STAR for Genome Index and Alignment

Question

[umeshtanwar2]

Hi. I am new for using STAR. I am generating the genome index for Arabidopsis thaliana (ftp://ftp.ensemblgenomes.org/pub/release-41/plants/fasta/arabidopsis_thaliana/dna/). I downloaded the FASTA files for each chromosome and the GTF file. My script was:

STAR --runThreadN 1 --runMode genomeGenerate --genomeDir /Documents/Umesh/Analysis123/star --genomeFastaFiles ~/Documents/Umesh/Analysis123/star/Arabidopsis_thaliana.TAIR10.dna.chromosome.1.fa ~/Documents/Umesh/Analysis123/star/Arabidopsis_thaliana.TAIR10.dna.chromosome.2.fa ~/Documents/Umesh/Analysis123/star/Arabidopsis_thaliana.TAIR10.dna.chromosome.3.fa ~/Documents/Umesh/Analysis123/star/Arabidopsis_thaliana.TAIR10.dna.chromosome.4.fa ~/Documents/Umesh/Analysis123/star/Arabidopsis_thaliana.TAIR10.dna.chromosome.5.fa ~/Documents/Umesh/Analysis123/star/Arabidopsis_thaliana.TAIR10.dna.chromosome.Mt.fa ~/Documents/Umesh/Analysis123/star/Arabidopsis_thaliana.TAIR10.dna.chromosome.Pt.fa --sjdbGTFfile ~/Documents/Umesh/Analysis123/star/Arabidopsis_thaliana.TAIR10.41.gtf sjdbOverhang 99

It is showing an error:

Jan 09 13:13:23 ..... started STAR run Jan 09 13:13:25 ...... FATAL ERROR, exiting

genomeGenerate.cpp:209:genomeGenerate: exiting because of OUTPUT FILE error: could not create output file /Documents/Umesh/Analysis123/star/chrName.txt Solution: check that the path exists and you have write permission for this file

I don't know what the problem is. Can someone help me out?

Answer 1

[GenoMax]

It looks like you are missing a ~ from this option.

--genomeDir ~/Documents/Umesh/Analysis123/star

[umeshtanwar2]

Thank you so much genomax. It started working.