File Info

Filename
.command.out
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/5ac133b273f4f53a41d219c4c4765c/.command.out
Size
1.5 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FASTQ_ALIGN_STAR:STAR_ALIGNMENT (659_Lx-T1-TRNA-1_B23MHV2LT4_1)
Attempt

Content

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	STAR --genomeDir ref_genome.fa.star.idx --readFilesIn input1/659_Lx-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz input2/659_Lx-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz --runThreadN 24 --outFileNamePrefix 659_Lx-T1-TRNA-1_B23MHV2LT4_1. --sjdbGTFfile ref_annot.gtf --outSAMattrRGline ID:659_Lx-T1-TRNA-1_B23MHV2LT4_1 SM:659_Lx-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 04 20:24:44 ..... started STAR run
Jun 04 20:24:44 ..... loading genome
Jun 04 20:25:01 ..... processing annotations GTF
Jun 04 20:25:10 ..... inserting junctions into the genome indices
Jun 04 20:26:24 ..... started mapping
Jun 04 20:51:58 ..... finished mapping
Jun 04 20:52:01 ..... started sorting BAM
Jun 04 20:55:26 ..... finished successfully