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
13:02:29.694 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 13:02:29 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
[Wed Jun 03 13:02:29 GMT 2026] Executing as ?@nf-ed8d0d96a6ef1dae44f84274179cfa2d-df819-z5q9r 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 2026-06-03 13:02:29 MarkDuplicates Start of doWork freeMemory: 105828704; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-03 13:02:29 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-03 13:02:29 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-03 13:02:33 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:110,018,371
INFO 2026-06-03 13:02:33 MarkDuplicates Tracking 885 as yet unmatched pairs. 26 records in RAM.
INFO 2026-06-03 13:02:34 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: chr1:228,146,888
INFO 2026-06-03 13:02:34 MarkDuplicates Tracking 1746 as yet unmatched pairs. 95 records in RAM.
INFO 2026-06-03 13:02:37 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 2s. Last read position: chr2:159,759,241
INFO 2026-06-03 13:02:37 MarkDuplicates Tracking 15347 as yet unmatched pairs. 376 records in RAM.
INFO 2026-06-03 13:02:38 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 1s. Last read position: chr3:51,993,725
INFO 2026-06-03 13:02:38 MarkDuplicates Tracking 15094 as yet unmatched pairs. 742 records in RAM.
INFO 2026-06-03 13:02:40 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: chr4:102,597,542
INFO 2026-06-03 13:02:40 MarkDuplicates Tracking 14256 as yet unmatched pairs. 185 records in RAM.
INFO 2026-06-03 13:02:42 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 1s. Last read position: chr5:176,506,768
INFO 2026-06-03 13:02:42 MarkDuplicates Tracking 13701 as yet unmatched pairs. 156 records in RAM.
INFO 2026-06-03 13:02:44 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 1s. Last read position: chr6:34,421,771
INFO 2026-06-03 13:02:44 MarkDuplicates Tracking 13729 as yet unmatched pairs. 1256 records in RAM.
INFO 2026-06-03 13:02:45 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: chr7:26,197,277
INFO 2026-06-03 13:02:45 MarkDuplicates Tracking 13131 as yet unmatched pairs. 1221 records in RAM.
INFO 2026-06-03 13:02:47 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: chr8:89,914,196
INFO 2026-06-03 13:02:47 MarkDuplicates Tracking 11845 as yet unmatched pairs. 282 records in RAM.
INFO 2026-06-03 13:02:50 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 3s. Last read position: chr9:133,349,561
INFO 2026-06-03 13:02:50 MarkDuplicates Tracking 12123 as yet unmatched pairs. 988 records in RAM.
INFO 2026-06-03 13:02:52 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 2s. Last read position: chr11:33,068,720
INFO 2026-06-03 13:02:52 MarkDuplicates Tracking 10630 as yet unmatched pairs. 703 records in RAM.
INFO 2026-06-03 13:02:54 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 1s. Last read position: chr12:6,945,786
INFO 2026-06-03 13:02:54 MarkDuplicates Tracking 9977 as yet unmatched pairs. 878 records in RAM.
INFO 2026-06-03 13:02:55 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: chr12:122,752,900
INFO 2026-06-03 13:02:55 MarkDuplicates Tracking 9343 as yet unmatched pairs. 133 records in RAM.
INFO 2026-06-03 13:02:58 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 3s. Last read position: chr15:28,076,562
INFO 2026-06-03 13:02:58 MarkDuplicates Tracking 8709 as yet unmatched pairs. 465 records in RAM.
INFO 2026-06-03 13:03:00 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 1s. Last read position: chr16:21,834,735
INFO 2026-06-03 13:03:00 MarkDuplicates Tracking 8034 as yet unmatched pairs. 651 records in RAM.
INFO 2026-06-03 13:03:01 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 1s. Last read position: chr17:7,318,111
INFO 2026-06-03 13:03:01 MarkDuplicates Tracking 7295 as yet unmatched pairs. 1082 records in RAM.
INFO 2026-06-03 13:03:04 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 2s. Last read position: chr17:76,039,898
INFO 2026-06-03 13:03:04 MarkDuplicates Tracking 6643 as yet unmatched pairs. 339 records in RAM.
INFO 2026-06-03 13:03:05 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 1s. Last read position: chr19:12,734,557
INFO 2026-06-03 13:03:05 MarkDuplicates Tracking 5761 as yet unmatched pairs. 755 records in RAM.
INFO 2026-06-03 13:03:07 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 1s. Last read position: chr20:35,277,516
INFO 2026-06-03 13:03:07 MarkDuplicates Tracking 5013 as yet unmatched pairs. 288 records in RAM.
INFO 2026-06-03 13:03:09 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 1s. Last read position: chr21:8,398,054
INFO 2026-06-03 13:03:09 MarkDuplicates Tracking 3586 as yet unmatched pairs. 634 records in RAM.
INFO 2026-06-03 13:03:11 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 2s. Last read position: chr22:38,495,046
INFO 2026-06-03 13:03:11 MarkDuplicates Tracking 2804 as yet unmatched pairs. 437 records in RAM.
INFO 2026-06-03 13:03:13 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chrY:19,721,298
INFO 2026-06-03 13:03:13 MarkDuplicates Tracking 1801 as yet unmatched pairs. 31 records in RAM.
INFO 2026-06-03 13:03:14 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 1s. Last read position: KI270733.1:134,152
INFO 2026-06-03 13:03:14 MarkDuplicates Tracking 587 as yet unmatched pairs. 587 records in RAM.
INFO 2026-06-03 13:03:15 MarkDuplicates Read 23345691 records. 0 pairs never matched.
INFO 2026-06-03 13:03:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 13716497016; totalMemory: 19595788288; maxMemory: 63585648640
INFO 2026-06-03 13:03:17 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-03 13:03:24 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-03 13:03:25 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-03 13:03:27 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-03 13:03:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 19517051936; totalMemory: 35467034624; maxMemory: 63585648640
INFO 2026-06-03 13:03:27 MarkDuplicates Marking 3945308 records as duplicates.
INFO 2026-06-03 13:03:27 MarkDuplicates Found 142496 optical duplicate clusters.
INFO 2026-06-03 13:03:27 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-03 13:03:46 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:19s. Time for last 10,000,000: 19s. Last read position: chr9:133,349,561
INFO 2026-06-03 13:04:06 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:39s. Time for last 10,000,000: 19s. Last read position: chr21:8,398,054
INFO 2026-06-03 13:04:13 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-03 13:04:13 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-03 13:04:13 MarkDuplicates Getting Memory Stats.
INFO 2026-06-03 13:04:13 MarkDuplicates Before output close freeMemory: 201855344; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-03 13:04:13 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-03 13:04:13 MarkDuplicates After output close freeMemory: 105281440; totalMemory: 134217728; maxMemory: 63585648640
[Wed Jun 03 13:04:13 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 1.73 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory