Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/0c95ee27a3afbad9e361a65c31958d/22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.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/a7/cc83e637a35079be1a37e6e76345c5/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/cc83e637a35079be1a37e6e76345c5/.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_2.Aligned.sortedByCoord.out.bam --OUTPUT 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bam --METRICS_FILE 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT 07:26:24.317 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 07:26:24 GMT 2026] MarkDuplicates --INPUT 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bam --METRICS_FILE 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.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 07:26:24 GMT 2026] Executing as ?@nf-a7cc83e637a35079be1a37e6e76345c5-a6d1b-7sb8d 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 07:26:24 MarkDuplicates Start of doWork freeMemory: 105830440; totalMemory: 134217728; maxMemory: 63585648640 INFO 2026-06-08 07:26:24 MarkDuplicates Reading input file and constructing read end information. INFO 2026-06-08 07:26:24 MarkDuplicates Will retain up to 230382784 data points before spilling to disk. INFO 2026-06-08 07:26:31 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 4s. Last read position: chr1:45,341,086 INFO 2026-06-08 07:26:31 MarkDuplicates Tracking 2150 as yet unmatched pairs. 3 records in RAM. INFO 2026-06-08 07:26:35 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 3s. Last read position: chr1:165,654,295 INFO 2026-06-08 07:26:35 MarkDuplicates Tracking 4023 as yet unmatched pairs. 1 records in RAM. INFO 2026-06-08 07:26:38 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 3s. Last read position: chr2:32,916,406 INFO 2026-06-08 07:26:38 MarkDuplicates Tracking 53413 as yet unmatched pairs. 3075 records in RAM. INFO 2026-06-08 07:26:41 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 3s. Last read position: chr2:189,006,343 INFO 2026-06-08 07:26:41 MarkDuplicates Tracking 55801 as yet unmatched pairs. 1120 records in RAM. INFO 2026-06-08 07:26:44 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 2s. Last read position: chr3:50,297,159 INFO 2026-06-08 07:26:44 MarkDuplicates Tracking 53852 as yet unmatched pairs. 1391 records in RAM. INFO 2026-06-08 07:26:48 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 3s. Last read position: chr4:22,442,754 INFO 2026-06-08 07:26:48 MarkDuplicates Tracking 52146 as yet unmatched pairs. 1055 records in RAM. INFO 2026-06-08 07:26:50 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 2s. Last read position: chr5:118,973,773 INFO 2026-06-08 07:26:50 MarkDuplicates Tracking 50260 as yet unmatched pairs. 1654 records in RAM. INFO 2026-06-08 07:26:54 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 4s. Last read position: chr6:26,156,731 INFO 2026-06-08 07:26:54 MarkDuplicates Tracking 48353 as yet unmatched pairs. 2900 records in RAM. INFO 2026-06-08 07:26:57 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 2s. Last read position: chr6:111,274,281 INFO 2026-06-08 07:26:57 MarkDuplicates Tracking 46241 as yet unmatched pairs. 770 records in RAM. INFO 2026-06-08 07:27:00 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 2s. Last read position: chr7:75,421,834 INFO 2026-06-08 07:27:00 MarkDuplicates Tracking 44435 as yet unmatched pairs. 1627 records in RAM. INFO 2026-06-08 07:27:03 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 3s. Last read position: chr8:30,504,372 INFO 2026-06-08 07:27:03 MarkDuplicates Tracking 42487 as yet unmatched pairs. 1949 records in RAM. INFO 2026-06-08 07:27:06 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 2s. Last read position: chr8:144,180,441 INFO 2026-06-08 07:27:06 MarkDuplicates Tracking 40709 as yet unmatched pairs. 143 records in RAM. INFO 2026-06-08 07:27:09 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chr9:134,765,706 INFO 2026-06-08 07:27:09 MarkDuplicates Tracking 38839 as yet unmatched pairs. 373 records in RAM. INFO 2026-06-08 07:27:12 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 3s. Last read position: chr10:119,042,185 INFO 2026-06-08 07:27:12 MarkDuplicates Tracking 36940 as yet unmatched pairs. 196 records in RAM. INFO 2026-06-08 07:27:15 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 2s. Last read position: chr11:65,554,300 INFO 2026-06-08 07:27:15 MarkDuplicates Tracking 34908 as yet unmatched pairs. 1613 records in RAM. INFO 2026-06-08 07:27:18 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 2s. Last read position: chr12:11,853,467 INFO 2026-06-08 07:27:18 MarkDuplicates Tracking 32866 as yet unmatched pairs. 2591 records in RAM. INFO 2026-06-08 07:27:22 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 3s. Last read position: chr12:119,179,587 INFO 2026-06-08 07:27:22 MarkDuplicates Tracking 30894 as yet unmatched pairs. 610 records in RAM. INFO 2026-06-08 07:27:24 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 2s. Last read position: chr14:51,720,247 INFO 2026-06-08 07:27:24 MarkDuplicates Tracking 28983 as yet unmatched pairs. 1767 records in RAM. INFO 2026-06-08 07:27:26 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 2s. Last read position: chr14:105,708,566 INFO 2026-06-08 07:27:26 MarkDuplicates Tracking 27316 as yet unmatched pairs. 82 records in RAM. INFO 2026-06-08 07:27:28 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 2s. Last read position: chr16:2,037,885 INFO 2026-06-08 07:27:28 MarkDuplicates Tracking 25381 as yet unmatched pairs. 2651 records in RAM. INFO 2026-06-08 07:27:30 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 2s. Last read position: chr16:30,700,847 INFO 2026-06-08 07:27:30 MarkDuplicates Tracking 23986 as yet unmatched pairs. 1248 records in RAM. INFO 2026-06-08 07:27:33 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 2s. Last read position: chr17:9,916,995 INFO 2026-06-08 07:27:33 MarkDuplicates Tracking 21808 as yet unmatched pairs. 3812 records in RAM. INFO 2026-06-08 07:27:35 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 2s. Last read position: chr17:50,190,354 INFO 2026-06-08 07:27:35 MarkDuplicates Tracking 19984 as yet unmatched pairs. 1978 records in RAM. INFO 2026-06-08 07:27:38 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 2s. Last read position: chr18:49,814,363 INFO 2026-06-08 07:27:38 MarkDuplicates Tracking 17651 as yet unmatched pairs. 261 records in RAM. INFO 2026-06-08 07:27:41 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 2s. Last read position: chr19:15,257,094 INFO 2026-06-08 07:27:41 MarkDuplicates Tracking 15342 as yet unmatched pairs. 3855 records in RAM. INFO 2026-06-08 07:27:44 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 2s. Last read position: chr19:45,306,833 INFO 2026-06-08 07:27:44 MarkDuplicates Tracking 12899 as yet unmatched pairs. 1397 records in RAM. INFO 2026-06-08 07:27:46 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 2s. Last read position: chr20:50,191,214 INFO 2026-06-08 07:27:46 MarkDuplicates Tracking 10646 as yet unmatched pairs. 551 records in RAM. INFO 2026-06-08 07:27:48 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 1s. Last read position: chr21:8,217,285 INFO 2026-06-08 07:27:48 MarkDuplicates Tracking 9044 as yet unmatched pairs. 3114 records in RAM. INFO 2026-06-08 07:27:50 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 1s. Last read position: chr21:8,399,111 INFO 2026-06-08 07:27:50 MarkDuplicates Tracking 8233 as yet unmatched pairs. 2293 records in RAM. INFO 2026-06-08 07:27:52 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,115 INFO 2026-06-08 07:27:52 MarkDuplicates Tracking 6903 as yet unmatched pairs. 961 records in RAM. INFO 2026-06-08 07:27:54 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 2s. Last read position: chr22:31,260,007 INFO 2026-06-08 07:27:54 MarkDuplicates Tracking 5189 as yet unmatched pairs. 1148 records in RAM. INFO 2026-06-08 07:27:57 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 2s. Last read position: chrX:143,581,717 INFO 2026-06-08 07:27:57 MarkDuplicates Tracking 3175 as yet unmatched pairs. 257 records in RAM. INFO 2026-06-08 07:27:59 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 2s. Last read position: GL000220.1:116,792 INFO 2026-06-08 07:27:59 MarkDuplicates Tracking 2521 as yet unmatched pairs. 43 records in RAM. INFO 2026-06-08 07:28:01 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 1s. Last read position: KI270733.1:128,201 INFO 2026-06-08 07:28:01 MarkDuplicates Tracking 2458 as yet unmatched pairs. 2455 records in RAM. INFO 2026-06-08 07:28:03 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 2s. Last read position: KI270733.1:176,024 INFO 2026-06-08 07:28:03 MarkDuplicates Tracking 77 as yet unmatched pairs. 74 records in RAM. INFO 2026-06-08 07:28:04 MarkDuplicates Read 35698267 records. 0 pairs never matched. INFO 2026-06-08 07:28:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 15127525848; totalMemory: 21609054208; maxMemory: 63585648640 INFO 2026-06-08 07:28:08 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk. INFO 2026-06-08 07:28:17 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2026-06-08 07:28:24 OpticalDuplicateFinder Large duplicate set. size = 1037 INFO 2026-06-08 07:28:24 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:2,982 INFO 2026-06-08 07:28:26 OpticalDuplicateFinder Large duplicate set. size = 1516 INFO 2026-06-08 07:28:26 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,231 INFO 2026-06-08 07:28:26 OpticalDuplicateFinder Large duplicate set. size = 1357 INFO 2026-06-08 07:28:26 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,988 INFO 2026-06-08 07:28:26 OpticalDuplicateFinder Large duplicate set. size = 1060 INFO 2026-06-08 07:28:26 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,705 INFO 2026-06-08 07:28:26 OpticalDuplicateFinder Large duplicate set. size = 1191 INFO 2026-06-08 07:28:26 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,407 INFO 2026-06-08 07:28:26 OpticalDuplicateFinder Large duplicate set. size = 1472 INFO 2026-06-08 07:28:26 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:24,243 INFO 2026-06-08 07:28:26 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2026-06-08 07:28:29 MarkDuplicates Sorting list of duplicate records. INFO 2026-06-08 07:28:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 22469806800; totalMemory: 38419824640; maxMemory: 63585648640 INFO 2026-06-08 07:28:30 MarkDuplicates Marking 18051978 records as duplicates. INFO 2026-06-08 07:28:30 MarkDuplicates Found 305008 optical duplicate clusters. INFO 2026-06-08 07:28:30 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2026-06-08 07:28:59 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:28s. Time for last 10,000,000: 28s. Last read position: chr7:75,421,834 INFO 2026-06-08 07:29:32 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:01:02s. Time for last 10,000,000: 33s. Last read position: chr16:2,037,885 INFO 2026-06-08 07:30:02 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:31s. Time for last 10,000,000: 29s. Last read position: chr21:8,444,115 INFO 2026-06-08 07:30:22 MarkDuplicates Writing complete. Closing input iterator. INFO 2026-06-08 07:30:22 MarkDuplicates Duplicate Index cleanup. INFO 2026-06-08 07:30:22 MarkDuplicates Getting Memory Stats. INFO 2026-06-08 07:30:22 MarkDuplicates Before output close freeMemory: 202426672; totalMemory: 234881024; maxMemory: 63585648640 INFO 2026-06-08 07:30:22 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2026-06-08 07:30:22 MarkDuplicates After output close freeMemory: 104308296; totalMemory: 134217728; maxMemory: 63585648640 [Mon Jun 08 07:30:22 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 3.98 minutes. Runtime.totalMemory()=134217728 Tool returned: 0 ls: *cram: No such file or directory ls: *.crai: No such file or directory