.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/e56269161c0bedddce3ef620cba45c/.command.log
Size: 835 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2)
Attempt

Content

  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/e56269161c0bedddce3ef620cba45c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/e56269161c0bedddce3ef620cba45c/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/4af1cf31b11a5d5f550862820ffbe5/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/063a6c236336087b84c32219e910bb/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

ls: *.sam: No such file or directory
ls: *.csi: No such file or directory
ls: *.crai: No such file or directory