.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/91/dbba21244455039c68f4394b62e775/.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/91/dbba21244455039c68f4394b62e775/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/91/dbba21244455039c68f4394b62e775/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
  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)

15:19:28.074 WARN  GATKReadFilterPluginDescriptor - Redundant enabled filter (NotDuplicateReadFilter) is enabled for this tool by default
15:19:28.120 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
15:19:28.199 INFO  Pileup - ------------------------------------------------------------
15:19:28.201 INFO  Pileup - The Genome Analysis Toolkit (GATK) v4.6.2.0
15:19:28.201 INFO  Pileup - For support and documentation go to https://software.broadinstitute.org/gatk/
15:19:28.201 INFO  Pileup - Executing as ?@nf-91dbba21244455039c68f4394b62e775-e2a52-smnbh on Linux v6.12.88 amd64
15:19:28.201 INFO  Pileup - Java runtime: OpenJDK 64-Bit Server VM v17.0.14+1-b1367.22
15:19:28.201 INFO  Pileup - Start Date/Time: June 5, 2026 at 3:19:28 PM UTC
15:19:28.201 INFO  Pileup - ------------------------------------------------------------
15:19:28.201 INFO  Pileup - ------------------------------------------------------------
15:19:28.202 INFO  Pileup - HTSJDK Version: 4.2.0
15:19:28.202 INFO  Pileup - Picard Version: 3.4.0
15:19:28.202 INFO  Pileup - Built for Spark Version: 3.5.0
15:19:28.203 INFO  Pileup - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:19:28.204 INFO  Pileup - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:19:28.204 INFO  Pileup - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:19:28.204 INFO  Pileup - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:19:28.204 INFO  Pileup - Deflater: IntelDeflater
15:19:28.204 INFO  Pileup - Inflater: IntelInflater
15:19:28.204 INFO  Pileup - GCS max retries/reopens: 20
15:19:28.204 INFO  Pileup - Requester pays: disabled
15:19:28.204 INFO  Pileup - Initializing engine
15:19:28.442 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
15:19:28.465 INFO  IntervalArgumentCollection - Processing 7353 bp from intervals
15:19:28.474 INFO  Pileup - Done initializing engine
15:19:28.474 INFO  ProgressMeter - Starting traversal
15:19:28.474 INFO  ProgressMeter -        Current Locus  Elapsed Minutes        Loci Processed      Loci/Minute
15:19:29.401 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
15:19:29.402 INFO  ProgressMeter -             unmapped              0.0                    97           6271.6
15:19:29.402 INFO  ProgressMeter - Traversal complete. Processed 97 total loci in 0.0 minutes.
15:19:29.402 INFO  Pileup - Shutting down engine
[June 5, 2026 at 3:19:29 PM UTC] org.broadinstitute.hellbender.tools.walkers.qc.Pileup done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=419430400
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