File Info

Filename
.command.out
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/a095ed51f541f346111783b9501b8d/.command.out
Size
1.5 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FASTQ_ALIGN_STAR:STAR_ALIGNMENT (659_c95-T1-TRNA-1_A23MVY2LT4_2)
Attempt

Content

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	STAR --genomeDir ref_genome.fa.star.idx --readFilesIn input1/659_c95-T1-TRNA-1_A23MVY2LT4_2_1.fastp.fastq.gz input2/659_c95-T1-TRNA-1_A23MVY2LT4_2_2.fastp.fastq.gz --runThreadN 24 --outFileNamePrefix 659_c95-T1-TRNA-1_A23MVY2LT4_2. --sjdbGTFfile ref_annot.gtf --outSAMattrRGline ID:659_c95-T1-TRNA-1_A23MVY2LT4_2 SM:659_c95-T1-TRNA-1_A23MVY2LT4_2 --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 07:40:25 ..... started STAR run
Jun 08 07:40:25 ..... loading genome
Jun 08 07:41:00 ..... processing annotations GTF
Jun 08 07:41:09 ..... inserting junctions into the genome indices
Jun 08 07:42:26 ..... started mapping
Jun 08 08:47:45 ..... finished mapping
Jun 08 08:47:48 ..... started sorting BAM
Jun 08 08:52:15 ..... finished successfully