.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/2e/5d69cdddb1ff6ddcbc847beb94ca59/.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/2e/5d69cdddb1ff6ddcbc847beb94ca59/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/8a5281a837c92a4fbdf2895f760dab/SW780_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/5d69cdddb1ff6ddcbc847beb94ca59/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/ba9f0ecb6cf27074a10aeda7adafec/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