.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/69f6927e670a03940b4733d6a5c8e2/.command.log
Size: 831 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1)
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/f9/69f6927e670a03940b4733d6a5c8e2/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/5acc309485ca3aa52aefc42f894e1e/1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/69f6927e670a03940b4733d6a5c8e2/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/cac3a11d8443394fe75d33063eb49e/1173_LV7_T1_RNA_SLD_01_A23T55JLT4_1.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