File Info

Filename
.command.out
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/467a172a351744d0022a2b489fe3f4/.command.out
Size
1.5 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FASTQ_ALIGN_STAR:STAR_ALIGNMENT (22Rv1_FFPE_RNA_0001_B23LG7FLT4_3)
Attempt

Content

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	STAR --genomeDir ref_genome.fa.star.idx --readFilesIn input1/22Rv1_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz input2/22Rv1_FFPE_RNA_0001_B23LG7FLT4_3_2.fastp.fastq.gz --runThreadN 24 --outFileNamePrefix 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3. --sjdbGTFfile ref_annot.gtf --outSAMattrRGline ID:22Rv1_FFPE_RNA_0001_B23LG7FLT4_3 SM:22Rv1_FFPE_RNA_0001_B23LG7FLT4_3 --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 07:20:38 ..... started STAR run
Jun 08 07:20:38 ..... loading genome
Jun 08 07:21:02 ..... processing annotations GTF
Jun 08 07:21:15 ..... inserting junctions into the genome indices
Jun 08 07:23:02 ..... started mapping
Jun 08 07:25:50 ..... finished mapping
Jun 08 07:25:54 ..... started sorting BAM
Jun 08 07:26:11 ..... finished successfully