STAR Aligment Running Problem

Question

[sehriban.buyukkilic]

Hi everone, I'm in trouble, I did genom index generation. and start to run STAR. But problem is STAR cannot open genomeParameters.txt. How ı can understand where is my genomeParameters.txt and solve this problem, pleaseeee help me :(

/truba_scratch/sbuyukkilic/rnaseq/STAR/STAR-2.7.10b/bin/Linux_x86_64_static/./STAR --runThreadN 10 --genomeDir /truba_scratch/sbuyukkilic/rnaseq --readFilesIn /truba_scratch/sbuyukkilic/files/SRR10727148_1.fastq --outFileNamePrefix ./align/SRR10727148_1.fastq
STAR version: 2.7.10b   compiled: 2022-11-01T09:53:26-04:00 :/home/dobin/data/STAR/STARcode/STAR.master/source
Dec 06 15:53:30 ..... started STAR run
Dec 06 15:53:30 ..... loading genome

EXITING because of FATAL ERROR: could not open genome file /truba_scratch/sbuyukkilic/rnaseq//genomeParameters.txt
SOLUTION: check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permsissions

Dec 06 15:53:30 ...... FATAL ERROR, exiting
-bash-4.2$ 

[swbarnes2]

Did you generate the index yourself? I might have seen that error before when using an index made with an older version of STAR.

[sehriban.buyukkilic]

Yeah, I did it by myself.

[GenoMax]

Based on other threads you posted are you sure the step of index creation actually worked (ref: STAR Aligment )? What does ls -lh /truba_scratch/sbuyukkilic/rnaseq/ show?

Answer 1

[GenoMax]

Looks like this file /truba_scratch/sbuyukkilic/rnaseq//genomeParameters.txt does not exist. As you can see STAR is not able to read/find that file.

--genomeDir option needs to point to the directory which contains all STAR index files.

[Ram]

Or the files exist but OP can't read them (like the error message says clearly). OP needs to:

stat /truba_scratch/sbuyukkilic/rnaseq/
ls /truba_scratch/sbuyukkilic/rnaseq/