.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (1173_J3R_T1_RNA_SLD_01_A23T55JLT4_2)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/41a52460686e50448d8fe844a522c6/.command.log
Size: 831 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (1173_J3R_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/84/41a52460686e50448d8fe844a522c6/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/da55bd6150f8002fdc7444070cea35/1173_J3R_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/41a52460686e50448d8fe844a522c6/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/90c352c5f0b24464db7941a27f4c09/1173_J3R_T1_RNA_SLD_01_A23T55JLT4_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