.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (FFPE_HD789_01_RNA_0002_B23LG7FLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/a092607f334fac00aca27c9398e21f/.command.log
Size: 831 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (FFPE_HD789_01_RNA_0002_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/5e/a092607f334fac00aca27c9398e21f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/a092607f334fac00aca27c9398e21f/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/e9ec6243d0ec6a8842644cd4316841/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/abf35c9b8a6909eca5c16eef2c6d8c/FFPE_HD789_01_RNA_0002_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