19:32:06.249 WARN GATKReadFilterPluginDescriptor - Redundant enabled filter (NotDuplicateReadFilter) is enabled for this tool by default
19:32:06.309 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
19:32:07.073 INFO Pileup - ------------------------------------------------------------
19:32:07.076 INFO Pileup - The Genome Analysis Toolkit (GATK) v4.6.2.0
19:32:07.076 INFO Pileup - For support and documentation go to https://software.broadinstitute.org/gatk/
19:32:07.076 INFO Pileup - Executing as ?@nf-2d1dd0a4e17bc48fa8de138ae3077ebf-927e4-mm5qw on Linux v6.12.88 amd64
19:32:07.076 INFO Pileup - Java runtime: OpenJDK 64-Bit Server VM v17.0.14+1-b1367.22
19:32:07.076 INFO Pileup - Start Date/Time: June 4, 2026 at 7:32:06 PM UTC
19:32:07.077 INFO Pileup - ------------------------------------------------------------
19:32:07.077 INFO Pileup - ------------------------------------------------------------
19:32:07.078 INFO Pileup - HTSJDK Version: 4.2.0
19:32:07.079 INFO Pileup - Picard Version: 3.4.0
19:32:07.079 INFO Pileup - Built for Spark Version: 3.5.0
19:32:07.080 INFO Pileup - HTSJDK Defaults.COMPRESSION_LEVEL : 2
19:32:07.081 INFO Pileup - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:32:07.081 INFO Pileup - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
19:32:07.081 INFO Pileup - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:32:07.081 INFO Pileup - Deflater: IntelDeflater
19:32:07.081 INFO Pileup - Inflater: IntelInflater
19:32:07.081 INFO Pileup - GCS max retries/reopens: 20
19:32:07.081 INFO Pileup - Requester pays: disabled
19:32:07.081 INFO Pileup - Initializing engine
19:32:07.368 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
19:32:07.400 INFO IntervalArgumentCollection - Processing 7353 bp from intervals
19:32:07.412 INFO Pileup - Done initializing engine
19:32:07.412 INFO ProgressMeter - Starting traversal
19:32:07.412 INFO ProgressMeter - Current Locus Elapsed Minutes Loci Processed Loci/Minute
19:32:09.093 INFO Pileup - 0 read(s) filtered by: WellformedReadFilter
0 read(s) filtered by: MappedReadFilter
14944 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
14944 total reads filtered out of 43040 reads processed
19:32:09.093 INFO ProgressMeter - unmapped 0.0 93 3319.5
19:32:09.093 INFO ProgressMeter - Traversal complete. Processed 93 total loci in 0.0 minutes.
19:32:09.093 INFO Pileup - Shutting down engine
[June 4, 2026 at 7:32:09 PM UTC] org.broadinstitute.hellbender.tools.walkers.qc.Pileup done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=511705088
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_tumor.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_tumor.pileup.txt -verbose -RF NotDuplicateReadFilter -RF CigarContainsNoNOperator -RF MatchingBasesAndQualsReadFilter