Entering edit mode
4.6 years ago
jeremy
•
0
Hello, I was wondering if anybody had experience using STAR with AWS. I have no problems running it locally, but am now transitioning it for use with snakemake/tibanna framework. With snakemake/tibanna, all the files you work with must be in an S3 bucket on AWS. So I put my genome index (that works locally for alignment) in an S3 bucket, referenced as such
S3.remote("rnaseq.raw/indexes/STAR_index"),
However, when I try this, I keep encountering the error
EXITING because of FATAL ERROR: could not open genome file rnaseq.raw/indexes/STAR_index/genomeParameters.txt
However, this file is definitely there in that folder. I can't find anything in the STAR docs about working with remote files. Does anybody have any experience with this?
Can you clarify if this question is about using STAR on AWS or about using STAR locally but with index in an S3 bucket? This may be a case of authentication error since the program is not able to
open
the file.