[ERRO] read faidx: open file.fasta.seqkit.fai: permission denied

Question

[Eleonora Tassara]

Hello, I'm trying to extract a specific nucleotide region from a fasta sequence of a chomosome. I created a fai index using:

$ seqkit faidx file.fasta

Then I run:

$ seqkit subseq -r 1268437:1269323 file.fasta

And this is the error:

[ERRO] read faidx: open file.fasta.seqkit.fai: permission denied

Do you have an idea how to resolve it?

Thank you in advance

[GenoMax]

There were no errors when you did the faidx indexing? Do you see file file.fasta.seqkit.fai created in this directory? Does it have read permissions by the account you are using?

[Eleonora Tassara]

When I run

$ seqkit faidx file.fasta

The output is:

[INFO] create FASTA index for file.fasta

In the same directory I see a file fasta.fai with reading permissions, but I don't have a file.fasta.seqkit.fai

[Joe]

Are you performing this operation within your home directory? (~)

[Eleonora Tassara]

No, I'm performing it in the directory in which I have the files

Answer 1

[GenoMax]

Looks like you can simply use faidx to extract the subsequence you need per usage page here.

$ seqkit faidx file.fasta name_you_want_to_extract:1268437-1269323 

[Eleonora Tassara]

Thank you, it worked!