Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/a1118b890c33ced99567881d245ca2/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/a1118b890c33ced99567881d245ca2/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1_2.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/ea/64bb71db35614ee027015bc4586297/.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/ea/64bb71db35614ee027015bc4586297/.command.run
==> STAGING COMPLETE (6 inputs)

	STAR --genomeDir ref_genome.fa.star.idx --readFilesIn input1/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz input2/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz --runThreadN 24 --outFileNamePrefix BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1. --sjdbGTFfile ref_annot.gtf --outSAMattrRGline ID:BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1 SM:BreastNB_FFPE_L01_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
May 28 20:06:31 ..... started STAR run
May 28 20:06:31 ..... loading genome
May 28 20:06:56 ..... processing annotations GTF
May 28 20:07:11 ..... inserting junctions into the genome indices
May 28 20:09:05 ..... started mapping
May 28 20:17:28 ..... finished mapping
May 28 20:17:30 ..... started sorting BAM
May 28 20:18:14 ..... finished successfully