.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (ColoN_FFPE_L07_RNA_01_B23LG7FLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/1f91660e3e1b59bc0db151f6259c37/.command.log
Size: 829 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (ColoN_FFPE_L07_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/a1/1f91660e3e1b59bc0db151f6259c37/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/d2b06966bb03c3b9fe3ca39ee3533d/ColoN_FFPE_L07_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/1f91660e3e1b59bc0db151f6259c37/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/377527b6189682012486af906b1c01/ColoN_FFPE_L07_RNA_01_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