Question: genomeGenerate: exiting because of *OUTPUT FILE* error: could not create output file ./GenomeDir//chrName.txt
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gravatar for yousefifariba6
8 weeks 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 • 154 views
ADD COMMENTlink modified 8 weeks ago by genomax91k • written 8 weeks ago by yousefifariba60

Does the genome directory exist in the star folder?

ADD REPLYlink written 8 weeks ago by rpolicastro2.0k

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 8 weeks ago • written 8 weeks ago by genomax91k

try this on the command line before you run it

mkdir /home/theory/Desktop/star/genome/
ADD REPLYlink written 8 weeks ago by benformatics2.0k
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