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/da/5f0b4e94c40683ce2acca17a73c04d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/141cb9b55199ed6713b6db8ca5197e/659_bhK-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz
  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/da/5f0b4e94c40683ce2acca17a73c04d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/141cb9b55199ed6713b6db8ca5197e/659_bhK-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

	STAR --genomeDir ref_genome.fa.star.idx --readFilesIn input1/659_bhK-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz input2/659_bhK-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz --runThreadN 24 --outFileNamePrefix 659_bhK-T1-TRNA-1_B23MHV2LT4_1. --sjdbGTFfile ref_annot.gtf --outSAMattrRGline ID:659_bhK-T1-TRNA-1_B23MHV2LT4_1 SM:659_bhK-T1-TRNA-1_B23MHV2LT4_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 07:33:14 ..... started STAR run
Jun 08 07:33:14 ..... loading genome
Jun 08 07:33:54 ..... processing annotations GTF
Jun 08 07:34:04 ..... inserting junctions into the genome indices
Jun 08 07:35:15 ..... started mapping
Jun 08 08:24:17 ..... finished mapping
Jun 08 08:24:20 ..... started sorting BAM
Jun 08 08:28:28 ..... finished successfully