Open whisperingkahuna opened 6 months ago
I also had the same issue. Just use a different species, such as banana "Macuminata" python -m jcvi.apps.fetch phytozome Macuminata
The seqids
will be different:
chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11
Pp01,Pp02,Pp03,Pp04,Pp05,Pp06,Pp07,Pp08
And I got the plot:
@whisperingkahuna
This is due to that Phytozome removed access to Vvinifera
(grape) for some reason. I'll have to use a different organism for the wiki tutorial. Thanks for reporting this issue.
Haibao
The wiki is temporarily upgraded to reflect the unavailability of grape via direct download. Please use the portal for a manual download.
I am using jcvi in google colab. It installs. I am following this tutorial.
Download data
I run this command
!python -m jcvi.apps.fetch phytozome
and it appears to be working fine
I get the following output.
I now run this command
!python -m jcvi.apps.fetch phytozome Vvinifera,Ppersica
I get this response
[01/02/24 17:57:20] INFO File .phytozome_directory_V12.xml exists. Download
I upload the file for reference. phytozome_directory_V12.zipI delete this file from the workspace and ran the below command again
!python -m jcvi.apps.fetch phytozome Vvinifera,Ppersica
I get this response
I don't know what the problem is. PS: I do not have a background in bioinformatics; I am helping someone execute the code. I would appreciate any lead