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_s1200_S21.Aligned.sortedByCoord.out.bam --OUTPUT rna_s1200_S21.md.bam --METRICS_FILE rna_s1200_S21.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
21:55:47.587 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
[Wed Jun 03 21:55:47 GMT 2026] MarkDuplicates --INPUT rna_s1200_S21.Aligned.sortedByCoord.out.bam --OUTPUT rna_s1200_S21.md.bam --METRICS_FILE rna_s1200_S21.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
[Wed Jun 03 21:55:47 GMT 2026] Executing as ?@nf-ecd690fe3f8146f89fd1af53a3fad053-97173-fv28h 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 2026-06-03 21:55:47 MarkDuplicates Start of doWork freeMemory: 105830008; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-03 21:55:47 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-03 21:55:47 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-03 21:55:51 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:111,230,487
INFO 2026-06-03 21:55:51 MarkDuplicates Tracking 1034 as yet unmatched pairs. 118 records in RAM.
INFO 2026-06-03 21:55:52 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 1s. Last read position: chr1:233,139,804
INFO 2026-06-03 21:55:52 MarkDuplicates Tracking 1667 as yet unmatched pairs. 10 records in RAM.
INFO 2026-06-03 21:55:54 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: chr2:177,215,659
INFO 2026-06-03 21:55:54 MarkDuplicates Tracking 14896 as yet unmatched pairs. 517 records in RAM.
INFO 2026-06-03 21:55:56 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 2s. Last read position: chr3:53,864,996
INFO 2026-06-03 21:55:56 MarkDuplicates Tracking 13980 as yet unmatched pairs. 387 records in RAM.
INFO 2026-06-03 21:55:58 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: chr4:143,538,860
INFO 2026-06-03 21:55:58 MarkDuplicates Tracking 13298 as yet unmatched pairs. 170 records in RAM.
INFO 2026-06-03 21:56:00 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 2s. Last read position: chr5:181,237,672
INFO 2026-06-03 21:56:00 MarkDuplicates Tracking 12925 as yet unmatched pairs. 430 records in RAM.
INFO 2026-06-03 21:56:02 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 2s. Last read position: chr6:43,499,011
INFO 2026-06-03 21:56:02 MarkDuplicates Tracking 11725 as yet unmatched pairs. 423 records in RAM.
INFO 2026-06-03 21:56:04 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: chr7:44,696,070
INFO 2026-06-03 21:56:04 MarkDuplicates Tracking 11025 as yet unmatched pairs. 519 records in RAM.
INFO 2026-06-03 21:56:06 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 2s. Last read position: chr8:100,706,769
INFO 2026-06-03 21:56:06 MarkDuplicates Tracking 10620 as yet unmatched pairs. 629 records in RAM.
INFO 2026-06-03 21:56:08 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: chr9:136,454,161
INFO 2026-06-03 21:56:08 MarkDuplicates Tracking 9488 as yet unmatched pairs. 187 records in RAM.
INFO 2026-06-03 21:56:10 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 1s. Last read position: chr11:46,547,131
INFO 2026-06-03 21:56:10 MarkDuplicates Tracking 8554 as yet unmatched pairs. 698 records in RAM.
INFO 2026-06-03 21:56:12 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 1s. Last read position: chr12:8,605,335
INFO 2026-06-03 21:56:12 MarkDuplicates Tracking 7708 as yet unmatched pairs. 836 records in RAM.
INFO 2026-06-03 21:56:13 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: chr12:124,911,968
INFO 2026-06-03 21:56:13 MarkDuplicates Tracking 7272 as yet unmatched pairs. 382 records in RAM.
INFO 2026-06-03 21:56:15 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 1s. Last read position: chr15:34,904,443
INFO 2026-06-03 21:56:15 MarkDuplicates Tracking 6276 as yet unmatched pairs. 471 records in RAM.
INFO 2026-06-03 21:56:17 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 2s. Last read position: chr16:22,513,880
INFO 2026-06-03 21:56:17 MarkDuplicates Tracking 5499 as yet unmatched pairs. 749 records in RAM.
INFO 2026-06-03 21:56:19 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 1s. Last read position: chr17:7,311,406
INFO 2026-06-03 21:56:19 MarkDuplicates Tracking 5063 as yet unmatched pairs. 1642 records in RAM.
INFO 2026-06-03 21:56:21 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 1s. Last read position: chr17:76,047,903
INFO 2026-06-03 21:56:21 MarkDuplicates Tracking 3797 as yet unmatched pairs. 369 records in RAM.
INFO 2026-06-03 21:56:23 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 2s. Last read position: chr19:10,689,198
INFO 2026-06-03 21:56:23 MarkDuplicates Tracking 2818 as yet unmatched pairs. 933 records in RAM.
INFO 2026-06-03 21:56:25 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 1s. Last read position: chr20:3,755,548
INFO 2026-06-03 21:56:25 MarkDuplicates Tracking 1890 as yet unmatched pairs. 439 records in RAM.
INFO 2026-06-03 21:56:27 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 1s. Last read position: chr22:36,518,625
INFO 2026-06-03 21:56:27 MarkDuplicates Tracking 1155 as yet unmatched pairs. 536 records in RAM.
INFO 2026-06-03 21:56:29 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 1s. Last read position: chrX:154,360,515
INFO 2026-06-03 21:56:29 MarkDuplicates Tracking 252 as yet unmatched pairs. 202 records in RAM.
INFO 2026-06-03 21:56:29 MarkDuplicates Read 21124841 records. 0 pairs never matched.
INFO 2026-06-03 21:56:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 13814058120; totalMemory: 19696451584; maxMemory: 63585648640
INFO 2026-06-03 21:56:31 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-03 21:56:36 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-03 21:56:38 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-03 21:56:39 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-03 21:56:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 19617722440; totalMemory: 35567697920; maxMemory: 63585648640
INFO 2026-06-03 21:56:40 MarkDuplicates Marking 3649536 records as duplicates.
INFO 2026-06-03 21:56:40 MarkDuplicates Found 12067 optical duplicate clusters.
INFO 2026-06-03 21:56:40 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-03 21:56:59 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:19s. Time for last 10,000,000: 19s. Last read position: chr9:136,454,161
INFO 2026-06-03 21:57:18 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:38s. Time for last 10,000,000: 19s. Last read position: chr22:36,518,625
INFO 2026-06-03 21:57:20 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-03 21:57:20 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-03 21:57:20 MarkDuplicates Getting Memory Stats.
INFO 2026-06-03 21:57:21 MarkDuplicates Before output close freeMemory: 201687376; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-03 21:57:21 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-03 21:57:21 MarkDuplicates After output close freeMemory: 104361456; totalMemory: 134217728; maxMemory: 63585648640
[Wed Jun 03 21:57:21 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 1.56 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory