.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/e6b06ed0b8ec16212974e5af2ec194/.command.log
Size: 835 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1)
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/c5/e6b06ed0b8ec16212974e5af2ec194/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/e6b06ed0b8ec16212974e5af2ec194/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/cd721685e1a602e76e763ab1de3fdd/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/7dfec696eb2e498ef8e543bc059437/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1.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