File Info

Filename
.command.out
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/5da4b0f0dc5b55b097fe818cf33f1e/.command.out
Size
1.5 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FASTQ_ALIGN_STAR:STAR_ALIGNMENT (aih-tih-sc-3924cb-R1_B23WHYVLT4_1)
Attempt

Content

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	STAR --genomeDir ref_genome.fa.star.idx --readFilesIn input1/aih-tih-sc-3924cb-R1_B23WHYVLT4_1_1.fastp.fastq.gz input2/aih-tih-sc-3924cb-R1_B23WHYVLT4_1_2.fastp.fastq.gz --runThreadN 24 --outFileNamePrefix aih-tih-sc-3924cb-R1_B23WHYVLT4_1. --sjdbGTFfile ref_annot.gtf --outSAMattrRGline ID:aih-tih-sc-3924cb-R1_B23WHYVLT4_1 SM:aih-tih-sc-3924cb-R1_B23WHYVLT4_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 07:36:13 ..... started STAR run
Jun 08 07:36:13 ..... loading genome
Jun 08 07:36:50 ..... processing annotations GTF
Jun 08 07:36:59 ..... inserting junctions into the genome indices
Jun 08 07:38:12 ..... started mapping
Jun 08 08:32:08 ..... finished mapping
Jun 08 08:32:11 ..... started sorting BAM
Jun 08 08:36:19 ..... finished successfully