Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/output_runs/dev_latest_regression_eks__47a821d--20260221-174447/preprocessing/recalibrated/HCC1395_BL/HCC1395_BL.recal.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/1e6b4ed92b96fbce77bb8dab186e1b/.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-rnd-pltf-dev-nextflow-scratch-01/work/e1/1e6b4ed92b96fbce77bb8dab186e1b/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict
Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/output_runs/dev_latest_regression_eks__47a821d--20260221-174447/preprocessing/recalibrated/HCC1395_BL/HCC1395_BL.recal.bam
==> STAGING COMPLETE (7 inputs)
19:32:06.186 WARN GATKReadFilterPluginDescriptor - Redundant enabled filter (NotDuplicateReadFilter) is enabled for this tool by default
19:32:06.247 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
19:32:07.069 INFO Pileup - ------------------------------------------------------------
19:32:07.072 INFO Pileup - The Genome Analysis Toolkit (GATK) v4.6.2.0
19:32:07.072 INFO Pileup - For support and documentation go to https://software.broadinstitute.org/gatk/
19:32:07.072 INFO Pileup - Executing as ?@nf-e11e6b4ed92b96fbce77bb8dab186e1b-94137-w87rq on Linux v6.12.88 amd64
19:32:07.072 INFO Pileup - Java runtime: OpenJDK 64-Bit Server VM v17.0.14+1-b1367.22
19:32:07.072 INFO Pileup - Start Date/Time: June 4, 2026 at 7:32:06 PM UTC
19:32:07.072 INFO Pileup - ------------------------------------------------------------
19:32:07.072 INFO Pileup - ------------------------------------------------------------
19:32:07.073 INFO Pileup - HTSJDK Version: 4.2.0
19:32:07.073 INFO Pileup - Picard Version: 3.4.0
19:32:07.073 INFO Pileup - Built for Spark Version: 3.5.0
19:32:07.075 INFO Pileup - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:32:07.075 INFO Pileup - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:32:07.075 INFO Pileup - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:32:07.076 INFO Pileup - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:32:07.076 INFO Pileup - Deflater: IntelDeflater
19:32:07.076 INFO Pileup - Inflater: IntelInflater
19:32:07.076 INFO Pileup - GCS max retries/reopens: 20
19:32:07.076 INFO Pileup - Requester pays: disabled
19:32:07.076 INFO Pileup - Initializing engine
19:32:07.388 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
19:32:07.422 INFO IntervalArgumentCollection - Processing 7353 bp from intervals
19:32:07.436 INFO Pileup - Done initializing engine
19:32:07.436 INFO ProgressMeter - Starting traversal
19:32:07.437 INFO ProgressMeter - Current Locus Elapsed Minutes Loci Processed Loci/Minute
19:32:08.296 INFO Pileup - 0 read(s) filtered by: WellformedReadFilter
0 read(s) filtered by: MappedReadFilter
2482 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
2482 total reads filtered out of 15009 reads processed
19:32:08.296 INFO ProgressMeter - unmapped 0.0 91 6356.2
19:32:08.297 INFO ProgressMeter - Traversal complete. Processed 91 total loci in 0.0 minutes.
19:32:08.297 INFO Pileup - Shutting down engine
[June 4, 2026 at 7:32:08 PM UTC] org.broadinstitute.hellbender.tools.walkers.qc.Pileup done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=360710144
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.recal.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