Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/467a172a351744d0022a2b489fe3f4/22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam
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/82/e7bf4c8c35e23f819c3c17f6613409/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/e7bf4c8c35e23f819c3c17f6613409/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai
==> 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 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam --OUTPUT 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.md.bam --METRICS_FILE 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:27:21.597 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 07:27:21 GMT 2026] MarkDuplicates --INPUT 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam --OUTPUT 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.md.bam --METRICS_FILE 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.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 07:27:21 GMT 2026] Executing as ?@nf-82e7bf4c8c35e23f819c3c17f6613409-80d55-rrrr7 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 07:27:21 MarkDuplicates Start of doWork freeMemory: 105828448; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:27:21 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:27:21 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:27:25 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:43,415,997
INFO 2026-06-08 07:27:25 MarkDuplicates Tracking 2361 as yet unmatched pairs. 3 records in RAM.
INFO 2026-06-08 07:27:26 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 1s. Last read position: chr1:156,137,005
INFO 2026-06-08 07:27:26 MarkDuplicates Tracking 4518 as yet unmatched pairs. 41 records in RAM.
INFO 2026-06-08 07:27:28 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 1s. Last read position: chr2:27,366,774
INFO 2026-06-08 07:27:28 MarkDuplicates Tracking 6469 as yet unmatched pairs. 6317 records in RAM.
INFO 2026-06-08 07:27:30 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:07s. Time for last 1,000,000: 2s. Last read position: chr2:113,437,951
INFO 2026-06-08 07:27:30 MarkDuplicates Tracking 60680 as yet unmatched pairs. 1740 records in RAM.
INFO 2026-06-08 07:27:32 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 1s. Last read position: chr3:13,637,781
INFO 2026-06-08 07:27:32 MarkDuplicates Tracking 58713 as yet unmatched pairs. 2417 records in RAM.
INFO 2026-06-08 07:27:33 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: chr3:143,972,170
INFO 2026-06-08 07:27:33 MarkDuplicates Tracking 56904 as yet unmatched pairs. 582 records in RAM.
INFO 2026-06-08 07:27:35 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: chr4:153,788,504
INFO 2026-06-08 07:27:35 MarkDuplicates Tracking 55099 as yet unmatched pairs. 250 records in RAM.
INFO 2026-06-08 07:27:37 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: chr5:149,362,802
INFO 2026-06-08 07:27:37 MarkDuplicates Tracking 53278 as yet unmatched pairs. 959 records in RAM.
INFO 2026-06-08 07:27:39 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 1s. Last read position: chr6:32,052,785
INFO 2026-06-08 07:27:39 MarkDuplicates Tracking 51384 as yet unmatched pairs. 2180 records in RAM.
INFO 2026-06-08 07:27:41 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: chr6:151,240,622
INFO 2026-06-08 07:27:41 MarkDuplicates Tracking 49647 as yet unmatched pairs. 424 records in RAM.
INFO 2026-06-08 07:27:42 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 1s. Last read position: chr7:94,430,251
INFO 2026-06-08 07:27:42 MarkDuplicates Tracking 47729 as yet unmatched pairs. 1309 records in RAM.
INFO 2026-06-08 07:27:44 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 1s. Last read position: chr8:37,841,922
INFO 2026-06-08 07:27:44 MarkDuplicates Tracking 45910 as yet unmatched pairs. 1722 records in RAM.
INFO 2026-06-08 07:27:45 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: chr8:144,512,966
INFO 2026-06-08 07:27:45 MarkDuplicates Tracking 44274 as yet unmatched pairs. 47 records in RAM.
INFO 2026-06-08 07:27:47 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 2s. Last read position: chr9:133,071,385
INFO 2026-06-08 07:27:47 MarkDuplicates Tracking 42190 as yet unmatched pairs. 606 records in RAM.
INFO 2026-06-08 07:27:50 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 2s. Last read position: chr10:102,656,900
INFO 2026-06-08 07:27:50 MarkDuplicates Tracking 40328 as yet unmatched pairs. 580 records in RAM.
INFO 2026-06-08 07:27:51 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 1s. Last read position: chr11:62,620,532
INFO 2026-06-08 07:27:51 MarkDuplicates Tracking 38406 as yet unmatched pairs. 2094 records in RAM.
INFO 2026-06-08 07:27:53 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 1s. Last read position: chr11:129,892,789
INFO 2026-06-08 07:27:53 MarkDuplicates Tracking 36370 as yet unmatched pairs. 40 records in RAM.
INFO 2026-06-08 07:27:54 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 1s. Last read position: chr12:57,614,578
INFO 2026-06-08 07:27:54 MarkDuplicates Tracking 34411 as yet unmatched pairs. 1255 records in RAM.
INFO 2026-06-08 07:27:56 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 1s. Last read position: chr13:110,419,985
INFO 2026-06-08 07:27:56 MarkDuplicates Tracking 32464 as yet unmatched pairs. 115 records in RAM.
INFO 2026-06-08 07:27:57 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 1s. Last read position: chr14:104,950,468
INFO 2026-06-08 07:27:57 MarkDuplicates Tracking 30665 as yet unmatched pairs. 867 records in RAM.
INFO 2026-06-08 07:27:59 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 1s. Last read position: chr15:68,187,090
INFO 2026-06-08 07:27:59 MarkDuplicates Tracking 28984 as yet unmatched pairs. 796 records in RAM.
INFO 2026-06-08 07:28:00 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 1s. Last read position: chr16:15,732,581
INFO 2026-06-08 07:28:00 MarkDuplicates Tracking 27028 as yet unmatched pairs. 1959 records in RAM.
INFO 2026-06-08 07:28:01 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 1s. Last read position: chr16:70,664,225
INFO 2026-06-08 07:28:01 MarkDuplicates Tracking 25687 as yet unmatched pairs. 602 records in RAM.
INFO 2026-06-08 07:28:03 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 1s. Last read position: chr17:35,986,587
INFO 2026-06-08 07:28:03 MarkDuplicates Tracking 23594 as yet unmatched pairs. 3736 records in RAM.
INFO 2026-06-08 07:28:05 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chr17:50,863,177
INFO 2026-06-08 07:28:05 MarkDuplicates Tracking 21384 as yet unmatched pairs. 1523 records in RAM.
INFO 2026-06-08 07:28:07 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 2s. Last read position: chr19:860,729
INFO 2026-06-08 07:28:07 MarkDuplicates Tracking 19168 as yet unmatched pairs. 6392 records in RAM.
INFO 2026-06-08 07:28:09 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 1s. Last read position: chr19:17,511,738
INFO 2026-06-08 07:28:09 MarkDuplicates Tracking 16368 as yet unmatched pairs. 3581 records in RAM.
INFO 2026-06-08 07:28:11 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 1s. Last read position: chr19:45,792,516
INFO 2026-06-08 07:28:11 MarkDuplicates Tracking 14100 as yet unmatched pairs. 1292 records in RAM.
INFO 2026-06-08 07:28:12 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 1s. Last read position: chr20:51,488,531
INFO 2026-06-08 07:28:12 MarkDuplicates Tracking 11884 as yet unmatched pairs. 540 records in RAM.
INFO 2026-06-08 07:28:14 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 1s. Last read position: chr21:8,216,882
INFO 2026-06-08 07:28:14 MarkDuplicates Tracking 10303 as yet unmatched pairs. 3721 records in RAM.
INFO 2026-06-08 07:28:14 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 0s. Last read position: chr21:8,397,444
INFO 2026-06-08 07:28:14 MarkDuplicates Tracking 9689 as yet unmatched pairs. 3103 records in RAM.
INFO 2026-06-08 07:28:15 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 0s. Last read position: chr21:8,441,974
INFO 2026-06-08 07:28:15 MarkDuplicates Tracking 7919 as yet unmatched pairs. 1325 records in RAM.
INFO 2026-06-08 07:28:16 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 1s. Last read position: chr21:44,456,542
INFO 2026-06-08 07:28:16 MarkDuplicates Tracking 6970 as yet unmatched pairs. 373 records in RAM.
INFO 2026-06-08 07:28:18 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 1s. Last read position: chrX:1,354,849
INFO 2026-06-08 07:28:18 MarkDuplicates Tracking 4804 as yet unmatched pairs. 1231 records in RAM.
INFO 2026-06-08 07:28:19 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 1s. Last read position: GL000220.1:114,010
INFO 2026-06-08 07:28:19 MarkDuplicates Tracking 3392 as yet unmatched pairs. 486 records in RAM.
INFO 2026-06-08 07:28:20 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 0s. Last read position: GL000220.1:158,088
INFO 2026-06-08 07:28:20 MarkDuplicates Tracking 2953 as yet unmatched pairs. 44 records in RAM.
INFO 2026-06-08 07:28:21 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 1s. Last read position: KI270733.1:130,991
INFO 2026-06-08 07:28:21 MarkDuplicates Tracking 2734 as yet unmatched pairs. 2733 records in RAM.
INFO 2026-06-08 07:28:22 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 1s. Last read position: KI270733.1:175,897
INFO 2026-06-08 07:28:22 MarkDuplicates Tracking 81 as yet unmatched pairs. 80 records in RAM.
INFO 2026-06-08 07:28:23 MarkDuplicates Read 38808735 records. 0 pairs never matched.
INFO 2026-06-08 07:28:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 15625343472; totalMemory: 22280142848; maxMemory: 63585648640
INFO 2026-06-08 07:28:26 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 07:28:33 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 07:28:37 OpticalDuplicateFinder Large duplicate set. size = 1896
INFO 2026-06-08 07:28:37 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-25,275
INFO 2026-06-08 07:28:39 OpticalDuplicateFinder Large duplicate set. size = 2561
INFO 2026-06-08 07:28:39 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:22,261
INFO 2026-06-08 07:28:39 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,057
INFO 2026-06-08 07:28:39 OpticalDuplicateFinder Large duplicate set. size = 2048
INFO 2026-06-08 07:28:39 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,103
INFO 2026-06-08 07:28:39 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:30,140
INFO 2026-06-08 07:28:39 OpticalDuplicateFinder Large duplicate set. size = 1695
INFO 2026-06-08 07:28:39 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-16,295
INFO 2026-06-08 07:28:39 OpticalDuplicateFinder Large duplicate set. size = 2017
INFO 2026-06-08 07:28:39 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-22,864
INFO 2026-06-08 07:28:39 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-32,216
INFO 2026-06-08 07:28:39 OpticalDuplicateFinder Large duplicate set. size = 2002
INFO 2026-06-08 07:28:39 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-17,032
INFO 2026-06-08 07:28:39 OpticalDuplicateFinder compared 2,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-27,233
INFO 2026-06-08 07:28:40 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 07:28:43 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 07:28:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 22201359456; totalMemory: 38151389184; maxMemory: 63585648640
INFO 2026-06-08 07:28:44 MarkDuplicates Marking 19396924 records as duplicates.
INFO 2026-06-08 07:28:44 MarkDuplicates Found 355425 optical duplicate clusters.
INFO 2026-06-08 07:28:44 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 07:29:11 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:26s. Time for last 10,000,000: 26s. Last read position: chr6:151,240,622
INFO 2026-06-08 07:29:36 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:51s. Time for last 10,000,000: 24s. Last read position: chr14:104,950,468
INFO 2026-06-08 07:30:00 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:16s. Time for last 10,000,000: 24s. Last read position: chr21:8,216,882
INFO 2026-06-08 07:30:24 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 07:30:24 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 07:30:24 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 07:30:25 MarkDuplicates Before output close freeMemory: 201790968; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 07:30:25 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 07:30:25 MarkDuplicates After output close freeMemory: 104307952; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 07:30:25 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 3.06 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory