File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/d9df5f8fa72c763eae872a9071ad39/.command.log
Size
1.5 KB
Task
NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1)
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/c8/d9df5f8fa72c763eae872a9071ad39/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/d9df5f8fa72c763eae872a9071ad39/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/a096db62109edfb8d9aede09e26b4c/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/f7c46891ee12480c88775c01ab5059/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/a096db62109edfb8d9aede09e26b4c/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.8SCde4ijmu/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.8SCde4ijmu/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.8SCde4ijmu/./star-fusion.preliminary
-sample contains 73993705 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.8SCde4ijmu/ctat_genome_lib_build_dir  -J /tmp/nxf.8SCde4ijmu/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.Chimeric.out.junction  -O /tmp/nxf.8SCde4ijmu/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.8SCde4ijmu/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.Chimeric.out.junction