.command.log - Workdir - NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE (HCC1395_BL;germline_cnv)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/2c93df225f65157460f29273b6d1ff/.command.log
Size: 959 bytes
Task: NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE (HCC1395_BL;germline_cnv)
Attempt

Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/2c93df225f65157460f29273b6d1ff/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/low_depth_grch38.tsv.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/2c93df225f65157460f29273b6d1ff/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/low_depth_header.txt
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/bbf35ef6342551bd720e395aaaa1ad/HCC1395_BL_BL.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/CustomBEDs/low_depth_grch38.tsv.gz
==> 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