.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/18fb3e148a4b3458ec48f1d222fba1/.command.log
Size: 835 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2)
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/20/18fb3e148a4b3458ec48f1d222fba1/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/18fb3e148a4b3458ec48f1d222fba1/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/7206381a0dcf13079d775f1600d86a/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/1b4d36560b17fde41db58926c426e7/SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_2.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