File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/356c65f0467afac247bd974d8d514d/.command.log
Size
1.5 KB
Task
NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (aih-tih-sc-75c3a9-R1_B23WHYVLT4_1)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/d859b1a79a168eb6584835a555b8b8/aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.Chimeric.out.junction
  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/4f/6438c7038d3d12aa4689a2f75e5de0/aih-tih-sc-75c3a9-R1_B23WHYVLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/356c65f0467afac247bd974d8d514d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/6438c7038d3d12aa4689a2f75e5de0/aih-tih-sc-75c3a9-R1_B23WHYVLT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/356c65f0467afac247bd974d8d514d/.command.run
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.11h0xoxOMZ/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.11h0xoxOMZ/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.11h0xoxOMZ/./star-fusion.preliminary
-sample contains 295003991 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.11h0xoxOMZ/ctat_genome_lib_build_dir  -J /tmp/nxf.11h0xoxOMZ/aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.Chimeric.out.junction  -O /tmp/nxf.11h0xoxOMZ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.11h0xoxOMZ/aih-tih-sc-75c3a9-R1_B23WHYVLT4_1.Chimeric.out.junction