.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/b59343211ed93627d791eb1d570043/.command.log
Size: 831 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2)
Attempt

Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/899915d2405ef08a254ea5ff631cd3/1173_JLC_T1_RNA_SLD_01_A23T55JLT4_2.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/e7/b59343211ed93627d791eb1d570043/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/b59343211ed93627d791eb1d570043/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/99c4a842d743ee7639c213c6493676/1173_JLC_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