Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/55180b7d0dcf010c9b9358090d25cd/659_cRa-T1-TRNA-1_B23WHTKLT4_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/2c/fa3fc5236d3a3816ee55f42d09a2e2/.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/2c/fa3fc5236d3a3816ee55f42d09a2e2/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/55180b7d0dcf010c9b9358090d25cd/659_cRa-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

	STAR --genomeDir ref_genome.fa.star.idx --readFilesIn input1/659_cRa-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz input2/659_cRa-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz --runThreadN 24 --outFileNamePrefix 659_cRa-T1-TRNA-1_B23WHTKLT4_1. --sjdbGTFfile ref_annot.gtf --outSAMattrRGline ID:659_cRa-T1-TRNA-1_B23WHTKLT4_1 SM:659_cRa-T1-TRNA-1_B23WHTKLT4_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 07:42:19 ..... started STAR run
Jun 08 07:42:19 ..... loading genome
Jun 08 07:42:59 ..... processing annotations GTF
Jun 08 07:43:14 ..... inserting junctions into the genome indices
Jun 08 07:44:53 ..... started mapping
Jun 08 08:37:55 ..... finished mapping
Jun 08 08:37:58 ..... started sorting BAM
Jun 08 08:41:55 ..... finished successfully