.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (786-O_FFPE_RNA_0001_B23LG7FLT4_2)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/d183a480ebb9232e2794afab166711/.command.log
Size: 825 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (786-O_FFPE_RNA_0001_B23LG7FLT4_2)
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/6c/d183a480ebb9232e2794afab166711/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/46684ef348b139d247eeb2ee8b39ae/786-O_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/d183a480ebb9232e2794afab166711/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/d4c8b5afe08cd46361b538a8d10336/786-O_FFPE_RNA_0001_B23LG7FLT4_2.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