File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/7d079e5ac7c499505293a520f606de/.command.log
Size
1.5 KB
Task
NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (FFPE_V4_0002_RNA_0001_B23WHYVLT4_1)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/04426f6e7216248473b56120b856c0/FFPE_V4_0002_RNA_0001_B23WHYVLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/04426f6e7216248473b56120b856c0/FFPE_V4_0002_RNA_0001_B23WHYVLT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/11ea7d13b884b58cba2e0efba70f64/FFPE_V4_0002_RNA_0001_B23WHYVLT4_1.Chimeric.out.junction
  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/1e/7d079e5ac7c499505293a520f606de/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/7d079e5ac7c499505293a520f606de/.command.run
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.xh5CnK7yFF/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.xh5CnK7yFF/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.xh5CnK7yFF/./star-fusion.preliminary
-sample contains 295014469 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.xh5CnK7yFF/ctat_genome_lib_build_dir  -J /tmp/nxf.xh5CnK7yFF/FFPE_V4_0002_RNA_0001_B23WHYVLT4_1.Chimeric.out.junction  -O /tmp/nxf.xh5CnK7yFF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.xh5CnK7yFF/FFPE_V4_0002_RNA_0001_B23WHYVLT4_1.Chimeric.out.junction