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 rna_s1221_S42.Aligned.sortedByCoord.out.bam --OUTPUT rna_s1221_S42.md.bam --METRICS_FILE rna_s1221_S42.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
20:35:54.724 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
[Tue Jun 02 20:35:54 GMT 2026] MarkDuplicates --INPUT rna_s1221_S42.Aligned.sortedByCoord.out.bam --OUTPUT rna_s1221_S42.md.bam --METRICS_FILE rna_s1221_S42.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
[Tue Jun 02 20:35:54 GMT 2026] Executing as ?@nf-78ef03efd18dd4a25cc1446a3eb6b7dd-dad7f-x765s 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 2026-06-02 20:35:54 MarkDuplicates Start of doWork freeMemory: 105830088; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-02 20:35:54 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-02 20:35:54 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-02 20:35:58 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:109,668,493
INFO 2026-06-02 20:35:58 MarkDuplicates Tracking 946 as yet unmatched pairs. 10 records in RAM.
INFO 2026-06-02 20:36:00 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: chr1:228,097,688
INFO 2026-06-02 20:36:00 MarkDuplicates Tracking 1795 as yet unmatched pairs. 123 records in RAM.
INFO 2026-06-02 20:36:02 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: chr2:159,748,300
INFO 2026-06-02 20:36:02 MarkDuplicates Tracking 15536 as yet unmatched pairs. 423 records in RAM.
INFO 2026-06-02 20:36:03 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: chr3:51,969,471
INFO 2026-06-02 20:36:03 MarkDuplicates Tracking 14870 as yet unmatched pairs. 437 records in RAM.
INFO 2026-06-02 20:36:05 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: chr4:102,578,927
INFO 2026-06-02 20:36:05 MarkDuplicates Tracking 14378 as yet unmatched pairs. 208 records in RAM.
INFO 2026-06-02 20:36:07 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: chr5:175,965,027
INFO 2026-06-02 20:36:07 MarkDuplicates Tracking 13796 as yet unmatched pairs. 135 records in RAM.
INFO 2026-06-02 20:36:09 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: chr6:34,417,468
INFO 2026-06-02 20:36:09 MarkDuplicates Tracking 13419 as yet unmatched pairs. 785 records in RAM.
INFO 2026-06-02 20:36:10 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: chr7:26,196,874
INFO 2026-06-02 20:36:10 MarkDuplicates Tracking 13012 as yet unmatched pairs. 988 records in RAM.
INFO 2026-06-02 20:36:12 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: chr8:85,477,248
INFO 2026-06-02 20:36:12 MarkDuplicates Tracking 11984 as yet unmatched pairs. 308 records in RAM.
INFO 2026-06-02 20:36:14 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 2s. Last read position: chr9:133,348,921
INFO 2026-06-02 20:36:14 MarkDuplicates Tracking 11452 as yet unmatched pairs. 274 records in RAM.
INFO 2026-06-02 20:36:16 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: chr11:32,934,959
INFO 2026-06-02 20:36:16 MarkDuplicates Tracking 10610 as yet unmatched pairs. 716 records in RAM.
INFO 2026-06-02 20:36:17 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 1s. Last read position: chr12:6,934,175
INFO 2026-06-02 20:36:17 MarkDuplicates Tracking 9909 as yet unmatched pairs. 861 records in RAM.
INFO 2026-06-02 20:36:19 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 1s. Last read position: chr12:122,361,130
INFO 2026-06-02 20:36:19 MarkDuplicates Tracking 9279 as yet unmatched pairs. 120 records in RAM.
INFO 2026-06-02 20:36:21 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 2s. Last read position: chr15:22,577,157
INFO 2026-06-02 20:36:21 MarkDuplicates Tracking 8657 as yet unmatched pairs. 458 records in RAM.
INFO 2026-06-02 20:36:22 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 1s. Last read position: chr16:21,456,352
INFO 2026-06-02 20:36:22 MarkDuplicates Tracking 8013 as yet unmatched pairs. 668 records in RAM.
INFO 2026-06-02 20:36:24 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 2s. Last read position: chr17:7,252,517
INFO 2026-06-02 20:36:24 MarkDuplicates Tracking 7263 as yet unmatched pairs. 1069 records in RAM.
INFO 2026-06-02 20:36:26 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 1s. Last read position: chr17:75,834,458
INFO 2026-06-02 20:36:26 MarkDuplicates Tracking 6654 as yet unmatched pairs. 356 records in RAM.
INFO 2026-06-02 20:36:28 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 2s. Last read position: chr19:12,666,543
INFO 2026-06-02 20:36:28 MarkDuplicates Tracking 5879 as yet unmatched pairs. 916 records in RAM.
INFO 2026-06-02 20:36:30 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 1s. Last read position: chr20:34,540,578
INFO 2026-06-02 20:36:30 MarkDuplicates Tracking 4974 as yet unmatched pairs. 290 records in RAM.
INFO 2026-06-02 20:36:31 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 1s. Last read position: chr21:8,397,807
INFO 2026-06-02 20:36:31 MarkDuplicates Tracking 3557 as yet unmatched pairs. 654 records in RAM.
INFO 2026-06-02 20:36:32 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 1s. Last read position: chr22:38,230,583
INFO 2026-06-02 20:36:32 MarkDuplicates Tracking 2612 as yet unmatched pairs. 300 records in RAM.
INFO 2026-06-02 20:36:33 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 1s. Last read position: chrY:12,912,799
INFO 2026-06-02 20:36:33 MarkDuplicates Tracking 1780 as yet unmatched pairs. 61 records in RAM.
INFO 2026-06-02 20:36:35 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 1s. Last read position: KI270733.1:133,680
INFO 2026-06-02 20:36:35 MarkDuplicates Tracking 831 as yet unmatched pairs. 829 records in RAM.
INFO 2026-06-02 20:36:35 MarkDuplicates Read 23361239 records. 2 pairs never matched.
INFO 2026-06-02 20:36:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 13717874272; totalMemory: 19595788288; maxMemory: 63585648640
INFO 2026-06-02 20:36:37 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-02 20:36:40 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-02 20:36:42 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-02 20:36:43 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-02 20:36:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 30791339728; totalMemory: 46741323776; maxMemory: 63585648640
INFO 2026-06-02 20:36:44 MarkDuplicates Marking 3947079 records as duplicates.
INFO 2026-06-02 20:36:44 MarkDuplicates Found 18255 optical duplicate clusters.
INFO 2026-06-02 20:36:44 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-02 20:37:02 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:18s. Time for last 10,000,000: 18s. Last read position: chr9:133,348,921
INFO 2026-06-02 20:37:22 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:38s. Time for last 10,000,000: 19s. Last read position: chr21:8,397,807
INFO 2026-06-02 20:37:29 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-02 20:37:29 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-02 20:37:29 MarkDuplicates Getting Memory Stats.
INFO 2026-06-02 20:37:29 MarkDuplicates Before output close freeMemory: 25804106152; totalMemory: 46741323776; maxMemory: 63585648640
INFO 2026-06-02 20:37:29 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-02 20:37:29 MarkDuplicates After output close freeMemory: 203989792; totalMemory: 234881024; maxMemory: 63585648640
[Tue Jun 02 20:37:29 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 1.58 minutes.
Runtime.totalMemory()=234881024
ls: *cram: No such file or directory
ls: *.crai: No such file or directory