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 dna_s739.Aligned.sortedByCoord.out.bam --OUTPUT dna_s739.md.bam --METRICS_FILE dna_s739.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:18:43.447 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 07:18:43 GMT 2026] MarkDuplicates --INPUT dna_s739.Aligned.sortedByCoord.out.bam --OUTPUT dna_s739.md.bam --METRICS_FILE dna_s739.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 07:18:43 GMT 2026] Executing as ?@nf-91df41f45a2f89b7c7d28c14b1a26d89-b9881-wdr57 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 07:18:43 MarkDuplicates Start of doWork freeMemory: 105492880; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:18:43 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:18:43 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:18:49 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:153,939,413
INFO 2026-06-08 07:18:49 MarkDuplicates Tracking 924 as yet unmatched pairs. 10 records in RAM.
INFO 2026-06-08 07:18:52 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 3s. Last read position: chr2:73,816,026
INFO 2026-06-08 07:18:52 MarkDuplicates Tracking 11387 as yet unmatched pairs. 693 records in RAM.
INFO 2026-06-08 07:18:55 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 3s. Last read position: chr3:12,298,654
INFO 2026-06-08 07:18:55 MarkDuplicates Tracking 10958 as yet unmatched pairs. 756 records in RAM.
INFO 2026-06-08 07:18:58 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 3s. Last read position: chr4:5,856,193
INFO 2026-06-08 07:18:58 MarkDuplicates Tracking 10409 as yet unmatched pairs. 472 records in RAM.
INFO 2026-06-08 07:19:01 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr5:132,645,042
INFO 2026-06-08 07:19:01 MarkDuplicates Tracking 9920 as yet unmatched pairs. 280 records in RAM.
INFO 2026-06-08 07:19:05 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 4s. Last read position: chr6:135,216,004
INFO 2026-06-08 07:19:05 MarkDuplicates Tracking 9269 as yet unmatched pairs. 208 records in RAM.
INFO 2026-06-08 07:19:09 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 3s. Last read position: chr7:117,777,499
INFO 2026-06-08 07:19:09 MarkDuplicates Tracking 8507 as yet unmatched pairs. 206 records in RAM.
INFO 2026-06-08 07:19:12 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 2s. Last read position: chr8:144,514,339
INFO 2026-06-08 07:19:12 MarkDuplicates Tracking 7877 as yet unmatched pairs. 26 records in RAM.
INFO 2026-06-08 07:19:14 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 2s. Last read position: chr10:45,778,926
INFO 2026-06-08 07:19:14 MarkDuplicates Tracking 7167 as yet unmatched pairs. 394 records in RAM.
INFO 2026-06-08 07:19:17 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 2s. Last read position: chr11:69,703,600
INFO 2026-06-08 07:19:17 MarkDuplicates Tracking 6414 as yet unmatched pairs. 344 records in RAM.
INFO 2026-06-08 07:19:22 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 4s. Last read position: chr12:103,774,955
INFO 2026-06-08 07:19:22 MarkDuplicates Tracking 5548 as yet unmatched pairs. 191 records in RAM.
INFO 2026-06-08 07:19:25 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 2s. Last read position: chr15:27,990,499
INFO 2026-06-08 07:19:25 MarkDuplicates Tracking 4783 as yet unmatched pairs. 438 records in RAM.
INFO 2026-06-08 07:19:27 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chr16:33,360,912
INFO 2026-06-08 07:19:27 MarkDuplicates Tracking 4058 as yet unmatched pairs. 376 records in RAM.
INFO 2026-06-08 07:19:30 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 3s. Last read position: chr17:45,264,324
INFO 2026-06-08 07:19:30 MarkDuplicates Tracking 3231 as yet unmatched pairs. 385 records in RAM.
INFO 2026-06-08 07:19:34 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 3s. Last read position: chr19:17,839,486
INFO 2026-06-08 07:19:34 MarkDuplicates Tracking 2356 as yet unmatched pairs. 506 records in RAM.
INFO 2026-06-08 07:19:37 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 2s. Last read position: chr20:59,006,858
INFO 2026-06-08 07:19:37 MarkDuplicates Tracking 1418 as yet unmatched pairs. 80 records in RAM.
INFO 2026-06-08 07:19:40 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 3s. Last read position: chrX:68,722,041
INFO 2026-06-08 07:19:40 MarkDuplicates Tracking 573 as yet unmatched pairs. 363 records in RAM.
INFO 2026-06-08 07:19:42 MarkDuplicates Read 17611547 records. 0 pairs never matched.
INFO 2026-06-08 07:19:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 12376857480; totalMemory: 17683185664; maxMemory: 63585648640
INFO 2026-06-08 07:19:47 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 07:19:59 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 07:20:02 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 07:20:04 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 07:20:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 17604463272; totalMemory: 33554432000; maxMemory: 63585648640
INFO 2026-06-08 07:20:05 MarkDuplicates Marking 5628985 records as duplicates.
INFO 2026-06-08 07:20:05 MarkDuplicates Found 150357 optical duplicate clusters.
INFO 2026-06-08 07:20:05 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 07:20:42 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:36s. Time for last 10,000,000: 36s. Last read position: chr11:69,703,600
INFO 2026-06-08 07:21:08 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 07:21:08 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 07:21:08 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 07:21:09 MarkDuplicates Before output close freeMemory: 202637872; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 07:21:09 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 07:21:09 MarkDuplicates After output close freeMemory: 104353840; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 07:21:09 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 2.43 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory