EXITING because of FATAL ERROR: could not open genome file

[Varsha]

Hi Dobin, 

I have been trying to use STAR however, I keep getting  the following error. I have all the read/write  and execute permissions for this file. The directory also contains the SA, SAIndex, chrLength.txt file etc. Could you please let me know what the problem might be? Also could you tell me what files should be generated in the genome

directory.

EXITING because of FATAL ERROR: could not open genome file /Homo_sapiens_Ensembl_GRCh37/Homo_sapiens/Ensembl/GRCh37/Sequence/STAR_Genome/genomeParameters.txt

SOLUTION: check that the path to genome files, specified in --genomDir is correct and the files are present, and have user read permissions

Thanks 

Varsha

[Varun Gupta]

Hi
You have to give the path of the genome directory where the files are stored, so it should be something like this

--genomeDir /Homo_sapiens_Ensembl_GRCh37/Homo_sapiens/Ensembl/GRCh37/Sequence/STAR_Genome/

and not

 /Homo_sapiens_Ensembl_GRCh37/Homo_sapiens/Ensembl/GRCh37/Sequence/STAR_Genome/genomeParameters.txt

You STAR_Genome directory has the files.
genomeParameters.txt is one of the files generated during genome generation step.

Hope this helps

Varun

[Varsha]

Hi 

This is what my run looks like, 

reference_genome="/Reference_Genomes/Homo_sapiens_Ensembl_GRCh37/Homo_sapiens/Ensembl/GRCh37/Sequence/STAR_Genome"

STAR \

--genomeDir "$reference_genome" \

--readFilesIn "$fastq_one" "$fastq_two" \

--outFileNamePrefix "$base_output_directory/Star_Mappings/$sample_name/" \

--runThreadN 2

the STAR_Genome directory contains

-rwxr-xr-x 1 varshar ms-lab         238 Jul  9  2013 chrLength.txt

-rwxr-xr-x 1 varshar ms-lab         302 Jul  9  2013 chrNameLength.txt

-rwxr-xr-x 1 varshar ms-lab          64 Jul  9  2013 chrName.txt

-rwxr-xr-x 1 varshar ms-lab         273 Jul  9  2013 chrStart.txt

-rwxr-xr-x 1 varshar ms-lab  3099328512 Jul  9  2013 Genome

-rwxr--r-- 1 varshar ms-lab         281 Mar  4 04:15 genomeParameters.txt

-rwxr-xr-x 1 varshar ms-lab 23584065962 Jul  9  2013 SA

-rwxr-xr-x 1 varshar ms-lab  1565873616 Jul  9  2013 SAindex

I am not sure where the problem lies.

Any input will be appreciated.

Thanks,

[Alexander Dobin]

Hi Varsha,

I agree with Varun, there is something wrong with your genome directory path. This path should be either absolute (starting from /), or relative to the directory STAR is run from.

From inside the STAR run directory you should be able to do `ls $reference_genome` and see the contents of genome directory. It appears that you are using absolute path, since your --genomeDir starts from / .

Cheers

Alex

On Tuesday, March 4, 2014 5:43:20 PM UTC-5, Varsha wrote:

Hi 

This is what my run looks like, 

reference_genome="/Reference_Genomes/Homo_sapiens_Ensembl_GRCh37/Homo_sapiens/Ensembl/GRCh37/Sequence/STAR_Genome"

STAR \

--genomeDir "$reference_genome" \

--readFilesIn "$fastq_one" "$fastq_two" \

--outFileNamePrefix "$base_output_directory/Star_Mappings/$sample_name/" \

--runThreadN 2

the STAR_Genome directory contains

-rwxr-xr-x 1 varshar ms-lab         238 Jul  9  2013 chrLength.txt

-rwxr-xr-x 1 varshar ms-lab         302 Jul  9  2013 chrNameLength.txt

-rwxr-xr-x 1 varshar ms-lab          64 Jul  9  2013 chrName.txt

-rwxr-xr-x 1 varshar ms-lab         273 Jul  9  2013 chrStart.txt

-rwxr-xr-x 1 varshar ms-lab  3099328512 Jul  9  2013 Genome

-rwxr--r-- 1 varshar ms-lab         281 Mar  4 04:15 genomeParameters.txt

-rwxr-xr-x 1 varshar ms-lab 23584065962 Jul  9  2013 SA

-rwxr-xr-x 1 varshar ms-lab  1565873616 Jul  9  2013 SAindex

I am not sure where the problem lies.

Any input will be appreciated.

Thanks,

On Tuesday, March 4, 2014 1:01:42 PM UTC-8, Varun Gupta wrote: