Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/7d0fde9eeb2d4e095bea8b3bd5949c/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_annot.gtf
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/cba97a8163abdb1c0d5a9e6b3970d5/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.star.idx
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/cba97a8163abdb1c0d5a9e6b3970d5/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/7d0fde9eeb2d4e095bea8b3bd5949c/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

	STAR --genomeDir ref_genome.fa.star.idx --readFilesIn input1/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz input2/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz --runThreadN 24 --outFileNamePrefix BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1. --sjdbGTFfile ref_annot.gtf --outSAMattrRGline ID:BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1 SM:BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1 --twopassMode None --chimSegmentMin 12 --chimJunctionOverhangMin 5 --chimMultimapNmax 50 --chimScoreJunctionNonGTAG -4 --chimScoreSeparation 1 --alignIntronMax 140000 --outReadsUnmapped None --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMunmapped Within --chimOutJunctionFormat 1 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignSJstitchMismatchNmax 5 -1 5 5 --chimMultimapScoreRange 3 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --alignInsertionFlush Right --alignSplicedMateMapLmin 30 --alignSplicedMateMapLminOverLmate 0.5 --quantMode GeneCounts --runRNGseed 1 --chimOutType Junctions WithinBAM --limitBAMsortRAM 38654705664
	STAR version: 2.7.10a   compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source
Jun 08 07:23:01 ..... started STAR run
Jun 08 07:23:01 ..... loading genome
Jun 08 07:23:27 ..... processing annotations GTF
Jun 08 07:23:41 ..... inserting junctions into the genome indices
Jun 08 07:25:34 ..... started mapping
Jun 08 07:41:25 ..... finished mapping
Jun 08 07:41:30 ..... started sorting BAM
Jun 08 07:42:52 ..... finished successfully