Thank you, it worked!
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[ERRO] read faidx: open file.fasta.seqkit.fai: permission denied
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
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GenoMax
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Eleonora Tassara •
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Eleonora Tassara •
1 answer
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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There were no errors when you did the
faidxindexing? Do you see filefile.fasta.seqkit.faicreated in this directory? Does it have read permissions by the account you are using?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
Are you performing this operation within your home directory? (
~)No, I'm performing it in the directory in which I have the files