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