File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/31969f1563984b27185a4eb466ccc4/.command.log
Size
1.3 KB
Task
NFCORE_SAREK:SAREK:CRAM_SAMPLE_INTEGRITY:BAM_NGSCHECKMATE:NGSCHECKMATE_NCM (1)
Attempt

Content

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  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/33/c44d80839c84a3712b5e69c8dc70cc/HCC1395_BL.ngscheckmate.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/31969f1563984b27185a4eb466ccc4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/54b75403f9e8ca6a47a5d2a8e62755/HCC1395_tumor.ngscheckmate.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/31969f1563984b27185a4eb466ccc4/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/719729f5e7810d4eaf8a8b72b06e27/Sig_18_Blood.ngscheckmate.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/7a042e851f17f36d9a3b1803813fc3/Sig_18_tissue.ngscheckmate.vcf.gz
==> STAGING COMPLETE (8 inputs)

Set the path to your reference file with the NCM_REF environment variable
eg. export NCM_REF=/<path>/<to>/<reference>

Generate Data Set from .
using this bed file : SNP_GRCh38_hg38_wChr.bed
ls: *.vcf: No such file or directory