.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (aih-tih-sc-f71b32-R1_B23WHYVLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/30de0412168a154ffc3b2284c7135b/.command.log
Size: 1.5 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (aih-tih-sc-f71b32-R1_B23WHYVLT4_1)
Attempt

Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/22b89dd7966516fac3dbdafe888b6b/aih-tih-sc-f71b32-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/fa/30de0412168a154ffc3b2284c7135b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/30de0412168a154ffc3b2284c7135b/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/984829ebb021881c81a4223711d2d8/aih-tih-sc-f71b32-R1_B23WHYVLT4_1.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/22b89dd7966516fac3dbdafe888b6b/aih-tih-sc-f71b32-R1_B23WHYVLT4_1_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.MLDQN00Bl9/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.MLDQN00Bl9/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.MLDQN00Bl9/./star-fusion.preliminary
-sample contains 295174180 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.MLDQN00Bl9/ctat_genome_lib_build_dir  -J /tmp/nxf.MLDQN00Bl9/aih-tih-sc-f71b32-R1_B23WHYVLT4_1.Chimeric.out.junction  -O /tmp/nxf.MLDQN00Bl9/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.MLDQN00Bl9/aih-tih-sc-f71b32-R1_B23WHYVLT4_1.Chimeric.out.junction