Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/ee925c5bfd728d1dc089aa5f59bf0a/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/ee925c5bfd728d1dc089aa5f59bf0a/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/4d20a971c93be1dc46f16704254326/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)
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_1.Aligned.sortedByCoord.out.bam --OUTPUT BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.md.bam --METRICS_FILE BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
20:10:15.455 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 20:10:15 GMT 2026] MarkDuplicates --INPUT BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.md.bam --METRICS_FILE BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_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
[Thu May 28 20:10:15 GMT 2026] Executing as ?@nf-9eee925c5bfd728d1dc089aa5f59bf0a-5121e-5l2bh 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 20:10:15 MarkDuplicates Start of doWork freeMemory: 105828064; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-05-28 20:10:15 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-05-28 20:10:15 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: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:114,464,347
INFO 2026-05-28 20:10:20 MarkDuplicates Tracking 2077 as yet unmatched pairs. 3 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: chr2:13,227,518
INFO 2026-05-28 20:10:23 MarkDuplicates Tracking 4105 as yet unmatched pairs. 3979 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: chr2:178,681,115
INFO 2026-05-28 20:10:26 MarkDuplicates Tracking 42299 as yet unmatched pairs. 796 records in RAM.
INFO 2026-05-28 20:10:28 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: chr3:105,577,790
INFO 2026-05-28 20:10:28 MarkDuplicates Tracking 40560 as yet unmatched pairs. 715 records in RAM.
INFO 2026-05-28 20:10:30 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: chr4:188,533,863
INFO 2026-05-28 20:10:30 MarkDuplicates Tracking 38896 as yet unmatched pairs. 12 records in RAM.
INFO 2026-05-28 20:10:33 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 2s. Last read position: chr6:3,224,944
INFO 2026-05-28 20:10:33 MarkDuplicates Tracking 37373 as yet unmatched pairs. 2094 records in RAM.
INFO 2026-05-28 20:10:35 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 2s. Last read position: chr6:151,223,784
INFO 2026-05-28 20:10:35 MarkDuplicates Tracking 35566 as yet unmatched pairs. 255 records in RAM.
INFO 2026-05-28 20:10:38 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 3s. Last read position: chr7:137,908,315
INFO 2026-05-28 20:10:38 MarkDuplicates Tracking 33757 as yet unmatched pairs. 491 records in RAM.
INFO 2026-05-28 20:10:41 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 2s. Last read position: chr8:143,866,188
INFO 2026-05-28 20:10:41 MarkDuplicates Tracking 32017 as yet unmatched pairs. 287 records in RAM.
INFO 2026-05-28 20:10:44 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 2s. Last read position: chr10:11,096,338
INFO 2026-05-28 20:10:44 MarkDuplicates Tracking 30077 as yet unmatched pairs. 1046 records in RAM.
INFO 2026-05-28 20:10:46 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 2s. Last read position: chr11:44,970,703
INFO 2026-05-28 20:10:46 MarkDuplicates Tracking 28488 as yet unmatched pairs. 1968 records in RAM.
INFO 2026-05-28 20:10:48 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 1s. Last read position: chr12:6,581,150
INFO 2026-05-28 20:10:48 MarkDuplicates Tracking 26455 as yet unmatched pairs. 1964 records in RAM.
INFO 2026-05-28 20:10:49 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 1s. Last read position: chr12:128,971,632
INFO 2026-05-28 20:10:49 MarkDuplicates Tracking 24587 as yet unmatched pairs. 83 records in RAM.
INFO 2026-05-28 20:10:51 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 1s. Last read position: chr14:104,893,056
INFO 2026-05-28 20:10:51 MarkDuplicates Tracking 22885 as yet unmatched pairs. 782 records in RAM.
INFO 2026-05-28 20:10:53 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 2s. Last read position: chr15:99,131,351
INFO 2026-05-28 20:10:53 MarkDuplicates Tracking 21043 as yet unmatched pairs. 31 records in RAM.
INFO 2026-05-28 20:10:55 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 2s. Last read position: chr16:66,604,864
INFO 2026-05-28 20:10:55 MarkDuplicates Tracking 19459 as yet unmatched pairs. 703 records in RAM.
INFO 2026-05-28 20:10:57 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 1s. Last read position: chr17:41,624,493
INFO 2026-05-28 20:10:57 MarkDuplicates Tracking 17459 as yet unmatched pairs. 2018 records in RAM.
INFO 2026-05-28 20:11:00 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chr18:44,949,891
INFO 2026-05-28 20:11:00 MarkDuplicates Tracking 15230 as yet unmatched pairs. 340 records in RAM.
INFO 2026-05-28 20:11:03 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: chr19:35,095,511
INFO 2026-05-28 20:11:03 MarkDuplicates Tracking 12773 as yet unmatched pairs. 2122 records in RAM.
INFO 2026-05-28 20:11:07 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 4s. Last read position: chr20:17,825,458
INFO 2026-05-28 20:11:07 MarkDuplicates Tracking 10436 as yet unmatched pairs. 749 records in RAM.
INFO 2026-05-28 20:11:10 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 3s. Last read position: chr21:8,216,846
INFO 2026-05-28 20:11:10 MarkDuplicates Tracking 8732 as yet unmatched pairs. 3451 records in RAM.
INFO 2026-05-28 20:11:12 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 1s. Last read position: chr21:8,397,478
INFO 2026-05-28 20:11:12 MarkDuplicates Tracking 8043 as yet unmatched pairs. 2759 records in RAM.
INFO 2026-05-28 20:11:14 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 2s. Last read position: chr21:8,442,047
INFO 2026-05-28 20:11:14 MarkDuplicates Tracking 6348 as yet unmatched pairs. 1054 records in RAM.
INFO 2026-05-28 20:11:16 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 1s. Last read position: chr22:20,566,657
INFO 2026-05-28 20:11:16 MarkDuplicates Tracking 5151 as yet unmatched pairs. 1122 records in RAM.
INFO 2026-05-28 20:11:18 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 2s. Last read position: chrX:154,349,653
INFO 2026-05-28 20:11:18 MarkDuplicates Tracking 3311 as yet unmatched pairs. 87 records in RAM.
INFO 2026-05-28 20:11:20 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 2s. Last read position: GL000220.1:116,801
INFO 2026-05-28 20:11:20 MarkDuplicates Tracking 2590 as yet unmatched pairs. 26 records in RAM.
INFO 2026-05-28 20:11:22 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 1s. Last read position: KI270733.1:126,207
INFO 2026-05-28 20:11:22 MarkDuplicates Tracking 2548 as yet unmatched pairs. 2547 records in RAM.
INFO 2026-05-28 20:11:24 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 2s. Last read position: KI270733.1:173,231
INFO 2026-05-28 20:11:24 MarkDuplicates Tracking 145 as yet unmatched pairs. 144 records in RAM.
INFO 2026-05-28 20:11:25 MarkDuplicates Read 28872614 records. 0 pairs never matched.
INFO 2026-05-28 20:11:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 13393970568; totalMemory: 19126026240; maxMemory: 63585648640
INFO 2026-05-28 20:11:27 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-05-28 20:11:32 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-05-28 20:11:36 OpticalDuplicateFinder Large duplicate set. size = 1773
INFO 2026-05-28 20:11:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-19,539
INFO 2026-05-28 20:11:38 OpticalDuplicateFinder Large duplicate set. size = 1080
INFO 2026-05-28 20:11:38 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,570
INFO 2026-05-28 20:11:38 OpticalDuplicateFinder Large duplicate set. size = 1082
INFO 2026-05-28 20:11:38 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,695
INFO 2026-05-28 20:11:38 OpticalDuplicateFinder Large duplicate set. size = 3753
INFO 2026-05-28 20:11:38 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:17,754
INFO 2026-05-28 20:11:38 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:16,581
INFO 2026-05-28 20:11:38 OpticalDuplicateFinder compared 3,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:10,668
INFO 2026-05-28 20:11:38 OpticalDuplicateFinder Large duplicate set. size = 2088
INFO 2026-05-28 20:11:38 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:6,283
INFO 2026-05-28 20:11:38 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:14,551
INFO 2026-05-28 20:11:38 OpticalDuplicateFinder Large duplicate set. size = 1949
INFO 2026-05-28 20:11:38 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:25,893
INFO 2026-05-28 20:11:38 OpticalDuplicateFinder Large duplicate set. size = 1568
INFO 2026-05-28 20:11:38 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-14,087
INFO 2026-05-28 20:11:38 OpticalDuplicateFinder Large duplicate set. size = 1741
INFO 2026-05-28 20:11:38 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-13,836
INFO 2026-05-28 20:11:38 OpticalDuplicateFinder Large duplicate set. size = 1758
INFO 2026-05-28 20:11:38 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:15,578
INFO 2026-05-28 20:11:39 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-05-28 20:11:40 MarkDuplicates Sorting list of duplicate records.
INFO 2026-05-28 20:11:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 22436234368; totalMemory: 38386270208; maxMemory: 63585648640
INFO 2026-05-28 20:11:41 MarkDuplicates Marking 13775306 records as duplicates.
INFO 2026-05-28 20:11:41 MarkDuplicates Found 214843 optical duplicate clusters.
INFO 2026-05-28 20:11:41 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-05-28 20:12:14 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:32s. Time for last 10,000,000: 32s. Last read position: chr10:11,096,338
INFO 2026-05-28 20:12:41 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:01:00s. Time for last 10,000,000: 27s. Last read position: chr20:17,825,458
INFO 2026-05-28 20:13:07 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-05-28 20:13:07 MarkDuplicates Duplicate Index cleanup.
INFO 2026-05-28 20:13:07 MarkDuplicates Getting Memory Stats.
INFO 2026-05-28 20:13:07 MarkDuplicates Before output close freeMemory: 17835628128; totalMemory: 38386270208; maxMemory: 63585648640
INFO 2026-05-28 20:13:07 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-05-28 20:13:07 MarkDuplicates After output close freeMemory: 203966264; totalMemory: 234881024; maxMemory: 63585648640
[Thu May 28 20:13:07 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 2.87 minutes.
Runtime.totalMemory()=234881024
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory