.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (FFPE_V4_0001_RNA_0003_B23MHV2LT4_2)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/0fce724663fd5673357aee3c01c392/.command.log
Size: 829 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (FFPE_V4_0001_RNA_0003_B23MHV2LT4_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/17/0fce724663fd5673357aee3c01c392/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/afd7714ccc31d9761cf50204f4a37b/FFPE_V4_0001_RNA_0003_B23MHV2LT4_2.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/0fce724663fd5673357aee3c01c392/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/15f7d615690c5e02da7a08acc5f63e/FFPE_V4_0001_RNA_0003_B23MHV2LT4_2.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