.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (aih-tih-sc-ea6ef3-R1_B23WHYVLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/d984fa4838bc8cf0181d5f1b7c9161/.command.log
Size: 1.5 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (aih-tih-sc-ea6ef3-R1_B23WHYVLT4_1)
Attempt

Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/4f569ad80cc35faa48468f894d6276/aih-tih-sc-ea6ef3-R1_B23WHYVLT4_1_2.fastp.fastq.gz
  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/2e/d984fa4838bc8cf0181d5f1b7c9161/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/35bb1280f2ca21fe7888ffef81700b/aih-tih-sc-ea6ef3-R1_B23WHYVLT4_1.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/d984fa4838bc8cf0181d5f1b7c9161/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/4f569ad80cc35faa48468f894d6276/aih-tih-sc-ea6ef3-R1_B23WHYVLT4_1_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.6uNdnHLf0x/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.6uNdnHLf0x/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.6uNdnHLf0x/./star-fusion.preliminary
-sample contains 294778940 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.6uNdnHLf0x/ctat_genome_lib_build_dir  -J /tmp/nxf.6uNdnHLf0x/aih-tih-sc-ea6ef3-R1_B23WHYVLT4_1.Chimeric.out.junction  -O /tmp/nxf.6uNdnHLf0x/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.6uNdnHLf0x/aih-tih-sc-ea6ef3-R1_B23WHYVLT4_1.Chimeric.out.junction