17:50:56.672 WARN GATKReadFilterPluginDescriptor - Redundant enabled filter (NotDuplicateReadFilter) is enabled for this tool by default
17:50:56.713 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
17:50:56.786 INFO Pileup - ------------------------------------------------------------
17:50:56.788 INFO Pileup - The Genome Analysis Toolkit (GATK) v4.6.2.0
17:50:56.788 INFO Pileup - For support and documentation go to https://software.broadinstitute.org/gatk/
17:50:56.788 INFO Pileup - Executing as ?@nf-48b5d3cdd4381b5e278a3ef1840fa4d0-9d4fa-jch92 on Linux v6.12.83 amd64
17:50:56.788 INFO Pileup - Java runtime: OpenJDK 64-Bit Server VM v17.0.14+1-b1367.22
17:50:56.789 INFO Pileup - Start Date/Time: May 28, 2026 at 5:50:56 PM UTC
17:50:56.789 INFO Pileup - ------------------------------------------------------------
17:50:56.789 INFO Pileup - ------------------------------------------------------------
17:50:56.789 INFO Pileup - HTSJDK Version: 4.2.0
17:50:56.789 INFO Pileup - Picard Version: 3.4.0
17:50:56.789 INFO Pileup - Built for Spark Version: 3.5.0
17:50:56.791 INFO Pileup - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:50:56.791 INFO Pileup - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:50:56.791 INFO Pileup - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:50:56.791 INFO Pileup - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:50:56.791 INFO Pileup - Deflater: IntelDeflater
17:50:56.791 INFO Pileup - Inflater: IntelInflater
17:50:56.791 INFO Pileup - GCS max retries/reopens: 20
17:50:56.791 INFO Pileup - Requester pays: disabled
17:50:56.792 INFO Pileup - Initializing engine
17:50:57.063 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
17:50:57.095 INFO IntervalArgumentCollection - Processing 7353 bp from intervals
17:50:57.104 INFO Pileup - Done initializing engine
17:50:57.104 INFO ProgressMeter - Starting traversal
17:50:57.105 INFO ProgressMeter - Current Locus Elapsed Minutes Loci Processed Loci/Minute
17:50:57.907 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
17:50:57.908 INFO ProgressMeter - unmapped 0.0 97 7256.9
17:50:57.908 INFO ProgressMeter - Traversal complete. Processed 97 total loci in 0.0 minutes.
17:50:57.908 INFO Pileup - Shutting down engine
[May 28, 2026 at 5:50:57 PM UTC] org.broadinstitute.hellbender.tools.walkers.qc.Pileup done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=310378496
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