genomeGenerate: exiting because of *OUTPUT FILE* error: could not create output file ./GenomeDir//chrName.txt

Question

[yousefifariba6]

I'm trying to run STAR alignment software on ubuntu to index the genome. The command is:

STAR --runThreadN 8 --runMode genomeGenerate –-genomeDir '/home/theory/Desktop/star/genome' --genomeFastaFiles '/home/theory/Desktop/star/ref.fa' --sjdbGTFfile '/home/theory/Desktop/star/apis_ref.gtf'

And it gives the error:

Aug 26 13:52:13 ..... started STAR run
Aug 26 13:52:13 ... starting to generate Genome files

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

Aug 26 13:52:19 ...... FATAL ERROR, exiting

what problem?

[rpolicastro]

Does the genome directory exist in the star folder?

[GenoMax]

Is the error you posted exactly what you see (or have you changed directory names)? Why are you using those single quotes around file names?

[benformatics]

try this on the command line before you run it

mkdir /home/theory/Desktop/star/genome/