02:44:30.765 WARN GATKReadFilterPluginDescriptor - Redundant enabled filter (NotDuplicateReadFilter) is enabled for this tool by default
02:44:30.813 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
02:44:32.304 INFO Pileup - ------------------------------------------------------------
02:44:32.307 INFO Pileup - The Genome Analysis Toolkit (GATK) v4.6.2.0
02:44:32.307 INFO Pileup - For support and documentation go to https://software.broadinstitute.org/gatk/
02:44:32.307 INFO Pileup - Executing as ?@nf-42e588b570f095560cfcee75957dc382-71c52-djjzk on Linux v6.12.88 amd64
02:44:32.307 INFO Pileup - Java runtime: OpenJDK 64-Bit Server VM v17.0.14+1-b1367.22
02:44:32.307 INFO Pileup - Start Date/Time: June 5, 2026 at 2:44:30 AM UTC
02:44:32.307 INFO Pileup - ------------------------------------------------------------
02:44:32.307 INFO Pileup - ------------------------------------------------------------
02:44:32.308 INFO Pileup - HTSJDK Version: 4.2.0
02:44:32.308 INFO Pileup - Picard Version: 3.4.0
02:44:32.308 INFO Pileup - Built for Spark Version: 3.5.0
02:44:32.310 INFO Pileup - HTSJDK Defaults.COMPRESSION_LEVEL : 2
02:44:32.310 INFO Pileup - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
02:44:32.310 INFO Pileup - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
02:44:32.310 INFO Pileup - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
02:44:32.310 INFO Pileup - Deflater: IntelDeflater
02:44:32.310 INFO Pileup - Inflater: IntelInflater
02:44:32.310 INFO Pileup - GCS max retries/reopens: 20
02:44:32.310 INFO Pileup - Requester pays: disabled
02:44:32.311 INFO Pileup - Initializing engine
02:44:32.591 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
02:44:32.616 INFO IntervalArgumentCollection - Processing 7353 bp from intervals
02:44:32.624 INFO Pileup - Done initializing engine
02:44:32.625 INFO ProgressMeter - Starting traversal
02:44:32.625 INFO ProgressMeter - Current Locus Elapsed Minutes Loci Processed Loci/Minute
02:44:33.278 INFO Pileup - 0 read(s) filtered by: WellformedReadFilter
0 read(s) filtered by: MappedReadFilter
2587 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
2587 total reads filtered out of 15770 reads processed
02:44:33.278 INFO ProgressMeter - unmapped 0.0 95 8728.9
02:44:33.278 INFO ProgressMeter - Traversal complete. Processed 95 total loci in 0.0 minutes.
02:44:33.278 INFO Pileup - Shutting down engine
[June 5, 2026 at 2:44:33 AM UTC] org.broadinstitute.hellbender.tools.walkers.qc.Pileup done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=494927872
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.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 HCC1395_BL.pileup.txt -verbose -RF NotDuplicateReadFilter -RF CigarContainsNoNOperator -RF MatchingBasesAndQualsReadFilter