Question: genomeGenerate: exiting because of *OUTPUT FILE* error: could not create output file ./GenomeDir//chrName.txt
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gravatar for yousefifariba6
6 months ago by
yousefifariba60 wrote:

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?

software error • 348 views
ADD COMMENTlink modified 6 months ago by GenoMax96k • written 6 months ago by yousefifariba60

Does the genome directory exist in the star folder?

ADD REPLYlink written 6 months ago by rpolicastro3.9k

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?

ADD REPLYlink modified 6 months ago • written 6 months ago by GenoMax96k

try this on the command line before you run it

mkdir /home/theory/Desktop/star/genome/
ADD REPLYlink written 6 months ago by benformatics2.0k
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