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!