Question: Genome Index Error in STAR:
gravatar for sbrashidx
14 months ago by
sbrashidx0 wrote:

I am ONLY trying to index my reference genome as the first step in order to subsequently align my reads using STAR. I am doing this through HPC. This is my very simple script:

STAR --runThreadN 4 --runMode genomeGenerate --genomeDir home/aubsxr/Wound_Healing/GENEINDEX \ --genomeFastaFiles MlScaffold09.nt

The error I get is as follows:

genomeGenerate.cpp:167:genomeGenerate: exiting because of OUTPUT FILE error: could not create output file home/aubsxr/Wound_Healing/GENEINDEX/chrName.txt Solution: check that the path exists and you have write permission for this file

The path exists and I have read/write permissions to all directories. I'm confused at what the problem could be?

Thanks so much!

indexing genome rna-seq star • 544 views
ADD COMMENTlink modified 14 months ago by Michael Dondrup48k • written 14 months ago by sbrashidx0

what is the output of

ls home/aubsxr/Wound_Healing/GENEINDEX


ADD REPLYlink written 14 months ago by Pierre Lindenbaum134k
gravatar for Michael Dondrup
14 months ago by
Bergen, Norway
Michael Dondrup48k wrote:

"The path" does not exist, you should take the error message seriously.*

You specified: home/aubsxr/Wound_Healing/GENEINDEX which is not an absolute path on Unix systems, you likely forgot the leading / so specify /home/aubsxr/Wound_Healing/GENEINDEX instead, as you did when checking that the path exists, and it should work.

*Why? Because file IO is about the most used function in any library and program, and chances that the c++ standard library is at fault here are extremely slim.

ADD COMMENTlink modified 14 months ago • written 14 months ago by Michael Dondrup48k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1056 users visited in the last hour