Config Error of anvi-display-pan

[Daniel Han]

Hello, I successfully ran anvi-split splitting pan.db into "core" and "accessory". Everything worked fine when I ran anvi-display-pan on core/Pan.db. However, when I rananvi-display-panon accessory/Pan.db, errors happened. The content of error was "Config Error: Apologies :( The code managed to came all the way down here without any item orders set for your project, which makes it impossible for anvi'o intearctive interface to display anything :/ Please check warning messages you may have on your screen."

TheDetailed Code:

(anvio-7.1) [dl@dl-KRPA-U16-Series All]$ anvi-display-pan -p Isolated_split_pan/accessory/PAN.db -g GENOMES-db/S_isolated-GENOMES.db
Interactive mode .............................: pan                                                                          
Functions found .............................................: COG20_FUNCTION, COG20_CATEGORY, antismash, COG20_PATHWAY      
Genomes storage .............................................: Initialized (storage hash: hash38501325)                      
Num genomes in storage ......................................: 57
Num genomes will be used ....................................: 57
Pan DB ......................................................: Initialized: Isolated_split_pan/accessory/PAN.db (v. 15)
Gene cluster homogeneity estimates ..........................: Functional: [YES]; Geometric: [YES]; Combined: [YES]
                                                                                                                             
* Gene clusters are initialized for all 26877 gene clusters in the database.

                                                                                                                             
WARNING
==============================================================
This pangenome (which you gracefully named as 'The accessory split from
"Streptomyces_isolated_pangenome"') does not seem to have any hierarchical
clustering of gene clusters it contains. Maybe you skipped the clustering step,
maybe anvi'o skipped it on your behalf because you had too many gene clusters or
something. Anvi'o will do its best to recover from this situation. But you will
very likely not be able to see a hierarchical dendrogram in the resulting
display even if everything goes alright.. In some cases using a parameter like
`--min-occurrence 2`, which would reduce the number of gene clusters by removing
singletons that appear in only one genome can help solve this issue and make
your pangenome great again.



Config Error: Apologies :( The code managed to came all the way down here without any item  
              orders set for your project, which makes it impossible for anvi'o intearctive
              interface to display anything :/ Please check warning messages you may have on
              your screen.

Thank you, I am looking forward to your reply.

[A. Murat Eren (Meren)]

I'm not sure what is the question here :) The error message explains very clearly why anvi-display-pan was not initiated.

Best wishes,

Meren.

--
Anvi'o Paper: https://peerj.com/articles/1319/
Project Page: http://merenlab.org/projects/anvio/
Code Repository: https://github.com/meren/anvio
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