.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (OvarianNP_FFPE_L01_RNA_01_B23LG7FLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/cd8308536bfd0ea138f35c8f4ec183/.command.log
Size: 1.5 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (OvarianNP_FFPE_L01_RNA_01_B23LG7FLT4_1)
Attempt

Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/355fa13c6547356a46005c7b15ba49/OvarianNP_FFPE_L01_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/5bb3cc3e0a2b3990c7256d3e27f4e3/OvarianNP_FFPE_L01_RNA_01_B23LG7FLT4_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/e3/cd8308536bfd0ea138f35c8f4ec183/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/cd8308536bfd0ea138f35c8f4ec183/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/355fa13c6547356a46005c7b15ba49/OvarianNP_FFPE_L01_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.evZTEW4Kff/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.evZTEW4Kff/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.evZTEW4Kff/./star-fusion.preliminary
-sample contains 10860033 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.evZTEW4Kff/ctat_genome_lib_build_dir  -J /tmp/nxf.evZTEW4Kff/OvarianNP_FFPE_L01_RNA_01_B23LG7FLT4_1.Chimeric.out.junction  -O /tmp/nxf.evZTEW4Kff/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.evZTEW4Kff/OvarianNP_FFPE_L01_RNA_01_B23LG7FLT4_1.Chimeric.out.junction