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genescf / GeneSCF

Gene Set Clustering based on Functional annotation
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unable to update GO database files #3

Closed univerchen closed 4 years ago

univerchen commented 5 years ago

I tried to update GO database, but failed. command line: ./prepare_database -db=GO_all -org=goa_human

The error is gzip: //geneSCF-master-source-v1.1-p2/class/lib/db/goa_human/gene_association.goa_human.gz: unexpected end of file cat: //geneSCF-master-source-v1.1-p2/class/lib/db/goa_human/gene_association.goa_human: No such file or directory cat: //geneSCF-master-source-v1.1-p2/class/lib/db/goa_human/gene_association.goa_human: No such file or directory Updating gene information... Do not panic. The processing is going on... rm: cannot remove '//geneSCF-master-source-v1.1-p2/class/lib/db/goa_human/gene_association.goa_human': No such file or directory Database retreived..You are now ready to use geneSCF with organism goa_human from --database GO Done....

The annotation files, like GO_all_gid.txt, is blank and 0 bytes. I use this in ubuntu 16.04. It works fine to update KEGG database. Does anyone know how to fix this? Thanks a lot.

decodebiology commented 5 years ago

Hello univerchen,

Thanks for reporting the error.

Due to changes in HTTP's request and response code, GeneSCF has to undergo some minor changes in the some of the modules. Downloading updated version (recently updated) solves issues related to database retrieval (prepare_database module).

Let me know if it solves your error.

univerchen commented 5 years ago

Hello! Thanks for your reply. I downloaded the newest version just now, and it works fine now. Thanks again!

decodebiology commented 5 years ago

Good to hear. Now I will close this issue. Feel free to report if there are any further issues in future. Thanks for using GeneSCF.