File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/9f81a9ab4d47b85e03591c8be7e736/.command.log
Size
1.5 KB
Task
NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (BreastNP_FFPE_L02_RNA_01_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/5b/17bf8ace65d43941c87253450d79d0/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/9f81a9ab4d47b85e03591c8be7e736/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/9f81a9ab4d47b85e03591c8be7e736/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/17bf8ace65d43941c87253450d79d0/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/ec3a10410562e6c89a0256d8bfdf6b/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Chimeric.out.junction
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.Kjmo1YMV5K/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.Kjmo1YMV5K/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.Kjmo1YMV5K/./star-fusion.preliminary
-sample contains 9022667 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.Kjmo1YMV5K/ctat_genome_lib_build_dir  -J /tmp/nxf.Kjmo1YMV5K/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Chimeric.out.junction  -O /tmp/nxf.Kjmo1YMV5K/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.Kjmo1YMV5K/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Chimeric.out.junction