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 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md.bam --METRICS_FILE 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:30:56.051 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 07:30:56 GMT 2026] MarkDuplicates --INPUT 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.md.bam --METRICS_FILE 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_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
[Mon Jun 08 07:30:56 GMT 2026] Executing as ?@nf-684d60d2b69965052c8400e0026ff4df-69bd0-c5fbp 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 07:30:56 MarkDuplicates Start of doWork freeMemory: 105849416; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:30:56 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:30:56 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:31:04 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 5s. Last read position: chr1:85,581,388
INFO 2026-06-08 07:31:04 MarkDuplicates Tracking 3034 as yet unmatched pairs. 4 records in RAM.
INFO 2026-06-08 07:31:07 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 3s. Last read position: chr1:218,285,319
INFO 2026-06-08 07:31:07 MarkDuplicates Tracking 5684 as yet unmatched pairs. 5 records in RAM.
INFO 2026-06-08 07:31:11 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 3s. Last read position: chr2:105,038,099
INFO 2026-06-08 07:31:11 MarkDuplicates Tracking 62256 as yet unmatched pairs. 2584 records in RAM.
INFO 2026-06-08 07:31:15 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 3s. Last read position: chr3:11,358,486
INFO 2026-06-08 07:31:15 MarkDuplicates Tracking 59526 as yet unmatched pairs. 3100 records in RAM.
INFO 2026-06-08 07:31:18 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 3s. Last read position: chr3:188,609,269
INFO 2026-06-08 07:31:18 MarkDuplicates Tracking 56829 as yet unmatched pairs. 386 records in RAM.
INFO 2026-06-08 07:31:22 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 4s. Last read position: chr5:69,419,528
INFO 2026-06-08 07:31:22 MarkDuplicates Tracking 54075 as yet unmatched pairs. 2287 records in RAM.
INFO 2026-06-08 07:31:26 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 3s. Last read position: chr6:27,838,958
INFO 2026-06-08 07:31:26 MarkDuplicates Tracking 51241 as yet unmatched pairs. 2674 records in RAM.
INFO 2026-06-08 07:31:30 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 3s. Last read position: chr7:1,485,289
INFO 2026-06-08 07:31:30 MarkDuplicates Tracking 48415 as yet unmatched pairs. 5466 records in RAM.
INFO 2026-06-08 07:31:34 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 3s. Last read position: chr7:99,486,627
INFO 2026-06-08 07:31:34 MarkDuplicates Tracking 45624 as yet unmatched pairs. 2669 records in RAM.
INFO 2026-06-08 07:31:37 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 3s. Last read position: chr7:150,372,421
INFO 2026-06-08 07:31:37 MarkDuplicates Tracking 43381 as yet unmatched pairs. 415 records in RAM.
INFO 2026-06-08 07:31:40 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 3s. Last read position: chr8:143,864,584
INFO 2026-06-08 07:31:40 MarkDuplicates Tracking 40828 as yet unmatched pairs. 1019 records in RAM.
INFO 2026-06-08 07:31:44 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 3s. Last read position: chr9:131,525,962
INFO 2026-06-08 07:31:44 MarkDuplicates Tracking 37798 as yet unmatched pairs. 716 records in RAM.
INFO 2026-06-08 07:31:48 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 3s. Last read position: chr10:122,248,597
INFO 2026-06-08 07:31:48 MarkDuplicates Tracking 35014 as yet unmatched pairs. 224 records in RAM.
INFO 2026-06-08 07:31:51 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 3s. Last read position: chr11:67,585,222
INFO 2026-06-08 07:31:51 MarkDuplicates Tracking 32140 as yet unmatched pairs. 1415 records in RAM.
INFO 2026-06-08 07:31:55 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 3s. Last read position: chr12:53,711,981
INFO 2026-06-08 07:31:55 MarkDuplicates Tracking 29369 as yet unmatched pairs. 2303 records in RAM.
INFO 2026-06-08 07:31:58 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 3s. Last read position: chr13:97,276,274
INFO 2026-06-08 07:31:58 MarkDuplicates Tracking 26505 as yet unmatched pairs. 314 records in RAM.
INFO 2026-06-08 07:32:01 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 3s. Last read position: chr15:45,676,118
INFO 2026-06-08 07:32:01 MarkDuplicates Tracking 23732 as yet unmatched pairs. 1140 records in RAM.
INFO 2026-06-08 07:32:05 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 3s. Last read position: chr16:18,401,590
INFO 2026-06-08 07:32:05 MarkDuplicates Tracking 20989 as yet unmatched pairs. 2270 records in RAM.
INFO 2026-06-08 07:32:09 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 3s. Last read position: chr17:7,577,620
INFO 2026-06-08 07:32:09 MarkDuplicates Tracking 18291 as yet unmatched pairs. 4701 records in RAM.
INFO 2026-06-08 07:32:13 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 3s. Last read position: chr17:50,195,611
INFO 2026-06-08 07:32:13 MarkDuplicates Tracking 15564 as yet unmatched pairs. 1970 records in RAM.
INFO 2026-06-08 07:32:16 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 3s. Last read position: chr19:4,652,153
INFO 2026-06-08 07:32:16 MarkDuplicates Tracking 12103 as yet unmatched pairs. 5247 records in RAM.
INFO 2026-06-08 07:32:19 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 3s. Last read position: chr19:41,709,834
INFO 2026-06-08 07:32:19 MarkDuplicates Tracking 8928 as yet unmatched pairs. 2070 records in RAM.
INFO 2026-06-08 07:32:22 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 2s. Last read position: chr20:41,172,466
INFO 2026-06-08 07:32:22 MarkDuplicates Tracking 5886 as yet unmatched pairs. 933 records in RAM.
INFO 2026-06-08 07:32:25 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 2s. Last read position: chr22:36,305,964
INFO 2026-06-08 07:32:25 MarkDuplicates Tracking 3143 as yet unmatched pairs. 976 records in RAM.
INFO 2026-06-08 07:32:29 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 3s. Last read position: GL000220.1:159,517
INFO 2026-06-08 07:32:29 MarkDuplicates Tracking 283 as yet unmatched pairs. 0 records in RAM.
INFO 2026-06-08 07:32:29 MarkDuplicates Read 25120674 records. 0 pairs never matched.
INFO 2026-06-08 07:32:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 14522951000; totalMemory: 20703084544; maxMemory: 63585648640
INFO 2026-06-08 07:32:33 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 07:32:43 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 07:32:47 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 07:32:50 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 07:32:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 21932977568; totalMemory: 37882953728; maxMemory: 63585648640
INFO 2026-06-08 07:32:50 MarkDuplicates Marking 3483156 records as duplicates.
INFO 2026-06-08 07:32:50 MarkDuplicates Found 231607 optical duplicate clusters.
INFO 2026-06-08 07:32:50 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 07:33:25 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:34s. Time for last 10,000,000: 34s. Last read position: chr7:150,372,421
INFO 2026-06-08 07:33:58 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:01:07s. Time for last 10,000,000: 32s. Last read position: chr17:50,195,611
INFO 2026-06-08 07:34:16 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 07:34:16 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 07:34:16 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 07:34:16 MarkDuplicates Before output close freeMemory: 202202976; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 07:34:16 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 07:34:16 MarkDuplicates After output close freeMemory: 104366672; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 07:34:16 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 3.34 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory