.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (U118MG_FFPE_RNA_0001_B23LG7FLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/6e2de888ee53a9b2b2c4f259a02bad/.command.log
Size: 827 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (U118MG_FFPE_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/4f/6e2de888ee53a9b2b2c4f259a02bad/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/6e2de888ee53a9b2b2c4f259a02bad/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/2edfb1cbe6036febeb2b1dd139d7f8/U118MG_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/8564425e28b0fbd6bc1d4832f11cfe/U118MG_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
==> 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