.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (PX_FFPE_kid_TRNA_nat_01_A23MVY2LT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/33bf78957fe629642675de64d118b7/.command.log
Size: 833 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:SAMTOOLS_VIEW_ALIGNMENT_CRAM (PX_FFPE_kid_TRNA_nat_01_A23MVY2LT4_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/ea/33bf78957fe629642675de64d118b7/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/ec781b9106a0ecd7faab40bf128131/PX_FFPE_kid_TRNA_nat_01_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/97485a7d809c0c4ccf93ad199265d8/PX_FFPE_kid_TRNA_nat_01_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/33bf78957fe629642675de64d118b7/.command.run
==> 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