.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (dna_s770)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/464ba56a9e7259eddec3b975882625/.command.log
Size: 1.3 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (dna_s770)
Attempt

Content

  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/2b4ae5726029c74278cbaf16867836/dna_s770_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/464ba56a9e7259eddec3b975882625/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/464ba56a9e7259eddec3b975882625/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/51c0141100d6d6ed2e74a9046977be/dna_s770.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/2b4ae5726029c74278cbaf16867836/dna_s770_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.SPyQv9tJ70/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.SPyQv9tJ70/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.SPyQv9tJ70/./star-fusion.preliminary
-sample contains 174402251 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.SPyQv9tJ70/ctat_genome_lib_build_dir  -J /tmp/nxf.SPyQv9tJ70/dna_s770.Chimeric.out.junction  -O /tmp/nxf.SPyQv9tJ70/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.SPyQv9tJ70/dna_s770.Chimeric.out.junction