.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_3)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/a9fd06049e94b2dbfec6482b2e5e5e/.command.log
Size: 835 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_3)
Attempt

Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/5124f879fb7ea1c0c1066a15fb294d/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
  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/88/a9fd06049e94b2dbfec6482b2e5e5e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/3d61b310224dff375fb3555658a1a2/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/a9fd06049e94b2dbfec6482b2e5e5e/.command.run
==> 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