.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (1173_LAF_T1_RNA_SLD_01_A23T55JLT4_2)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/b5cddc02e9247dd060d177f32669a0/.command.log
Size: 831 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (1173_LAF_T1_RNA_SLD_01_A23T55JLT4_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/95/b5cddc02e9247dd060d177f32669a0/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/7c1a7ae5483b4f04015da13ade979d/1173_LAF_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/b5cddc02e9247dd060d177f32669a0/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/0f64a9924a8c6a5da0530fe7c59467/1173_LAF_T1_RNA_SLD_01_A23T55JLT4_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