.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (aih-tih-sc-f14fdc-R1_B23WHYVLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/1b6d8848c24075f38ec07111a5d2f0/.command.log
Size: 1.5 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (aih-tih-sc-f14fdc-R1_B23WHYVLT4_1)
Attempt

Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/2f6209bf5aebd13ad8654449e63ba3/aih-tih-sc-f14fdc-R1_B23WHYVLT4_1_1.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/b6/1b6d8848c24075f38ec07111a5d2f0/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/1b6d8848c24075f38ec07111a5d2f0/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/2f6209bf5aebd13ad8654449e63ba3/aih-tih-sc-f14fdc-R1_B23WHYVLT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/7e1a6d137b9f98ab4520f74794075a/aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.Chimeric.out.junction
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.uapUXpTuOo/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.uapUXpTuOo/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.uapUXpTuOo/./star-fusion.preliminary
-sample contains 295326268 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.uapUXpTuOo/ctat_genome_lib_build_dir  -J /tmp/nxf.uapUXpTuOo/aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.Chimeric.out.junction  -O /tmp/nxf.uapUXpTuOo/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.uapUXpTuOo/aih-tih-sc-f14fdc-R1_B23WHYVLT4_1.Chimeric.out.junction