20:31:14.115 WARN GATKReadFilterPluginDescriptor - Redundant enabled filter (NotDuplicateReadFilter) is enabled for this tool by default
20:31:14.197 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
20:31:14.335 INFO Pileup - ------------------------------------------------------------
20:31:14.339 INFO Pileup - The Genome Analysis Toolkit (GATK) v4.6.2.0
20:31:14.339 INFO Pileup - For support and documentation go to https://software.broadinstitute.org/gatk/
20:31:14.339 INFO Pileup - Executing as ?@nf-2ac4df5048ae04a8844be67a7a43c13d-d7356-kf7zd on Linux v6.12.83 amd64
20:31:14.339 INFO Pileup - Java runtime: OpenJDK 64-Bit Server VM v17.0.14+1-b1367.22
20:31:14.340 INFO Pileup - Start Date/Time: May 28, 2026 at 8:31:14 PM UTC
20:31:14.340 INFO Pileup - ------------------------------------------------------------
20:31:14.340 INFO Pileup - ------------------------------------------------------------
20:31:14.341 INFO Pileup - HTSJDK Version: 4.2.0
20:31:14.341 INFO Pileup - Picard Version: 3.4.0
20:31:14.341 INFO Pileup - Built for Spark Version: 3.5.0
20:31:14.343 INFO Pileup - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:31:14.344 INFO Pileup - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:31:14.344 INFO Pileup - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:31:14.344 INFO Pileup - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:31:14.344 INFO Pileup - Deflater: IntelDeflater
20:31:14.344 INFO Pileup - Inflater: IntelInflater
20:31:14.344 INFO Pileup - GCS max retries/reopens: 20
20:31:14.344 INFO Pileup - Requester pays: disabled
20:31:14.345 INFO Pileup - Initializing engine
20:31:14.844 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
20:31:14.901 INFO IntervalArgumentCollection - Processing 7353 bp from intervals
20:31:14.919 INFO Pileup - Done initializing engine
20:31:14.920 INFO ProgressMeter - Starting traversal
20:31:14.921 INFO ProgressMeter - Current Locus Elapsed Minutes Loci Processed Loci/Minute
20:31:19.834 INFO Pileup - 0 read(s) filtered by: WellformedReadFilter
0 read(s) filtered by: MappedReadFilter
30096 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
30096 total reads filtered out of 105155 reads processed
20:31:19.834 INFO ProgressMeter - unmapped 0.1 100 1221.2
20:31:19.835 INFO ProgressMeter - Traversal complete. Processed 100 total loci in 0.1 minutes.
20:31:19.835 INFO Pileup - Shutting down engine
[May 28, 2026 at 8:31:19 PM UTC] org.broadinstitute.hellbender.tools.walkers.qc.Pileup done. Elapsed time: 0.10 minutes.
Runtime.totalMemory()=352321536
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_tissue.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_tissue.pileup.txt -verbose -RF NotDuplicateReadFilter -RF CigarContainsNoNOperator -RF MatchingBasesAndQualsReadFilter