Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Cannot run genscf with a locally constructed database for E. coli #17

Open
nicolasginet opened this issue Sep 27, 2022 · 1 comment
Open

Comments

@nicolasginet
Copy link

Dear Author,

I am desperately in need of your GeneSCF results but I cannot manage to make it work. I am working on E. coli MG1655 and when I prepared the database with ecocyc I realized that the file format was not good (wrong order of informations, a "t" instead of a "~" and other stuff). I then decided to reconstruct a GO_BP_sym.txt from UNIPROT (see the following attachment). But I still get errors after running your script. I pasted the message from the terminal window if this can help ...
Many thanks for your help !
Nicolas GINET, research scinetist at CNRS
[GO_BP_sym.txt] (https://github.com/genescf/GeneSCF/files/9657541/GO_BP_sym.txt)

root@lemale:/media/pc-ma-le/DATA/Bioinfo/GeneSCF# ./geneSCF -m=normal -i=Input/BACCHATposFC4.list -o=Output/ -t=sym -db=GO_BP -bg=4000 --plot=yes -org=eco
processing in 'normal' mode started....mardi 27 septembre 2022, 17:26:48 (UTC+0200)
=> Finished retriving database...
=> Calculating statistics...
Note:Only KEGG and Geneontology supports multiple organisms (GeneSCF-xx/org_codes_help). If you choose REACTOME/NCG database please specify organism as 'Hs'. Currently REACTOME and NCG in GeneSCF only supports Human (Hs).
GO_BP last updated 2022-09-27 16:54
Illegal division by zero at /media/pc-ma-le/DATA/Bioinfo/GeneSCF/class/lib/List/Vectorize/lib/List.pl line 599, chunk 1.
mardi 27 septembre 2022, 17:26:48 (UTC+0200) finished processing
root@lemale:/media/pc-ma-le/DATA/Bioinfo/GeneSCF#

@decodebiology
Copy link
Collaborator

Sorry for my very delayed response. To accommodate '-org=eco' you must have directory $GeneSCF_source_DIR/class/lib/db/eco/GO_BP_sym.txt. I hope this works.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants