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

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

index seqkit subseq fai • 1.0k views
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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?

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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

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

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

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14 months ago
GenoMax 142k

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 
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Thank you, it worked!

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