Genome Index Error in STAR:

Question

[sbrashidx]

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!

[Pierre Lindenbaum]

what is the output of

ls home/aubsxr/Wound_Healing/GENEINDEX

?

Answer 1

[Michael]

"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.