.command.log - Workdir - NFCORE_SAREK:SAREK:CRAM_SAMPLE_INTEGRITY:BAM_CONTAMINATION_ANALYSIS:CONPAIR_PILEUP (HCC1395_tumor)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/42aa799cf34ee58c609c8875b798f0/.command.log
Size: 5.0 KB
Task: NFCORE_SAREK:SAREK:CRAM_SAMPLE_INTEGRITY:BAM_CONTAMINATION_ANALYSIS:CONPAIR_PILEUP (HCC1395_tumor)
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-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_tumor/HCC1395_tumor.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/42aa799cf34ee58c609c8875b798f0/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_tumor/HCC1395_tumor.recalibrated.bam
  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/e6/42aa799cf34ee58c609c8875b798f0/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict
==> STAGING COMPLETE (7 inputs)

15:19:29.803 WARN  GATKReadFilterPluginDescriptor - Redundant enabled filter (NotDuplicateReadFilter) is enabled for this tool by default
15:19:29.880 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
15:19:29.975 INFO  Pileup - ------------------------------------------------------------
15:19:29.977 INFO  Pileup - The Genome Analysis Toolkit (GATK) v4.6.2.0
15:19:29.977 INFO  Pileup - For support and documentation go to https://software.broadinstitute.org/gatk/
15:19:29.977 INFO  Pileup - Executing as ?@nf-e642aa799cf34ee58c609c8875b798f0-26a5f-cj4t7 on Linux v6.12.88 amd64
15:19:29.977 INFO  Pileup - Java runtime: OpenJDK 64-Bit Server VM v17.0.14+1-b1367.22
15:19:29.978 INFO  Pileup - Start Date/Time: June 5, 2026 at 3:19:29 PM UTC
15:19:29.978 INFO  Pileup - ------------------------------------------------------------
15:19:29.978 INFO  Pileup - ------------------------------------------------------------
15:19:29.978 INFO  Pileup - HTSJDK Version: 4.2.0
15:19:29.978 INFO  Pileup - Picard Version: 3.4.0
15:19:29.978 INFO  Pileup - Built for Spark Version: 3.5.0
15:19:29.980 INFO  Pileup - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:19:29.980 INFO  Pileup - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:19:29.980 INFO  Pileup - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:19:29.980 INFO  Pileup - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:19:29.980 INFO  Pileup - Deflater: IntelDeflater
15:19:29.980 INFO  Pileup - Inflater: IntelInflater
15:19:29.980 INFO  Pileup - GCS max retries/reopens: 20
15:19:29.980 INFO  Pileup - Requester pays: disabled
15:19:29.981 INFO  Pileup - Initializing engine
15:19:30.296 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
15:19:30.325 INFO  IntervalArgumentCollection - Processing 7353 bp from intervals
15:19:30.335 INFO  Pileup - Done initializing engine
15:19:30.336 INFO  ProgressMeter - Starting traversal
15:19:30.336 INFO  ProgressMeter -        Current Locus  Elapsed Minutes        Loci Processed      Loci/Minute
15:19:31.616 INFO  Pileup - 0 read(s) filtered by: WellformedReadFilter 
0 read(s) filtered by: MappedReadFilter 
15605 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 
15605 total reads filtered out of 45296 reads processed
15:19:31.616 INFO  ProgressMeter -             unmapped              0.0                    97           4546.9
15:19:31.616 INFO  ProgressMeter - Traversal complete. Processed 97 total loci in 0.0 minutes.
15:19:31.617 INFO  Pileup - Shutting down engine
[June 5, 2026 at 3:19:31 PM UTC] org.broadinstitute.hellbender.tools.walkers.qc.Pileup done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=528482304
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.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_tumor.pileup.txt -verbose -RF NotDuplicateReadFilter -RF CigarContainsNoNOperator -RF MatchingBasesAndQualsReadFilter