Question: STAR alignment error: Genome_genomeGenerate.cpp:208:genomeGenerate: exiting because of *OUTPUT FILE* error: could not create output file ./GenomeDir/
0
gravatar for salamandra
16 months ago by
salamandra240
salamandra240 wrote:

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

STAR --runThreadN 4 --runMode genomeGenerate --genomeFastaFiles $GENOME --sjdbGTFfile $ANOTATION --sjdbOverhang 99

And it gives the error:

Jun 28 15:21:51 ..... started STAR run
Jun 28 15:21:51 ... starting to generate Genome files
Genome_genomeGenerate.cpp:208: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

I have 'read and write' permissions for both input files. As suggested somewhere, I have tried to reduce the number of threads, and to increase the limit number of files that can be open at the same time with:

ulimit 10000000
ulimit -n

Nothing worked. Any ideas?

rna-seq star • 1.4k views
ADD COMMENTlink modified 16 months ago • written 16 months ago by salamandra240
1
gravatar for genomax
16 months ago by
genomax73k
United States
genomax73k wrote:

At a minimum add --genomeDir some_dir that you actually have write permissions to write to, so a specific location is available to store the indexes.

ADD COMMENTlink modified 16 months ago • written 16 months ago by genomax73k

you were right. it was missing

ADD REPLYlink written 16 months ago by salamandra240
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