Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/9b7e7b2ef1237e3e9faba4ba632e7a/A549_FFPE_01_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/b7/aefe4d47fd7db59788c99bcea82f5e/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/aefe4d47fd7db59788c99bcea82f5e/.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 A549_FFPE_01_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md.bam --METRICS_FILE A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT 20:06:48.366 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 20:06:48 GMT 2026] MarkDuplicates --INPUT A549_FFPE_01_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT A549_FFPE_01_RNA_0001_B23LG7FLT4_1.md.bam --METRICS_FILE A549_FFPE_01_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 20:06:48 GMT 2026] Executing as ?@nf-b7aefe4d47fd7db59788c99bcea82f5e-414f5-5snk2 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 20:06:48 MarkDuplicates Start of doWork freeMemory: 105828824; totalMemory: 134217728; maxMemory: 63585648640 INFO 2026-05-28 20:06:48 MarkDuplicates Reading input file and constructing read end information. INFO 2026-05-28 20:06:48 MarkDuplicates Will retain up to 230382784 data points before spilling to disk. INFO 2026-05-28 20:06:52 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr11:85,484,188 INFO 2026-05-28 20:06:52 MarkDuplicates Tracking 3363 as yet unmatched pairs. 107 records in RAM. INFO 2026-05-28 20:06:54 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: chr21:8,397,817 INFO 2026-05-28 20:06:54 MarkDuplicates Tracking 2284 as yet unmatched pairs. 1528 records in RAM. INFO 2026-05-28 20:06:56 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: GL000220.1:158,237 INFO 2026-05-28 20:06:56 MarkDuplicates Tracking 595 as yet unmatched pairs. 10 records in RAM. INFO 2026-05-28 20:06:57 MarkDuplicates Read 3581598 records. 0 pairs never matched. INFO 2026-05-28 20:06:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 4839636944; totalMemory: 8623489024; maxMemory: 63585648640 INFO 2026-05-28 20:06:58 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk. INFO 2026-05-28 20:07:05 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2026-05-28 20:07:05 OpticalDuplicateFinder Large duplicate set. size = 1023 INFO 2026-05-28 20:07:05 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,988 INFO 2026-05-28 20:07:05 OpticalDuplicateFinder Large duplicate set. size = 1633 INFO 2026-05-28 20:07:05 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:7,318 INFO 2026-05-28 20:07:05 OpticalDuplicateFinder Large duplicate set. size = 1079 INFO 2026-05-28 20:07:05 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,777 INFO 2026-05-28 20:07:05 OpticalDuplicateFinder Large duplicate set. size = 1488 INFO 2026-05-28 20:07:05 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,939 INFO 2026-05-28 20:07:05 OpticalDuplicateFinder Large duplicate set. size = 1161 INFO 2026-05-28 20:07:05 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,551 INFO 2026-05-28 20:07:05 OpticalDuplicateFinder Large duplicate set. size = 2807 INFO 2026-05-28 20:07:05 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:7,796 INFO 2026-05-28 20:07:05 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:4,430 INFO 2026-05-28 20:07:05 OpticalDuplicateFinder Large duplicate set. size = 3437 INFO 2026-05-28 20:07:05 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,596 INFO 2026-05-28 20:07:05 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:4,123 INFO 2026-05-28 20:07:05 OpticalDuplicateFinder compared 3,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:14,696 INFO 2026-05-28 20:07:06 OpticalDuplicateFinder Large duplicate set. size = 1057 INFO 2026-05-28 20:07:06 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:8,904 INFO 2026-05-28 20:07:06 OpticalDuplicateFinder Large duplicate set. size = 1885 INFO 2026-05-28 20:07:06 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,933 INFO 2026-05-28 20:07:06 OpticalDuplicateFinder Large duplicate set. size = 2644 INFO 2026-05-28 20:07:06 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,251 INFO 2026-05-28 20:07:06 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,925 INFO 2026-05-28 20:07:06 OpticalDuplicateFinder Large duplicate set. size = 2886 INFO 2026-05-28 20:07:06 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:29,647 INFO 2026-05-28 20:07:06 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:17,641 INFO 2026-05-28 20:07:06 OpticalDuplicateFinder Large duplicate set. size = 1148 INFO 2026-05-28 20:07:06 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,026 INFO 2026-05-28 20:07:06 OpticalDuplicateFinder Large duplicate set. size = 1259 INFO 2026-05-28 20:07:06 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,860 INFO 2026-05-28 20:07:06 OpticalDuplicateFinder Large duplicate set. size = 1769 INFO 2026-05-28 20:07:06 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-26,812 INFO 2026-05-28 20:07:06 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2026-05-28 20:07:06 MarkDuplicates Sorting list of duplicate records. INFO 2026-05-28 20:07:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 10692196760; totalMemory: 26642219008; maxMemory: 63585648640 INFO 2026-05-28 20:07:06 MarkDuplicates Marking 355212 records as duplicates. INFO 2026-05-28 20:07:06 MarkDuplicates Found 1035 optical duplicate clusters. INFO 2026-05-28 20:07:06 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2026-05-28 20:07:15 MarkDuplicates Writing complete. Closing input iterator. INFO 2026-05-28 20:07:15 MarkDuplicates Duplicate Index cleanup. INFO 2026-05-28 20:07:15 MarkDuplicates Getting Memory Stats. INFO 2026-05-28 20:07:15 MarkDuplicates Before output close freeMemory: 10755878776; totalMemory: 26742882304; maxMemory: 63585648640 INFO 2026-05-28 20:07:15 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2026-05-28 20:07:15 MarkDuplicates After output close freeMemory: 203715096; totalMemory: 234881024; maxMemory: 63585648640 [Thu May 28 20:07:15 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.45 minutes. Runtime.totalMemory()=234881024 Tool returned: 0 ls: *cram: No such file or directory ls: *.crai: No such file or directory