File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/016e3f86893254554f83b444db0407/.command.log
Size
1.5 KB
Task
NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (aih-tih-sc-7c6c07-R1_B23WHYVLT4_1)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/bf9f9b2dc57aaf99a96eb6c9ac3ea1/aih-tih-sc-7c6c07-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/22/016e3f86893254554f83b444db0407/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/016e3f86893254554f83b444db0407/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/3e7e0bce575cd44248f4576937dfaa/aih-tih-sc-7c6c07-R1_B23WHYVLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/3e7e0bce575cd44248f4576937dfaa/aih-tih-sc-7c6c07-R1_B23WHYVLT4_1_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.7XlfVCHAaN/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.7XlfVCHAaN/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.7XlfVCHAaN/./star-fusion.preliminary
-sample contains 295151796 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.7XlfVCHAaN/ctat_genome_lib_build_dir  -J /tmp/nxf.7XlfVCHAaN/aih-tih-sc-7c6c07-R1_B23WHYVLT4_1.Chimeric.out.junction  -O /tmp/nxf.7XlfVCHAaN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.7XlfVCHAaN/aih-tih-sc-7c6c07-R1_B23WHYVLT4_1.Chimeric.out.junction