No root node identified error

[Divya Nandakumar]

Hi,

I get an error when I try to run the Gene Ontology analysis. The log details are below

Operating system: OS X 10.9.5

Running GO-Elite version 1.2.5

Primary GO-Elite Parameters
species: Hs
results-directory: /GO analysis/output3
filter_method: z-score
z_threshold: 1.96
p_val_threshold: 0.05
change_threshold: 2
sort_only_by_zscore: yes
analysis_method: UI
criterion_input_folder: /GO analysis/input
custom_sets_folder:
ORA Parameters
mod: Ensembl
permutations: 2000
resources_to_analyze: Gene Ontology
Performing over-representation analysis (ORA) on Blue.txt
Using: all.txt for the denominator.
* * * * * * * * * * Ensembl-Symbol.txt imported
Building 2000 permuted ID sets * * * * * * * * * * completed in 5.0 seconds
Analyzing input ID list with available ontologies
NO ROOT NODE IDENTIFIED... SHOULD BE: biological_process
Analyzing input ID list with available gene-sets
Warning!!! Either the MOD you have selected: Ensembl
is missing the appropriate relationshipfiles necessary to run GO-Elite
or you have selected an invalid resource to analyze. Either replace
the missing MOD files in Databases/Hs sub-directories or
select a different MOD at run-time.


I am able to obtain other reports such as Biomarkers, KEGG etc, but get an error every time I try something associated with ontologies.

I checked the databases folder and I am able to see the files in the gene-go folder.

Can you please help me and tell me if I am doing something wrong??

[Nathan Salomonis]

Hi Divya,

This problem occurs when you download all resources because GO-Slim changed it's download link and the software pulls down an empty file that causes a problem. This is fixed in the current GO-Elite version that is available with the software AltAnalyze, however, the fix in your version is to open your OBO folder folder in GO-Elite and delete the GO-Slim file (goslim_pir.obo) prior to running. This will fix everything!

Best,

Nathan

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