.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (SW780_FFPE_RNA_0001_B23LG7FLT4_2)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/a2ca0cd49c3a7cb219c1bc9014edfc/.command.log
Size: 825 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (SW780_FFPE_RNA_0001_B23LG7FLT4_2)
Attempt

Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/4080e18bdc2f8794e2bd031b81f590/SW780_FFPE_RNA_0001_B23LG7FLT4_2.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/78/a2ca0cd49c3a7cb219c1bc9014edfc/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/a2ca0cd49c3a7cb219c1bc9014edfc/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/47/b8ef08ecdfb8dd65c3cd9da5a7ad92/SW780_FFPE_RNA_0001_B23LG7FLT4_2.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