.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (tih_rna_sample_00136_B23WHTKLT4_2)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/152408dd6d4783654300ce1ca17c40/.command.log
Size: 1.5 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (tih_rna_sample_00136_B23WHTKLT4_2)
Attempt

Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/0da41f3e02a8cb3db0294316236a86/tih_rna_sample_00136_B23WHTKLT4_2_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/27/d2399606fa384285f96f378f870299/tih_rna_sample_00136_B23WHTKLT4_2.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/152408dd6d4783654300ce1ca17c40/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/152408dd6d4783654300ce1ca17c40/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/0da41f3e02a8cb3db0294316236a86/tih_rna_sample_00136_B23WHTKLT4_2_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.HxQAgx9K4G/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.HxQAgx9K4G/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.HxQAgx9K4G/./star-fusion.preliminary
-sample contains 98626830 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.HxQAgx9K4G/ctat_genome_lib_build_dir  -J /tmp/nxf.HxQAgx9K4G/tih_rna_sample_00136_B23WHTKLT4_2.Chimeric.out.junction  -O /tmp/nxf.HxQAgx9K4G/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.HxQAgx9K4G/tih_rna_sample_00136_B23WHTKLT4_2.Chimeric.out.junction