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ksamuk / pixy

Software for painlessly estimating average nucleotide diversity within and between populations
https://pixy.readthedocs.io/
MIT License
115 stars 14 forks source link

Hello, While running the pixy software after converting vcf file with invariant sites using bcftools, I am getting the following error:UnicodeDecodeError: 'utf-8' codec cant decode byte 0x8b in position 1: invalid start byte; Could you please help me to resolve this error? #76

Closed kanikaghildiyal closed 1 year ago

ksamuk commented 1 year ago

Hi there, pixy currently doesn't support sample or chromosome/contig names with special characters, particularly semi-colons, commas, or letters with accent characters etc. We are hoping to resolve this in a future release. In the meantime, the solution is to simplify your sample or chromosome/contig names before running pixy.

kanikaghildiyal commented 1 year ago

Hi,

Thank you for the suggestion! I tried to make changes in the vcf file and it looks like this now:

[image: image.png] However, I am still getting the same error: unicode decode error: 'utf-8' codec cant decode byte 0x8b in position 1: invalide start byte

Could you please help me with this?

Thanks and regards, Kanika

On Wed, Apr 5, 2023 at 7:57 PM Kieran Samuk @.***> wrote:

Hi there, pixy currently doesn't support sample or chromosome/contig names with special characters, particularly semi-colons, commas, or letters with accent characters etc. We are hoping to resolve this in a future release. In the meantime, the solution is to simplify your sample or chromosome/contig names before running pixy.

— Reply to this email directly, view it on GitHub https://github.com/ksamuk/pixy/issues/76#issuecomment-1497584656, or unsubscribe https://github.com/notifications/unsubscribe-auth/A4FH4TZXAJPWCLDGSJ4ZWGLW7V6NHANCNFSM6AAAAAAWT2KPII . You are receiving this because you authored the thread.Message ID: @.***>

ksamuk commented 1 year ago

Hi, unfortunately, pixy doesn't have support for this type of dataset at the moment, so you'll have to wait until we fully address this issue in a later release.

amanda128891 commented 1 year ago

Hi there,

I know you closed this issue but I just ran into the same problem. I'm going to try to rework the sample names in my VCF but if this issue could be addressed that would make things a lot easier!

Thanks, -Amanda