.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/8fa7fe2a07073bece8a88609e86a7c/.command.log
Size: 835 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (BreastNP_FFPE_L03_RNA_01_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/c6/8fa7fe2a07073bece8a88609e86a7c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/5a8966bec5d146d12802b7b8467a55/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/8fa7fe2a07073bece8a88609e86a7c/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/1fe52a363a5178c4ba1cdfc8e4a78f/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.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