the problem of Mus_musculus.GRCm38.dna.primary_assembly.fa

[kenny...@gmail.com]

Hi everyone,

    i have a problem when i want to creat genomedir on my u disk,i have download the Mus_musculus.GRCm38.dna.primary_assembly.fa and Mus_musculus.GRCm38.90,when i run 

STAR   --runThreadN 30 --runMode genomeGenerate --genomeDir ./ --genomeFastaFiles Mus_musculus.GRCm38.dna.primary_assembly.fa --sjdbGTFfile Mus_musculus.GRCm38.90.gtf

It have problem with "EXITING because of INPUT ERROR: the file format of the genomeFastaFile: Mus_musculus.GRCm38.dna.primary_assembly.fais not fasta: the first character is   , not > .

 Solution: check formatting of the fasta file. Make sure the file is uncompressed (unzipped)."

I am sure I have download fully and uncompressed it.

Could someone tell me how to solve this problems?Is this bacause I use the path of udisk? when i run ll, it comes out:

drwxrwxrwx 0 root root        512 Dec  1 10:11 ./

drwxrwxrwx 0 root root        512 Dec  1 10:10 ../

-rwxrwxrwx 1 root root        546 Dec  2 09:49 genomeParameters.txt*

-rwxrwxrwx 1 root root      13041 Dec  2 09:49 Log.out*

-rwxrwxrwx 1 root root  756721066 Dec  1 10:34 Mus_musculus.GRCm38.90.gtf*

-rwxrwxrwx 1 root root 2776390504 Dec  2 09:07 Mus_musculus.GRCm38.dna.primary_assembly.fa*

drwxrwxrwx 0 root root        512 Dec  2 09:49 _STARtmp/

Hope u can tell me.

Thanks.

[Alexander Dobin]

Hi @kennyzhao94

what is the output of 

$ head Mus_musculus.GRCm38.dna.primary_assembly.fa

Cheers

Alex