.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (FFPE_V4_0001_RNA_0003_B23MHV2LT4_2)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/5c4cceb4251eb6820acc4094310479/.command.log
Size: 829 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (FFPE_V4_0001_RNA_0003_B23MHV2LT4_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/60/5c4cceb4251eb6820acc4094310479/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/7d91b421d07bc48e4bd1929884d81d/FFPE_V4_0001_RNA_0003_B23MHV2LT4_2.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/5c4cceb4251eb6820acc4094310479/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/f8c73df09182e4b0272819acf78b19/FFPE_V4_0001_RNA_0003_B23MHV2LT4_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