File Info

Filename
.command.out
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/6a433b48423cb1b81bcb42ff22b6ec/.command.out
Size
1.5 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FASTQ_ALIGN_STAR:STAR_ALIGNMENT (659_bKP-T1-TRNA-1_B23MHV2LT4_1)
Attempt

Content

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	STAR --genomeDir ref_genome.fa.star.idx --readFilesIn input1/659_bKP-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz input2/659_bKP-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz --runThreadN 24 --outFileNamePrefix 659_bKP-T1-TRNA-1_B23MHV2LT4_1. --sjdbGTFfile ref_annot.gtf --outSAMattrRGline ID:659_bKP-T1-TRNA-1_B23MHV2LT4_1 SM:659_bKP-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 20:26:55 ..... started STAR run
Jun 04 20:26:55 ..... loading genome
Jun 04 20:27:12 ..... processing annotations GTF
Jun 04 20:27:20 ..... inserting junctions into the genome indices
Jun 04 20:28:26 ..... started mapping
Jun 04 21:04:53 ..... finished mapping
Jun 04 21:04:56 ..... started sorting BAM
Jun 04 21:08:46 ..... finished successfully