Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/8af83348c10fab5a0aa13fa2175d18/22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam 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/c7/26385c53c21a21363909bcf6b800b9/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/26385c53c21a21363909bcf6b800b9/.command.run Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai ==> 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 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.md.bam --METRICS_FILE 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT 20:09:32.489 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 [Thu May 28 20:09:32 GMT 2026] MarkDuplicates --INPUT 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 22Rv1_FFPE_RNA_0001_B23LG7FLT4_1.md.bam --METRICS_FILE 22Rv1_FFPE_RNA_0001_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 --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 [Thu May 28 20:09:32 GMT 2026] Executing as ?@nf-c726385c53c21a21363909bcf6b800b9-7dbd0-qd67v on Linux 6.12.83 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 2026-05-28 20:09:32 MarkDuplicates Start of doWork freeMemory: 105492176; totalMemory: 134217728; maxMemory: 63585648640 INFO 2026-05-28 20:09:32 MarkDuplicates Reading input file and constructing read end information. INFO 2026-05-28 20:09:32 MarkDuplicates Will retain up to 230382784 data points before spilling to disk. INFO 2026-05-28 20:09:37 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:40,861,919 INFO 2026-05-28 20:09:37 MarkDuplicates Tracking 2155 as yet unmatched pairs. 23 records in RAM. INFO 2026-05-28 20:09:40 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: chr1:155,942,448 INFO 2026-05-28 20:09:40 MarkDuplicates Tracking 4099 as yet unmatched pairs. 7 records in RAM. INFO 2026-05-28 20:09:43 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 3s. Last read position: chr2:15,541,965 INFO 2026-05-28 20:09:43 MarkDuplicates Tracking 6092 as yet unmatched pairs. 5935 records in RAM. INFO 2026-05-28 20:09:46 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 2s. Last read position: chr2:96,276,932 INFO 2026-05-28 20:09:46 MarkDuplicates Tracking 63747 as yet unmatched pairs. 1882 records in RAM. INFO 2026-05-28 20:09:48 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: chr2:238,246,421 INFO 2026-05-28 20:09:48 MarkDuplicates Tracking 62098 as yet unmatched pairs. 148 records in RAM. INFO 2026-05-28 20:09:52 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 3s. Last read position: chr3:113,632,779 INFO 2026-05-28 20:09:52 MarkDuplicates Tracking 60352 as yet unmatched pairs. 1068 records in RAM. INFO 2026-05-28 20:09:55 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 2s. Last read position: chr4:82,429,614 INFO 2026-05-28 20:09:55 MarkDuplicates Tracking 58508 as yet unmatched pairs. 725 records in RAM. INFO 2026-05-28 20:09:57 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 2s. Last read position: chr5:134,371,536 INFO 2026-05-28 20:09:57 MarkDuplicates Tracking 56774 as yet unmatched pairs. 1609 records in RAM. INFO 2026-05-28 20:09:59 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 2s. Last read position: chr6:19,838,130 INFO 2026-05-28 20:09:59 MarkDuplicates Tracking 54989 as yet unmatched pairs. 3009 records in RAM. INFO 2026-05-28 20:10:03 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 3s. Last read position: chr6:73,466,596 INFO 2026-05-28 20:10:03 MarkDuplicates Tracking 53056 as yet unmatched pairs. 1057 records in RAM. INFO 2026-05-28 20:10:06 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 3s. Last read position: chr7:44,107,866 INFO 2026-05-28 20:10:06 MarkDuplicates Tracking 51204 as yet unmatched pairs. 1986 records in RAM. INFO 2026-05-28 20:10:09 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 2s. Last read position: chr7:144,365,132 INFO 2026-05-28 20:10:09 MarkDuplicates Tracking 49577 as yet unmatched pairs. 321 records in RAM. INFO 2026-05-28 20:10:11 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 2s. Last read position: chr8:138,929,847 INFO 2026-05-28 20:10:11 MarkDuplicates Tracking 47647 as yet unmatched pairs. 1054 records in RAM. INFO 2026-05-28 20:10:13 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 1s. Last read position: chr9:87,967,563 INFO 2026-05-28 20:10:13 MarkDuplicates Tracking 45923 as yet unmatched pairs. 1698 records in RAM. INFO 2026-05-28 20:10:15 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 2s. Last read position: chr10:24,546,081 INFO 2026-05-28 20:10:15 MarkDuplicates Tracking 43890 as yet unmatched pairs. 1598 records in RAM. INFO 2026-05-28 20:10:18 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 2s. Last read position: chr11:862,567 INFO 2026-05-28 20:10:18 MarkDuplicates Tracking 42178 as yet unmatched pairs. 3303 records in RAM. INFO 2026-05-28 20:10:21 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 2s. Last read position: chr11:66,315,615 INFO 2026-05-28 20:10:21 MarkDuplicates Tracking 40423 as yet unmatched pairs. 1524 records in RAM. INFO 2026-05-28 20:10:23 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 1s. Last read position: chr12:9,165,193 INFO 2026-05-28 20:10:23 MarkDuplicates Tracking 38534 as yet unmatched pairs. 2926 records in RAM. INFO 2026-05-28 20:10:25 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 2s. Last read position: chr12:107,382,429 INFO 2026-05-28 20:10:25 MarkDuplicates Tracking 36606 as yet unmatched pairs. 974 records in RAM. INFO 2026-05-28 20:10:27 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 2s. Last read position: chr14:23,957,084 INFO 2026-05-28 20:10:27 MarkDuplicates Tracking 34570 as yet unmatched pairs. 2772 records in RAM. INFO 2026-05-28 20:10:29 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 1s. Last read position: chr14:105,587,599 INFO 2026-05-28 20:10:29 MarkDuplicates Tracking 32584 as yet unmatched pairs. 756 records in RAM. INFO 2026-05-28 20:10:31 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 1s. Last read position: chr15:75,356,397 INFO 2026-05-28 20:10:31 MarkDuplicates Tracking 30779 as yet unmatched pairs. 593 records in RAM. INFO 2026-05-28 20:10:33 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 1s. Last read position: chr16:16,374,889 INFO 2026-05-28 20:10:33 MarkDuplicates Tracking 29044 as yet unmatched pairs. 1839 records in RAM. INFO 2026-05-28 20:10:34 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 1s. Last read position: chr16:78,582,099 INFO 2026-05-28 20:10:34 MarkDuplicates Tracking 27697 as yet unmatched pairs. 477 records in RAM. INFO 2026-05-28 20:10:36 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 2s. Last read position: chr17:38,010,689 INFO 2026-05-28 20:10:36 MarkDuplicates Tracking 25688 as yet unmatched pairs. 3527 records in RAM. INFO 2026-05-28 20:10:38 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 1s. Last read position: chr17:50,199,816 INFO 2026-05-28 20:10:38 MarkDuplicates Tracking 23582 as yet unmatched pairs. 1417 records in RAM. INFO 2026-05-28 20:10:41 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 2s. Last read position: chr18:76,441,644 INFO 2026-05-28 20:10:41 MarkDuplicates Tracking 21515 as yet unmatched pairs. 109 records in RAM. INFO 2026-05-28 20:10:43 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 2s. Last read position: chr19:15,265,438 INFO 2026-05-28 20:10:43 MarkDuplicates Tracking 19263 as yet unmatched pairs. 3994 records in RAM. INFO 2026-05-28 20:10:45 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 1s. Last read position: chr19:42,410,535 INFO 2026-05-28 20:10:45 MarkDuplicates Tracking 16998 as yet unmatched pairs. 1712 records in RAM. INFO 2026-05-28 20:10:47 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 2s. Last read position: chr20:35,716,793 INFO 2026-05-28 20:10:47 MarkDuplicates Tracking 14819 as yet unmatched pairs. 827 records in RAM. INFO 2026-05-28 20:10:49 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 2s. Last read position: chr21:8,214,876 INFO 2026-05-28 20:10:49 MarkDuplicates Tracking 13915 as yet unmatched pairs. 6317 records in RAM. INFO 2026-05-28 20:10:51 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 2s. Last read position: chr21:8,258,727 INFO 2026-05-28 20:10:51 MarkDuplicates Tracking 12255 as yet unmatched pairs. 4642 records in RAM. INFO 2026-05-28 20:10:52 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 1s. Last read position: chr21:8,397,818 INFO 2026-05-28 20:10:52 MarkDuplicates Tracking 11586 as yet unmatched pairs. 3971 records in RAM. INFO 2026-05-28 20:10:54 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 1s. Last read position: chr21:8,441,654 INFO 2026-05-28 20:10:54 MarkDuplicates Tracking 9215 as yet unmatched pairs. 1591 records in RAM. INFO 2026-05-28 20:10:55 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,535 INFO 2026-05-28 20:10:55 MarkDuplicates Tracking 8672 as yet unmatched pairs. 1046 records in RAM. INFO 2026-05-28 20:10:57 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 1s. Last read position: chr22:32,066,989 INFO 2026-05-28 20:10:57 MarkDuplicates Tracking 6896 as yet unmatched pairs. 1035 records in RAM. INFO 2026-05-28 20:10:59 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 2s. Last read position: chrX:106,999,703 INFO 2026-05-28 20:10:59 MarkDuplicates Tracking 5017 as yet unmatched pairs. 497 records in RAM. INFO 2026-05-28 20:11:01 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 1s. Last read position: GL000220.1:114,450 INFO 2026-05-28 20:11:01 MarkDuplicates Tracking 4298 as yet unmatched pairs. 521 records in RAM. INFO 2026-05-28 20:11:02 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 1s. Last read position: GL000220.1:158,121 INFO 2026-05-28 20:11:02 MarkDuplicates Tracking 3819 as yet unmatched pairs. 39 records in RAM. INFO 2026-05-28 20:11:03 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 1s. Last read position: GL000220.1:160,819 INFO 2026-05-28 20:11:03 MarkDuplicates Tracking 3780 as yet unmatched pairs. 0 records in RAM. INFO 2026-05-28 20:11:05 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 1s. Last read position: KI270733.1:133,167 INFO 2026-05-28 20:11:05 MarkDuplicates Tracking 1021 as yet unmatched pairs. 1021 records in RAM. INFO 2026-05-28 20:11:06 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 1s. Last read position: KI270733.1:176,186 INFO 2026-05-28 20:11:06 MarkDuplicates Tracking 93 as yet unmatched pairs. 93 records in RAM. INFO 2026-05-28 20:11:07 MarkDuplicates Read 42807085 records. 0 pairs never matched. INFO 2026-05-28 20:11:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 15861941760; totalMemory: 22615687168; maxMemory: 63585648640 INFO 2026-05-28 20:11:09 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk. INFO 2026-05-28 20:11:13 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2026-05-28 20:11:17 OpticalDuplicateFinder Large duplicate set. size = 1127 INFO 2026-05-28 20:11:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,021 INFO 2026-05-28 20:11:17 OpticalDuplicateFinder Large duplicate set. size = 1555 INFO 2026-05-28 20:11:17 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-19,539 INFO 2026-05-28 20:11:18 OpticalDuplicateFinder Large duplicate set. size = 1410 INFO 2026-05-28 20:11:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,822 INFO 2026-05-28 20:11:18 OpticalDuplicateFinder Large duplicate set. size = 1324 INFO 2026-05-28 20:11:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:7,521 INFO 2026-05-28 20:11:18 OpticalDuplicateFinder Large duplicate set. size = 1129 INFO 2026-05-28 20:11:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,331 INFO 2026-05-28 20:11:18 OpticalDuplicateFinder Large duplicate set. size = 1398 INFO 2026-05-28 20:11:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:1,372 INFO 2026-05-28 20:11:18 OpticalDuplicateFinder Large duplicate set. size = 3772 INFO 2026-05-28 20:11:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,687 INFO 2026-05-28 20:11:18 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,921 INFO 2026-05-28 20:11:18 OpticalDuplicateFinder compared 3,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,131 INFO 2026-05-28 20:11:18 OpticalDuplicateFinder Large duplicate set. size = 3603 INFO 2026-05-28 20:11:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,239 INFO 2026-05-28 20:11:18 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-13,933 INFO 2026-05-28 20:11:18 OpticalDuplicateFinder compared 3,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,445 INFO 2026-05-28 20:11:18 OpticalDuplicateFinder Large duplicate set. size = 1787 INFO 2026-05-28 20:11:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,590 INFO 2026-05-28 20:11:18 OpticalDuplicateFinder Large duplicate set. size = 2912 INFO 2026-05-28 20:11:18 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,529 INFO 2026-05-28 20:11:18 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-27,362 INFO 2026-05-28 20:11:18 OpticalDuplicateFinder Large duplicate set. size = 3394 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-13,480 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,365 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder compared 3,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,401 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder Large duplicate set. size = 1038 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:23,773 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder Large duplicate set. size = 1266 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-25,623 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder Large duplicate set. size = 1481 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:23,514 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder Large duplicate set. size = 4026 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,672 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,305 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder compared 3,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-22,703 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder compared 4,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:21,953 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder Large duplicate set. size = 1072 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:5,328 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder Large duplicate set. size = 1012 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:10,368 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder Large duplicate set. size = 1325 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,887 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder Large duplicate set. size = 1957 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,350 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder Large duplicate set. size = 2431 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,140 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-27,589 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder Large duplicate set. size = 1090 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,293 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder Large duplicate set. size = 1021 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,130 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder Large duplicate set. size = 2379 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-13,893 INFO 2026-05-28 20:11:19 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,349 INFO 2026-05-28 20:11:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2026-05-28 20:11:22 MarkDuplicates Sorting list of duplicate records. INFO 2026-05-28 20:11:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 27301612264; totalMemory: 43251662848; maxMemory: 63585648640 INFO 2026-05-28 20:11:23 MarkDuplicates Marking 20469729 records as duplicates. INFO 2026-05-28 20:11:23 MarkDuplicates Found 330560 optical duplicate clusters. INFO 2026-05-28 20:11:23 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2026-05-28 20:11:44 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:20s. Time for last 10,000,000: 20s. Last read position: chr6:73,466,596 INFO 2026-05-28 20:12:07 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:44s. Time for last 10,000,000: 23s. Last read position: chr14:23,957,084 INFO 2026-05-28 20:12:33 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:10s. Time for last 10,000,000: 26s. Last read position: chr20:35,716,793 INFO 2026-05-28 20:12:54 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:30s. Time for last 10,000,000: 20s. Last read position: GL000220.1:160,819 INFO 2026-05-28 20:13:04 MarkDuplicates Writing complete. Closing input iterator. INFO 2026-05-28 20:13:04 MarkDuplicates Duplicate Index cleanup. INFO 2026-05-28 20:13:04 MarkDuplicates Getting Memory Stats. INFO 2026-05-28 20:13:04 MarkDuplicates Before output close freeMemory: 201712328; totalMemory: 234881024; maxMemory: 63585648640 INFO 2026-05-28 20:13:04 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2026-05-28 20:13:04 MarkDuplicates After output close freeMemory: 104282000; totalMemory: 134217728; maxMemory: 63585648640 [Thu May 28 20:13:04 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 3.54 minutes. Runtime.totalMemory()=134217728 Tool returned: 0 ls: *cram: No such file or directory ls: *.crai: No such file or directory