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_2.Aligned.sortedByCoord.out.bam --OUTPUT A549_FFPE_01_RNA_0001_B23LG7FLT4_2.md.bam --METRICS_FILE A549_FFPE_01_RNA_0001_B23LG7FLT4_2.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:23:36.701 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 07:23:36 GMT 2026] MarkDuplicates --INPUT A549_FFPE_01_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT A549_FFPE_01_RNA_0001_B23LG7FLT4_2.md.bam --METRICS_FILE A549_FFPE_01_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 <optimized capture of last three ':' separated fields as numeric values> --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 07:23:36 GMT 2026] Executing as ?@nf-61d8425149544fe61ff11f95e87ec5dd-46f2b-s52nn 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 07:23:36 MarkDuplicates Start of doWork freeMemory: 105828800; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:23:36 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:23:36 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:23:42 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr21:8,442,520
INFO 2026-06-08 07:23:42 MarkDuplicates Tracking 329 as yet unmatched pairs. 20 records in RAM.
INFO 2026-06-08 07:23:44 MarkDuplicates Read 1496510 records. 0 pairs never matched.
INFO 2026-06-08 07:23:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 2585981912; totalMemory: 6341787648; maxMemory: 63585648640
INFO 2026-06-08 07:23:47 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 07:23:58 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 07:23:59 OpticalDuplicateFinder Large duplicate set. size = 1122
INFO 2026-06-08 07:23:59 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:5,312
INFO 2026-06-08 07:23:59 OpticalDuplicateFinder Large duplicate set. size = 1256
INFO 2026-06-08 07:23:59 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:21,751
INFO 2026-06-08 07:23:59 OpticalDuplicateFinder Large duplicate set. size = 1220
INFO 2026-06-08 07:23:59 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:20,942
INFO 2026-06-08 07:23:59 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 07:23:59 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 07:23:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 16933350152; totalMemory: 32883343360; maxMemory: 63585648640
INFO 2026-06-08 07:23:59 MarkDuplicates Marking 134679 records as duplicates.
INFO 2026-06-08 07:23:59 MarkDuplicates Found 474 optical duplicate clusters.
INFO 2026-06-08 07:23:59 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 07:24:05 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 07:24:05 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 07:24:05 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 07:24:05 MarkDuplicates Before output close freeMemory: 29229346816; totalMemory: 45164265472; maxMemory: 63585648640
INFO 2026-06-08 07:24:05 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 07:24:05 MarkDuplicates After output close freeMemory: 203899232; totalMemory: 234881024; maxMemory: 63585648640
[Mon Jun 08 07:24:05 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.48 minutes.
Runtime.totalMemory()=234881024
ls: *cram: No such file or directory
ls: *.crai: No such file or directory