.command.out - Workdir - NFCORE_RNAFUSION:RNAFUSION:FASTQ_ALIGN_STAR:STAR_ALIGNMENT (1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1)

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/9432b492030b76af3248c3b7e8a412/.command.out
Size: 1.5 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FASTQ_ALIGN_STAR:STAR_ALIGNMENT (1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1)
Attempt

Content

	STAR --genomeDir ref_genome.fa.star.idx --readFilesIn input1/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz input2/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz --runThreadN 24 --outFileNamePrefix 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1. --sjdbGTFfile ref_annot.gtf --outSAMattrRGline ID:1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1 SM:1173_CRX_T1_RNA_SLD_01_A23T55JLT4_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 07:25:44 ..... started STAR run
Jun 08 07:25:44 ..... loading genome
Jun 08 07:26:05 ..... processing annotations GTF
Jun 08 07:26:16 ..... inserting junctions into the genome indices
Jun 08 07:27:34 ..... started mapping
Jun 08 07:29:20 ..... finished mapping
Jun 08 07:29:25 ..... started sorting BAM
Jun 08 07:29:38 ..... finished successfully