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_3.Aligned.sortedByCoord.out.bam --OUTPUT A549_FFPE_01_RNA_0001_B23LG7FLT4_3.md.bam --METRICS_FILE A549_FFPE_01_RNA_0001_B23LG7FLT4_3.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT 07:23:50.235 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 07:23:50 GMT 2026] MarkDuplicates --INPUT A549_FFPE_01_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam --OUTPUT A549_FFPE_01_RNA_0001_B23LG7FLT4_3.md.bam --METRICS_FILE A549_FFPE_01_RNA_0001_B23LG7FLT4_3.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 07:23:50 GMT 2026] Executing as ?@nf-a4098746d67bde52743cf85398eaf34b-f5310-8sckf 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 07:23:50 MarkDuplicates Start of doWork freeMemory: 105828992; totalMemory: 134217728; maxMemory: 63585648640 INFO 2026-06-08 07:23:50 MarkDuplicates Reading input file and constructing read end information. INFO 2026-06-08 07:23:50 MarkDuplicates Will retain up to 230382784 data points before spilling to disk. INFO 2026-06-08 07:23:55 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr10:104,479,813 INFO 2026-06-08 07:23:55 MarkDuplicates Tracking 5690 as yet unmatched pairs. 127 records in RAM. INFO 2026-06-08 07:23:57 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: chr21:8,217,329 INFO 2026-06-08 07:23:57 MarkDuplicates Tracking 4267 as yet unmatched pairs. 3190 records in RAM. INFO 2026-06-08 07:23:59 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 2s. Last read position: chr22:11,630,472 INFO 2026-06-08 07:23:59 MarkDuplicates Tracking 1083 as yet unmatched pairs. 64 records in RAM. INFO 2026-06-08 07:24:02 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 2s. Last read position: KI270733.1:131,106 INFO 2026-06-08 07:24:02 MarkDuplicates Tracking 515 as yet unmatched pairs. 515 records in RAM. INFO 2026-06-08 07:24:03 MarkDuplicates Read 4557021 records. 0 pairs never matched. INFO 2026-06-08 07:24:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 8582976264; totalMemory: 12381585408; maxMemory: 63585648640 INFO 2026-06-08 07:24:05 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk. INFO 2026-06-08 07:24:15 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2026-06-08 07:24:15 OpticalDuplicateFinder Large duplicate set. size = 1293 INFO 2026-06-08 07:24:15 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 07:24:15 OpticalDuplicateFinder Large duplicate set. size = 1430 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-21,699 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder Large duplicate set. size = 1233 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:8,143 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder Large duplicate set. size = 1570 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,228 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder Large duplicate set. size = 1288 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-18,002 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder Large duplicate set. size = 1334 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,115 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder Large duplicate set. size = 4503 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:31,969 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:21,621 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder compared 3,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-13,440 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder compared 4,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,238 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder Large duplicate set. size = 3645 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,185 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,981 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder compared 3,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:6,574 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder Large duplicate set. size = 1037 INFO 2026-06-08 07:24:15 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 2026-06-08 07:24:15 OpticalDuplicateFinder Large duplicate set. size = 1476 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-19,281 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder Large duplicate set. size = 2971 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-30,299 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,552 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder Large duplicate set. size = 3118 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,031 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,629 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder compared 3,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-13,860 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder Large duplicate set. size = 1313 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-13,755 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder Large duplicate set. size = 1223 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:10,854 INFO 2026-06-08 07:24:15 OpticalDuplicateFinder Large duplicate set. size = 1250 INFO 2026-06-08 07:24:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,360 INFO 2026-06-08 07:24:16 OpticalDuplicateFinder Large duplicate set. size = 1688 INFO 2026-06-08 07:24:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-27,411 INFO 2026-06-08 07:24:16 OpticalDuplicateFinder Large duplicate set. size = 1180 INFO 2026-06-08 07:24:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,274 INFO 2026-06-08 07:24:16 OpticalDuplicateFinder Large duplicate set. size = 3455 INFO 2026-06-08 07:24:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:25,772 INFO 2026-06-08 07:24:16 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:5,005 INFO 2026-06-08 07:24:16 OpticalDuplicateFinder compared 3,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,318 INFO 2026-06-08 07:24:16 OpticalDuplicateFinder Large duplicate set. size = 1102 INFO 2026-06-08 07:24:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:11,218 INFO 2026-06-08 07:24:16 OpticalDuplicateFinder Large duplicate set. size = 1619 INFO 2026-06-08 07:24:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,916 INFO 2026-06-08 07:24:16 OpticalDuplicateFinder Large duplicate set. size = 1959 INFO 2026-06-08 07:24:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,592 INFO 2026-06-08 07:24:16 OpticalDuplicateFinder Large duplicate set. size = 1137 INFO 2026-06-08 07:24:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-29,304 INFO 2026-06-08 07:24:16 OpticalDuplicateFinder Large duplicate set. size = 2154 INFO 2026-06-08 07:24:16 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-18,698 INFO 2026-06-08 07:24:16 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:27,390 INFO 2026-06-08 07:24:16 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2026-06-08 07:24:16 MarkDuplicates Sorting list of duplicate records. INFO 2026-06-08 07:24:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 12302798176; totalMemory: 28252831744; maxMemory: 63585648640 INFO 2026-06-08 07:24:16 MarkDuplicates Marking 482601 records as duplicates. INFO 2026-06-08 07:24:16 MarkDuplicates Found 1336 optical duplicate clusters. INFO 2026-06-08 07:24:16 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2026-06-08 07:24:32 MarkDuplicates Writing complete. Closing input iterator. INFO 2026-06-08 07:24:32 MarkDuplicates Duplicate Index cleanup. INFO 2026-06-08 07:24:32 MarkDuplicates Getting Memory Stats. INFO 2026-06-08 07:24:32 MarkDuplicates Before output close freeMemory: 12114658952; totalMemory: 28252831744; maxMemory: 63585648640 INFO 2026-06-08 07:24:32 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2026-06-08 07:24:32 MarkDuplicates After output close freeMemory: 203702144; totalMemory: 234881024; maxMemory: 63585648640 [Mon Jun 08 07:24:32 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.71 minutes. Runtime.totalMemory()=234881024 ls: *cram: No such file or directory ls: *.crai: No such file or directory