Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/dda9190b5ec239ae35d4f1f57d7430/.command.sh Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_BL/HCC1395_BL.recalibrated.bam Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_BL/HCC1395_BL.recalibrated.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/dda9190b5ec239ae35d4f1f57d7430/.command.run Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict ==> STAGING COMPLETE (7 inputs) 20:33:20.006 WARN GATKReadFilterPluginDescriptor - Redundant enabled filter (NotDuplicateReadFilter) is enabled for this tool by default 20:33:20.048 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/conda/envs/conpair/share/gatk4-4.6.2.0-0/gatk-package-4.6.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 20:33:20.116 INFO Pileup - ------------------------------------------------------------ 20:33:20.118 INFO Pileup - The Genome Analysis Toolkit (GATK) v4.6.2.0 20:33:20.118 INFO Pileup - For support and documentation go to https://software.broadinstitute.org/gatk/ 20:33:20.118 INFO Pileup - Executing as ?@nf-27dda9190b5ec239ae35d4f1f57d7430-f36cf-vm722 on Linux v6.12.88 amd64 20:33:20.118 INFO Pileup - Java runtime: OpenJDK 64-Bit Server VM v17.0.14+1-b1367.22 20:33:20.118 INFO Pileup - Start Date/Time: June 8, 2026 at 8:33:20 PM UTC 20:33:20.118 INFO Pileup - ------------------------------------------------------------ 20:33:20.118 INFO Pileup - ------------------------------------------------------------ 20:33:20.119 INFO Pileup - HTSJDK Version: 4.2.0 20:33:20.119 INFO Pileup - Picard Version: 3.4.0 20:33:20.119 INFO Pileup - Built for Spark Version: 3.5.0 20:33:20.120 INFO Pileup - HTSJDK Defaults.COMPRESSION_LEVEL : 2 20:33:20.120 INFO Pileup - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 20:33:20.120 INFO Pileup - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 20:33:20.120 INFO Pileup - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 20:33:20.121 INFO Pileup - Deflater: IntelDeflater 20:33:20.121 INFO Pileup - Inflater: IntelInflater 20:33:20.121 INFO Pileup - GCS max retries/reopens: 20 20:33:20.121 INFO Pileup - Requester pays: disabled 20:33:20.121 INFO Pileup - Initializing engine 20:33:20.349 INFO FeatureManager - Using codec BEDCodec to read file file:///opt/conpair/conpair/markers/GRCh38.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.liftover.bed 20:33:20.374 INFO IntervalArgumentCollection - Processing 7353 bp from intervals 20:33:20.381 INFO Pileup - Done initializing engine 20:33:20.382 INFO ProgressMeter - Starting traversal 20:33:20.382 INFO ProgressMeter - Current Locus Elapsed Minutes Loci Processed Loci/Minute 20:33:21.060 INFO Pileup - 0 read(s) filtered by: WellformedReadFilter 0 read(s) filtered by: MappedReadFilter 2587 read(s) filtered by: NotDuplicateReadFilter 0 read(s) filtered by: PassesVendorQualityCheckReadFilter 0 read(s) filtered by: NotSecondaryAlignmentReadFilter 0 read(s) filtered by: CigarContainsNoNOperator 0 read(s) filtered by: MatchingBasesAndQualsReadFilter 2587 total reads filtered out of 15770 reads processed 20:33:21.061 INFO ProgressMeter - unmapped 0.0 95 8407.1 20:33:21.061 INFO ProgressMeter - Traversal complete. Processed 95 total loci in 0.0 minutes. 20:33:21.061 INFO Pileup - Shutting down engine [June 8, 2026 at 8:33:21 PM UTC] org.broadinstitute.hellbender.tools.walkers.qc.Pileup done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=478150656 Using GATK jar /opt/conda/envs/conpair/share/gatk4-4.6.2.0-0/gatk-package-4.6.2.0-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 -Xmx12g -jar /opt/conda/envs/conpair/share/gatk4-4.6.2.0-0/gatk-package-4.6.2.0-local.jar Pileup -R Homo_sapiens_assembly38.fasta -I HCC1395_BL.recalibrated.bam -L /opt/conpair/conpair/markers/GRCh38.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.liftover.bed -O HCC1395_BL.pileup.txt -verbose -RF NotDuplicateReadFilter -RF CigarContainsNoNOperator -RF MatchingBasesAndQualsReadFilter