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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#
The text was updated successfully, but these errors were encountered:
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.
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#
The text was updated successfully, but these errors were encountered: