.command.log - Workdir - NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE (HCC1395_BL;sentieon_haplotyper_rf)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/e96e1d55a05f70f5d4675e5400162d/.command.log
Size: 987 bytes
Task: NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE (HCC1395_BL;sentieon_haplotyper_rf)
Attempt

Content

  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/repeatmasker_grch38.bed.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/e96e1d55a05f70f5d4675e5400162d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/e96e1d55a05f70f5d4675e5400162d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/repeatmasker_grch38.bed.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/835856a703dbcee8ab82e72e820a62/HCC1395_BL.deconflicted_germline.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/repeatmasker_header.txt
==> STAGING COMPLETE (6 inputs)

ls: *.vcf: No such file or directory
ls: *.bcf: No such file or directory
ls: *.bcf.gz: No such file or directory