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
2.3 years ago by
salamandra330
salamandra330 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 • 3.1k views
ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by salamandra330
2
gravatar for genomax
2.3 years ago by
genomax91k
United States
genomax91k 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 2.3 years ago • written 2.3 years ago by genomax91k

you were right. it was missing

ADD REPLYlink written 2.3 years ago by salamandra330
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1001 users visited in the last hour