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Not working with either GO or KEGG dbs #22

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Jrosen-code opened this issue Jan 14, 2025 · 2 comments
Open

Not working with either GO or KEGG dbs #22

Jrosen-code opened this issue Jan 14, 2025 · 2 comments

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@Jrosen-code
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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

@decodebiology
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Please provide your input gene list to reproduce the error.

@Jrosen-code
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Sure, I know the name says gene ids but they are hugo gene symbols.
SCFhighGeneIDs.txt

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