.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (U118MG_FFPE_RNA_0001_B23LG7FLT4_3)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/882f52b3af61b67e9da5cab9f658ce/.command.log
Size: 827 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (U118MG_FFPE_RNA_0001_B23LG7FLT4_3)
Attempt

Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/096f032fe902f64495f8f7e00c6774/U118MG_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam
  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/32/882f52b3af61b67e9da5cab9f658ce/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/a3628d6a2285daa7c10082976745b3/U118MG_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/882f52b3af61b67e9da5cab9f658ce/.command.run
==> 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