merenlab / anvio

An analysis and visualization platform for 'omics data
http://merenlab.org/software/anvio
GNU General Public License v3.0
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Config Error of anvi-display-pan #2088

Closed DanielHan4545 closed 1 year ago

DanielHan4545 commented 1 year ago

Short description of the problem

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.

anvi'o version

anvio-7.1

System info

Ubuntu

Detailed description of the issue

`(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]

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.

meren commented 1 year ago

This is not a problem. As the error message mentions it, there are way too many gene clusters to display using the standard anvi-display-pan approach.