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 <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
[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
ls: *cram: No such file or directory
ls: *.crai: No such file or directory