.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (A673_FFPE_RNA_0001_B23LG7FLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/c5fe3c749c9bad747f5dbbf920dc7e/.command.log
Size: 823 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (A673_FFPE_RNA_0001_B23LG7FLT4_1)
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/7f/c5fe3c749c9bad747f5dbbf920dc7e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/4384ffd54210c48ab7fc4bdeb3bb13/A673_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/c5fe3c749c9bad747f5dbbf920dc7e/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/c9d08ed8bdfdb6136dc1aa50bd1fdb/A673_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
==> 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