.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (EndoN_FFPE_L02_RNA_01_B23LG7FLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/00e698dad2258fecd28c6b7ed2313e/.command.log
Size: 829 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (EndoN_FFPE_L02_RNA_01_B23LG7FLT4_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/d6/00e698dad2258fecd28c6b7ed2313e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/7f0144a2170fc8c7876350a4d3a45a/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/00e698dad2258fecd28c6b7ed2313e/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/42/42fdedddc30c04977a3c74b9feda10/EndoN_FFPE_L02_RNA_01_B23LG7FLT4_1.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