01:58:14.187 WARN GATKReadFilterPluginDescriptor - Redundant enabled filter (NotDuplicateReadFilter) is enabled for this tool by default 01:58:14.230 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 01:58:14.305 INFO Pileup - ------------------------------------------------------------ 01:58:14.307 INFO Pileup - The Genome Analysis Toolkit (GATK) v4.6.2.0 01:58:14.307 INFO Pileup - For support and documentation go to https://software.broadinstitute.org/gatk/ 01:58:14.307 INFO Pileup - Executing as ?@nf-6c4e381f6aaac37bab09c7e58414a218-c2ac5-nhpll on Linux v6.12.88 amd64 01:58:14.307 INFO Pileup - Java runtime: OpenJDK 64-Bit Server VM v17.0.14+1-b1367.22 01:58:14.307 INFO Pileup - Start Date/Time: June 5, 2026 at 1:58:14 AM UTC 01:58:14.307 INFO Pileup - ------------------------------------------------------------ 01:58:14.307 INFO Pileup - ------------------------------------------------------------ 01:58:14.308 INFO Pileup - HTSJDK Version: 4.2.0 01:58:14.308 INFO Pileup - Picard Version: 3.4.0 01:58:14.308 INFO Pileup - Built for Spark Version: 3.5.0 01:58:14.309 INFO Pileup - HTSJDK Defaults.COMPRESSION_LEVEL : 2 01:58:14.309 INFO Pileup - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 01:58:14.309 INFO Pileup - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 01:58:14.309 INFO Pileup - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 01:58:14.309 INFO Pileup - Deflater: IntelDeflater 01:58:14.310 INFO Pileup - Inflater: IntelInflater 01:58:14.310 INFO Pileup - GCS max retries/reopens: 20 01:58:14.310 INFO Pileup - Requester pays: disabled 01:58:14.310 INFO Pileup - Initializing engine 01:58:14.557 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 01:58:14.580 INFO IntervalArgumentCollection - Processing 7353 bp from intervals 01:58:14.592 INFO Pileup - Done initializing engine 01:58:14.593 INFO ProgressMeter - Starting traversal 01:58:14.593 INFO ProgressMeter - Current Locus Elapsed Minutes Loci Processed Loci/Minute 01:58:15.466 INFO Pileup - 0 read(s) filtered by: WellformedReadFilter 0 read(s) filtered by: MappedReadFilter 2556 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 2556 total reads filtered out of 19410 reads processed 01:58:15.466 INFO ProgressMeter - unmapped 0.0 97 6666.7 01:58:15.466 INFO ProgressMeter - Traversal complete. Processed 97 total loci in 0.0 minutes. 01:58:15.466 INFO Pileup - Shutting down engine [June 5, 2026 at 1:58:15 AM UTC] org.broadinstitute.hellbender.tools.walkers.qc.Pileup done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=419430400 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 Sig_18_Blood.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 Sig_18_Blood.pileup.txt -verbose -RF NotDuplicateReadFilter -RF CigarContainsNoNOperator -RF MatchingBasesAndQualsReadFilter