File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/5a1da46aa2d5937f2cd4bfdb9c20cc/.command.log
Size
1.5 KB
Task
NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (BT-20_FFPE_RNA_0001_B23LG7FLT4_2)
Attempt

Content

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  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/79/5a1da46aa2d5937f2cd4bfdb9c20cc/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/5a1da46aa2d5937f2cd4bfdb9c20cc/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/eac656c045b42cd5f5b3825266dd5a/BT-20_FFPE_RNA_0001_B23LG7FLT4_2_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/3e543b9fe691f4fe4913ef352c2dc8/BT-20_FFPE_RNA_0001_B23LG7FLT4_2.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/eac656c045b42cd5f5b3825266dd5a/BT-20_FFPE_RNA_0001_B23LG7FLT4_2_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.l9e3yOnM0d/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.l9e3yOnM0d/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.l9e3yOnM0d/./star-fusion.preliminary
-sample contains 85474037 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.l9e3yOnM0d/ctat_genome_lib_build_dir  -J /tmp/nxf.l9e3yOnM0d/BT-20_FFPE_RNA_0001_B23LG7FLT4_2.Chimeric.out.junction  -O /tmp/nxf.l9e3yOnM0d/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.l9e3yOnM0d/BT-20_FFPE_RNA_0001_B23LG7FLT4_2.Chimeric.out.junction