.command.log - Workdir - NFCORE_SAREK:SAREK:CRAM_SAMPLE_INTEGRITY:BAM_CONTAMINATION_ANALYSIS:CONPAIR_PILEUP (Sig_18_Blood)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/b5d3cdd4381b5e278a3ef1840fa4d0/.command.log
Size: 5.0 KB
Task: NFCORE_SAREK:SAREK:CRAM_SAMPLE_INTEGRITY:BAM_CONTAMINATION_ANALYSIS:CONPAIR_PILEUP (Sig_18_Blood)
Attempt
Content

  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/b5d3cdd4381b5e278a3ef1840fa4d0/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/b5d3cdd4381b5e278a3ef1840fa4d0/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_Blood/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_Blood/Sig_18_Blood.recalibrated.bam
==> STAGING COMPLETE (7 inputs)

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