decodebiology
commented
8 years ago Thanks for trying GeneSCF.
Problems associated with your commandline:
1) Missing background genes (All parameters are necessary)
./geneSCF -m=update -i=GEnes_Go.txt -t=sym -o=/Go_Prupe -db=KEGG -p=yes -org=pper -bg=NumberOfBackgroundGenes**
2) The output path you gave is a root path. That is the reason, GeneSCF could not able to create any files. If your directory 'Go_Prupe' and input file is in current path use as below (or use complete path to your output directory and input file),
./geneSCF -m=update -i=./GEnes_Go.txt -t=sym -o=./Go_Prupe/ -db=KEGG -p=yes -org=pper -bg=#NumberOfBackgroundGenes
From your error 'cat: /Go_Prupe/GEnes_Go.txt_user_mapped.list' I can see that the problem is associated with your path to output directory.
Input gene_list format:
https://www.biostars.org/p/186074/#186110
Recommendations:
1) GeneSCF only works on Linux system, it has been successfully tested on Ubuntu, Mint and Cent OS. Other distributions of Linux might work as well.
2) Use updated version of GeneSCF.
Check example codes:
https://www.biostars.org/p/108669/
https://www.biostars.org/p/205677/#205679
Let me know if you still have problems.
Tcvalenzuela
Hi to all I'm trying to make an analysis of gene ontology in a set of differentially expressed genes of prunus persica. To do so I provide to the program with a list in a .txt file with all the prupes of my analysis and run the following code line [CODE] ./geneSCF -m=update -i=GEnes_Go.txt -t=sym -o=/Go_Prupe -db=KEGG -p=yes -org=pper [/CODE]
and I get the following
[CODE] Since you have selected 'update' mode. It will take a while to prepare new updated database Connecting remote RUD.. processing started....mar ago 30 11:13:14 CLST 2016 Retreiving 129 KEGG pathways for pper Do not panic. The processing is going on... Database retreived..You are now ready to use geneSCF with organism pper from --database KEGG Done....mar ago 30 11:20:23 CLST 2016 =>processing in update started....mar ago 30 11:20:23 CLST 2016 => Finished retriving database... => Calculating statistics... find: «pper/class/lib/db/yes/kegg_database.txt»: No existe el archivo o el directorio 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). KEGG last updated
Example input types
gid | sym => Retreving gene list for yes from KEGG sh: 1: cannot create pper/mapping/DB/GEnes_Go.txt_gene_list.txt: Directory nonexistent => Mapping user list Can't open perl script "pper/class/scripts/mappingIDS.pl": No existe el archivo o el directorio sh: 1: cannot create /Go_Prupe/GEnes_Go.txt_user_mapped.list: Directory nonexistent cat: /Go_Prupe/GEnes_Go.txt_user_mapped.list: No existe el archivo o el directorio sh: 1: cannot create pper/mapping/GEnes_Go.txt_input_list.txt: Directory nonexistent wc: pper/mapping/GEnes_Go.txt_input_list.txt: No existe el archivo o el directorio Note: There were genes mapped from 324 user provided unique genes (0 %) Please cross-check your gene identifier.mar ago 30 11:20:25 CLST 2016 finished processing [/CODE]
And I don't know where to look for the missing files, please help