 OpticalDuplicateFinder Large duplicate set. size = 1032 INFO 2026-06-08 07:52:24 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,287 INFO 2026-06-08 07:52:24 OpticalDuplicateFinder Large duplicate set. size = 1015 INFO 2026-06-08 07:52:24 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,358 INFO 2026-06-08 07:52:24 OpticalDuplicateFinder Large duplicate set. size = 2225 INFO 2026-06-08 07:52:24 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:14,373 INFO 2026-06-08 07:52:24 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,612 INFO 2026-06-08 07:52:25 OpticalDuplicateFinder Large duplicate set. size = 1143 INFO 2026-06-08 07:52:25 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,382 INFO 2026-06-08 07:52:25 OpticalDuplicateFinder Large duplicate set. size = 1212 INFO 2026-06-08 07:52:25 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-27,120 INFO 2026-06-08 07:52:25 OpticalDuplicateFinder Large duplicate set. size = 1106 INFO 2026-06-08 07:52:25 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,671 INFO 2026-06-08 07:52:25 OpticalDuplicateFinder Large duplicate set. size = 1077 INFO 2026-06-08 07:52:25 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,082 INFO 2026-06-08 07:52:26 OpticalDuplicateFinder Large duplicate set. size = 1702 INFO 2026-06-08 07:52:26 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-27,427 INFO 2026-06-08 07:52:26 OpticalDuplicateFinder Large duplicate set. size = 1051 INFO 2026-06-08 07:52:26 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,014 INFO 2026-06-08 07:52:26 OpticalDuplicateFinder Large duplicate set. size = 1022 INFO 2026-06-08 07:52:26 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,944 INFO 2026-06-08 07:52:26 OpticalDuplicateFinder Large duplicate set. size = 1170 INFO 2026-06-08 07:52:26 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,296 INFO 2026-06-08 07:52:26 OpticalDuplicateFinder Large duplicate set. size = 1068 INFO 2026-06-08 07:52:26 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:21,063 INFO 2026-06-08 07:52:26 OpticalDuplicateFinder Large duplicate set. size = 1120 INFO 2026-06-08 07:52:26 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:7,933 INFO 2026-06-08 07:52:26 OpticalDuplicateFinder Large duplicate set. size = 1087 INFO 2026-06-08 07:52:26 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-14,653 INFO 2026-06-08 07:52:26 OpticalDuplicateFinder Large duplicate set. size = 1099 INFO 2026-06-08 07:52:26 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-31,181 INFO 2026-06-08 07:52:27 OpticalDuplicateFinder Large duplicate set. size = 1385 INFO 2026-06-08 07:52:27 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,673 INFO 2026-06-08 07:52:27 OpticalDuplicateFinder Large duplicate set. size = 2510 INFO 2026-06-08 07:52:27 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:4,794 INFO 2026-06-08 07:52:27 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:1,235 INFO 2026-06-08 07:52:27 OpticalDuplicateFinder Large duplicate set. size = 1180 INFO 2026-06-08 07:52:27 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:3,775 INFO 2026-06-08 07:52:27 OpticalDuplicateFinder Large duplicate set. size = 1672 INFO 2026-06-08 07:52:27 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:14,567 INFO 2026-06-08 07:52:27 OpticalDuplicateFinder Large duplicate set. size = 1374 INFO 2026-06-08 07:52:27 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,493 INFO 2026-06-08 07:52:27 OpticalDuplicateFinder Large duplicate set. size = 1051 INFO 2026-06-08 07:52:27 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,587 INFO 2026-06-08 07:52:27 OpticalDuplicateFinder Large duplicate set. size = 1357 INFO 2026-06-08 07:52:27 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:13,451 INFO 2026-06-08 07:52:27 OpticalDuplicateFinder Large duplicate set. size = 1475 INFO 2026-06-08 07:52:27 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,511 INFO 2026-06-08 07:52:27 OpticalDuplicateFinder Large duplicate set. size = 1233 INFO 2026-06-08 07:52:27 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,464 INFO 2026-06-08 07:52:28 OpticalDuplicateFinder Large duplicate set. size = 1528 INFO 2026-06-08 07:52:28 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:15,594 INFO 2026-06-08 07:52:28 OpticalDuplicateFinder Large duplicate set. size = 1005 INFO 2026-06-08 07:52:28 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,523 INFO 2026-06-08 07:52:28 OpticalDuplicateFinder Large duplicate set. size = 1048 INFO 2026-06-08 07:52:28 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:6,857 INFO 2026-06-08 07:52:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2026-06-08 07:52:56 MarkDuplicates Sorting list of duplicate records. INFO 2026-06-08 07:53:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300748288; totalMemory: 53250883584; maxMemory: 63585648640 INFO 2026-06-08 07:53:02 MarkDuplicates Marking 124497124 records as duplicates. INFO 2026-06-08 07:53:03 MarkDuplicates Found 3182500 optical duplicate clusters. INFO 2026-06-08 07:53:03 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2026-06-08 07:53:29 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:26s. Time for last 10,000,000: 26s. Last read position: chr1:153,618,888 INFO 2026-06-08 07:53:55 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:52s. Time for last 10,000,000: 26s. Last read position: chr2:99,376,425 INFO 2026-06-08 07:54:21 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:18s. Time for last 10,000,000: 25s. Last read position: chr2:240,590,746 INFO 2026-06-08 07:54:45 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:42s. Time for last 10,000,000: 23s. Last read position: chr4:168,903,884 INFO 2026-06-08 07:55:10 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:02:07s. Time for last 10,000,000: 25s. Last read position: chr6:31,817,343 INFO 2026-06-08 07:55:36 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:33s. Time for last 10,000,000: 25s. Last read position: chr7:56,104,372 INFO 2026-06-08 07:56:01 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:58s. Time for last 10,000,000: 25s. Last read position: chr8:143,860,571 INFO 2026-06-08 07:56:27 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:03:24s. Time for last 10,000,000: 25s. Last read position: chr10:79,709,868 INFO 2026-06-08 07:56:54 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:03:51s. Time for last 10,000,000: 26s. Last read position: chr11:119,420,191 INFO 2026-06-08 07:57:17 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:04:14s. Time for last 10,000,000: 22s. Last read position: chr13:110,357,492 INFO 2026-06-08 07:57:39 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:04:36s. Time for last 10,000,000: 22s. Last read position: chr16:2,277,625 INFO 2026-06-08 07:58:03 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:05:00s. Time for last 10,000,000: 23s. Last read position: chr17:7,557,407 INFO 2026-06-08 07:58:26 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:05:23s. Time for last 10,000,000: 23s. Last read position: chr17:50,190,543 INFO 2026-06-08 07:58:50 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:05:47s. Time for last 10,000,000: 23s. Last read position: chr17:74,958,982 INFO 2026-06-08 07:59:13 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:06:10s. Time for last 10,000,000: 22s. Last read position: chr19:35,725,570 INFO 2026-06-08 07:59:36 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:06:33s. Time for last 10,000,000: 22s. Last read position: chr21:8,397,804 INFO 2026-06-08 07:59:57 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:06:54s. Time for last 10,000,000: 21s. Last read position: chrX:153,954,664 INFO 2026-06-08 08:00:07 MarkDuplicates Writing complete. Closing input iterator. INFO 2026-06-08 08:00:07 MarkDuplicates Duplicate Index cleanup. INFO 2026-06-08 08:00:07 MarkDuplicates Getting Memory Stats. INFO 2026-06-08 08:00:07 MarkDuplicates Before output close freeMemory: 201587096; totalMemory: 234881024; maxMemory: 63585648640 INFO 2026-06-08 08:00:07 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2026-06-08 08:00:07 MarkDuplicates After output close freeMemory: 104210720; totalMemory: 134217728; maxMemory: 63585648640 [Mon Jun 08 08:00:07 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 14.84 minutes. Runtime.totalMemory()=134217728 Tool returned: 0 ls: *cram: No such file or directory ls: *.crai: No such file or directory