.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (SW780_FFPE_RNA_0001_B23LG7FLT4_3)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/156a8fe702826a38578d84cdf50fcd/.command.log
Size: 825 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (SW780_FFPE_RNA_0001_B23LG7FLT4_3)
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/49/156a8fe702826a38578d84cdf50fcd/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/ee018aa9e6ed8279e80e938e738760/SW780_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/156a8fe702826a38578d84cdf50fcd/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/547b171f3f7ae7187eeca9af4afd2a/SW780_FFPE_RNA_0001_B23LG7FLT4_3.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