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I am running into an issue where my list of hugo symbols will not work with geneSCF for either KEGG or GO, KEGG runs the best but it still gives me the error:
"Note: There were 0 genes mapped from 5 user provided unique genes (0 %)
Please cross-check your gene identifier.Tue Jan 14 12:18:50 EST 2025 finished processing"
I know its not an identifier issue because when i manually run the symbols against the kegg DB I am able to identify the gene without issue.
The GO error is less informative:
jjoemr@DESKTOP-HITDCS2:~$ sudo GeneSCF-1.1-p3.beta/geneSCF -m=normal -i=genExplore/SCFhighimpactlist.txt -t=sym
-o=genExplore/final_results/ -db=GO_all -p=no -bg=4315 -org=goa_human
processing in 'normal' mode started....Tue Jan 14 12:24:03 EST 2025
=> 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_all last updated 2025-01-14 10:55
Illegal division by zero at /home/joemr/GeneSCF-1.1-p3.beta/class/lib/List/Vectorize/lib/List.pl line 599, chunk 1.
Tue Jan 14 12:24:03 EST 2025 finished processing
The text was updated successfully, but these errors were encountered:
Hi and thank you for creating this tool.
I am running into an issue where my list of hugo symbols will not work with geneSCF for either KEGG or GO, KEGG runs the best but it still gives me the error:
"Note: There were 0 genes mapped from 5 user provided unique genes (0 %)
Please cross-check your gene identifier.Tue Jan 14 12:18:50 EST 2025 finished processing"
I know its not an identifier issue because when i manually run the symbols against the kegg DB I am able to identify the gene without issue.
The GO error is less informative:
jjoemr@DESKTOP-HITDCS2:~$ sudo GeneSCF-1.1-p3.beta/geneSCF -m=normal -i=genExplore/SCFhighimpactlist.txt -t=sym
-o=genExplore/final_results/ -db=GO_all -p=no -bg=4315 -org=goa_human
processing in 'normal' mode started....Tue Jan 14 12:24:03 EST 2025
=> 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_all last updated 2025-01-14 10:55
Illegal division by zero at /home/joemr/GeneSCF-1.1-p3.beta/class/lib/List/Vectorize/lib/List.pl line 599, chunk 1.
Tue Jan 14 12:24:03 EST 2025 finished processing
The text was updated successfully, but these errors were encountered: