.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (1173_GXL_T1_RNA_SLD_01_A23T55JLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/8463e02f1ab7ce11189da423db0c88/.command.log
Size: 831 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (1173_GXL_T1_RNA_SLD_01_A23T55JLT4_1)
Attempt

Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/74f7bb631afd2d9baccde59a6a1a35/1173_GXL_T1_RNA_SLD_01_A23T55JLT4_1.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/9d/8463e02f1ab7ce11189da423db0c88/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/8463e02f1ab7ce11189da423db0c88/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/42ac4d786e3518d1ea68598424a247/1173_GXL_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