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/17/3c15023005fc6ecaab130723455b3f/.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/17/3c15023005fc6ecaab130723455b3f/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/e754d1dbb1f9187c7c568eac722643/rna_s1221_S42_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/e754d1dbb1f9187c7c568eac722643/rna_s1221_S42_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

	STAR --genomeDir ref_genome.fa.star.idx --readFilesIn input1/rna_s1221_S42_1.fastp.fastq.gz input2/rna_s1221_S42_2.fastp.fastq.gz --runThreadN 24 --outFileNamePrefix rna_s1221_S42. --sjdbGTFfile ref_annot.gtf --outSAMattrRGline ID:rna_s1221_S42 SM:rna_s1221_S42 --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 03 12:58:02 ..... started STAR run
Jun 03 12:58:02 ..... loading genome
Jun 03 12:58:16 ..... processing annotations GTF
Jun 03 12:58:25 ..... inserting junctions into the genome indices
Jun 03 12:59:36 ..... started mapping
Jun 03 13:00:48 ..... finished mapping
Jun 03 13:00:50 ..... started sorting BAM
Jun 03 13:00:58 ..... finished successfully