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/36/17ff620bae81001efa734f313dd819/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/17ff620bae81001efa734f313dd819/.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/21/77f6521aa147bd4bf2fd365c3f16aa/rna_s1221_S42.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 rna_s1221_S42.Aligned.sortedByCoord.out.bam --OUTPUT rna_s1221_S42.md.bam --METRICS_FILE rna_s1221_S42.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
15:28:29.863 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
[Tue Jun 02 15:28:29 GMT 2026] MarkDuplicates --INPUT rna_s1221_S42.Aligned.sortedByCoord.out.bam --OUTPUT rna_s1221_S42.md.bam --METRICS_FILE rna_s1221_S42.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
[Tue Jun 02 15:28:29 GMT 2026] Executing as ?@nf-3617ff620bae81001efa734f313dd819-a592d-zbzjj 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 2026-06-02 15:28:29 MarkDuplicates Start of doWork freeMemory: 105829192; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-02 15:28:29 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-02 15:28:29 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-02 15:28:33 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:110,018,371
INFO 2026-06-02 15:28:33 MarkDuplicates Tracking 885 as yet unmatched pairs. 26 records in RAM.
INFO 2026-06-02 15:28:35 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 2s. Last read position: chr1:228,146,888
INFO 2026-06-02 15:28:35 MarkDuplicates Tracking 1746 as yet unmatched pairs. 95 records in RAM.
INFO 2026-06-02 15:28:37 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: chr2:159,759,241
INFO 2026-06-02 15:28:37 MarkDuplicates Tracking 15347 as yet unmatched pairs. 376 records in RAM.
INFO 2026-06-02 15:28:39 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: chr3:51,993,725
INFO 2026-06-02 15:28:39 MarkDuplicates Tracking 15094 as yet unmatched pairs. 742 records in RAM.
INFO 2026-06-02 15:28:41 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: chr4:102,597,542
INFO 2026-06-02 15:28:41 MarkDuplicates Tracking 14256 as yet unmatched pairs. 185 records in RAM.
INFO 2026-06-02 15:28:43 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 2s. Last read position: chr5:176,506,768
INFO 2026-06-02 15:28:43 MarkDuplicates Tracking 13701 as yet unmatched pairs. 156 records in RAM.
INFO 2026-06-02 15:28:46 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 2s. Last read position: chr6:34,421,771
INFO 2026-06-02 15:28:46 MarkDuplicates Tracking 13729 as yet unmatched pairs. 1256 records in RAM.
INFO 2026-06-02 15:28:48 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: chr7:26,197,277
INFO 2026-06-02 15:28:48 MarkDuplicates Tracking 13131 as yet unmatched pairs. 1221 records in RAM.
INFO 2026-06-02 15:28:49 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: chr8:89,914,196
INFO 2026-06-02 15:28:49 MarkDuplicates Tracking 11845 as yet unmatched pairs. 282 records in RAM.
INFO 2026-06-02 15:28:51 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: chr9:133,349,561
INFO 2026-06-02 15:28:51 MarkDuplicates Tracking 12123 as yet unmatched pairs. 988 records in RAM.
INFO 2026-06-02 15:28:53 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 1s. Last read position: chr11:33,068,720
INFO 2026-06-02 15:28:53 MarkDuplicates Tracking 10630 as yet unmatched pairs. 703 records in RAM.
INFO 2026-06-02 15:28:54 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:23s. Time for last 1,000,000: 1s. Last read position: chr12:6,945,786
INFO 2026-06-02 15:28:54 MarkDuplicates Tracking 9977 as yet unmatched pairs. 878 records in RAM.
INFO 2026-06-02 15:28:56 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 1s. Last read position: chr12:122,752,900
INFO 2026-06-02 15:28:56 MarkDuplicates Tracking 9343 as yet unmatched pairs. 133 records in RAM.
INFO 2026-06-02 15:28:58 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 1s. Last read position: chr15:28,076,562
INFO 2026-06-02 15:28:58 MarkDuplicates Tracking 8709 as yet unmatched pairs. 465 records in RAM.
INFO 2026-06-02 15:28:59 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 1s. Last read position: chr16:21,834,735
INFO 2026-06-02 15:28:59 MarkDuplicates Tracking 8034 as yet unmatched pairs. 651 records in RAM.
INFO 2026-06-02 15:29:01 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 2s. Last read position: chr17:7,318,111
INFO 2026-06-02 15:29:01 MarkDuplicates Tracking 7295 as yet unmatched pairs. 1082 records in RAM.
INFO 2026-06-02 15:29:04 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 2s. Last read position: chr17:76,039,898
INFO 2026-06-02 15:29:04 MarkDuplicates Tracking 6643 as yet unmatched pairs. 339 records in RAM.
INFO 2026-06-02 15:29:06 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 2s. Last read position: chr19:12,734,557
INFO 2026-06-02 15:29:06 MarkDuplicates Tracking 5761 as yet unmatched pairs. 755 records in RAM.
INFO 2026-06-02 15:29:08 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 1s. Last read position: chr20:35,277,516
INFO 2026-06-02 15:29:08 MarkDuplicates Tracking 5013 as yet unmatched pairs. 288 records in RAM.
INFO 2026-06-02 15:29:09 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 1s. Last read position: chr21:8,398,054
INFO 2026-06-02 15:29:09 MarkDuplicates Tracking 3586 as yet unmatched pairs. 634 records in RAM.
INFO 2026-06-02 15:29:11 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 1s. Last read position: chr22:38,495,046
INFO 2026-06-02 15:29:11 MarkDuplicates Tracking 2804 as yet unmatched pairs. 437 records in RAM.
INFO 2026-06-02 15:29:13 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 1s. Last read position: chrY:19,721,298
INFO 2026-06-02 15:29:13 MarkDuplicates Tracking 1801 as yet unmatched pairs. 31 records in RAM.
INFO 2026-06-02 15:29:14 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 1s. Last read position: KI270733.1:134,152
INFO 2026-06-02 15:29:14 MarkDuplicates Tracking 587 as yet unmatched pairs. 587 records in RAM.
INFO 2026-06-02 15:29:14 MarkDuplicates Read 23345691 records. 0 pairs never matched.
INFO 2026-06-02 15:29:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 13820519976; totalMemory: 19696451584; maxMemory: 63585648640
INFO 2026-06-02 15:29:16 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-02 15:29:22 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-02 15:29:23 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-02 15:29:25 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-02 15:29:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 22033633952; totalMemory: 37983617024; maxMemory: 63585648640
INFO 2026-06-02 15:29:25 MarkDuplicates Marking 3945308 records as duplicates.
INFO 2026-06-02 15:29:25 MarkDuplicates Found 142496 optical duplicate clusters.
INFO 2026-06-02 15:29:25 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-02 15:29:44 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:18s. Time for last 10,000,000: 18s. Last read position: chr9:133,349,561
INFO 2026-06-02 15:30:02 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:36s. Time for last 10,000,000: 17s. Last read position: chr21:8,398,054
INFO 2026-06-02 15:30:08 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-02 15:30:08 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-02 15:30:08 MarkDuplicates Getting Memory Stats.
INFO 2026-06-02 15:30:08 MarkDuplicates Before output close freeMemory: 201522736; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-02 15:30:08 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-02 15:30:08 MarkDuplicates After output close freeMemory: 104347504; totalMemory: 134217728; maxMemory: 63585648640
[Tue Jun 02 15:30:08 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 1.64 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory