.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (HeadNeckN_FFPE_L09_RNA_01_B23LG7FLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/30101559e291b0472b128cd3da5d6c/.command.log
Size: 837 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (HeadNeckN_FFPE_L09_RNA_01_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/17/30101559e291b0472b128cd3da5d6c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/30101559e291b0472b128cd3da5d6c/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/82b978e1669a987bf45e287f81ecaa/HeadNeckN_FFPE_L09_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/3c5224672911e145f68511184c8bd5/HeadNeckN_FFPE_L09_RNA_01_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