STAR --genomeDir ref_genome.fa.star.idx --readFilesIn input1/PX_FFPE_esp_TRNA_nat_02_A23MVY2LT4_1_1.fastp.fastq.gz input2/PX_FFPE_esp_TRNA_nat_02_A23MVY2LT4_1_2.fastp.fastq.gz --runThreadN 24 --outFileNamePrefix PX_FFPE_esp_TRNA_nat_02_A23MVY2LT4_1. --sjdbGTFfile ref_annot.gtf --outSAMattrRGline ID:PX_FFPE_esp_TRNA_nat_02_A23MVY2LT4_1 SM:PX_FFPE_esp_TRNA_nat_02_A23MVY2LT4_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 07:40:27 ..... started STAR run
Jun 08 07:40:27 ..... loading genome
Jun 08 07:41:01 ..... processing annotations GTF
Jun 08 07:41:10 ..... inserting junctions into the genome indices
Jun 08 07:42:23 ..... started mapping
Jun 08 08:46:38 ..... finished mapping
Jun 08 08:46:42 ..... started sorting BAM
Jun 08 08:50:50 ..... finished successfully