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 BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.md.bam --METRICS_FILE BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
20:10:14.869 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
[Thu May 28 20:10:14 GMT 2026] MarkDuplicates --INPUT BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.md.bam --METRICS_FILE BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.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
[Thu May 28 20:10:14 GMT 2026] Executing as ?@nf-45d5f7081e8fb7cae324302fcc38c56c-2c16f-hnxj5 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 2026-05-28 20:10:14 MarkDuplicates Start of doWork freeMemory: 105494968; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-05-28 20:10:14 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-05-28 20:10:14 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-05-28 20:10:20 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:154,170,699
INFO 2026-05-28 20:10:20 MarkDuplicates Tracking 1705 as yet unmatched pairs. 1 records in RAM.
INFO 2026-05-28 20:10:23 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 3s. Last read position: chr2:55,232,826
INFO 2026-05-28 20:10:23 MarkDuplicates Tracking 35667 as yet unmatched pairs. 1233 records in RAM.
INFO 2026-05-28 20:10:26 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 2s. Last read position: chr3:20,101,400
INFO 2026-05-28 20:10:26 MarkDuplicates Tracking 34226 as yet unmatched pairs. 1783 records in RAM.
INFO 2026-05-28 20:10:29 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 3s. Last read position: chr3:195,784,165
INFO 2026-05-28 20:10:29 MarkDuplicates Tracking 32705 as yet unmatched pairs. 248 records in RAM.
INFO 2026-05-28 20:10:31 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 2s. Last read position: chr5:138,467,809
INFO 2026-05-28 20:10:31 MarkDuplicates Tracking 31133 as yet unmatched pairs. 740 records in RAM.
INFO 2026-05-28 20:10:35 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 3s. Last read position: chr6:138,424,240
INFO 2026-05-28 20:10:35 MarkDuplicates Tracking 29481 as yet unmatched pairs. 288 records in RAM.
INFO 2026-05-28 20:10:38 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 3s. Last read position: chr7:100,992,948
INFO 2026-05-28 20:10:38 MarkDuplicates Tracking 27829 as yet unmatched pairs. 2864 records in RAM.
INFO 2026-05-28 20:10:40 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 2s. Last read position: chr7:100,996,313
INFO 2026-05-28 20:10:40 MarkDuplicates Tracking 27567 as yet unmatched pairs. 2602 records in RAM.
INFO 2026-05-28 20:10:42 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 1s. Last read position: chr7:100,998,122
INFO 2026-05-28 20:10:42 MarkDuplicates Tracking 26740 as yet unmatched pairs. 1775 records in RAM.
INFO 2026-05-28 20:10:44 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 1s. Last read position: chr7:101,000,813
INFO 2026-05-28 20:10:44 MarkDuplicates Tracking 26156 as yet unmatched pairs. 1191 records in RAM.
INFO 2026-05-28 20:10:46 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 2s. Last read position: chr7:101,003,735
INFO 2026-05-28 20:10:46 MarkDuplicates Tracking 25897 as yet unmatched pairs. 932 records in RAM.
INFO 2026-05-28 20:10:48 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 2s. Last read position: chr8:143,859,092
INFO 2026-05-28 20:10:48 MarkDuplicates Tracking 24244 as yet unmatched pairs. 415 records in RAM.
INFO 2026-05-28 20:10:51 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 2s. Last read position: chr10:7,799,859
INFO 2026-05-28 20:10:51 MarkDuplicates Tracking 22222 as yet unmatched pairs. 1021 records in RAM.
INFO 2026-05-28 20:10:54 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 2s. Last read position: chr11:3,702,314
INFO 2026-05-28 20:10:54 MarkDuplicates Tracking 20774 as yet unmatched pairs. 2063 records in RAM.
INFO 2026-05-28 20:10:57 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 2s. Last read position: chr12:4,744,050
INFO 2026-05-28 20:10:57 MarkDuplicates Tracking 18659 as yet unmatched pairs. 1513 records in RAM.
INFO 2026-05-28 20:11:00 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 2s. Last read position: chr13:49,746,972
INFO 2026-05-28 20:11:00 MarkDuplicates Tracking 17050 as yet unmatched pairs. 281 records in RAM.
INFO 2026-05-28 20:11:03 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 2s. Last read position: chr15:61,911,972
INFO 2026-05-28 20:11:03 MarkDuplicates Tracking 15389 as yet unmatched pairs. 632 records in RAM.
INFO 2026-05-28 20:11:05 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 1s. Last read position: chr16:21,599,760
INFO 2026-05-28 20:11:05 MarkDuplicates Tracking 13493 as yet unmatched pairs. 992 records in RAM.
INFO 2026-05-28 20:11:07 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 2s. Last read position: chr17:19,188,047
INFO 2026-05-28 20:11:07 MarkDuplicates Tracking 11735 as yet unmatched pairs. 1545 records in RAM.
INFO 2026-05-28 20:11:09 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 2s. Last read position: chr18:76,379,957
INFO 2026-05-28 20:11:09 MarkDuplicates Tracking 9862 as yet unmatched pairs. 31 records in RAM.
INFO 2026-05-28 20:11:12 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 2s. Last read position: chr19:39,899,624
INFO 2026-05-28 20:11:12 MarkDuplicates Tracking 7992 as yet unmatched pairs. 1153 records in RAM.
INFO 2026-05-28 20:11:14 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 2s. Last read position: chr20:62,324,486
INFO 2026-05-28 20:11:14 MarkDuplicates Tracking 6262 as yet unmatched pairs. 172 records in RAM.
INFO 2026-05-28 20:11:17 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 3s. Last read position: chr21:8,399,901
INFO 2026-05-28 20:11:17 MarkDuplicates Tracking 4952 as yet unmatched pairs. 1252 records in RAM.
INFO 2026-05-28 20:11:20 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 2s. Last read position: chr22:31,104,234
INFO 2026-05-28 20:11:20 MarkDuplicates Tracking 3398 as yet unmatched pairs. 566 records in RAM.
INFO 2026-05-28 20:11:23 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 3s. Last read position: GL000220.1:114,342
INFO 2026-05-28 20:11:23 MarkDuplicates Tracking 1686 as yet unmatched pairs. 281 records in RAM.
INFO 2026-05-28 20:11:25 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 2s. Last read position: KI270733.1:133,178
INFO 2026-05-28 20:11:25 MarkDuplicates Tracking 318 as yet unmatched pairs. 315 records in RAM.
INFO 2026-05-28 20:11:26 MarkDuplicates Read 26600672 records. 0 pairs never matched.
INFO 2026-05-28 20:11:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 13147701200; totalMemory: 18790481920; maxMemory: 63585648640
INFO 2026-05-28 20:11:28 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-05-28 20:11:34 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-05-28 20:11:41 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-05-28 20:11:43 MarkDuplicates Sorting list of duplicate records.
INFO 2026-05-28 20:11:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 20959850592; totalMemory: 36909875200; maxMemory: 63585648640
INFO 2026-05-28 20:11:44 MarkDuplicates Marking 15476100 records as duplicates.
INFO 2026-05-28 20:11:44 MarkDuplicates Found 287618 optical duplicate clusters.
INFO 2026-05-28 20:11:44 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-05-28 20:12:09 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:25s. Time for last 10,000,000: 25s. Last read position: chr7:101,000,813
INFO 2026-05-28 20:12:33 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:49s. Time for last 10,000,000: 23s. Last read position: chr18:76,379,957
INFO 2026-05-28 20:12:50 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-05-28 20:12:50 MarkDuplicates Duplicate Index cleanup.
INFO 2026-05-28 20:12:50 MarkDuplicates Getting Memory Stats.
INFO 2026-05-28 20:12:50 MarkDuplicates Before output close freeMemory: 13908723472; totalMemory: 36909875200; maxMemory: 63585648640
INFO 2026-05-28 20:12:50 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-05-28 20:12:50 MarkDuplicates After output close freeMemory: 203938840; totalMemory: 234881024; maxMemory: 63585648640
[Thu May 28 20:12:50 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 2.59 minutes.
Runtime.totalMemory()=234881024
ls: *cram: No such file or directory
ls: *.crai: No such file or directory