.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/820dabda22105dd7c8e9da700e556c/.command.log
Size: 835 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1)
Attempt

Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/cba97a8163abdb1c0d5a9e6b3970d5/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
  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/66/820dabda22105dd7c8e9da700e556c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/b880940c7903f4a5934e55d1a55917/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/820dabda22105dd7c8e9da700e556c/.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