File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/b2e507ed6e5add3171da6704a81dba/.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/1c/afea95248bacb8f5500cfb7c2832a5/HCC1395_BL.ngscheckmate.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/b2e507ed6e5add3171da6704a81dba/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/b55c900c10e1f83a0d90d3ae0f6624/HCC1395_tumor.ngscheckmate.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/b2e507ed6e5add3171da6704a81dba/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/5fe2ec60e3844a6a241d735659ccdf/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/cc/965403792a4cc7e865a5d09bc499c8/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